.. _release_notes: EasyBuild release notes ======================= The latest version of EasyBuild provides support for building and installing **1,798** different software packages, including 31 different (compiler) toolchains. It contains 212 software-specific easyblocks and 36 generic easyblocks, alongside 8,964 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. .. _release_notes_eb411: EasyBuild v4.1.1 (January 16th 2020) ------------------------------------ bugfix/update release **framework** * various enhancements, including: * add ``check_log_for_errors`` function (in ``easybuild.tools.run``) to detect and handle multiple errors (`#3118 `_) * implement support for ``eb --show-ec`` to show contents of specified easyconfig file (`#3132 `_) * also update ``$XDG_DATA_DIR`` (share/) and ``$GI_TYPELIB_PATH`` environment variables (lib*/girepository-*) in generated module files (`#3133 `_) * add support for ``--copy-ec`` to copy easyconfig file to specified location (`#3142 `_) * mention ``--disable-*`` option in ``--help`` output for boolean options enabled by default (`#3151 `_) * add ``--cuda-compute-capabilities`` configuration option (`#3161 `_) * various bug fixes, including: * ignore imports from ``vsc`` namespace made from pkgutil.py (`#3120 `_) * only actually change permissions using ``os.chmod`` in ``adjust_permissions`` if the current permissions are not correct already (`#3125 `_) * use ``shutil.copyfile`` to just copy file contents if target path exists and is owned by someone else (`#3127 `_) * fix or avoid warnings that commonly arise in build log (`#3129 `_) * disable buffering in ``asyncprocess.Popen`` using ``bufsize=0``, to fix ``run_cmd_qa`` missing output (`#3130 `_) * update pip & install wheel package in generated Singularity container recipes (`#3136 `_) * avoid crash in ``modify_env`` & unset ``unset_env_vars`` when using (older versions) of Python 3.5 & 3.6 by using ``list(...)`` (`#3140 `_) * take into account that lib64 could be a symlink to lib (or vice versa) in ``get_software_libdir`` function (`#3141 `_) * only parse docstring if it exists in ``gen_easyblock_doc_section_rst`` function (`#3144 `_) * only add useful entries for ``$CPATH``, ``$(LD_)LIBRARY_PATH`` and ``$PATH`` (non-empty directories) (`#3145 `_, `#3152 `_) * fix ``--list-software=detailed`` when using Python 3 by leveraging ``sort_looseversions`` function from ``py2vs3`` module (`#3146 `_) * ensure subdirectories in software install directory have correct search (exec) permission (`#3147 `_) * take into account that a checksum value may be a tuple of valid checksum in ``EasyBlock.check_checksums`` (`#3153 `_) * other changes: * bump to Lmod 8.2.9 in GitHub CI config (`#3115 `_) * update copyright statements for 2020 (`#3149 `_) * make Hound CI code style checker ignore "Black would make changes" produced by flake8-black (`#3162 `_) **easyblocks** * new software-specific easyblock for cryptography (to fix missing ``-pthread`` for all versions) (`#1874 `_) * minor enhancements, including: * update WPS easyblock for v3.6 & newer (`#1315 `_) * update FSL easyblock to support FSL v6.0.2 & newer (`#1860 `_) * add ``setup_cmake_env`` function in CMakeMake easyblock which can be leveraged in other easyblocks, and use it for OpenFOAM (`#1869 `_) * remove obsolete configure options for Python + build with optimizations/LTO enabled for recent Python versions (`#1876 `_) * update WPS easyblock for recent versions: set ``$WRF_DIR`` to point to location of WRF installation (`#1886 `_) * make sure ``$LIBLAPACK_MT`` is set before using it in ESMF easyblock (`#1887 `_) * remove useless ``PATH`` entries + add ``PKG_CONFIG_PATH`` in imkl easyblock (`#1900 `_) * enhance tbb easyblock to support building on POWER (`#1912 `_) * enhance TensorFlow easyblock to pick up on ``--cuda-compute-capabilities``, and issue a warning if no CUDA compute capabilities are specified (`#1913 `_) * add custom easyconfig parameter ``build_type`` to generic CMakeMake easyblock (`#1915 `_, `#1922 `_) * various bug fixes, including: * fix for conda packages that rely on particular versions of Python (`#1836 `_) * fix path for intel and netCDF lib directories in NCL easyblock (`#1862 `_) * fix CUDA 10.1 installation on POWER (`#1871 `_) * change Bazel easyblock to prefer using Java dependency rather than included JDK (fix for POWER9) (`#1875 `_) * remove optarch warning in GROMACS for Cray toolchains (`#1879 `_) * also fix ``$WM_COMPILE_OPTION`` in OpenFOAM rc scripts to make debug builds work correctly (`#1880 `_) * limit MPI ranks used for running WRF test cases to max. 4 + include contents of rsl.error.0000 output file in case test failed (`#1884 `_) * update ``$PYTHONPATH`` + add ``python -c 'import mrtrix3'`` as sanity check command for recent MRtrix versions (`#1889 `_) * update sanity check in SAMtools easyblock for version 1.10 (`#1890 `_) * make sure ``$PYTHONNOUSERSITE`` it set when performing sanity check for (bundles of) Python package(s) (`#1891 `_) * fix install dir subdir for WPS v4.0+ that is considered for ``$PATH`` and ``$LD_LIBRARY_PATH`` (`#1895 `_) * impi: don't rebuild libfabric if the source code is not present (`#1896 `_) * also copy component patches to self.cfg in Bundle generic easyblock (`#1897 `_) * skip patch step in Bundle generic easyblock (per-component patches are still applied) (`#1898 `_) * derive easyblock for iccifort only from icc easyblock (not ifort), to avoid adding include subdir to ``$CPATH`` (`#1899 `_) * add ``export LANG=C`` to preinstallopts instead of install_script path in CUDA easyblock (`#1902 `_) * stop setting updating ``$CPATH`` and ``$LIBRARY_PATH`` for GCC and GCCcore, not required (`#1903 `_) * remove ``$LIBRARY_PATH`` entries in iccifort easyblock, already known to icc et al (`#1904 `_) * use major/minor version of Python command being used if ``req_py_majver``/``req_py_minver`` are not specified (`#1907 `_) * define ``$EB_PYTHON`` in module for EasyBuild installation, to make sure correct Python version is used at runtime (`#1908 `_) * fix Python easyblock to allow configuring build of Python v3.8 (``Setup.dist`` script was renamed to ``Setup``) (`#1909 `_) * fix netCDF easyblock for version 4.4.0 (`#1911 `_) * correct comment about when we set ``RUNPARALLEL`` in HDF5 easyblock (`#1914 `_) * do not sanity check on MATLAB compiler, since it requires a separate license (`#1916 `_) * build HDF5 without MPI C++ extension to avoid breaking linkage for C software that requires HDF5 (`#1918 `_, `#1919 `_) * override ``set_pylibdirs`` method in ``VersionIndependentPythonPackage`` to hard set ``self.pylibdir`` to 'lib' (`#1924 `_) * other changes: * increase timeout for interactive installation command in CUDA easyblock to 1000 sec. (`#1878 `_) * disable running of ``sudo apt-get update`` in GitHub CI config, since it's failing (and we don't really need it) (`#1882 `_) * stop requiring Python dep for SWIG, just configure with ``--without-python`` if Python is not a dependency (`#1894 `_) * update copyright statements for 2020 (`#1905 `_) * make Hound CI code style checker ignore "Black would make changes" produced by flake8-black (`#1923 `_) **easyconfigs** * added example easyconfig files for 27 new software packages: * Autoconf-archive (`#9658 `_), breseq (`#9603 `_), CrossMap (`#9483 `_), CSBDeep (`#9560 `_), CNT-ILP (`#9323 `_), cytoolz (`#9453 `_), Faber (`#9553 `_), Fiji (`#8748 `_), GARLI (`#9404 `_), Globus-CLI (`#9565 `_), GtkSourceView (`#9526 `_), gradunwarp (`#9648 `_), gsettings-desktop-schemas (`#9529 `_), HyPhy (`#9405 `_), horton (`#7449 `_), IGMPlot (`#9438 `_), LEMON (`#9323 `_), Meld (`#9530 `_), mhcflurry (`#9554 `_), NCIPLOT (`#9419 `_), ncl (`#9632 `_), OpenSlide (`#9499 `_), openslide-python (`#9499 `_), pythran (`#9488 `_, `#9594 `_), Qualimap (`#9411 `_), TinyDB (`#9555 `_), TreeShrink (`#9381 `_) * added additional easyconfigs for various supported software packages, including: * Beast 1.10.4, Boost.Python 1.71.0, Clang 9.0.1, ESMF 8.0.0, FSL 6.0.3, fastp 0.20.0, freeglut 3.2.1, GDAL 3.0.2, GEOS 3.8.0, GROMACS 2019.4, GSL 2.6, hwloc 2.1.0, Jellyfish 2.3.0, Julia 1.3.1, LibTIFF 4.1.0, libxml2 2.9.10, lxml 4.4.2, Mothur 1.43.0, mayavi 4.7.1, molmod 1.4.5, netCDF-C++4 4.3.1, netCDF-Fortran 4.5.2, numactl 2.0.13, OpenFOAM 7, OpenFOAM v1912, OpenMM 7.4.1, OpenMPI 4.0.2, PLUMED 2.5.3, PROJ 6.2.1, plotly.py 4.4.1, pocl 1.4, QuickFF 2.2.4, R 3.6.2 w/ foss/2019b and fosscuda/2019b, ReFrame 2.20, SAMtools 1.10, SUNDIALS 5.1.0, SWIG 4.0.1, Salmon 1.0.0, SuiteSparse 5.6.0, snakemake 5.7.1, TensorFlow 2.1.0 w/ fosscuda/2019b, torchvision 0.4.2, WPS 4.1, WRF 4.1.3 * added easyconfigs for ``intel/2020.00`` toolchain (`#9575 `_) * minor enhancements, including: * add POWER9 support to CUDA 10.1 easyconfigs (`#9442 `_) * build CMake in parallel (`#9543 `_) * use NCCL for GPU ops in Horovod 0.18.2 easyconfig (`#9562 `_) * update Java/1.8 wrapper to Java/1.8.0_231 (for x86_64) (`#9585 `_) * various bug fixes, including: * fix remote launch of broker and workers for SCOOP (`#9366 `_) * fix failing RPATH sanity check for NCL 6.6.2 due to missing dependencies (+ add easyconfig using ``foss/2018b``) (`#9388 `_) * add missing 'wheel' extensions to Spark 2.4.0 easyconfig using ``intel/2018b`` toolchain (`#9424 `_) * add missing OS dependencies in Java 1.8 easyconfig used on POWER systems (`#9454 `_) * fix build of recent Bazel versions on Power9 + stick to Java/1.8 as dependency (`#9455 `_) * fix CMake 3.15.3 build on Power (+ enable building in parallel) (`#9469 `_) * fix source URLs in xorg-macros easyconfigs (`#9477 `_, `#9578 `_) * add missing wcwidth extension to Python 2.7.15 + 2.7.16 easyconfigs & enable 'pip check' in sanity check (`#9479 `_) * remove (wrong) ``GI_TYPELIB_PATH`` and ``XDG_DATA_DIRS`` in various easyconfigs (`#9528 `_, `#9577 `_, `#9615 `_) * use xorg-macros as dependency in X11 easyconfigs (rather than installing it as a bundle component) (`#9546 `_) * fix lpsymphony extension for R-bundle-Bioconductor (`#9548 `_) * add correct 'old-versions' source URL to all Mesa easyconfigs (`#9569 `_) * add missing SHA256 checksums for Armadillo (`#9572 `_) * also define ``$AUGUSTUS_BIN_PATH`` and ``$AUGUSTUS_SCRIPTS_PATH`` in generated module file for AUGUSTUS (`#9579 `_) * add SSL OS dependencies for GDAL 3.0.0 (`#9586 `_) * add missing jupyter_contrib_core extension for IPython 7.7.0+ + consistently include jupyter_nbextensions_configurator extension (`#9587 `_) * patch libcxx (Clang 8.0.0) on pcc64le for incomplete IBM128 long double in GCC (`#9590 `_) * patch for GCCcore 8.2.0 to fix '__float128 is not supported on this target' on ppc64le (`#9591 `_) * fix broken easyconfigs for cyvcf2 v0.11.5 by adding missing 'monotonic' extension (`#9601 `_) * use absolute path for extraction to allow relocating the build dir for g2log-1.0 (`#9604 `_) * add alternate SHA256 checksum for kallisto-0.43.1 after re-release under same version without code changes (`#9611 `_) * add additional valid checksum for MASS 7.3-51.4 extension in R 3.6.0 easyconfigs (`#9621 `_) * update ctffind website (`#9622 `_) * make sure we use easybuild Clang in pocl easyconfigs (`#9624 `_) * make ``postinstallcmds`` independent of current working directory in OpenCV 3.1.0 easyconfigs (`#9628 `_) * update ``source_urls`` to include old releases folder in libsodium easyconfigs (`#9632 `_) * fix source URLs for ant v1.10.5 - v1.10.7 (`#9633 `_) * update URLs to new location of libxc (`#9635 `_) * add alternate SHA256 checksum for rda_1.0.2-2.1 extension in R 3.6.0 (`#9644 `_) * update source URLs in QCA 2.1.0 easyconfigs (`#9647 `_) * fix Python 3.5.1 easyconfig: bitstring 3.1.3 sources no longer available on PyPI (`#9649 `_) * fix tesseract 4.1.0 dependencies (`#9650 `_) * make ICU 64.2 depend on Python3 instead of Python 2, to avoid picking up system Python 3.x (`#9652 `_) * use ``True`` (boolean value) rather than ``'True'`` (string value) for boolean easyconfig parameters (`#9657 `_) * fix pyfits easyconfig by adding missing d2to1 extension (`#9687 `_) * other changes: * disable running of ``sudo apt-get update`` in GitHub CI config, since it's failing (and we don't really need it) (`#9492 `_) * require that ``sanity_pip_check`` is enabled in new/changed easyconfigs (`#9516 `_, `#9576 `_) * update copyright statements for 2020 (`#9598 `_) * allow missing '-Python-*' versionsuffix for existing easyconfig files changed in PRs (`#9634 `_) .. _release_notes_eb410: EasyBuild v4.1.0 (December 4th 2019) ------------------------------------ bugfix/update release **framework** * various enhancements, including: * performance improvements: * skip validation when copying EasyConfig object for extension (`#3071 `_) * correctly specify that ActiveMNS & co are singleton classes when using Python 3 (`#3073 `_) * don't call out to prohibitively expensive ``getRootLoggerName`` in ``getLogger``, just use 'root' instead (`#3074 `_) * fix inconsistent module path usage that leads to repeated reloading in HMNS (`#3099 `_) * add support for specifying different dependency version based on processor architecture (`#3047 `_) * support use of glob patterns for paths to files with external modules metadata (`#3075 `_) * take into account that external modules may not be visible directly (due to module hierarchy) (`#3083 `_) * add support for including 'extensions' statement in Lua modules with Lmod 8.2.8+ (`#3085 `_, `#3107 `_, `#3110 `_) * add support for ``--sync-pr-with-develop`` (`#3087 `_) * add support for ``--new-branch-github``, ``--new-pr-from-branch``, ``--sync-branch-with-develop``, ``--update-branch-github`` (`#3103 `_) * fix typo in docstring for ``new_branch_github`` (`#3106 `_) * various bug fixes, including: * correctly handle ``iccifortcuda`` toolchain with standalone ``iccifort`` in ``det_toolchain_compilers`` (`#3055 `_) * init git repo with ``git.repo.clone()`` instead of ``copy_dir()`` (`#3062 `_) * fix regular expression so depends-on statements are recognized correctly in Tcl module files (`#3065 `_) * update GitPython to latest version that supports Python 2.6 in requirements.txt to fix broken ``test_new_update_pr`` (`#3066 `_) * imply ``--disable-pre-create-installdir`` with ``--inject-checksums`` (`#3069 `_) * handle patches in extensions more like normal patches (`#3067 `_) * take into account that ``platform.linux_distribution`` and ``platform.dist`` was removed in Python 3.8 (`#3078 `_) * always include mandatory easyconfig parameters in dumped easyconfig (`#3081 `_) * hide backup module file when using Lmod 6.x (fixes `#9302 `_) (`#3089 `_) * add better error message when mandatory key is missing from a dictionary easyconfig parameter (`#3092 `_) * also create symlinks for default modules in class module folders (`#3093 `_) * fix semantics of ``--set-default-module``: only set default for specified easyconfigs, not for the ones that are installed as dependencies via ``--robot`` (`#3094 `_) * fix various issues in extracting comments from original easyconfig file and including them again in dumped easyconfig (`#3095 `_) * don't use ``%(version)s`` template in ``exts_default_options`` in dumped easyconfig (`#3096 `_) * fix generated module statements in case only a single version is listed in ``multi_deps`` (`#3097 `_) * fix broken ``test_show_system_info`` on macOS due to 'Python' binary (`#3105 `_) * take into account that dependency version could be a dict rather than a string value in template_constant_dict (`#3111 `_) * other changes: * deprecate running EasyBuild with Python 2.6 via new ``check_python_version()`` function (`#3076 `_) * deprecate support for using Lmod 6.x (`#3077 `_) * trim set of test configurations in Travis CI (`#3086 `_) * flesh out ``env_vars_external_module`` from ``Toolchain._simulated_load_dependency_module`` (`#3088 `_) **easyblocks** * new software-specific easyblock for cuDNN, to allow setting ``cudnnarch`` (`#1855 `_) * refactored software-specific easyblock for Xmipp, based on Scons (`#1837 `_) * minor enhancements, including: * add ``prebuildopts`` to Bazel build command (`#1838 `_) * add support to Toolchain generic easyblock for defining $EB* environment variables for toolchain components that use an external module (`#1849 `_) * add support for running 'pip check' during sanity check in generic PythonPackage easyblock (`#1853 `_) * various bug fixes, including: * clean up ``/tmp/cuda-installer.log`` in CUDA easyblock, to avoid segfault in cuda-installer (`#1835 `_) * minor fix to name of Gctf binary (`#1840 `_) * move BLAS toolchain existence check earlier in SuperLU easyblock (`#1842 `_) * fixes for TensorFlow easyblocks w.r.t. Bazel build options & ``__init__`` in top-level google-protobuf package dir (`#1843 `_) * fix support for sequential version in MUMPS easyblock (`#1845 `_) * change default value of ``files_to_copy`` to None in MakeCp generic easyblock + code cleanup & use ``change_dir``, ``copy_dir``, ``copy_file`` and ``mkdir`` function from ``filetools`` (`#1848 `_) * prepend ``-L$EBROOTZLIB/lib`` to ``LDFLAGS`` in SCOTCH easyblock (`#1850 `_) * improve configuration in netCDF and netcdf4_python easyblocks (`#1852 `_) * fix CUDA header paths for TensorFlow versions < 1.14 (`#1854 `_) * handle incorrect regex better in generic CmdCp easyblock (`#1861 `_) * add missing docstrings in cmakeninja easyblock (`#1867 `_) * other changes: * add GitHub Actions workflow to run easybuild-easyblocks test suite (`#1844 `_) **easyconfigs** * added example easyconfig files for 46 new software packages: * Amara (`#9340 `_), anvio (`#9387 `_), Arriba (`#9226 `_, `#9244 `_), attr (`#7824 `_), bibtexparser (`#9284 `_), bwa-meth (`#9217 `_), CITE-seq-Count (`#9237 `_), CoordgenLibs (`#9374 `_), dtcmp (`#9052 `_), fatslim (`#9193 `_), GromacsWrapper (`#9177 `_), GULP (`#9243 `_), hdf5storage (`#9195 `_), ITSTool (`#7260 `_), kim-api (`#8786 `_), kwant (`#9238 `_), libarchive (`#9052 `_), libcircle (`#9052 `_), libxml2-python (`#7260 `_), lifelines (`#9215 `_), lwgrp (`#9052 `_), maeparser (`#9374 `_), MaxQuant (`#9281 `_), MethylDackel (`#9216 `_), MoviePy (`#9205 `_), mpifileutils (`#9052 `_), mpiP (`#9059 `_), nanofilt (`#8502 `_), NOVOPlasty (`#9326 `_), openkim-models (`#8786 `_), parallel-fastq-dump (`#9218 `_), pasta (`#9348 `_), pyqstem (`#9277 `_), python-Levenshtein (`#9237 `_), RapidJSON (`#9373 `_), RDFlib (`#9346 `_), RQGIS3 (`#9125 `_), Short-Pair (`#9376 `_), SpliceMap (`#9375 `_), TRIQS-cthyb (`#9230 `_), TRIQS-dft_tools (`#9230 `_), TRIQS-tprf (`#9230 `_), UMI-tools (`#9237 `_), VarDict (`#7283 `_), Xmipp (`#9257 `_), XSD (`#9347 `_) * added additional easyconfigs for various supported software packages, including: * awscli 1.16.290, BLIS 0.6.0, Bazel 1.1.0, Biopython 1.75, Blender 2.81, bokeh 1.4.0, CONCOCT 1.1.0, CUDA 10.2.89, Catch2 2.11.0, CellRanger 3.1.0, CheckM 1.0.18, dask 2.8.0, deepTools 3.3.1, FastANI 1.2, Flye 2.6, GDCM 3.0.4, GTDB-Tk 0.3.2, Glade 3.8.6, Hadoop 2.9.2, h5py 2.10.0, hypothesis 4.44.2, IPython 7.9.0, Kaiju 1.7.2, Kraken 1.1.1, libsodium 1.0.18, MEGAHIT 1.2.8, Mesa 19.2.1, MetaBAT 2.14, matplotlib 3.1.1, metaWRAP 1.2.2,cNCCL 2.4.8, NGS 2.10.0, NiBabel 2.5.1, netCDF 4.7.1, networkx 2.4, numba 0.46.0, OpenCV 3.4.7, OpenCoarrays 2.8.0, OpenEXR 2.4.0, OpenFOAM v1906, OpenImageIO 2.0.12, ParaView 5.6.2, Pillow 6.2.1, PyTorch 1.3.1, PyYAML 5.1.2, Pysam 0.15.3, picard 2.21.1, prokka 1.14.5, protobuf 3.10.0, R-keras 2.2.5.0, Racon 1.4.7, SCOTCH 6.0.9, SRPRISM 3.1.1, Salmon 0.14.2, SciPy-bundle 2019.10, Subread 2.0.0, scikit-image 0.16.2, scikit-learn 0.21.3, TRIQS 2.2.1, TensorFlow 1.15.0, TensorFlow 2.0.0 w/ fosscuda/2019b, Tkinter 3.7.4, ToFu 1.4.1, tbb 2019_U9, Xerces-C++ 3.2.2, Xmipp 3.19.04, yaff 1.6.0 * added easyconfigs for ``intelcuda/2019a`` toolchain (`#9271 `_) * minor enhancements, including: * tweak Java 1.8 wrapper to use different Java version on POWER systems (`#9081 `_) * add jupyter_nbextensions_configurator extension to IPython 7.7.0 easyconfigs (`#9133 `_) * add additional extensions to R 3.6.0 easyconfigs (`#9184 `_, `#9275 `_) * add additional extensions to R-bundle-Bioconductor 3.9 easyconfig (`#9185 `_, `#9349 `_, `#9410 `_) * enhance sanity check in cutadapt 1.18 easyconfigs + consistently use PythonBundle & ``use_pip`` (`#9219 `_) * update cuDNN 7.6.4.38 easyconfigs to support both x86_64 and ppc64le (`#9331 `_) * tweak NCCL 2.4.8 easyconfig to support x86_64 and ppc64le (`#9336 `_) * define ``$SPARK_HOME`` in generated module file for Spark 2.4.0 (`#9408 `_) * add sanity check command for matplotlib 3.x with Python 3 to check import from mpl_toolkits (`#9413 `_, `#9414 `_) * various bug fixes, including: * explicitly set ``SYSCONFDIR`` configure option in TurboVNC easyconfig (`#9137 `_) * patch pigz Makefile so zlib provided by EasyBuild is picked up (`#9138 `_) * add libjpeg-turbo as dependency to recent LibTIFF easyconfigs, to avoid picking up LibTIFF installed in system (`#9146 `_) * add freetype as dependency to OpenImageIO, to avoid picking up freetyype installed in system (`#9147 `_, `#9152 `_) * fix definition of ``fosscuda/2019b`` to make sure it works with hierarchical MNS (`#9178 `_) * add missing setuptools_scm extension required to build dateutil extension in Python 3.7.0 easyconfigs (`#9209 `_) * add Python as build dependency for recent Bazel versions (`#9223 `_, `#9299 `_, `#9342 `_) * fix homepage & description in Bioconductor easyconfigs (`#9225 `_) * fix checksum in Stacks 2.41 easyconfig after sneaky re-release (`#9232 `_) * apply fixes to ImageJ 1.51k easyconfig (`#9245 `_) * consistently use patch for OpenCV 3.4.7 (`#9279 `_) * use protobuf 3.10.0 as build dep for TensorFlow 2.0.0 w/ fosscuda/2019b + use nodocs variant of git as build dep (`#9298 `_) * add Jasper dependency to Qt5 v.5.13.1 (`#9313 `_) * fix Python 3.7.2 required OpenSSL version for old OS to the one provided on the same toolchain (`#9324 `_) * add missing extensions required by Sphinx & pytest to easyconfigs for Python 3.7.2 and 3.7.4 (`#9329 `_) * update TensorFlow v1.14.0 + v2.0.0 CUDA patch to handle compiler wrappers like ccache (`#9333 `_) * patch binutils 2.31.1 and 2.32 to fix compatibility with RHEL8 (`#9335 `_) * add missing extensions in TensorFlow 2.0.0 easyconfigs (+ update to tensorboard/tensorflow-estimator 2.0.1) (`#9338 `_) * fix logic to determine location of scripts dir + ensure right compiler flags are used in KAT easyconfigs (`#9360 `_) * add missing GCCcore-6.3.0_fix-sanitizer_linux.patch in GCCcore 6.4.0 easyconfig (`#9362 `_) * fix linker errors when linking with libhts.a for MetaBAT 2.12.1 (`#9379 `_) * add egg-info file via patch in VTK v8.2.0, for Pytho 2.7.15, 3.7.2, 3.7.4 (`#9386 `_) * promote binutils to a runtime dependency for Python in GCCcore based builds (`#9402 `_) * fix archive URL typo for ncdf4 (`#9407 `_) * fix problems with mpl_toolkits namespace for matplotlib easyconfigs using Python 2 (`#9415 `_, `#9416 `_, `#9417 `_) * other changes: * ignore commented out lines in easyconfig files when checking for http:// URLs (`#9224 `_) * add GitHub Actions workflow to run easybuild-easyconfigs test suite (`#9231 `_, `#9255 `_) * archive old patches for Xmipp 3.1 (`#9256 `_) * speed up easyconfigs test suite by avoiding re-parsing and re-ordering of easyconfigs (`#9236 `_) * only run easyconfigs test suite with Python 2.7 & 3.6 + Lmod 7 in Travis CI (`#9297 `_) * archive ACML easyconfigs (`#9367 `_) * update CMake build in Eigen 3.3.7 to use more recent toolchain (`#9398 `_) .. _release_notes_eb401: EasyBuild v4.0.1 (October 15th 2019) ------------------------------------ bugfix/update release **framework** * various enhancements, including: * add '``parallel``' to list of config templates (`#3036 `_) * add GitHub Actions workflow to run easybuild-framework test suite (`#3039 `_) * add '``retest``' as a reason to ``--close-pr``, to close/re-open PRs to trigger re-test in Travis (`#3040 `_) * define ``$EB_SCRIPT_PATH`` in '``eb``' wrapper script, and consider it before location of '``eb``' determined via ``$PATH`` in ``get_paths_for`` function (`#3046 `_) * add support for ``--remove-ghost-install-dirs`` configuration option, and warn about (potential) ghost install dirs by default when ``--force``/``--rebuild`` is used (`#3050 `_) * various bug fixes, including: * update bootstrap script to support installing EasyBuild v4.0 (`#3017 `_) * fix broken ``test_download_repo`` due to archiving of easyconfigs (`#3019 `_, `#3023 `_) * avoid that ``--inject-checksums`` introduces list of patches for extensions as a single long line (`#3025 `_, `#3034 `_) * enhance regex in ``fix_shebang`` method to fix more Python/Perl shebangs + avoid patching binary files (`#3029 `_) * delete test gist that is created by ``--check-github`` (`#3031 `_) * disable templates when defining easyconfig parameters in ``EasyConfig.set_keys()`` (`#3037 `_) * avoid setting GC3Pie's max_in_flight to ``None`` if ``--job-max-jobs`` is not specified (`#3038 `_) * fix use of ``obtain_file`` method for extensions (`#3042 `_) * error out if some GC3Pie job failed (`#3044 `_) **easyblocks** * one new generic easyblock: ``CMakeNinja`` (`#1829 `_) * new software-specific easyblock for Gctf (`#1827 `_), MotionCor2 (`#1819 `_) * minor enhancements, including: * update OpenFOAM easyblock for changes in version 1906 w.r.t. wamke rules (`#1772 `_) * add ``%(cudaarch)s`` template variable so that it can be used in sources (`#1797 `_) * update Boost easyblock for versions >=1.71.0 (`#1814 `_) * update RepeatMasker easyblock for version 4.0.9 (`#1815 `_) * add ``--verbose`` flag to '``pip install``' when running EB in debug mode (`#1822 `_) * update TensorFlow easyblock to support TensorFlow 2.0 (`#1823 `_) * add support in TensorFlow easyblock to run a custom test script as smoke test (`#1824 `_) * add support for installing QScintilla on top of PyQt5 (`#1825 `_) * update VEP easyblock to make installation compatible with ``Bio::EnsEMBL::XS`` (`#1828 `_) * various bug fixes, including: * enhance TensorFlow easyblock to support installing TF 1.14.0 with CUDA and MPI support (`#1811 `_, `#1816 `_) * avoid ``UnicodeDecodeError`` when reading '``configure``' script and checking for '``Generated by GNU Autoconf``' in ``ConfigureMake`` (`#1817 `_, `#1821 `_) * don't require '``python``' command to install libxml2 without Python bindings (`#1818 `_) * make sure "``generic=True``" actually turns on generic build in GCC easyblock (`#1826 `_) * fix compatibility of Trilinos easyblock with Python 3 (`#1831 `_) **easyconfigs** * added example easyconfig files for 58 new software packages: * ADOL-C (`#9098 `_), ALFA (`#9106 `_), ASTRID (`#9088 `_), Annif (`#8536 `_), bnpy (`#8989 `_), bpp-core (`#9064 `_), bpp-phyl (`#9064 `_), bpp-seq (`#9064 `_), Clang-Python-bindings (`#9084 `_), CPB (`#5869 `_), Centrifuge (`#8714 `_), Chromaprint (`#9047 `_), Con3F (`#8755 `_), DeepSurv (`#8096 `_), Essentia (`#9054 `_), FastRFS (`#9088 `_), GAT (`#5871 `_), Gaia (`#9049 `_), Gctf (`#9097 `_), GenomeMapper (`#5872 `_), Infomap (`#9091 `_), kpcalg (`#8740 `_), libglvnd (`#9111 `_, `#9130 `_), libsamplerate (`#9046 `_), libssh (`#8865 `_), libzip (`#9073 `_), MetaboAnalystR (`#8773 `_), Metaxa2 (`#8939 `_), MotionCor2 (`#8942 `_), NFFT (`#9085 `_), PhyML (`#9103 `_), PlaScope (`#8714 `_), PyCharm (`#9100 `_), pbcopper (`#8928 `_), pbmm2 (`#8929 `_), phylokit (`#9088 `_), phylonaut (`#9088 `_), phyx (`#9090 `_), pycma (`#8834 `_), Q6 (`#9069 `_), Qt5Webkit (`#9120 `_), ROME (`#9050 `_, `#9062 `_), rioxarray (`#9007 `_), SVDquest (`#9088 `_), savvy (`#9124 `_), sciClone (`#7806 `_), shapAAR (`#8983 `_), shrinkwrap (`#9124 `_), Structure (`#5866 `_), trimAl (`#9063 `_), thurstonianIRT (`#9080 `_), TurboVNC (`#9110 `_, `#9111 `_, `#9128 `_), Tracer (`#8970 `_), TagLib (`#9048 `_), TRIQS (`#8835 `_), THetA (`#8875 `_), vcfnp (`#5862 `_), WebSocket++ (`#8842 `_) * added additional easyconfigs for various supported software packages, including: * Armadillo 9.700.2, arpack-ng 3.7.0, BLASR 5.3.3, Bazel 0.26.1 + Bazel 0.29.1, Cufflinks 20190706, DL_POLY_Classic 1.10, FFmpeg 4.2.1, Go 1.13.1, Horovod 0.18.1, IOR 3.2.1, Julia 1.2.0, LLVM 9.0.0, Mesa 19.1.7, Molden 6.1, Mono 6.4.0.198, NCO 4.8.1, , Net-core 3.0.0, Nim 1.0.0, OpenFOAM 2.2.x, PGI 19.7, PLUMED 2.5.2, PMIx 3.1.4, PostgreSQL 11.3, psycopg2 2.8.3, QGIS 3.4.12, QScintilla 2.11.2, Qt5 5.13.1, ReFrame 2.19, Rust 1.37.0, Spack 0.12.1, TAMkin 1.2.6, TensorFlow 1.14.0 w/ fosscuda/2019a, TensorFlow 2.0.0 w/ foss/2019a, UCX 1.6.1, VEP 96.0, xarray 0.13.0 * added easyconfigs for ``fosscuda/2019a`` toolchain (`#9066 `_) * minor enhancements, including: * add EBImage extension to easyconfig for R-bundle-Bioconductor 3.9 (`#8982 `_) * add check for ``http://`` URLs in easyconfig files added/changed in PRs (`#9012 `_) * add bbmle/emdbook/SOAR/rasterVis/tictoc extensions to R 3.6.0 easyconfigs (`#9037 `_) * updated PyQt5 5.12.1 easyconfig to also build sip files + minor readability changes (`#9071 `_) * enabled ``SQLITE_ENABLE_COLUMN_METADATA``, which is needed for GDAL (and QGIS) (`#9118 `_) * also install include/GL/internal/ for recent Mesa installations (`#9129 `_) * various bug fixes, including: * add ncurses as dependency to lftp (`#8646 `_) * add patch for gettext 0.19.8* to avoid picking up global git config that could break the installation (`#8957 `_) * fix source URLs in GlimmerHMM easyconfigs (`#8980 `_) * add patch for PyTorch 1.2.0 to use version of torchvision that is compatible with PyTorch 1.2.0 (`#8986 `_) * clarify the comment regarding the optarch setting in ITK-5.0.1 (`#8991 `_) * fix homepage & description in easyconfig file for YAPS (`#8993 `_) * add patch for PyTorch 1.2.0 to fix failing softmax test on Intel Sandy Bridge (`#9010 `_) * fix permissions for TRF (`#9034 `_) * ICU needs Python 2.7+ to build, so add that as builddependency (`#9053 `_) * fix urls for Anaconda and Miniconda (`#9087 `_) * use a cuDNN version that has support for the CUDA version in ``fosscuda/2019a`` (CUDA 10.1) in PyTorch, TensorFlow and Theano easyconfigs (`#9112 `_) * other changes: * make sources in CUDA 10.1.105 use ``%(cudaarch)s`` template value (to use different source on POWER systems) (`#8136 `_) * update ``Java/1.8`` wrapper to ``Java/1.8.0_221`` (`#9038 `_) * allow divergent Java dep version as long as it's indicated by versionsuffix (`#9041 `_) .. _release_notes_eb400: EasyBuild v4.0.0 (September 20th 2019) -------------------------------------- feature release (incl. backwards-incompatible changes) **framework** * **fixed compatibility with Python 3.5+** (`#2708 `_, `#2713 `_, `#2714 `_, `#2719 `_, `#2721 `_, `#2723 `_, `#2729 `_, `#2743 `_, `#2744 `_, `#2751 `_, `#2756 `_, `#2759 `_, `#2761 `_, `#2762 `_, `#2765 `_, `#2766 `_, `#2767 `_, `#2768 `_, `#2774 `_, `#2775 `_, `#2778 `_, `#2780 `_, `#2785 `_, `#2787 `_, `#2789 `_, `#2791 `_, `#2792 `_, `#2794 `_, `#2800 `_, `#2801 `_, `#2805 `_, `#2806 `_, `#2895 `_, `#2932 `_, `#2982 `_, `#2992 `_, `#3007 `_, `#3011 `_) * supported Python versions: 2.6, 2.7, 3.5, 3.6, 3.7 * some functionality from the Python standard library should be imported from the new ``easybuild.tools.py2vs3`` package * see :ref:`py2_py3_compatibility` & :ref:`eb4_relocated_functions_classes_constants` * **ingested relevant code from** ``vsc-base`` & ``vsc-install`` (`#2708 `_, `#2713 `_, `#2714 `_, `#2763 `_, `#2790 `_, `#2993 `_) * ``vsc-base`` & ``vsc-install`` are no longer required as dependencies * the functionality that was provided by these packages is now (mostly) available from the ``easybuild.base`` package * any import statements from the '``vsc``' namespace will result in an error * see also :ref:`eb4_changes_ingested_vsc_base` and :ref:`eb4_relocated_functions_classes_constants` * ``setuptools`` **is longer required** (neither for installing or using EasyBuild) (`#2836 `_, `#2837 `_, `#2984 `_, `#2986 `_, `#2988 `_) * see also :ref:`eb4_no_required_deps` * this required moving some classes and constants, see :ref:`eb4_relocated_functions_classes_constants` * **the** '``dummy``' **toolchain is deprecated and replaced by the** '``system``' **toolchain** (`#2877 `_, `#3001 `_) * if '``dummy``' is still used as a toolchain in easyconfig files, a warning will be printed * use "``toolchain = SYSTEM``" instead * for more information, see :ref:`system_toolchain` * **a warning is printed when local variables in easyconfig file don't follow the recommended naming scheme** (`#2938 `_, `#2968 `_) * see also :ref:`easyconfig_files_local_variables` * **names of software installation directories are independent of module naming scheme by enabling** ``--fixed-installdir-naming-scheme`` **by default** (`#2999 `_) * see :ref:`eb4_changes_fixed_installdir_naming_scheme` for more information * various other small enhancements, including: * use requests instead of urllib2 for 403 errors (`#2695 `_) * use pip requirements file in Travis (`#2874 `_) * add support for ``--fix-deprecated-easyconfigs`` (`#2881 `_, 2898, `#2938 `_) * add ``-L$EBROOTIMKL/lib/intel64`` to ``$LDFLAGS`` for MKL (`#2930 `_) * handle dict-type checksums in check_checksums_for (`#2974 `_) * allow that ``icc`` & ``ifort`` are not actual dependencies in ``iccifort`` toolchain module (`#2995 `_) * define mapping for ``iccifort``->``intel`` for ``iccifort`` compiler-only toolchain for HMNS (`#2996 `_) * also consider concatenation of compiler module names to determine details of toolchain compiler component (`#2997 `_) * update metadata for Cray-provided external modules (`#3013 `_) * various bug fixes, including: * update the PyPI trove classifiers in setup.py (`#2875 `_) * reverse lists for ``$LDFLAGS`` and ``$CPPFLAGS`` (`#2931 `_) * enhance/fix to_template_str function to do a better job at using template values in dumped easyconfigs (`#2948 `_) * also take into account ``--filter-deps`` when finalizing parsed dependencies to fix problem with dependency filters using version ranges (`#2983 `_) * fix broken ``--from-pr`` tests due to archiving of easyconfigs (`#2985 `_) * fixes required to avoid breaking Cray support (`#3008 `_) * fixes for ``--read-only-installdir``: avoid crash with ``ModuleRC`` easyblock + also make log file in installdir read-only (`#3012 `_) * other changes: * add check to ensure that ``--robot`` argument specifies an existing directory (`#2086 `_) * remove old scripts that are no longer useful (+ minor fixes to others) (`#2897 `_) * use '``command -v``' to avoid requiring '``which``' in '``eb``' command (`#2979 `_) * add ``modluafooter`` & ``modtclfooter`` at the end of the generated module file (`#3003 `_) * print warning when '``eb``' command is not found in ``$PATH`` and for empty robot search path (`#3006 `_) **easyblocks** * fixes due to backwards-incompatible changes in easybuild-framework v4.0.0 * use ``is_system_toolchain()`` rather than checking toolchain name against DUMMY_TOOLCHAIN_NAME constant (`#1690 `_, `#1728 `_) * fix compatibility of various easyblocks with Python 3 (`#1640 `_, `#1644 `_, `#1648 `_, `#1721 `_, `#1794 `_, `#1808 `_, `#1795 `_, `#1796 `_, `#1807 `_, `#1809 `_) * new software-specific easyblocks for ``OpenMPI`` (`#1789 `_, `#1801 `_), ``iccifort`` (`#1799 `_) and ``numexpr`` (`#1803 `_, `#1804 `_) * various other enhancements, including: * removed checks for Boussinesq and sonic solvers for OpenFOAM 7, since those have been deprecated (`#1733 `_) * update Paraver easyblock to support recent versions (`#1790 `_) * various bug fixes, including: * update the PyPI trove classifiers (`#1723 `_) * make the plugins build use the correct Tcl library version in VMD easyblock (`#1786 `_) * use ``*_MT libs`` for BLAS/LAPACK only if ``openmp`` is enabled in Trilinos easyblock (`#1791 `_) * filter out empty entries in ``$CPATH`` or ``$C_INCLUDE_PATH`` when building Perl, since that breaks the build (`#1800 `_) * set ``$XDG_CACHE_HOME`` in TensorFlow easyblock to avoid that ``pip`` (ab)uses ``$HOME/.cache`` (`#1802 `_) * don't load modules for dependencies in ``CrayToolchain.prepare_step`` (`#1805 `_) * other changes: * drop requirement for setuptools as runtime dependency (`#1689 `_) * enable '``check_ldshared``' in generic PythonPackage easyblock by default for recent Python versions (`#1788 `_) * stop trying to use ``setuptools.setup`` in ``setup.py``, always use ``distutils.core.setup`` instead (`#1793 `_) **easyconfigs** * fixes due to changes in easybuild-framework v4.0.0 * use ``SYSTEM`` toolchain rather than deprecated ``dummy`` toolchain (`#8369 `_, `#8711 `_, `#8822 `_) * fix names of local variables (`#8682 `_-`#8688 `_, `#8690 `_, `#8695 `_-`#8702 `_, `#8709 `_, `#8710 `_, `#8715 `_, `#8717 `_, `#8718 `_, `#8720 `_-`#8732 `_, `#8822 `_) * enable ``--local-var-naming-check=error`` for easyconfigs tests (`#8784 `_) * stick to '``dummy``' toolchain for now in easyconfig for latest EasyBuild 3.x (`#8829 `_) * fix compatibility with Python 3: also run easyconfigs tests with Python 3.5, 3.6 and 3.7 (`#7778 `_, `#7836 `_, `#8293 `_) * added easyconfigs for new common toolchains: ``foss/2019b`` (`#8567 `_), ``intel/2019b`` (`#8681 `_) * ``iccifort`` is now installed as a single entity (no more separate ``icc``/``ifort`` installations from ``intel/2019b`` onwards) (see also `#8879 `_) * ``versionsuffix`` has been stripped down for toolchain components (GCC/binutils/OpenBLAS versions are no longer included) * see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html * added example easyconfig files for 28 new software packages: * AGFusion (`#8840 `_), Bonmin (`#8855 `_), causalml (`#8871 `_), ClonalFrameML (`#6082 `_), Control-FREEC (`#8794 `_), corner (`#8886 `_), CVXPY (`#8662 `_), cytosim (`#8368 `_), dill (`#8885 `_), Dsuite (`#8713 `_), GDCHART (`#8679 `_), gifsicle (`#8664 `_), guenomu (`#8677 `_), JsonCpp (`#8841 `_), libxml++ (`#8896 `_), LOHHLA (`#7227 `_), Longshot (`#8830 `_), MDBM (`#8850 `_), nglview (`#8860 `_), ownCloud (`#6804 `_), ptemcee (`#8884 `_), pubtcrs (`#7500 `_), pyiron (`#8860 `_), qpth (`#8665 `_), QtKeychain (`#6804 `_), rgdal (`#8826 `_), smallgenomeutilities (`#8507 `_), umis (`#8812 `_) * added additional easyconfigs for various supported software packages, including: * Blosc 1.17.0, bokeh 1.3.4, cURL 7.66.0, csvkit 1.0.4, dask 2.3.0, Extrae 3.7.1, FSL 6.0.1, GLibmm 2.49.7, git 2.23.0, IPython 7.7.0, numexpr 2.7.0, OSU-Micro-Benchmarks 5.6.2, OpenBLAS 0.3.7, OpenSSL 1.1.1d, ParaView 5.5.2, Paraver 4.8.1, Perl 5.30.0, PnetCDF 1.10.0, Porechop 0.2.4, PyTables 3.5.2, PyTorch 1.2.0, Python 2.7.16 + 3.7.4, parallel 20190622, phonopy 2.2.0, QIIME2 2019.7, Qiskit 0.12.0, REMORA 1.8.3, scikit-image 0.15.0, spglib-python 1.14.1.post0, torchvision 0.3.0, X11 20190717 * various additional minor enhancements, including: * add several extensions to R 3.6.0 easyconfigs (`#8843 `_, `#8881 `_) * add pRoloc to R-bundle-Bioconductor v3.9 (`#8882 `_) * clean up OpenMPI 3.1.* and 4.* easyconfigs to use custom OpenMPI easyblock (`#8889 `_, `#8890 `_) * update numexpr easyconfigs to use custom easyblock for numexpr (`#8901 `_) * switch to ``PythonBundle`` & enable use_pip in old dask easyconfig files (`#8922 `_) * update ``CrayCCE``, ``CrayGNU``, ``CrayIntel`` and ``CrayPGI`` toolchains to 19.06 (`#8944 `_) * various bug fixes, including: * make TensorFlow 1.7.0 work for AMD CPUs (`#6256 `_) * make sure that right Python wrapper is used in VTK8 (`#7296 `_) * update the PyPI trove classifiers (`#8298 `_) * add missing checksum for matplotlib v3.0.3 (`#8643 `_) * add patch to ``plugins/Make-arch`` to use the correct Tcl library version in VMD (`#8820 `_) * fix issue where '``print_qiime_config.py -t``' sanity check command fails for QIIME 1.9.1 because of missing subdir in ``$PYTHONPATH`` (`#8838 `_) * update homepage info in likwid (`#8846 `_) * disable threading in ``preprocessCore`` extension included with Bioconductor 3.9 to work around conflict with OpenBLAS's threading (`#8847 `_) * add ``-lrt`` patch to PyTorch 1.1.0 easyconfig (`#8852 `_) * fix incorrect escaping in SIP configure options in PyQt5 easyconfigs (`#8856 `_) * add missing Autotools build dep for fastq-tools (`#8858 `_) * add missing deps for zlib, bzip2, and XZ for angsd (`#8867 `_) * apply patch to R package uroot in R 3.6.0 (`#8872 `_) * consider archive source URL for all extensions in R-tesseract easyconfig (`#8897 `_) * add pkg-config build dep for tesseract v4.0.0 (`#8898 `_) * fix ``source_urls`` in byacc easyconfig files (`#8899 `_, `#8908 `_) * add missing cairo dependency to PRINSEQ easyconfig file (`#8902 `_) * configure OpenMPI 1.10.x with ``--without-ucx`` to avoid problems when ``ucx-devel`` is installed in the OS (`#8903 `_) * add GDAL 3.0.0 for Python 2.7.15 and fix the Python 3.7.2 version (`#8912 `_) * fix homepage & description in scikit-image easyconfigs (`#8916 `_) * add faulthandler patches to Python 3.7.0 easyconfigs (`#8832 `_) * other changes: * archive ancient CUDA 5.0.35 easyconfigs with creative way of determining sources (`#7796 `_) * remove ancient easyconfigs from archive (`#8542 `_) * archive easyconfigs using deprecated toolchains (`#8557 `_, `#8558 `_, `#8585 `_) * archive ancient versions of GC3Pie/GCC/OpenMPI/ORCA (`#8586 `_) & CPLEX (`#8765 `_) * rename SALMON to SALMON-TDDFT to fix name clash with Salmon (`#8613 `_) * bump AnnotationDb version in bundle for Bioconductor 3.9 (`#8854 `_) * stop trying to use ``setuptools.setup`` in ``setup.py``, always use ``distutils.core.setup`` instead (`#8866 `_, `#8892 `_, `#8894 `_) * archive easyconfigs using ancient ``Cray*`` toolchains (`#8945 `_) .. _release_notes_eb394: EasyBuild v3.9.4 (August 23rd 2019) ----------------------------------- bugfix/update release **framework** * various enhancements, including: * add support for specifying checksum via dict providing a filename-to-checksum mapping (`#2946 `_) * enhance 'completed' message with how much time was needed for the installation (`#2956 `_) * add support for specifying tuple of alternative checksums (`#2958 `_) * support using '``system``' as alias for '``dummy``' toolchain + ``SYSTEM`` constant (`#2960 `_) * ensure '``docurls``' easyconfig parameter value is a list of string values, not a single string value (`#2963 `_) * automatically enable ``--ignore-osdeps`` when using ``--check-contrib`` or ``--check-style`` (`#2965 `_) * various bug fixes, including: * escape '``+``' in search queries + handle invalid search queries better (`#2967 `_) * also consider extension patches when determining for which easyconfig a given patch file is intended in ``--new-pr``/``--update-pr`` (`#2969 `_) * unset ``$CDPATH`` early on if it is defined (`#2970 `_) * create specified temporary log directory if it doesn't exist yet in ``init_logging`` (`#2972 `_) * don't indicate first multi_deps version as default in module help text when ``multi_deps_load_default=False`` (`#2973 `_) * other changes: * deprecate toolchains older than ``gompi/2016a`` and ``foss/2016a`` (#2951) **easyblocks** * new software-specific easyblock for MSM (`#1770 `_, `#1775 `_, `#1776 `_) * minor enhancements, including: * allow specifying the license file directly in MATLAB easyblock (`#1712 `_) * enhance CPLEX easyblock to also build Python bindings (`#1738 `_) * workaround for XCrySDen for Tcl 8.6 (`#1749 `_) * update WIEN2k easyblock to support version 19.1 (`#1758 `_) * resolve custom ``%(cudaarch)s`` template value for CUDA sources (`#1766 `_) * enhance sanity check for Blender to make sure that Cycles render engine is available (`#1779 `_) * various bug fixes, including: * only check for qtwebengine in custom easyblock for Qt(5) if glibc is sufficiently recent (`#1771 `_) * correctly define ``comp.src`` in Bundle easyblock, to fix compatibility with easyblocks that leverage ``self.src`` (`#1777 `_) * fix ``Bundle.check_checksums`` to checksums for extensions are also checked (`#1778 `_) **easyconfigs** * added example easyconfig files for 36 new software packages: * ArrayFire (`#8461 `_), BRAKER (`#8437 `_), bwidget (`#8477 `_), Catch2 (`#8703 `_), core-counter (`#8749 `_), CubeGUI (`#6328 `_), CubeLib (`#6328 `_), CubeWriter (`#6328 `_), dagitty (`#8606 `_), enaBrowserTool (`#8795 `_), GEMMA (`#8270 `_), GeneMark-ET (`#8437 `_), GenomeThreader (`#8437 `_), ieeg-cli (`#8793 `_, `#8811 `_), Judy (`#8543 `_), Julia (`#8578 `_), libaio (`#8543 `_), libtirpc (`#8792 `_), magick (`#8545 `_), MSM (`#8556 `_), MSPC (`#8531 `_), mygene (`#8809 `_), OpenMolcas (`#7699 `_), PhiPack (`#8750 `_), plc (`#8796 `_), plotly.py (`#8756 `_), pymemcache (`#8663 `_), PySCF (`#8736 `_), qcint (`#8736 `_), Qiskit (`#7592 `_), QuaZIP (`#8672 `_), re2c (`#8543 `_), SeqAn3 (`#8651 `_), snippy (`#8635 `_), spaln (`#8437 `_), V8 (`#8676 `_) * added additional easyconfigs for various supported software packages, including: * ASE 3.18.0, BEDTools 2.28.0, Bowtie 1.2.3, bzip2 1.0.8, CPLEX 12.9, CUDA 10.1 update 2, cyvcf2 0.11.5, EIGENSOFT 7.2.1, GC3Pie 2.5.2, GCC(core) 9.2.0, GPAW 19.8.1, GlobalArrays 5.7, IMB 2019.3, imageio 2.5.0, jemalloc 5.2.0, nodejs 10.15.3, PyTorch 1.1.0, pybedtools 0.8.0, Quandl 3.4.8, R 3.6.0 w/ intel/2019a, R-bundle-Bioconductor 3.9, Salmon 0.14.1, Scalasca 2.5, Score-P 6.0, Stacks 2.41, TensorFlow 1.14.0, ToFu 1.4.0, WIEN2k 19.1, Wannier90 3.0.0, XCrySDen 1.5.60 * minor enhancements, including: * add patch and dependencies to easyconfig for Qt5 5.12.3 to fix Xlib support & enhance the installation (`#8544 `_) * update nodejs to version 10.15.3 and build libnode and libv8 shared libs (`#8546 `_) * add extensions to R 3.6.0 easyconfig: ``MIIVsem`` (`#8565 `_), ``medflex`` (`#8680 `_), ``Rserve``/``spls`` (`#8758 `_), ``Boruta``/``CovSel``/``ctmle``/``BayesPen`` (`#8805 `_) * include PyQtWebEngine bindings in easyconfig for PyQt5 5.12.1 using Python 3.7.2 (`#8572 `_) * switch GLX backend to Gallium in Mesa-19.0.1 (`#8594 `_) * various bug fixes, including: * fix typo in description in GroopM easyconfig file (`#8346 `_) * add missing bugfix patch to easyconfig for OpenMPI 3.1.4 (`#8566 `_) * downgrade AtomPAW to last supported version in ABINIT 8.10.3 (`#8571 `_) * switch easyconfig for glew 2.1.0 to ``ConfigureMake`` easyblock (`#8595 `_) * fix checksum for source tarball in ``foss/2018b`` easyconfig of NAMD v2.13 (`#8602 `_) * update URL for bzip2 easyconfigs (`#8614 `_) * add patch for M4 1.4.17 to fix installation on top of glibc 2.28 (`#8666 `_) * add patch for Bison 3.0.4 to fix installation on top of glibc 2.28 (`#8675 `_) - avoid needless requirement for matplotlib < 3.0.0 in MultiQC easyconfigs (`#8691 `_) * fix checksum in OpenMPI 1.8.8 easyconfigs (`#8692 `_) * add alternative checksums for ``nlme``/``mgcv``/``foreign``/``boot`` extensions in R 3.5.1 and 3.6.0 easyconfigs (`#8564 `_, `#8762 `_) * add missing core-counter dependency for worker 1.6.8 (`#8749 `_) * add missing pkg-config build dependency in various easyconfigs for (`#8763 `_, `#8775 `_, `#8777 `_, `#8776 `_, `#8764 `_, `#8787 `_, `#8816 `_) * add patch to Python 3.7.2 easyconfig to fix faulthandler segfault (`#8781 `_) * set ``$CPLUS_INCLUDE_PATH`` in easyconfigs for older matplotlib versions (`#8785 `_) * patch out removed glibc 2.28 header from GCC libsanitizer (`#8789 `_) * include ``sysmacros.h`` directly to work around removal from glibc header in numactl easyconfig (`#8790 `_) * adapt gzip's bundled gnulib for glibc 2.28 (`#8791 `_) * add libtirpc and depend on it in easyconfig for libdap 3.20.3 (`#8792 `_) * add missing YAML extension to Perl 5.28.0 easyconfig (required by BioPerl scripts) (`#8806 `_) * other changes: * remove broken easyconfigs for ciftify due to non-trivial missing dependencies (`#8560 `_) .. _release_notes_eb393: EasyBuild v3.9.3 (July 8th 2019) ---------------------- bugfix/update release **framework** * various enhancements, including: * add a URL whatis line to generated module files (`#2933 `_) * various bug fixes, including: * stick to Ubuntu Trusty when testing with Python 2.6 in Travis (`#2928 `_) * honor ``--tmp-logdir`` when determining location of temporary log file (`#2937 `_) **easyblocks** * minor enhancements, including: * also install docs and demos in Rosetta easyblock (`#1745 `_) * update HEALPix easyblock to work with latest version of HEALPix' ``configure.sh`` (`#1752 `_) * make HPCG log pattern more generic, it changed in 3.1 (`#1753 `_) * allow bootstrapping GCC with profile-guided optimizations (`#1756 `_) * only require vsc-base for EasyBuild 2.x and 3.x in EasyBuildMeta easyblock (`#1757 `_) * extend question patterns with '``https``' URL entry in Modeller easyblock for recent versions (`#1762 `_) * ``modextrapaths`` implemented on easyblock level, ``sanity_check_step``, ``gcc_target`` added in HEALPix easyblock (`#1763 `_) * update OpenBLAS easyblock to be aware of POWER9 support in OpenBLAS 0.3.6 (`#1765 `_) * various bug fixes, including: * stick to Ubuntu Trusty when testing with Python 2.6 in Travis (`#1751 `_) * fix scripts installation path in SNPhylo easyblock (`#1759 `_) * be more patient when running interactive ``Allwmake.firstInstall`` command for recent OpenFOAM-Extend versions (`#1761 `_) * also add ``--without-go`` configure option for SWIG as we "disable everything by default" (`#1754 `_) * don't assume cmake arguments when configure_cmd is set in CMakeMake easyblock (`#1750 `_) **easyconfigs** * added example easyconfig files for 25 new software packages: * Arb (`#8137 `_), AtomPAW (`#8506 `_), ciftify (`#8457 `_), cysignals (`#8459 `_), deal.II (`#8440 `_), FastQTL (`#8449 `_), FLINT (`#8137 `_), gdbgui (`#8488 `_), gearshifft (`#8482 `_), jbigkit (`#8442 `_), lavaan (`#8539 `_), libRmath (`#8449 `_), OR-Tools (`#8364 `_, `#8523 `_), p4est (`#8440 `_), ppl (`#8459 `_), pplpy (`#8459 `_), PRISMS-PF (`#8440 `_), PyAPS3 (`#8398 `_), pyEGA3 (`#8418 `_), ReFrame (`#8481 `_), S4 (`#8487 `_), SALMON (`#8478 `_), TM-align (`#8510 `_), UnZip (`#8474 `_), XTandem (`#8517 `_) * added additional easyconfigs for various supported software packages, including: * ABINIT 8.10.3, CFITSIO 3.47, GDB 8.3, GROMACS 2019.3, HEALPix 3.50, HPCG 3.1, Nilearn 0.5.2, OpenBLAS 0.3.6, Xerces-C++ 3.2.0 * minor enhancements, including: * update easyconfig for CFITSIO 3.45 with https and sanity check (`#8472 `_) * add AtomPAW and Wannier90 support to ABINIT 8.10.2 easyconfig (`#8506 `_) * add '``resample``' extension to R 3.5.1 + 3.6.0 easyconfigs (`#8538 `_) * various bug fixes, including: * fix source URLs for Mesa 17.{2,3} with fosscuda toolchain (`#8446 `_) * add in Boost dependency to canu-1.8 easyconfigs using ``foss`` toolchain (`#8470 `_) * stick to Ubuntu Trusty when testing with Python 2.6 in Travis (`#8483 `_) * fix incorrect order of extensions for Python-2.7.14 easyconfigs (``pycparser`` and ``cffi`` must come before ``cryptography``) (`#8495 `_) * suppress installation of ``libbfd`` and ``libopcode`` for GDB (`#8496 `_) * fix KronaTools easyconfigs to make sure symlinks in bin are not broken (`#8508 `_) * make additional configopts in PETSc easyconfigs work after uncommenting (`#8522 `_) * add ``pkg-config`` build dep to easyconfig for pocl 1.2 (`#8528 `_) * download correct source tarball for Net-core 2.1.8 (`#8530 `_) * fix '``Permission denied``' error when running '``cp -a``' for ANTs 2.3.1 installation by first removing the ``.git`` subdirectories causing them (`#8535 `_) * fix checksum for boot 1.3-22 extension in R 3.6.0 easyconfig (`#8537 `_) .. _release_notes_eb392: EasyBuild v3.9.2 (June 9th 2019) -------------------------------- bugfix/update release **framework** - various enhancements, including: - enhance (experimental) support for generating Singularity container recipes/images (`#2884 `_, `#2900 `_, `#2902 `_, `#2903 `_, `#2907 `_, `#2909 `_, `#2910 `_, `#2913 `_, `#2915 `_) - add support for specifying container configuration via ``--container-config`` (``--container-base`` option has been removed) - add support for providing custom template for container recipe via ``--container-template-recipe`` - add support for '``sif``' Singularity 3.x container image format - add support for specifying non-image based Singularity bootstrap agents - install default set of OS packages in container recipes starting from scratch - configure Lmod and update Lmod spider cache in generated Singularity container recipes - configure EasyBuild via environment variables (to allow overriding configuration settings via options to '``eb``' command) - also consider ``/tmp/easybuild/sources`` in source path (to allow seeding in sources in container build environment) - updated documentation is available at https://easybuild.readthedocs.io/en/latest/Containers.html - various bug fixes, including: - make sure that easyconfig file for EasyBuild version being bootstrapped is found in robot search path (`#2899 `_) - remove interpreter options when fixing script shebang (`#2905 `_, `#2906 `_) - fix crash on iterated installation when using Cray toolchains (`#2914 `_) - disable checking of read/exec permissions when checking for availability of '``sudo``' command (`#2918 `_) - other changes: - stick to vsc-base < 2.9.0 in bootstrap script to avoid requiring '``future``' dependency (`#2892 `_) **easyblocks** - new software-specific easyblock for ELPA (`#1621 `_) - minor enhancements, including: - allow Boost to build both Python 2 and Python 3 libraries (`#1718 `_) - update CPLEX sanity check: convert tool was removed in CPLEX 12.8 (`#1737 `_) - don't try to patch ``CROSSTOOL`` script for recent Bazel versions (since it's no longer there) (`#1741 `_) - various bug fixes, including: - fix version check on using '``-log``' option to '``Allwmake``' in OpenFOAM easyblock (`#1739 `_) - fix GROMACS easyblock for list-type ``configopts`` (`#1740 `_) - fix configure step for GROMACS version < 4.6 (`#1742 `_) **easyconfigs** - added example easyconfig files for 17 new software packages: - adjustText (`#8354 `_), cowsay (`#8380 `_), fxtract (`#8426 `_), google-java-format (`#8373 `_), libtar (`#8379 `_), mkl-service (`#8390 `_), msprime (`#8371 `_), pygrib (`#8395 `_), pyhdf (`#8394 `_), pyproj (`#8395 `_), PyStan (`#8410 `_), Racon (`#8358 `_), rapidtide (`#8256 `_), SingleM (`#8428 `_), smafa (`#8420 `_), SVDetect (`#8399 `_), Unicycler (`#8376 `_) - added additional easyconfigs for various supported software packages, including: - BLAST+ 2.9.0, Boost.Python 1.70.0, DIAMOND 0.9.24, EMAN2 2.3, ecCodes 2.12.5, GDAL 3.0.0, ImageMagick 7.0.8-46, Libint 2.5.0, matplotlib 2.2.4, NLopt 2.6.1, OrfM 0.7.1, PGI 19.4, PostgreSQL 11.3, R 3.6.0, R-bundle-Bioconductor 3.8, Rust 1.35.0, STAR 2.7.1a - minor enhancements, including: - use CMake rather than configure script for libxc 4.3.4 (`#8361 `_, `#8453 `_) - add '``cobs``' extension to R 3.5.1 easyconfigs (`#8389 `_) - add sanity check command to PSI4 1.2.1 easyconfigs to ensure that '``import psi4``' works (`#8393 `_) - include the provided backports patch in QuantumESPRESSO-6.4.1 (`#8405 `_) - add ``Logger::Simple``, ``Scalar::Util::Numeric``, ``YAML``, ``Object::InsideOut`` extensions to Perl 5.28.1 easyconfig (`#8432 `_) - update Java 1.8 to 1.8.0_212 (`#8443 `_) - various bug fixes, including: - add missing build dependency on gettext to ATK/2.28.1 for fosscuda/2018b (`#8402 `_) - add patch to fix OpenBLAS v0.3.1 matrices multiplication issue (`#8396 `_) - make Eigen a build dependency for nanopolish (`#8448 `_) - other changes: - clean up ELPA 2018.11.001 easyconfig to use custom easyblock for ELPA (`#8360 `_) - remove unused checksum for ``ballgown`` extension in Bioconductor 3.7 easyconfigs (`#8363 `_) .. _release_notes_eb391: EasyBuild v3.9.1 (May 20th 2019) -------------------------------- bugfix/update release **framework** * various enhancements, including: * add function to determine whether specified easyblock is generic or not (`#2838 `_) * add support to ``apply_regex_substitutions`` function to skip creation of backup (`#2844 `_) * add support for ``%(pymajver)s`` (& co) (`#2850 `_) * add support for '``fix_python_shebang_for``' and '``fix_perl_shebang_for``' easyconfig parameters (`#2878 `_) * add ``multi_deps`` information to generated module, help and whatis sections (`#2882 `_) * add support for '``eb --missing``' ('``eb -M``') (`#2883 `_) * see also https://easybuild.readthedocs.io/en/latest/Using_the_EasyBuild_command_line.html#getting-an-overview-of-missing-installations-missing-m * various bug fixes, including: * only call '``scontrol release``' when there's at least one job submitted (`#2834 `_) * fix small bug in ``find_eb_script`` + various minor issues with tests (related to environment in which tests are run) (`#2835 `_) * list build dependencies *before* runtime dependencies, so dependencies listed via ``multi_deps`` are loaded first in toolchain environment (`#2839 `_) * allow setting parallel to ``0`` or ``False`` to disable adding the ``-j`` argument (`#2842 `_) * be more careful when using single quotes for Tcl syntax (`#2847 `_) * append to existing ``.modulerc`` file rather than overwriting it (if ``--force`` is used) (`#2848 `_) * correctly resolve template values used for extensions (`#2852 `_) * update template values after updating iterative easyconfig parameters (`#2854 `_) * add top-level directories of hierarchical module naming scheme to ``$MODULEPATH`` before loading dependencies (`#2857 `_) * inject dependencies specified via ``multi_deps`` before normal build dependencies (`#2861 `_) * include Python version(s) in PR titles auto-generated by ``--new-pr`` (`#2863 `_, `#2880 `_) * update ``HierarchicalMNS`` for GCCcore toolchain (`#2870 `_) * bump iteration index counter at the correct time (`#2886 `_) * don't specify ``--ntasks-per-node`` when submitting Slurm jobs (`#2887 `_) * fix order of easyconfig parameters in output generated by '``eb --avail-easyconfig-params --output-format rst``' (`#2888 `_) * other changes: * lower required version in Slurm job backend to 16.05 (`#2833 `_) * add Lmod 8 to test suite (`#2849 `_) * deprecate useless 'skip_lower' named argument in template_constant_dict, always define ``*lower`` templates (`#2856 `_) * fix Python classifiers in ``setup.py``, should be (only) Python 2.6 & 2.7 (`#2876 `_) **easyblocks** * one new generic easyblock: ``CMakeMakeCp`` (`#1725 `_) * new software-specific easyblock for Blender (`#1595 `_), Lua (`#1396 `_), OpenBLAS (`#1693 `_, `#1697 `_) * OpenBLAS easyblock also supports installation on POWER systems * minor enhancements, including: * enhance VMD easyblock to also build Surf & Stride + pick up netCDF for VMD >= 1.9.3 (`#1314 `_) * update CGAL easyblock to support CGAL 4.12 & newer (`#1679 `_) * update QuantumESPRESSO easyblock for v6.4.1 (`#1692 `_) * enhance Advisor & VTune easyblocks, since no license is required starting with version 2019 update 3 (`#1694 `_, `#1695 `_) * handle new multi-deps Python setup with ``$EBPYTHONPREFIXES`` for Tensorflow (`#1702 `_) * make CHARMM easyblock pick up on ``prebuildopts`` and ``runtest`` (`#1707 `_) * change default value for ``'use_pip``' to None, so we can discriminate from '``use_pip``' being set to False explicitly (`#1709 `_) * make PythonPackage aware of ``(pre)testopts`` (`#1715 `_) * enable GPU offloading in Clang if CUDA is included as a dep (`#1716 `_) * add support to Clang easyblock for also building libc++ and RTTI (`#1717 `_) * rebuild internal libfabric for impi 2019.x & more recent (`#1730 `_) * update Q&A patterns in SAS easyblock for version 9.4 + add support for custom license file path (`#1731 `_) * various bug fixes, including: * only install mkl-dnn by default with TensorFlow on x86-64 systems (`#1666 `_) * make sure ``ldconfig`` can be found before using it in CUDA easyblock (`#1684 `_) * use temporary directory for pip cache (rather than ``$HOME/.cache/pip``) in ``PythonPackage`` easyblock (`#1687 `_) * allow oversubscription when testing FFTW on top of OpenMPI >= 3.0 (`#1688 `_) * make sure ``$HOME/.cache/pip`` isn't used while installing Tkinter (`#1691 `_) * set default ``exts_filter`` in ``PythonBundle``, so already installed extensions in a bundle can be skipped (`#1701 `_) * instruct Bazel to not use ``$HOME/.cache/bazel`` in TensorFlow easyblock (`#1704 `_) * also set ``$XDG_CACHE_HOME`` during installation of Python, to ensure that '``pip``' that comes along with it doesn't touch ``$HOME/.cache/pip`` (`#1705 `_) * use ``-fp-model precise`` if FMA instructions are missing in GROMACS easyblock (`#1706 `_) * make sure Perl install dir follows a standard format (`#1708 `_) * attach ``source_urls`` directly to sources for components in generic ``Bundle`` easyblock (`#1711 `_) * avoid that ``--no-build-isolation`` option is specified multiple times in ``PythonPackage`` easyblock (`#1713 `_) * fix prefix in impi compiler wrappers (`#1727 `_) * only embed zlib in binutils if it is listed a build dependency (`#1732 `_) * other changes: * fix Python classifiers in ``setup.py``, should be (only) Python 2.6 & 2.7 (`#1724 `_) **easyconfigs** * added easyconfigs for new toolchains: * ``fosscuda/2019a`` (`#8063 `_), ``gimkl/2018b`` (`#8287 `_), ``gomkl/2018b`` (`#8216 `_), ``gomkl/2019a`` (`#8218 `_), intelcuda/2019a (`#8069 `_) * added example easyconfig files for 52 new software packages: * ADDA (`#8207 `_), AMD-LibM (`#7164 `_), AMD-RNG (`#7165 `_), AMD-SecureRNG (`#7165 `_), ARGoS (`#8039 `_, `#8104 `_), ARWEN (`#8213 `_), Canvas (`#7716 `_), cdsapi (`#7970 `_), charmm (`#8202 `_), emcee (`#7989 `_), FlexiDot (`#8228 `_, `#8275 `_), FreeImage (`#8039 `_), Hello (`#7704 `_), HLAminer (8094), hypothesis (`#8307 `_), imgaug (`#8229 `_), INTEGRATE (`#8193 `_, `#8304 `_), INTEGRATE-Neo (`#8094 `_), IRkernel (`#8050 `_, `#8099 `_), JiTCODE (`#7148 `_, `#8327 `_), libFLAME (`#7163 `_), libpsml (`#5859 `_), LibSoup (`#8116 `_), libutempter (`#6426 `_), LS-PrePost (`#8070 `_), LUSCUS (`#7191 `_, `#8105 `_, `#8285 `_), memory-profiler (`#8255 `_), metaWRAP (`#7896 `_), Net-core (`#7716 `_), netMHC (`#8094 `_), Nextflow (`#8195 `_), nvtop (`#8024 `_), openpyxl (`#8121 `_), py-cpuinfo (`#8245 `_), pyFFTW (`#8198 `_), PyQtGraph (`#7525 `_, `#8253 `_), R-tesseract (`#7933 `_), RBFOpt (`#8178 `_), rnaQUAST (`#8040 `_), RStan (`#7996 `_), scikit-multilearn (`#8142 `_), simpy (`#8177 `_, `#8250 `_), SMARTdenovo (`#7630 `_), socat (`#8305 `_), SymEngine (`#7148 `_, `#8327 `_), unixODBC (`#8074 `_), VAtools (`#7938 `_), VirtualGL (`#8008 `_), WebKitGTK+ (`#8118 `_, `#8241 `_), xmlf90 (`#5858 `_), YAPS (`#7976 `_), zingeR (`#7264 `_) * added additional easyconfigs for various supported software packages, including: * Boost 1.70.0, cairo 1.16.0, CGAL 4.14, Clang 8.0, cutadapt 2.1, dask 1.1.4, ELPA 2018.11.001, FFmpeg 4.1.3, GCC 9.1.0, GEOS 3.7.2, GLib 2.60.1, gmsh 4.2.2, GROMACS 2019.2, GTK+ 3.24.8, h5py 2.9.0, hwloc 1.11.12, Hypre 2.15.1, Mathematica 12.0.0, matplotlib 3.0.3, Mesa 19.0.1, NBO 7.0, NCL 6.6.2, NCO 4.7.9, NiBabel 2.4.0, numba 0.43.1, OpenMPI 3.1.4, OrthoFinder 2.3.3, PCMSolver 1.2.3, PETSc 3.11.1, PROJ 6.0.0, PyQt5 5.12.1, PyTorch 1.0.1, PyYAML 5.1, Qt5 5.12.3, QuantumESPRESSO 6.4.1, R 3.5.1 (w/ intel/2018b), RNAIndel 1.0.0, Ruby 2.6.3, scikit-learn 0.20.3, SLEPc 3.11.0, sympy 1.4, Tkinter 3.7.2, Vim 8.1.1209, VTK 8.2.0, wrf-python 1.3.1, wxPython 4.0.4, wxWidgets 3.0.4, xarray 0.12.1, zstd 1.4.0 * minor enhancements, including: * enable auto-download of VMD 1.9.3 + add patches for Surf and Stride (`#7305 `_) * add mlegp extension in R 3.5.1 easyconfigs (`#7814 `_) * add pkg-config file to bzip2 easyconfigs (`#8200 `_) * allow use of '``use_pip = False``' in easyconfigs if pip doesn't work (`#8220 `_) * various bug fixes, including: * fix checksums for nlme extensions in R easyconfigs (`#7814 `_, `#8054 `_) * add missing XZ dependency for Pysam > 0.12 (`#7971 `_) * define ``$GRACE_HOME`` in Grace easyconfigs, so that font dir can be located (`#8048 `_) * ``$XDG_DATA_DIRS`` must be set for GTK+ (`#8089 `_) * add missing FriBidi dependency for Pango 1.43.0 (`#8103 `_) * add (back) custom ``sanity_check_paths`` in recent Pango easyconfigs (`#8106 `_) * fix missing extensions in cutadapt 1.16 easyconfigs (`#8130 `_) * add missing cURL dependency for recent SAMtools versions (`#8131 `_) * add singledispatch extension to Python 2.7.15 easyconfig using ``GCCcore/8.2.0`` toolchain (`#8164 `_) * add missing X11 dependency for Gdk-Pixbuf 2.38.1 (`#8222 `_) * make sure ``hdf5r`` picks up HDF5 dependency in R 3.5.1 easyconfigs (`#8223 `_) * enable zstd compression in GRASS 7.6.0 easyconfig (`#8224 `_) * add missing ICU dependency on ICU for Harfbuzz 2.4.0 (`#8226 `_) * disable AVX512 DGEMM kernels in OpenBLAS 0.3.5 (`#8227 `_) * fix homepage/description in OrthoFinder easyconfig (`#8234 `_) * add ``Parallel::ForkManager`` extension to Perl 5.28.x easyconfigs (`#8247 `_) * replace LibUUID dependencies with util-linux (`#8258 `_) * add jemalloc & pkg-config as build deps for Salmon 0.12.0 (`#8264 `_) * fix MAJIQ easyconfig by fixing order of extensions + avoid numpy test hang (`#8272 `_) * fix shebang in GLib Python script + clarify runtime dependency on Python (`#8277 `_) * add pkg-config and expat as (build) dependency for DBus (`#8283 `_) * define ``$GI_TYPELIB_PATH`` in GTK+ and Pango easyconfigs (`#8246 `_, `#8286 `_) * add pkg-config build dep to PROJ 6.0.0 easyconfig (`#8309 `_) * fix source URLS in recent libcerf easyconfigs (`#8332 `_, `#8243 `_) * make zlib a real dependency rather than a build dep in recent binutils easyconfigs (>= 2.28) (`#8340 `_) * add fix-ib-query patch to OpenMPI 2.1.x and 3.0.x easyconfigs (`#8341 `_) * set ``$XDG_CACHE_HOME`` to $TMPDIR before '``pip install``' in Arrow 0.12.0 easyconfigs (`#8347 `_) * other changes: * remove xbitmaps dependency from motif (`#7530 `_) * require custom ``sanity_check_paths`` in easyconfigs touched in PRs when generic easyblock is used (`#8101 `_, `#8123 `_) * use CMake built with GCCcore toolchain when installing Eigen 3.3.4+ (`#8261 `_) * fix Python classifiers in ``setup.py``, should be (only) Python 2.6 & 2.7 (`#8299 `_) * use custom easyblock for OpenBLAS in OpenBLAS 0.3.x easyconfigs (`#8345 `_, `#8339 `_) .. _release_notes_eb390: EasyBuild v3.9.0 (April 12th 2019) ---------------------------------- feature release **framework** * various enhancements, including: * add ``(pre)testopts`` easyconfig parameters (`#2793 `_) * add support for ``multi_deps`` easyconfig parameter (`#2741 `_, `#2810 `_, `#2811 `_, `#2812 `_, `#2813 `_, `#2825 `_, `#2826 `_, `#2827 `_, `#2828 `_) * various bug fixes, including: * fix argument name in ``close_pr`` (`#2752 `_) * fix undefined variable '``prefix``' in ``Compiler._set_compiler_vars`` (`#2757 `_) * fix test account for GitHub-related tests (`#2760 `_) * make sure read permissions are always set in ``permissions_step`` (`#2770 `_) * make test for ``dep_graph`` function robust against changing order of lines in resulting dot file (`#2772 `_) * fix problem with ``import_available_modules`` when running from easybuild-framework directory (`#2786 `_) * prepend location of test easyblocks to ``$PYTHONPATH`` to ``test_generate_software_list``, rather than append (`#2788 `_) * use pid in backup name candidate to reduce risk of two processes colliding (`#2796 `_) * automatically enable ``--ignore-osdeps`` when using ``--preview-pr`` (`#2799 `_) * use temporary checkout of repository as robot path for ``--new-pr`` and ``--update-pr`` to determine locations for patch files (`#2803 `_) * avoid relying on order in which keys are processed in ``to_dependency`` (`#2804 `_) * fix yeb format to work with PyYAML 5 (`#2809 `_) * fix typo in error message for use of unknown easyconfig parameter (`#2817 `_) * enhance ``log_file_format`` to fix problem when ``%(name)s`` template value is used for log directory (`#2818 `_) * iterate over subdirectories in order in ``find_egg_dir_for`` of bootstrap script, to ensure oldest vsc-install is picked (`#2819 `_) * replace ``-Wl,--enable-new-dtags`` compiler option with ``-Wl,--disable-new-dtags`` in RPATH wrapper script (`#2821 `_) * updated ``COMPILER_F77`` for PGI >= 19.1 (`#2823 `_) * added ``FFTW_STATIC_LIBS_MT`` to ``FFTW_MAP_CLASS``, otherwise ``FFTW_STATIC_LIBS_MT`` are incorrectly defined (`#2822 `_) * sort available version list when selecting/generating easyconfig (`#2732 `_) * other changes: * use ``assertEqual`` rather than ``assertEquals`` (which is deprecated) (`#2746 `_) * test with Tmod 4.1.4 (packaged in RHEL8) in Travis CI (`#2747 `_) * replace deps by hidden deps instead of removing them from the lists (`#2748 `_) * ensure non-zero exit code for all test subsuites (+ fix trivial style issues) (`#2773 `_) * silence printed deprecation warnings for easyconfigs/toolchains while running (easyconfigs) test suite (`#2781 `_) * avoid printing of messages/warnings in framework test suite (`#2782 `_) * enable silent mode for ``--new-pr`` and ``--update-pr`` (`#2802 `_) * update Travis config to reflect that PyYAML 5.x is no longer compatible with Python 2.6 (`#2807 `_) **easyblocks** * new software-specific easyblock for TensorRT (`#1627 `_) * minor enhancements, including: * make sure CMake doesn't pick up on system Boost in CMakeMake generic easyblock (`#1618 `_) * modified ``ConfigureMake`` and ``CMakeMake`` generic easyblocks to allow changing ``configure_cmd``, ``build_cmd`` and ``install_cmd`` to fit various needs (`#1628 `_, `#1658 `_) * update ANSYS easyblock to deal with changed versioning scheme (`#1631 `_) * add extra path to builddir for SNPhylo >= 20160204 (`#1632 `_) * add better support for TensorRT to TensorFlow (`#1634 `_) * add support for newer versions of wxPython to wxPython easyblock (`#1635 `_) * update OCaml easyblock to support OPAM 2.x (`#1638 `_) * update sanity check in TensorFlow easyblock for TensorFlow 1.13.x (`#1642 `_) * make ``ConfigureMake``, ``MesonNinja`` and ``SCons`` generic easyblocks aware of pretestopts (`#1645 `_) * add support for installing Python packages with '``pip``' without using ``--ignore-installed`` (`#1647 `_) * add support to ``CMakeMake`` easyblock to specify compilers using absolute file path (`#1652 `_, `#1655 `_) * stop checking for deprecated ``pgf77`` in sanity check of PGI easyblock (`#1653 `_) * accommodate version 10.1 in CUDA easyblock (`#1654 `_) * install ``sitecustomize.py`` with Python to support Python package installations for multiple Python versions in a single directory (`#1657 `_) * enhance SAMtools easyblock to also install ``libhts.a`` and include/htslib (when applicable) (`#1661 `_) * tweak ``PythonPackage`` & ``PythonBundle`` to update ``$EBPYTHONPREFIXES`` rather than ``$PYTHONPATH`` for multi-Python installations + make ``sanity_check_step`` aware of multi_deps (`#1664 `_, `#1678 `_) * replace ``-openmp`` with ``-fopenmp`` when building TINKER with Intel compilers (+ modernize easyblock) (`#1668 `_) * make sure Meson is configured with ``-Dlibdir=lib`` so it doesn't install libraries in ``lib/x86_64-linux-gnu`` on Debian/Ubuntu multiarch systems (`#1673 `_) * allow for external libfabric via ``ofi_libfabric`` parameter in impi easyblock (`#1676 `_) * pass down compiler names and options to Qt5 5.8 & more recent via corresponding ``QMAKE_*`` configuration options (`#1677 `_) * various bug fixes, including: * create symlinks to ``.modulerc`` in symlinked module directories (`#1636 `_) * add missing import in FFTW easyblock (`#1641 `_) * fix finding of Python 3 include subdir + ``libpython*.so`` in OpenBabel easyblock (`#1633 `_) * add ``no_qa`` pattern for interactive installation command for ABAQUS (`#1637 `_) * make serial, smpar and dm+sm builds of WRF work and pass tests (`#1646 `_) * configure CP2K with correct ``DATA_DIR`` value rather than relying on ``$CP2K_DATA_DIR`` environment variable (`#1650 `_) * CP2K fixes: only call configure_LAPACK/ScaLAPACK when imkl is not used, prefer using 2^2 MPI processes for tests (`#1651 `_) * also take into account custom easyconfig parameters from ``CMakeMake`` in BamTools easyblock (`#1656 `_) * make sure Perl scripts are installed in the right location (`#1660 `_) * make sure setenv is used for CUDA_PATH etc. (`#1663 `_) * cleanup ``sanity_check_paths`` in numpy & scipy easyblocks (`#1665 `_, `#1667 `_) * always set ``self.pylibdir`` in ``PythonPackage.set_pylibdirs()``, which is important when installing Python packages for multiple Python versions via ``multi_deps`` (`#1671 `_) * fix custom definition of ``load_module`` method in LAPACK module (`#1675 `_) * other changes: * replace '``except OSError, err:``' pattern with '``except OSError as err:``' (for compatibility with Python 3.x) (`#1639 `_) * clean up Java easyblock to use ``filetools`` functionality (`#1649 `_) **easyconfigs** * added easyconfigs for new toolchains: ``intel/2019.02`` (`#7598 `_), ``intel/2019.03`` (`#7846 `_) * added example easyconfig files for 68 new software packages: * ACT (`#7928 `_), aiohttp (`#7728 `_), at-spi2-atk and at-spi2-core (`#7658 `_), Bader (`#7804 `_), barrnap (`#7738 `_), BCEL (`#7937 `_), biscuit (`#5868 `_), bitarray (`#7772 `_), BlobTools (`#7565 `_, `#7583 `_), bmtagger (`#7890 `_), bsddb3 (`#7642 `_), CheckM (`#7712 `_), Cheetah (`#7952 `_), CONCOCT (`#7891 `_), cyvcf2 (`#8031 `_), DAS_Tool (`#7741 `_), ExaBayes (`#7801 `_), FastANI (`#7992 `_), fastp (`#7693 `_), Flask (`#7734 `_), giflib (`#7663 `_), Giza (`#7843 `_), glew (`#7685 `_), gpustat (`#8025 `_), GRASS (`#7489 `_), GTDB-Tk (`#7995 `_), HPCX (`#7725 `_), IntelPython (`#7920 `_), KNIME (`#7554 `_), KronaTools (`#7721 `_), KyotoCabinet (`#7955 `_), Leptonica (`#7932 `_), libepoxy (`#7655 `_), libpsl (`#7666 `_), MAGMA (`#7829 `_), MATLAB-Engine (`#7758 `_), MaxBin (`#7767 `_), MetaBAT (`#7746 `_, `#7931 `_), MinPath (`#7763 `_), ncdu (`#7505 `_), NGSadmix (`#7524 `_), NIMBLE (`#7564 `_), PCAngsd (`#7727 `_), pizzly (`#7724 `_), Ploticus (`#7545 `_), pocl (`#7681 `_), POT (`#8011 `_), ProjectQ (`#7576 `_), pullseq (`#7740 `_), pyBigWig (`#7600 `_), Pyke3 (`#8034 `_), PyRETIS (`#8041 `_), RDKit (`#7973 `_), RNAIndel (`#8009 `_), scikit-optimize (`#7613 `_), SciPy-bundle (`#7922 `_), sep (`#8032 `_), slidingwindow (`#7909 `_), SPLASH (`#7843 `_), SqueezeMeta (`#7771 `_), SRPRISM (`#7890 `_), taxator-tk (`#7894 `_), TensorRT (`#7584 `_), tesseract (`#7932 `_), Transrate (`#5108 `_), VCF-kit (`#7786 `_, `#7882 `_), VV (`#7297 `_) * added additional easyconfigs for various supported software packages, including: * AFNI 19.0.01, Arrow 0.7.1, BLAST+ 2.8.1, CUDA 10.1.105, GCC(core) 8.3.0, GTK+ 3.22.30, Java (OpenJDK) 11(.0.2), Meson 0.50.0, MultiQC 1.7, Nim 0.19.2, Ninja 1.9.0, netCDF 4.6.2, netCDF-Fortran 4.4.5, PCRE 8.43, Perl 5.28.1, PGI 19.1, Python 3.7.2, RELION 3.0.4, Ruby 2.6.1, SCons 3.0.4, SQLite 3.27.2, SuiteSparse 5.4.0, TINKER 8.6.1, TensorFlow 1.13.1, X11 20190311 * minor enhancements, including: * add various extensions to R 3.5.1 easyconfigs: ``asnipe`` (`#7572 `_), ``liquidSVM`` (`#7597 `_), ``oddsratio``/``mltools``/``h2o`` (`#7744 `_), ``mlegp`` (`#7814 `_), ``bartMachine``/``lqa`` (`#7865 `_), ``PresenceAbsence``/``GUTS``/``GenSA`` (`#7905 `_), ``parsedate`` (`#7935 `_), ``circular`` (`#7975 `_) * add ``ujson`` extension in recent Python easyconfigs (`#7517 `_) * run various checks on easyconfigs that are touched in pull requests and involve Python packages (`#7754 `_) * add ``cpanminus`` extension to recent Perl easyconfigs (`#7866 `_) * also install ANTs scripts (and set ``$ANTSPATH`` as required by those scripts) (`#7940 `_) * add missing ``configopts`` in GATE 8.1 easyconfig to enable Davis feature (`#8000 `_) * various bug fixes, including: * add patch for Mesa 18.1.1 to detect MIT-SHM (`#7536 `_) * add proper description to MINC-2.4.03 (`#7551 `_) * add libunwind dependency to recent Mesa easyconfig when building with foss/GCC (`#7629 `_) * add/reorder missing/misplaced extensions in Python 2.7.15 and 3.6.6 easyconfigs (`#7696 `_) * fix Jellyfish dependency in easyconfig for Kraken 1.0 (Jellyfish 1.x is required) (`#7743 `_) * use ``https://`` in most recent XZ easyconfigs (`#7782 `_) * add patch for OpenMPI 3.1.x to fix ib-query '``Invalid argument``' error (`#7789 `_) * build OpenBLAS with ``-fno-tree-vectorize`` (asm constraint bugs for <0.3.6) + cleanup & SHA256 checksums (`#7790 `_, `#7793 `_) * extra patch for TensorFlow 1.12.0 to remove ``-B/usr/bin`` from ``linker_bin_path_flag`` in ``cuda_configure.bzl`` (`#7800 `_) * fix easyconfig for STAR-Fusion 1.5.0 (`#7802 `_) * fix checksums for boot/nlme extensions in R easyconfigs (`#7814 `_, `#8054 `_) * add patch for OpenMPI 3.x to fix UCX memory leak (`#7535 `_, `#7824 `_) * replace ``ncurses-devel`` OS dependency in CMake easyconfigs using ``dummy`` toolchain with proper ncurses dependency (`#7834 `_) * use ``PythonBundle`` for ``snakemake-5.2.4-foss-2018b-Python-3.6.6.eb`` (+ fix moduleclass) (`#7842 `_) * use correct ``buildopts`` + add missing zlib dependency in StringTie 1.3.5 easyconfig (`#7845 `_) * update GStreamer to not enable dw and fix some missing dependencies (`#7889 `_) * add missing XZ dependency to most recent Pysam easyconfigs (`#7897 `_) * expat: add configure option ``--without-docbook`` to avoid docbook2X dependency (`#7930 `_) * fix source URLs for mawk (`#7960 `_) * fix LWM2, OTF2, OPARI2, and Score-P download URLs (`#7994 `_) * use ``https://`` in homepage & source_urls for OpenMPI and hwloc easyconfigs (`#8013 `_, `#8014 `_, `#8015 `_ and `#8016 `_) * add missing bokeh dependency for dask 1.0.0 (+ add dask-jobqueue) (`#8029 `_) * fix checking of binutils build dep in easyconfig tests (`#8038 `_) * other changes: * avoid use of ``.items()`` in R (bundle) easyconfigs, to fix compatibility with EasyBuild running on top of Python 3 (`#7791 `_) * trim down test configuration: only test with Lmod 6.x with Tcl/Lua on Python 2.6/2.7 (`#7795 `_, `#7798 `_) * use ``%(pyshortver)s`` template in (old) SIP easyconfigs (`#7797 `_) * add PyTorch to whitelist for not having '``use_pip``' enabled (`#7844 `_) * don't use local variable '``pylibdir``' in list comprehension in PyQt easyconfig, since that doesn't work in Python 3 (`#7848 `_) * use pip instead of setup.py with h5py/2.7.1 and 2017b toolchains (`#7864 `_) * prefer ``https://`` over ``ftp://`` for source_urls in recent GROMACS easyconfigs (`#7948 `_) * rename arrow to Arrow for old easyconfig (`#8007 `_) .. _release_notes_eb381: EasyBuild v3.8.1 (January 29th 2019) ------------------------------------ bugfix/update release **framework** * various minor enhancements, including: * speed up checking of OS dependencies (`#2703 `_) * add support for '``eb --show-system-info``' (`#2722 `_) * add support for '``%(arch)s``' template value in easyconfig files (x86-64, aarch64, ppc64le, ...) (`#2728 `_) * various bug fixes, including: * add timestamp to reprod dir while in tmp space (`#2705 `_) * avoid '``+``' in directory name for ``g++`` rpath wrapper (`#2710 `_) * pre-install vsc-install < 0.11.4 in bootstrap script to avoid requiring '``mock``' Python package (`#2717 `_) * fix check in ``--merge-pr`` whether PR is eligible for merging in to only consider the status of the last test report (`#2720 `_) * don't recreate build directory when '``buildininstalldir``' is enabled for iterative installations (`#2724 `_) * filter (CUDA) ``lib*/stubs`` paths in RPATH wrapper script (`#2725 `_) * other changes: * replace '``except IOError, err:``' pattern with '``except IOError as err:``' for compatibility with Python 3.x (`#2711 `_) * make all ``print`` statements compatible with Python 3 (`#2715 `_) * avoid use of ``sys.maxint`` in dependencies_for (`#2716 `_) **easyblocks** * minor enhancements, including: * update Ferret easyblock to handle Ferret 7.3 (`#1349 `_) * add support for defining ``$LDSHARED`` when installing Python packages if Python's value doesn't use toolchain compiler ($CC) (`#1455 `_) * update CP2K easyblock to add support for CP2K 6.1, and fix incorrect LibInt references (`#1545 `_) * make OpenFOAM easyblock handle debug build (`#1609 `_) * handle multiple installation keys for MATLAB (`#1610 `_) * run '``make check``' in parallel for GROMACS since it involves more compilation (`#1611 `_) * update OpenCV easyblock for recent versions (3.4.x >= 3.4.4 + 4.0.x) (`#1616 `_) * various bug fixes, including: * check current ``start_dir`` value before appending '``src``' subdirectory in MrBayes easyblock (`#1582 `_) * avoid that (system) Intel compilers are always considered when building SuiteSparse (`#1612 `_) * fix missing import statement in ROOT easyblock (`#1614 `_) * answer SELinux question with '``no``' in Mathematica easyblock (`#1617 `_) * disable "build isolation" feature in pip > 10.x in PythonPackage generic easyblock (`#1623 `_) * other changes * cleanup in Perl and PerlModule easyblocks (`#1603 `_) **easyconfigs** * added easyconfigs for new toolchains ``foss/2019a`` (`#7371 `_), ``intel/2019a`` (`#7372 `_) and ``iomkl/2019.01`` (`#7375 `_) * see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html * added example easyconfig files for 43 new software packages: * Assimulo (`#6740 `_), C3D (`#7059 `_), CellMix (`#7422 `_), CESM-deps (`#6654 `_, `#6675 `_, `#6823 `_), DSA (`#7422 `_), DeMixT (`#7422 `_), deconf (`#7422 `_), DeconICA (`#7422 `_), double-conversion (`#7307 `_), dxpy (`#7079 `_), EPIC (`#7422 `_), expect (`#7387 `_), Flye (`#7430 `_), FMILibrary (`#6740 `_), FMRIprep (`#7059 `_), FUSE (`#7078 `_), GDCM (`#7310 `_), HDDM (`#7396 `_), ICA-AROMA (`#7059 `_), IntaRNA (`#7334 `_), imageio (`#6738 `_), KWIML (`#7308 `_), kWIP (`#7444 `_), MagresPython (`#7395 `_), medaka (`#7426 `_), MINC (`#7311 `_), MuSiC (`#7422 `_), netMHCIIpan (`#7377 `_), NIfTI (`#7311 `_), OPERA (`#7408 `_), psrecord (`#7331 `_), pyfits (`#7273 `_), PyFMI (`#6740 `_), PyGWAS (`#5852 `_), Pylint (`#6675 `_), QDD (`#7284 `_), RERconverge (`#7289 `_), samclip (`#7226 `_), SCIPhI (`#7419 `_), swarm (`#7453 `_), VXL (`#7309 `_), wrf-python (`#6736 `_), xCell (`#7422 `_) * added additional easyconfigs for various supported software packages, including: * Amber 18, Arrow 0.12.0, Biopython 1.73, Boost 1.69.0, CP2K 6.1, canu 1.8, Ferret 7.3, GATE 8.1.p01, GROMACS 2019, Geant4 10.5, HPL 2.3, libxsmm 1.10, matplotlib 3.0.2, NEURON 7.6.5, Octave 4.4.1, OpenBLAS 0.3.5, OpenCV 3.4.5 + 4.0.1, OpenFOAM v1812, PGI 18.10, PLUMED 2.5.0, ROOT 6.14.06, Theano 1.0.3, TopHat 2.1.2, Yade 2018.02b * minor enhancements, including: * add additional extensions to R 3.5.1 easyconfigs: * statnet (`#7370 `_), NMF, ComICS, dtangle, MCMCpack, shinythemes (`#7420 `_), csSAM (`#7423 `_), bridgedist (`#7477 `_) * add DeconRNASeq and GSVA extensions to R-bundle-Bioconductor 3.7 easyconfigs (`#7421 `_) * also install header files and CMake module for SeqAn 2.4.0 built with ``foss/2018b`` (`#7434 `_) * add download URL for ``intel/2018a`` components (`#7436 `_) * add missing checksums for protobuf easyconfigs using dummy toolchain (`#7492 `_) * various bug fixes, including: * fix source URL in Doxygen easyconfigs (`#7324 `_) * add fallback source URL for recent pigz versions (`#7346 `_) * promote FriBiDi to runtime dep of Pango rather than only build dep (`#7369 `_) * add ``--without-systemdsystemunitdir`` configure option to recent DBus easyconfigs (`#7373 `_) * fix issue of building M4 1.4.18 with glibc 2.28 (`#7384 `_) * fix broken source URLs in MariaDB easyconfigs (`#7413 `_) * bump up build dependency of flex 2.6.4 from Bison 3.0.4 to 3.0.5 (`#7414 `_) * disable building of OpenColorIO Python bindings since Python is not included as a dependency (`#7416 `_) * add missing build dependencies in old Harfbuzz/Pango easyconfigs (2016a generation) (`#7433 `_) * fix XML-LibXML linking with Intel compiler and GCCcore Perl (`#7440 `_) * prevent non-critical error from stopping Guile v1.8.8 build (`#7446 `_) * use ``%(arch)s`` template rather than hardcoding '``x86_64``' in XML-Parser easyconfigs (`#7450 `_) * use uniform configopts for Guile 1.8.8 (`#7452 `_) * fix configopts in PyQt5 easyconfig files to avoid installation of files in Python/Qt5 installation directories (`#7470 `_) * other changes: * fix homepage in easyconfigs for ``foss`` toolchains (`#7482 `_) and ``intel`` toolchains (`#7483 `_) .. _release_notes_eb380: EasyBuild v3.8.0 (December 18th 2018) ------------------------------------- feature release **framework** * various enhancements, including: * support use of version ranges in ``--filter-deps`` (`#2357 `_) * add support for ``--list-prs`` (`#2400 `_, `#2668 `_) * add support for ``--close-pr`` (`#2401 `_) * allow setting ``optarch`` compiler flags in the easyconfig via ``toolchainopts`` easyconfig parameter (`#2595 `_) * add option to skip pre-creation of install directory: ``--disable-pre-create-installdir`` (`#2629 `_, `#2637 `_) * flesh out setting up of configuration into dedicated '``set_up_configuration``' function (`#2638 `_) * clean error when '``eb``' is cancelled by user (`#2641 `_) * add support for using Slurm as backend for ``--job``, via ``--job-backend=Slurm`` (`#2642 `_, `#2666 `_) * save easyblocks along with easyconfig in '``reprod``' subdirectory of install directory (`#2653 `_) * add support for deprecating easyconfig files & toolchains (`#2656 `_) * changed ``EasyConfig.update`` to be able to specify not to allow duplicate values (`#2657 `_) * move adding of dependencies to prepare step instead of check readiness step (`#2674 `_) * add support for disabling mapping of (sub)toolchains when ``--try-toolchain`` is used, via ``--disable-map-toolchains`` (`#2682 `_) * add '``astro``' and '``quantum``' module classes (`#2693 `_) * various bug fixes, including: * make ``--from-pr`` always try to apply PR patch on top of PR target branch (`#2631 `_) * fix bug that could cause to silently overwrite an existing easyconfig when using ``--try-*`` (`#2635 `_) * don't pass down specific environment variables into submitted jobs (`#2643 `_) * update template constants for source URLs to use https (`#2648 `_) * fix lib64 fallback for '``lib``'/'``lib64``' dirs entry in ``sanity_check_paths`` (`#2649 `_) * change PGI F90 Fortran compiler to pgf90 (`#2650 `_) * use ``--set-upstream-to`` in ``install-EasyBuild-develop.sh`` script to deal with deprecated/no longer supported ``--set-upstream`` (`#2651 `_) * fix order of keys in '``toolchain``' value for dumped easyconfig file (name, version) + run style check on dumped easyconfigs in dump tests (`#2660 `_) * ensure checksums beside sources in dumped easyconfigs (`#2661 `_) * fix problems with easyconfig file saved in '``reprod``' directory by copying it before running any installation steps (`#2664 `_) * make print functions more robust w.r.t. arguments being passed to format the message to be printed (`#2670 `_) * use '``git am``' to apply patch for PRs in ``fetch_easyconfigs_from_pr`` (`#2680 `_) * correctly define ``$LIBFFT_MT`` for Intel MKL (`#2688 `_) * don't always require easyconfig files to resolve dependencies (`#2690 `_, `#2692 `_, `#2697 `_, `#2698 `_, `#2699 `_) * fixes for Travis CI config: * stop testing with Lmod 6.6.3, testing with Lmod 6.5.1 is sufficient (`#2627 `_) * Python 2.6 requires python-daemon 1.x as dep for GC3Pie (`#2673 `_) * stick to idna<2.8 with Python 2.6 in Travis + distable broken test for HgRepository (`#2678 `_) * other changes: * always skip symlinks in ``adjust_permissions`` (`#2644 `_) * flesh out '``avail_easyblocks``' function from support for ``--list-easyblocks`` (`#2663 `_) * deprecate the ``ictce`` toolchain (`#2667 `_) * deprecate ``goolf`` and ``goolfc`` toolchains (`#2676 `_) * deprecate ``intel`` toolchains older than ``intel/2016a`` (+ ``iccifort`` & ``iimpi`` subtoolchains) (`#2677 `_) * deprecate ancient ``gompi`` toolchain versions (`#2684 `_) * use '``tar xzf``' (gzip) rather than '``tar xZf``' (ancient ``compress``) to unpack ``*.tar.Z`` source files (`#2686 `_) * flesh out '``set_parallel``' method to it can be called separately (`#2687 `_) **easyblocks** * new generic easyblocks: * ``PythonBundle`` for installing a bundle of Python packages (`#1553 `_) * ``MesonNinja`` for installing using Meson & Ninja (`#1561 `_) * new software specific easyblock for ``RepeatMasker`` (`#1600 `_) * minor enhancements, including: * add ``-fno-delete-null-pointer-checks`` compiler flag for OpenFOAM versions older than v3.0 (`#1311 `_) * add support for building Tau with OTF included as dependency (`#1313 `_) * add support for Intel MPI version 2019 (`#1546 `_) * also populate the include dir for CP2K (`#1554 `_) * add custom easyconfig parameter in GCC easyblock to control use of gold linker: ``use_gold_linker`` (`#1555 `_) * replace '``-``' with '``_``' in default '``import``' check for Python packages (`#1560 `_) * update WRF and WPS to support version 4 (`#1563 `_) * adapt PSI easyblock for PSI4 > 1.2 (`#1568 `_) * update Siesta easyblock to 4.1-b4 and add custom test_step (`#1573 `_) * enhance Mothur easyblock to support use of Boost and HDF5 as dependencies (`#1576 `_) * enhance sanity check for icc & ifort: also check for ``compilers_and_libraries_*/linux`` subdirectory (`#1577 `_) * update Trinity easyblock for latest version 2.8 (`#1579 `_) * add version check in sanity check step of SCOTCH easyblock (+ code cleanup) (`#1580 `_) * add support in Clang easyblock to skip running of all tests (`#1584 `_) * update WRF easyblock to allow serial HDF5 + pick up on parallel netCDF (`#1592 `_) * avoid hardcoding '``PREFIX=``' in build/install options when using ``SCons`` easyblock (`#1594 `_) * enable TensorFlow to detect any MPI runtime (`#1597 `_) * enhance ``Bundle`` easyblock to allow installation of bundle components with additional easyblocks + build components in parallel (`#1598 `_) * enhance Trilinos easyblock to support building against MKL (`#1601 `_) * various bug fixes, including: * make FDTD_Solutions easyblock do the install by copying files instead of '``rpm rebuild``' (`#1307 `_) * re-add missing ``VT_(S)LIB_DIR`` env variable to itac module (`#1309 `_) * fix in QuantumESPRESSO easyblock: ifort compiler needs ``-assume byterecl`` (`#1556 `_) * extract targets from buildopts in Quantumespresso easyblock (`#1558 `_) * fixes for TensorFlow easyblock (`#1559 `_) * pass ``$PYTHONPATH`` while building TensorFlow * disable cross-compilation mode if optarch is set * fix sanity check for installing TensorFlow as extension * added a test to disable compiling FFTW with MPI if the toolchain does not support MPI (`#1562 `_) * fix permissions problem with CUDA nvvp tar files + correctly handle numactl symlink in LLVM subdir in PGI easyblock (`#1569 `_) * fix TensorFlow test tempdir problem (`#1572 `_) * tweak VMD easyblock so that ``configopts`` don't contain duplicate values (otherwise it fails to rebuild) (`#1575 `_) * fix running netcdf4-python tests to also support installation as extension (`#1578 `_) * added the openmp flags in the linker flags in MUMPS easyblock (`#1585 `_) * avoid hardcoding ``--with-rdma`` configure option in MVAPICH2 easyblock (`#1586 `_) * fix location of path-to-source argument in configure command of ``CMakeMake`` (`#1591 `_) * fix GROMACS use of MKL for non-Intel compilers (e.g. gomkl toolchain) (`#1596 `_) * other changes * inform Hound CI about Python 2 builtins (`#1604 `_) **easyconfigs** * added easyconfigs for new toolchains: ``intel/2018.04`` (`#7171 `_), ``intel/2019.00`` (`#7218 `_), ``intel/2019.01`` (`#7219 `_) * added example easyconfig files for 36 new software packages: * 4ti2 (`#7040 `_), ARPACK++ (`#6750 `_), CellRanger (`#7242 `_), CharLS (`#6762 `_) cscope (`#7057 `_), ctags (`#7057 `_), datamash (`#6693 `_), dcm2niix (`#6762 `_), DCMTK (`#6761 `_), deepdiff (`#7109 `_), Drake (`#7182 `_), fast5 (`#7250 `_), gap (`#7040 `_), Gerris (`#7211 `_), GPAW-setups (`#6984 `_), iCount (`#7080 `_), ipyparallel (`#6797 `_), Kratos (`#7149 `_), LCov (`#7160 `_), libvdwxc (`#6984 `_), libwebp (`#7065 `_), lrslib (`#7040 `_), MuPeXI (`#6991 `_), netMHCpan (`#6991 `_), Normaliz (`#7040 `_), OpenColorIO (`#7146 `_), OpenJPEG (`#7216 `_), PHLAT (`#7036 `_), poppler (`#7069 `_), RECON (`#7042 `_), RepeatMasker (`#7281 `_), TreeMix (`#7133 `_), unrar (`#7117 `_), utf8proc (`#7083 `_), VSEARCH (`#7153 `_), XMDS2 (`#7121 `_) * added additional easyconfigs for various supported software packages, including: * CheMPS2 1.8.8, Clang 6.0.1 + 7.0.0, dask 1.0.0, FFmpeg 4.1, GCC(core) 6.5.0 + 7.4.0, GPAW 1.4.0, HMMER 3.2.1, IPython 7.2.0, ITK 4.13.1, Keras 2.2.4, LLVM 7.0.0, Mothur 1.41.0, MultiQC 1.6, NAMD 2.13, OpenBLAS 0.3.4, OpenMPI 3.1.3 + 4.0.0, PSI4 1.2.1, Qt5 5.11.2, QuantumESPRESSO 6.3, Rust 1.30.1, Spark 2.4.0, Spyder 3.3.1, TensorFlow 1.11.0 + 1.12.0 * minor enhancements, including: * install misc tools for angsd (`#6995 `_) * add libXp component to X11 bundle for GCCcore 6.4.0 (`#7062 `_) * also install shared libraries for LZO (`#7073 `_) * add extensions to R 3.5.1 easyconfigs: ``gllvm`` (`#7123 `_), ``grpreg`` (`#7140 `_), ``gamlss`` + ``gamlss.tr`` (`#7263 `_) * install Tk private headers (`#7155 `_) * add ``File::Next`` extension to Perl 5.28.0 easyconfig (`#7276 `_) * various bug fixes, including: * fix installation of scikit-image 0.13.x by including missing required ``PyWavelets`` extension (`#7061 `_) * add missing dependencies to easyconfig for GC3Pie 2.5.0 (`#7066 `_) * stop setting ignored '``full_sanity_check``' easyconfig parameter in easyconfigs (`#7094 `_) * add missing checksums in X11/2016* easyconfigs (`#7095 `_) * add missing checksums in X11/2017* easyconfigs (`#7096 `_) * add missing ``cffi`` & ``pycparser`` extensions to recent Python easyconfigs (`#7105 `_, `#7118 `_) * fix homepage in QuantumESPRESSO easyconfigs (`#7114 `_) * use empty toolchain version in picard easyconfigs to ensure Java dependency is loaded during installation (`#7116 `_) * fix checksum for ``mgcv`` extension in R 3.5.* easyconfigs (`#7122 `_) * add missing 'patsy' extension in ARCH easyconfig + switch to using ``PythonBundle`` easyblock (`#7124 `_) * add missing (dummy) sklearn extension in NeuroKit easyconfig (`#7126 `_) * fix order of extensions in recent IPython easyconfigs to make '``pip check``' pass (`#7131 `_) * fix missing required Python packages in ASE 3.16.2 easyconfigs (`#7139 `_) * fix ``source_urls`` in CP2K easyconfigs (for official releases) (`#7240 `_) * update SCOTCH 6.0.5 easyconfigs in-place to 6.0.6 to fix wrong download URL (`#7159 `_) * add Autotools build dep in patchelf easyconfig (`#7175 `_) * STREAM fixes: use https + versioned source (`#7193 `_) * fix checksum in Molden easyconfig (`#7251 `_) * fix source URL for ADMIXTURE (`#7258 `_) * fix source URLs & versions + build procedure for SKESA (`#7275 `_) * fix checksum for TRF 4.09 (`#7278 `_) * add missing zlib dependency for NSS (`#7293 `_) * add required build deps for QtWebEngine in recent Qt5 easyconfigs (`#7300 `_) * fix ImageMagick source URLs: use ``launchpad.net`` for old versions, switch to GitHub for 7.0.8-* onwards (`#7301 `_) * other changes: * update ``Java/1.8`` wrapper to Java 1.8.0_192 (`#7097 `_) * don't enable ``optarch`` toolchain option in VCFtools easyconfigs, since it's enabled by default (`#7106 `_) * stop using lowopt in libxc 4.2.3 easyconfigs (`#7115 `_) * deprecate easyconfigs for ``ictce`` toolchains + ``intel`` toolchains older than ``intel/2016a`` (`#7231 `_) * deprecate easyconfigs for ``goolf(c)`` + corresponding ``gompi(c)`` subtoolchains (`#7243 `_) .. _release_notes_eb371: EasyBuild v3.7.1 (October 18th 2018) ------------------------------------ bugfix/update release **framework** - various enhancements, including: - generate ``.modulerc.lua`` when Lua syntax and Lmod >= 7.8 is used (`#2597 `_) - allow ``--force`` to use regex if ``--try-toolchain`` can not map intelligently (`#2605 `_) - add support for disabling modules tool version check (`#2610 `_) - add support to ``ModuleGenerator.modulerc`` method to also write ``.modulerc`` file (`#2611 `_) - check whether module file being wrapped exists in same directory as module wrapper when using Lmod 6.x (`#2611 `_) - various bug fixes, including: - stop relying on '``easy_install``' in bootstrap script, use '``python -m easy_install``' instead (`#2590 `_) - fix templating of values in ``list_software`` function (`#2591 `_) - fix composing of ``lib64`` fallback paths in sanity check (`#2602 `_) - determine ``file_info`` for all easyconfigs before any actual copying in ``copy_easyconfigs`` function (`#2604 `_) - also check for module wrappers in ``ModulesTool.exist`` method (`#2606 `_) - add trailing newline to module load message if it's not there yet (`#2613 `_) - retain all dependencies when determining dependency tree of a toolchain (`#2617 `_) - protect ``exts_lists`` from templating in ``dump`` method (`#2619 `_) - making CUDA capability detection more robust (`#2621 `_) - other changes: - lower required Lmod version to 6.5.1 (`#2593 `_) **easyblocks** - new software specific easyblocks for fastStructure (`#1529 `_) - minor enhancements, including: - support bypassing use of system type obtained with recent ``config.guess`` in ``ConfigureMake`` (`#1531 `_) - enhance generated module file for FreeSurfer (`#1543 `_) - add option in Qt easyblock to check for QtWebEngine component in sanity check (`#1544 `_) - also install CP2K as a library + code cleanup in CP2K easyblock (`#1547 `_) - various bug fixes, including: - fix checking for downloaded dependencies for stand-alone installations in ``PythonPackage`` generic easyblock (`#1530 `_) - also specify ``--host`` option to configure script based on config.guess result in ``ConfigureMake`` easyblock (`#1532 `_) - use short module name when creating module wrapper in ``ModuleRC`` generic easyblock (`#1535 `_) - use ``DOT_MODULERC`` constant in ``ModuleRC`` easyblock rather than hardcoding '``.modulerc``' (`#1533 `_) - use ``--no-deps`` when installing .whl in TensorFlow easyblock if extension are being installed, move test run to sanity check (`#1537 `_) - use ``os.getcwd()`` rather than ``self.startdir`` in TensorFlow easyblock to fix installation of TensorFlow as extension in a bundle (`#1540 `_) - add symlink to wrapped module file when creating ``.modulerc`` in temporary location (`#1539 `_) - properly handle Python dependency in Qscintilla easyblock (`#1499 `_) - other changes: - cleanup Tarball easyblock by using ``copy_dir`` function (`#1541 `_) **easyconfigs** - added easyconfigs for new toolchain ``foss/2018.08`` with GCC/8.2.0 (`#6992 `_) - added example easyconfig files for 26 new software packages: - ARCH (`#6939 `_), fbm (`#6948 `_), GenomeTester4 (`#6970 `_), GlobusConnectPersonal (`#6974 `_), MMseqs2 (`#6964 `_), NAG (`#5772 `_), NAGfor (`#5772 `_), NSPR (`#7005 `_), NSS (`#7005 `_), NeuroKit (`#6947 `_), novoalign (`#6944 `_), OptiType (`#6924 `_), OrthoFinder (`#6964 `_), pandas-datareader (`#6938 `_), pFUnit (`#6949 `_), PMIx (`#6930 `_), PSolver (`#6888 `_), PyDatastream (`#6951 `_), PyFR (`#6846 `_), Pyomo (`#6910 `_), Quandl (`#6950 `_), RTG-Tools (`#6862 `_), seq2HLA (`#6969 `_), suds (`#6951 `_), UCX (`#6931 `_), XMLSec (`#6929 `_) - added additional easyconfigs for various supported software packages, including: - binutils 2.31.1, dask 0.19.4, GCC(core) 8.2.0, OpenBLAS 0.3.3, OpenMPI 3.1.2, Pillow 5.3.0, PyCUDA 2018.1 - minor enhancements, including: - add clustree + plotly extensions (+ deps) for R 3.5.1 (`#6901 `_) - add tclsh symlink to recent Tcl easyconfigs (`#6915 `_) - update GROMACS 2016.3 with NVML patches (`#6936 `_) - use ``make=make`` in build options for ParMGridGen easyconfigs (`#6952 `_) - add ``Data::Dump`` as extension to Perl (dependency for GIMIC) (`#7004 `_) - various bug fixes, including: - inhibit ``-Werror`` in binutils 2.26 as new system GCC has case fallthrough warnings (`#5793 `_) - change fastStructure easyconfig to use custom easyblock (`#6893 `_) - fix toolchain for tbb dependency in ``Bowtie2-2.3.4.2-foss-2018b.eb`` (`#6927 `_) - fix uroot installation in R-3.5.1-foss-2018b (`#6934 `_) - add missing Python packages in TensorFlow 1.10.x easyconfigs (`#6940 `_) - add missing dep for Szip in 2017b builds of netCDF (`#6942 `_) - fix missing comment from ``OpenBabel-2.4.1-fix-link-path-tests.patch`` (`#6943 `_) - add patch to Python 3.6.1 - 3.6.3 that removes comment in comment (`#6946 `_) - add missing ``ulimit_unlimited=True`` (see issue `#6484 `_) in the newest Python builds (`#6959 `_) - solve '``version UUID_1.0 not found``' problem in LibUUID easyconfigs (`#6962 `_) - eliminate dependency on ancient problematic LibUUID library, replace with util-linux (`#6963 `_) - force building of ``ccmake`` for CMake 3.12.1 + fix deps (`#6967 `_) - fix broken installation for Python 3.6.2 & 3.6.3 with PyNaCl as dep for paramiko extension by explicitly including previous PyNaCl version as extension (`#6971 `_) - fix source URL for ADMIXTURE (no https) + add SHA256 checksum (`#6982 `_) - add missing NSS/DBus dependencies to Qt 5.10.1 easyconfigs built with foss toolchain to ensure that QtWebEngine component gets installed (`#7005 `_) - add '``openssl``' OS deps in Perl 5.28.0 easyconfig for ``Net::ssleay`` (`#7008 `_) - add missing checksum for ipaddress extension in Python easyconfigs (`#7021 `_ and `#7033 `_) - add missing extensions to Python 2.7.14 (`#7022 `_ and `#7023 `_), 3.6.2 (`#7025 `_), 3.6.3 (`#7027 `_) and 3.6.4 (`#7029 `_ and `#7030 `_) - add missing OS dependencies for git (`#7028 `_) - create default configuration for RTG-Tools (`#7032 `_) - also run checks on changed files when target branch for PR is something different than 'develop' (`#7034 `_) - other changes: - removed dead 'bzip.org' source URL for bzip2 source tarball (`#6983 `_) .. _release_notes_eb370: EasyBuild v3.7.0 (September 25th 2018) -------------------------------------- feature release **framework** - minimal Lmod version requirement bumped to 6.6.3 (`#2575 `_) - various enhancements, including: - add support to bootstrap script to force install specific EasyBuild version (`#2382 `_, `#2580 `_) - consider potential of multiple subtoolchains when resolving dependencies (`#2464 `_, `#2465 `_, `#2466 `_, `#2585 `_) - fall back to downloading using the ``requests`` Python package (if installed) when ``urllib2`` fails due to SSL error (`#2538 `_) - make ``--try-toolchain`` more aware of subtoolchains (`#2539 `_) - subtoolchain of original toolchains are now mapped to subtoolchains of target toolchain - add support for BLIS and goblf toolchain that uses BLIS for BLAS (`#2540 `_) - allow skipping of sanity check step via '``skipsteps``' easyconfig parameter (`#2549 `_) - add support for ``--check-contrib`` (`#2551 `_) - equivalent with ``--check-style``, but also verifies presence of SHA256 checksums (+ more checks in the future) - added support to 'download' sources from git (`#2555 `_) - see https://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html#downloading-from-a-git-repository - add '``parse``' hook to add support for applying site-specific customisations to the 'raw' easyconfig (`#2562 `_, `#2566 `_) - see https://easybuild.readthedocs.io/en/develop/Hooks.html - lift invalidating of module caches into helper method that can be used by easyblocks (`#2571 `_) - always dump a fully parsed easyconfig to the '``reprod``' subdir of the installation directory (`#2574 `_) - add '``modulerc``' method to ``ModuleGenerator`` class (`#2575 `_) - various bug fixes, including: - make GC3Pie stop build process if a dependency failed (`#2474 `_) - filter out patched files in test/ in ``fetch_easyconfigs_from_pr`` (`#2547 `_) - check GC3pie version using the ``pkg_resources`` API rather than using ``__version__`` (which was removed in GC3Pie 2.5.0) (`#2554 `_) - fix enforcing of checksums for extensions (`#2561 `_, `#2570 `_, `#2579 `_) - skip running of configuration checks while only a single configuration level is taken into account during ``--show-config`` (`#2567 `_) - fix error statements in modules tool version checks (`#2576 `_) - fix finding of software subdirectory for specified patch file in ``--new-pr``/``--update-pr`` (`#2577 `_) - take into account dependency 'wrappers' in check_conflicts (`#2583 `_) - stick to pycparser < 2.19 with Python 2.6 in Travis config (`#2584 `_) - other changes: - use ``namelower`` as default for '``github_account``' easyconfig parameter (`#2528 `_) - use ``.counts()`` rather than deprecated ``.stats()`` for GC3Pie (`#2573 `_) **easyblocks** - new generic easyblock: ``ModuleRC`` (`#1503 `_, `#1518 `_) - new software specific easyblocks for BWISE (`#1497 `_) and VEP (`#1512 `_) - minor enhancements, including: - update QuantumESPRESSO easyblock: stop building in installation dir, do not use external FoX dependency, support for recent versions (`#1312 `_) - updates to TensorFlow easyblock: - require cuDNN if CUDA support is enabled, enable mkl-dnn by default, fix problem with internal protobuf problem, add awareness for TensorRT & NCCL (`#1453 `_) - add support for IntelMPI (`#1507 `_) - update WIEN2k easyblock for version 18.1 (`#1460 `_) - add CUDA '``stubs``' subdirectory to $LIBRARY_PATH (`#1464 `_) - add support for building ScaLAPACK on top of BLIS (`#1467 `_) - handle X11 better and make '``static``' a build flag in Amber easyblock (`#1468 `_) - update Boost easyblock for Boost 1.67.0 (name change in Python 3.x library files) (`#1472 `_) - add CEI/bin to $PATH for ANSYS 19 & newer (`#1476 `_) - enhance SCons easyblock to enable building in parallel (`#1477 `_) - add awareness for CCOLAMD and CAMD in Trilinos easyblock (`#1480 `_) - add support to apply (binary) patches after main CUDA install (`#1481 `_, `#1483 `_) - add support for only building Python bindings (+ code cleanup) in Boost easyblock (`#1484 `_, `#1495 `_) - provide control over subdirectory in which R packages are installed (`#1485 `_) - added regex to fix ``$WM_PROJECT_VERSION`` correctly in OpenFOAM easyblock (`#1489 `_) - improve PGI siterc so it allows ``-pthread`` switch (`#1494 `_) - customise ``check_checksums method`` in Bundle easyblock to fix checking of checksums for components (`#1496 `_) - include a pkgconfig file '``hdf5.pc``' to HDF5 installations (`#1504 `_) - (download &) use an updated ``config.guess`` script in generic ConfigureMake easyblock (`#1506 `_, `#1522 `_, `#1523 `_, `#1524 `_) - make ``IntelBase`` generic easyblock aware of ``(pre)installopts`` (`#1509 `_) - update Siesta easyblock for v3.2 to 4.1-b3 (`#1510 `_) - take ``(pre)installopts`` into account in RPackage generic easyblock (`#1513 `_) - update DOLFIN easyblock for latest version (`#2018 `_.1) (`#1521 `_) - various bug fixes, including: - drop useless definition of ``$NLSPATH`` in ``IntelBase`` + fix ipp library paths (`#1442 `_) - fix order of arguments in log message in ``PythonPackage`` easyblock (`#1459 `_) - run ``ldconfig`` in post-install step of CUDA easyblock to create missing symlinks in 'stubs' subdirectory (`#1473 `_) - take into account that only name/version may be specified for some components in ``Bundle`` easyblock (`#1474 `_) - make SuperLU easyblock consider both ``lib`` and ``lib64`` subdirectories (`#1479 `_) - use short build dir for Trilinos to dance around "``Argument list too long``" problem + link with ``libmetis.a`` (`#1486 `_) - correct check for Red Hat 6 based OS in TensorFlow easyblock (`#1487 `_) - improve configuration choice in FSL easyblock (`#1498 `_) - don't check for ``mcc`` in MATLAB sanity check as it requires a specific toolbox license (`#1514 `_) - make sure Bazel doesn't write files in $HOME/.cache when building TensorFlow (`#1519 `_) - enable VSX on POWER for FFTW >= 3.3.7 (`#1520 `_) - add ``librt`` as dependency when linking Trilinos with SuiteSparse (`#1525 `_) - other changes: - switch to using CMake install procedure for Eigen 3.3.4 & newer (`#1482 `_) - bump Lmod version used in Travis config to 6.6.3 (now required by framework) (`#1505 `_) **easyconfigs** - added easyconfigs for new toolchains: ``fosscuda/2017b`` (`#6706 `_), ``intelcuda/#2017b`` (`#6709 `_), ``iomkl/2018b`` (`#6661 `_) - added example easyconfig files for 49 new software packages: - alleleCount (`#6676 `_), BCALM (`#6796 `_), BDBag (`#6672 `_), BFC (`#6647 `_), Bio-DB-HTS (`#6854 `_), bioawk (`#6865 `_), biomart-perl (`#6745 `_), BLIS (`#6614 `_), Boost.Python (`#6763 `_), BWISE (`#6802 `_), CapnProto (`#6542 `_), CaVEMan (`#6708 `_), CCL (`#5802 `_), cDNA_Cupcake (`#6787 `_), cget (`#6780 `_), coevol (`#6589 `_, `#6642 `_), Delly (`#6735 `_), earthengine-api (`#6556 `_), fineRADstructure (`#6586 `_), GIMIC (`#6575 `_), GitPython (`#6850 `_), HiC-Pro (`#5873 `_), Inelastica (`#6831 `_), JAXFrontCE (`#6837 `_), jq (`#6632 `_), KAT (`#6808 `_), KMC (`#6553 `_), Kraken2 (`#6569 `_), Lighter (`#6553 `_), Mash (`#6542 `_), MetaPhlAn2 (`#6600 `_), Minimac4 (`#6781 `_), mordecai (`#6670 `_), NCCL (`#5802 `_), NxTrim (`#6646 `_), parasail (`#6601 `_), PheWAS (`#6030 `_), Pilon (`#6553 `_), python-parasail (`#6601 `_), SearchGUI (`#6637 `_), shovill (`#6553 `_), SKESA (`#6553 `_), snakemake (`#6851 `_), strelka (`#6742 `_), SWIPE (`#6795 `_), ToFu (`#6322 `_), tqdm (`#6721 `_), TRUST (`#6601 `_), VEP (`#6854 `_) - added additional easyconfigs for various supported software packages, including: - Bazel 0.16.0, Boost 1.67.0 + 1.68.0, CUDA 10.0.1, DOLFIN (FEniCS) 2018.1, FSL 5.0.11, GC3Pie 2.5.0, GROMACS 2018.3, HTSlib + SAMtools 1.9, IPython 6.4.0, matplotlib 3.0.0, OpenCoarrays 2.2.0, OpenFOAM 6 & v1806, PyTorch 0.4.1, Python 3.6.6, R 3.5.1, TensorFlow 1.10.1, Trilinos 12.12.1, WIEN2k 18.1 - minor enhancements, including: - add test to enforce SHA256 checksums in touched files in pull requests to develop (`#5005 `_) - add various extensions to recent R easyconfigs (`#6590 `_, `#6686 `_, `#6858 `_) - add ``mpmath`` extension to Python 3.6.4 + 3.7.0 easyconfigs (`#6607 `_, `#6713 `_) - add Java 1.8 easyconfig that can be updated in-place to more recent JDK 1.8.x (`#6712 `_) - see also https://easybuild.readthedocs.io/en/latest/Wrapping_dependencies.html - add ``iso_c_binding`` support to arpack-ng 3.6.2 (`#6718 `_) - add ``XML::Parser``, ``XML::RegExp`` & ``XML::DOM`` extensions to Perl(`#6744 `_) - add ``tabulate`` extension to all Python > 3.6 easyconfigs (`#6809 `_) - enable MPI version of arpack-ng 3.5.0 (`#6840 `_) - add ``wish`` symlink to ``wish8.6`` in recent Tk easyconfigs (`#6870 `_) - add ``libXp`` and ``printproto`` to X11 bundle (`#6873 `_) - various bug fixes, including: - define '``_GNU_SOURCE``' to ensure that '``reallocarray``' is defined in flex 2.6.4 easyconfigs, fixes bootstrap crash (`#5792 `_, `#6766 `_) - added tabix dependency in VCFtools (`#6584 `_) - added zlib dependency to BWA (`#6591 `_), BEDTools (`#6592 `_), VCFtools (`#6653 `_) - add checksums to googletest easyconfigs (`#6611 `_) - fix source URL + add checksum to wkhtmltopdf-0.12.3-Linux-x86_64.eb (`#6628 `_, `#6641 `_) - don't use external FoX dependency in QuantumESPRESSO 6.2 (`#6638 `_) - update hwloc easyconfigs with libxml2 and libpciaccess dependencies (`#6639 `_) - fix gettext build dep for Mono-5.10.0.160 (`#6640 `_) - remove no longer existing config option ``--enable-mpi-thread-multiple`` in OpenMPI 3.x easyconfigs (`#6645 `_) - fix homepage in recent HDF5 easyconfigs (`#6687 `_) - add expat dependency to Mesa v18.1.1 (`#6706 `_) - add missing ``--with-trio-flavor=netcdf`` flag to ABINIT 8.x easyconfigs (`#6711 `_) - remove useless definition of $TORCH_CUDA_ARCH_LIST in PyTorch easyconfig that doesn't use CUDA (`#6719 `_) - fix builing GCCcore 6.3.0 on recent OSs by backporting patches from 6.4.0 (`#6727 `_) - fix ``source_urls`` in bzip2 easyconfigs (`#6728 `_) - specify location of dependencies in configure options for libgd (to avoid system libraries being used instead) (`#6731 `_) - also install docs/man pages in recent git easyconfigs (versions 2.1x.y) (`#6751 `_) - add CMake build dep for Eigen 3.3.4 (`#6756 `_, `#6784 `_) - add expat dependency to Perl 5.26.0 (`#6758 `_) - add ncurses OS dependency to CMake for Debian distros (`#6783 `_) - fix checksums for pkgmaker, rngtools & RcppProgress extensions in R 3.4.3 easyconfigs (`#6815 `_) - add pkg-config build dependency to GTS (`#6819 `_) - do not check if hwloc-dump-hwdata utility was installed, since it's only built on x86 systems (`#6836 `_) - patch libxc 3.x and 4.0.x to compile on POWER (`#6868 `_) - consistently add patch for paycheck extension in Python 3.6/3.7 to fix UTF8 issue with README (`#6892 `_) - other changes: - bump Lmod version used in Travis config to 6.6.3 (now required by framework) (`#6834 `_) .. _release_notes_eb362: EasyBuild v3.6.2 (July 11th 2018) --------------------------------- bugfix/update release **framework** * various enhancements, including: * add support for including environment variable that is resolved at "module load time" in user module path (`#2395 `_) * ``{RUNTIME_ENV::EXAMPLE}`` is replaced by value of ``$EXAMPLE`` when module is loaded * also support generating Docker container recipes & image via ``--containerize`` (still experimental) (`#2479 `_) * add support for specifying source URLs directly in '``sources``' (`#2520 `_) * perform early 'raw' parse of provided easyconfig file to check for syntax error or faulty inputs (`#2523 `_) * add '``bitbucket_account``' easyconfig parameter and template, and let ``BITBUCKET*`` templates use it (`#2525 `_) * various bug fixes, including: * take into account ``--filter-deps`` when re-loading build dependencies in ``extensions_step`` (`#2516 `_) * fix for offline use of bootstrap script: ignore errors when determining source URLs if source tarballs are provided (`#2517 `_) * fix error message that is raised for incorrect type of value in ``sanity_check_paths`` (`#2524 `_) * other changes: * move flake8 config into ``setup.cfg`` + fix style issues in ``easybuild/tools/options.py`` (`#2511 `_) * make test that verifies that ``BuildOptions`` does not support updating a bit more flexible (`#2518 `_) **easyblocks** * new software-specific easyblock for OpenCV (`#1444 `_) * minor enhancements, including: * use ``$CPATH``/``$LD_LIBRARY_PATH`` for CMake's ``find_path``/``find_library`` functions in ``CMakeMake`` easyblock (`#1165 `_) * make cdft lib compilation optional for Intel MKL, by detecting MPI availability (`#1393 `_) * add ``use_glibcxx11_abi`` easyconfig parameter in Boost easyblock (`#1434 `_) * enable filtering of paths in ``$CPATH`` and ``$LIBRARY_PATH`` in TensorFlow easyblock (`#1436 `_) * add support for building GROMACS with ``--optarch=GENERIC`` (`#1440 `_) * check current stack limit and set it to '``unlimited``' if possible in Python easyblock (`#1441 `_) * trivial update for Q&A in SAS easyblock (`#1448 `_) * allow skipping tests when installing Perl extensions, by setting '``runtest``' to ``False`` (`#1451 `_) * add support for installing Intel products using serial numbers (`#1452 `_) * update version check to FFTW 3.3.8 for tests to pass on POWER (ppc64le) (`#1454 `_) * various bug fixes, including: * build MPFR in GCC stage 1 without LTO if (system) GCC used is too old (`#1435 `_) * make sure xmlpatterns always gets built with Qt (`#1437 `_) * fix symlink check in NWChem easyblock + use ``change_dir``/``remove_file``/``symlink`` functions (`#1438 `_) * other changes: * move flake8 configuration to ``setup.cfg`` and make HoundCI aware of it (`#1430 `_) **easyconfigs** * added easyconfigs for new toolchains: ``foss/2018b`` (`#6424 `_), ``fosscuda/2018b`` (`#6555 `_) and ``intel/2018b`` (`#6409 `_) * added example easyconfig files for 28 new software packages: * CUnit (`#6469 `_), eggnog-mapper (`#6513 `_), FANN (`#6468 `_), FTGL (`#6421 `_), FreeFem++ (`#5918 `_), fastStructure (`#6448 `_), fastq-tools (`#5396 `_), fullrmc (`#6422 `_), GDGraph (`#6529 `_), heaptrack (`#6450 `_), libgpuarray (`#5429 `_), lz4 (`#6449 `_), MAJIQ (`#5983 `_), makedepf90 (`#6504 `_), nanopolish (`#6464 `_), opencv_contrib (`#6441 `_), PRC (`#6477 `_), Pillow-SIMD (`#6152 `_), Pytorch (`#6152 `_), poretools (`#6467 `_), pystran (`#6395 `_), R-keras (`#6530 `_), Scoary (`#6521 `_), Scrappie (`#6469 `_), torchvision (`#6152 `_), WISExome (`#6524 `_), WannierTools (`#6539 `_), zstd (`#6449 `_, `#6452 `_) * added additional easyconfigs for various supported software packages, including: * GROMACS 2018.2, HDF5 1.10.2, IPython 6.3.1, Kraken 1.0, Mesa 18.1.1, netCDF 4.6.1, NWChem 6.8, OpenBLAS 0.3.1, OpenMPI 3.1.1, Perl 5.28.0, Python 2.7.15, R 3.5.0, X11 20180604 * minor enhancements, including: * add hint on file name differences between downloaded and expected in cuDNN easyconfig (`#6042 `_) * add '``gee``' extension to R 3.4.4 easyconfigs (`#6376 `_) * enable building of MPI libraries in VTK 8.1.0 easyconfigs (`#6460 `_, `#6429 `_) * minor changes, including: * rename '``Canu``' to '``canu``' for v1.7 (`#6389 `_) * update existing easyconfigs for OpenCV 3.4.1 to use new custom easyblock for OpenCV (`#6509 `_) * fix software name in ``Bsoft`` easyconfig (`#6557 `_) * various bug fixes, including: * fix SAMtools dependency for ChimPipe, required SAMtools < 1.0 (`#5930 `_) * skip installing of documentation in easyconfig for jemalloc 5.0.1 (`#6428 `_) * stop including GCCcore 6.4.0 as build dep for GCCcore 8.1.0 (`#6431 `_) * no longer needed with updated GCC easyblock * add patch for GCCcore 6.4.0 to fix compilation problems on glibc 2.26 systems (`#6432 `_, `#6495 `_) * fix checksums for ``pkgmaker``/``rngtools``/``RWeka``/``RcppProgress``/``mgcv`` extensions in R 3.4.4 easyconfigs (`#6446 `_, `#6502 `_) * added necessary compiler flag for Guile 1.8.8 (`#6457 `_) * build hwloc 1.11.10 with ``-fno-tree-vectorize`` to avoid segfaulting lstopo on Intel Skylake (`#6461 `_) * add patch for binutils 2.30 to fix assertion failure (`#6463 `_) * sync extensions in ``Python-3.6.4-iomkl-2018a.eb`` easyconfig with other Python 3.6.4 easyconfigs using 2018a toolchain (`#6471 `_) * enable checking/setting of unlimited stack limit in Python 3.6.x easyconfigs using an '``intel``' toolchain (`#6485 `_, `#6492 `_) * add missing ``libxml2`` dependency for HDF5 1.10.1 (`#6498 `_) * also copy eggnog-mapper scripts (`#6522 `_) * fix missing dependencies for Perl modules included as extensions for Perl 5.26.1 (`#6532 `_) and 5.28.0 (`#6533 `_) * fix location of include directory in libffi 3.2.1 easyconfigs (`#6565 `_) * other changes * also check for multiple dependency variants in easyconfigs using GCCcore 7.3.0 & newer (`#6444 `_) .. _release_notes_eb361: EasyBuild v3.6.1 (May 26th 2018) -------------------------------- bugfix/update release **framework** * various enhancements, including: * add support for enabling fallback in sanity check to consider ``lib64`` equivalent for seemingly missing libraries (`#2477 `_) * add ``GITHUB_LOWER_SOURCE`` constant (`#2491 `_) * add '``exts_download_dep_fail``' as known easyconfig parameter (`#2493 `_) * add support for passing custom messages on failing sanity check for extensions (`#2494 `_) * add definition for ``fosscuda`` toolchain (`#2507 `_) * various bug fixes, including: * make ``--inject-checksums`` always re-order ``source_urls``/``sources``/``patches``/``checksums`` (`#2487 `_) * fix git remote url in ``CONTRIBUTING.md`` (`#2490 `_) * make ``flake8`` happy in ``easyblock.py`` (`#2492 `_) * handle missing permissions for adding labels in ``--new-pr`` (`#2497 `_) * restore tweaked ``$TMPDIR`` value after loading module (for sanity check) (`#2498 `_) * enhance ``get_module_path`` function to auto-detect generic vs software-specific easyblock class names (`#2502 `_) * don't blindly overwrite an existing easyconfig in ``tweak_one`` (`#2504 `_) * take account that ``PlaintextKeyring`` may be provided via ``keyrings.alt`` (`#2505 `_) * prepend location for temporary module file to ``$MODULEPATH`` with high priority + mark it as default in ``load_fake_module`` method (`#2506 `_) **easyblocks** * minor enhancements, including: * add support for detecting auto-downloaded dependencies in ``PythonPackage`` easyblock (`#1377 `_) * disabled by default, can be enabled using "``download_dep_fail = True``" in easyconfig file * add support to enable integration of pscom in psmpi easyblock (`#1397 `_) * set ``$CMAKE_*_PATH`` when ``CMake`` is loaded in ``PythonPackage`` easyblock (`#1398 `_) * update WIEN2k easyblock for v17 (`#1405 `_) * disable jemalloc support in TensorFlow on CentOS 6 & co (+ minor cleanups) (`#1412 `_) * update Maple easyblock to support recent versions (`#1414 `_) * enable ``nc-config`` usage for netCDF in ESMF >=7.1 (`#1419 `_) * enhance PETSc easyblock for version 3.9 (`#1421 `_) * check output of MATLAB installation command for invalid installation key error (`#1423 `_) * fix suffix for Boost Python library in Boost 1.67.0 & newer (`#1424 `_) * support adding specific paths to ``$PATH`` for generic Binary easyblock via '``prepend_to_path``' custom easyconfig parameter (`#1426 `_) * minor changes, including: * assume PGI Community edition is used when no license file is specified (`#1427 `_) * various bug fixes, including: * fix imkl sanity check overwriting base libs with interface libs (`#1392 `_) * install Chimera in a subdirectory to avoid its dependencies being added to the environment (`#1413 `_) * add conditional so "``--with-x``" is only added to configopts if left unspecified in R easyblock (`#1415 `_) * make ``configure`` and ``make`` look for FoX in ``$EBROOTFOX`` in QuantumESPRESSO easyblock (`#1420 `_) * fix path for ``$ICEM_ACN`` in ANSYS easyblock (`#1422 `_) * avoid hardcoding defaults in question patterns in Doris easyblock (`#1428 `_) **easyconfigs** * added easyconfigs for new toolchains ``fosscuda/2018a`` (`#6363 `_) and ``giolfc/2017b`` (`#5799 `_) * added example easyconfig files for 24 new software packages: * BAGEL (`#6332 `_), Bottleneck (`#6334 `_), cisTEM (`#6370 `_), cftime (`#6337 `_), dotNET-Core-Runtime (`#6345 `_), ecCodes (`#6235 `_), feh (`#6300 `_), Graphene (`#5043 `_), gffread (`#6306 `_), HOME (`#6227 `_), HiCExplorer (`#6342 `_), ICU (`#6371 `_), Imlib2 (`#6300 `_), KmerGenie (`#5929 `_), libgeotiff (`#6262 `_), NetPIPE (`#6062 `_), Pandoc (`#6247 `_), Pisces (`#6347 `_), Proteinortho (`#6333 `_), pyshp (`#6364 `_), SIMPLE (`#6019 `_), STIR (`#6349 `_), SimpleElastix (`#6114 `_), wxWidgets (`#6370 `_) * added additional easyconfigs for various supported software packages, including: * Boost 1.67.0, ESMF 7.1.0r, GATK 4.0.4.0, GCC 8.1.0, GROMACS 2018, OpenBLAS 0.3.0, PETSc 3.9.1, PGI 18.4, TensorFlow 1.8.0, WIEN2k 17.1 * minor enhancements, including: * add ``py_expression_eval`` extension to (recent) Python 2.7.14 & 3.6.4 easyconfigs (`#6285 `_) * add ``README`` for Java with information on downloading source tarball (`#6294 `_) * add several extensions to Perl 5.26.1 easyconfigs, incl ``Dist::Zilla`` & dependencies (`#6297 `_) * also include archive URLs for Bioconductor 3.6 (`#6311 `_) * add ``README.md`` file for installing icc/ifort (`#6317 `_) * various bug fixes, including: * consistently specify '``intel-mkl``' component in recent Intel MKL easyconfigs (`#6234 `_) * add ``pkg-config`` as build dependency to libdrm (`#6243 `_) * add ``pkg-config`` build dep to most recent libdrm easyconfigs (`#6244 `_) * fix checksum for foreign extension in R 3.4.3 and R 3.4.4 easyconfigs (`#6245 `_) * fix installation of Libint 2.4.2 by building with ``-std=c++11`` (`#6251 `_) * fix source spec for networkx 2.1 extension in scikit-image easyconfig (`#6254 `_) * avoid that Nipype downloads dependencies for included extensions (`#6261 `_, `#6263 `_) * consistently include patch for FLTK 1.3.4 (`#6265 `_) * fix Perl shebang in MCL v14.137 scripts (`#6269 `_) * add patch to build particular source file of matrixStats extension in R 3.4.4 easyconfig with ``-O1`` to work around ICE in Skylake systems (`#6278 `_) * add ``pkg-config`` build dependency to FFmpeg >= 3.3.1 (`#6291 `_) * change back checksum for libdap 3.19.1 (`#6305 `_) * add patch for Automake 1.15 to fix issue with recent Perl versions (`#6358 `_) * fix ``glog`` causing intel error in Intel compilers on Intel Skylake (`#6360 `_) * include ICU as dependency in recent R easyconfigs (v3.4.3 & v3.4.4) (`#6371 `_) * fix checksum for RSEM 1.3.0 after sneaky re-release (`#6379 `_) .. _release_notes_eb360: EasyBuild v3.6.0 (April 26th 2018) ---------------------------------- feature release **framework** * (experimental) support for generating Singularity container recipes & (optionally) images via '``sudo singularity``' (`#2332 `_, `#2480 `_, `#2481 `_, `#2482 `_, `#2483 `_) * see documentation at http://easybuild.readthedocs.io/en/latest/Containers.html * include ``-ftree-vectorize`` and ``-fno-math-errno`` in default compiler optimisation flags for GCC (`#2388 `_) * this significantly improves performance of generated binaries when building with a GCC-based toolchain * can be disabled if needed via the ``vectorize`` toolchain option * several enhancements/fixes to GitHub integration support: * loosen commit message requirements for ``--new-pr`` w.r.t. to patches as long as all easyconfigs are new (`#2438 `_) * automatically add '``new``' and/or '``update``' labels in ``--new-pr`` (`#2384 `_) * add ``force_in_dry_run=True`` to ``copy_file`` in ``copy_patch_files`` (`#2442 `_) * test for custom commit message when deleting a file instead of when adding a patch (`#2443 `_) * make ``diff_stat`` pattern also match output of older git versions in tests for ``--new``/``update-pr`` (`#2444 `_) * remove duplicates from ``--new-pr`` title (`#2478 `_) * add support for "``eb --fetch``" to only download sources (even without having a modules tool installed) (`#2457 `_) * add definitions for a bunch of new toolchains: * ``golf`` (`#2458 `_), ``gmkl`` (`#2460 `_), ``gomkl`` (`#2455 `_), ``pmkl`` (`#2460 `_) * toolchains including CUDA: ``gmklc``, ``gomklc``, ``iimklc``, ``iompic``, ``iomklc`` (`#2461 `_) * various minor enhancements, including: * avoid that '``--inject-checksums``' adds lines longer than 120 characters (`#2434 `_) * enable caching of ``$HOME/.cache/pip`` in Travis config (`#2435 `_) * replace raw strings with bytes literal as iterator sentinels in checksum calculation (`#2446 `_) * new command-line option '``--job-max-jobs``' to cap nr of submitted build jobs with GC3Pie (`#2378 `_) * add configuration for houndci + flake8 (`#2451 `_) * add ``Accept`` header when downloading file (`#2437 `_) * include running of '``eb --check-github``' in Travis config (`#2449 `_, `#2454 `_) * flesh out common code blocks in ``test/framework/options.py`` (`#2452 `_) * support '``depends_on``' load statements in generated modules via ``--module-depends-on`` and ``module_depends_on`` easyconfig parameter (`#2391 `_) * fix compatibility with Modules v4.1.x (`#2470 `_) * add support to ``run_cmd`` to enable streaming output (`#2476 `_) * various bug fixes, including: * determine whether included easyblocks are generic or not based on class they define (`#2432 `_) * make sure GitHub token is used in test for ``--preview-pr`` (`#2436 `_) * take into account that toolchain components may be hidden when determining toolchain composition (`#2440 `_) * stick to autopep8 1.3.4 when testing with Python 2.6 (`#2462 `_) * strip off ``.lua`` extension when backing up modules to ensure Lmod 6.x doesn't pick up on them (`#2463 `_) * check for ``modulecmd.tcl`` before modulecmd in bootstrap script to discriminate between Modules 4.1.x vs 3.2.10 (`#2468 `_) * fix ``derive_alt_pypi_url`` after PyPI switching to sha256 in package URLs + fix broken test for ``pypi_source_urls`` + fix bootstrap script (`#2471 `_) * make sure that both '``get_git_revision``' and '``this_is_easybuild``' return regular strings rather than Unicode strings (`#2472 `_) **easyblocks** * new software-specific easyblock for Nim (`#1402 `_) * minor enhancements, including: * enhance ``RPackage`` easyblock to support installing from unpacked sources (`#1383 `_) * add support to ``PythonPackage`` easyblock to install with '``pip install --editable``' (`#1384 `_) * add ``$EBROOTIFORT/include`` in ``$CPATH`` for ifort (`#1385 `_) * add houndci + flake8 configuration (`#1388 `_) * add additional location to ``$PATH`` for FLUENT installations (`#1389 `_) * make ``PythonPackage`` generic easyblock aware of '``unpack_options``' easyconfig parameter (`#1391 `_) * minor updates to ABAQUS easyblock to support latest version (`#1394 `_) * add support for extracting sources in ``Binary`` easyblock (`#1401 `_) * various bug fixes, including: * fix linking to FFTW for Doris: should be ``-lfftw3f`` (`#1387 `_) * fix for installing TensorFlow 1.6.0: use the absolute path for the C compiler when compiling with GPU support (`#1386 `_) * also take ``lib64`` into account for binutils libraries (`#1399 `_) * make sanity check in MPICH easyblock aware of libraries in ``lib64`` subdir (`#1403 `_) * take into account that ``self.debuggerpath`` may not be set in icc easyblock (`#1408 `_) * extend noqa in configure step of Qt easyblock (`#1409 `_) **easyconfig** * added easyconfigs for new toolchain golf/2018a (`#6080 `_) * added example easyconfig files for 39 new software packages: * ARAGORN (`#6138 `_, `#6219 `_), amask (`#6105 `_), BamBam (`#5490 `_), Bandage (`#6053 `_), bcgTree (`#6057 `_), biobambam2 (`#6040 `_), CODEX2 (`#5972 `_), coverage (`#5964 `_), DANPOS2 (`#5870 `_), EasyQC (`#6175 `_), elastix (`#6074 `_), FRANz (`#6035 `_), Filtlong (`#6050 `_), FriBidi (`#6181 `_), Gblocks (`#6057 `_), Grace (`#6036 `_), LMfit (`#6119 `_), libmaus2 (`#6040 `_), MathGL (`#6033 `_), MiGEC (`#6047 `_), MiXCR (`#6045 `_), Miniconda3 (`#6075 `_), Multiwfn (`#5403 `_), mosdepth (`#6169 `_), Nim (`#6167 `_), Porechop (`#6051 `_), propy (`#6091 `_), Roary (`#6056 `_), Rtree (`#6222 `_), SALib (`#6145 `_), SMRT-Link (`#6218 `_), SimpleITK (`#6172 `_), spectral.methods (`#6104 `_), supernova (`#6193 `_), TEToolkit (`#5912 `_), tbl2asn (`#6139 `_), udocker (`#5770 `_), vartools (`#6102 `_), XCfun (`#5975 `_) * added new easyconfigs for existing toolchains: * ``gmpich/2017.08`` (`#6143 `_), ``goolfc/2018a`` (`#6129 `_), ``intel/2018.02`` (`#6077 `_), ``iomkl/2018.02`` (`#6088 `_) * added additional easyconfigs for various supported software packages, including: * ABINIT 8.6.3, Anaconda2 5.1.0, Anaconda3 5.1.0, binutils 2.30, dask 0.17.2, FFmpeg 4.0, GCC(core) 7.3.0, GROMACS 2016.5, HTSlib 1.8, LLVM 6.0.0, Mesa 17.3.6, netCDF 4.6.0, Octave 4.2.2, OpenCV 3.4.1, PLUMED 2.4.1, PROJ 5.0.0, PostgreSQL 10.3, Qt5 5.10.1, R 3.4.4, SAMtools 1.8, Spack 0.11.2, TensorFlow 1.7.0, VTK 8.1.0 * minor enhancements, including: * add test to ensure there's only one variant for each dependency in dep graph of easyconfigs using particular toolchains (`#5970 `_, `#6023 `_) * add extensions required by CODEX2 v20180227 to Bioconductor w/ R 3.4.3 (`#5972 `_) * add config file for https://pre-commit.com/ (`#5785 `_) * add custom sanity check paths for GraphicsMagick consistently (`#5997 `_) * add custom sanity check paths to recent Ghostscript easyconfigs (`#5998 `_) * add svd, Rssa, JBTools, RUnit, DistributionUtils and gapfill extensions for R 3.4.3 (`#6099 `_) * add additional extensions to Bioconductor 3.6 bundle (`#6136 `_) * add xlrd extension to recent Python 2.x and 3.x easyconfigs (`#6162 `_) * minor changes, including: * use gettext 0.19.8.1 on top of libxml2 2.9.7 as dep for git built with ``foss/2018a`` (`#5993 `_) * bump hwloc dep for OpenMPI 2.1.2 that is part of ``iomkl/2018a`` to v1.11.8 (`#5994 `_) * use non-interactive plotting backend by default for matplotlib 2.1.2 (`#6024 `_) * don't use bare Perl as dependency for git with ``foss/2018a``, use variant with extensions (`#6058 `_) * various bug fixes, including: * fix ``moduleclass`` & add custom ``sanity_check_paths`` in gettext easyconfigs (`#5991 `_) * drop use of ``--disable-dlopen`` in (recent) OpenMPI easyconfigs due to negative performance impact (`#6060 `_) * add missing XZ dep in Python 3.6.4 easyconfigs built with ``*/2018a`` toolchain (`#6065 `_) * add 10 packages that were previously downloaded in Python 3.6.4 easyconfigs (`#6081 `_) * add patch for Tensorflow 1.6 & 1.7 to include missing -lrt link flag (needed in CentOS6) (`#6089 `_) * fix checksums for R extensions that were updated in place in easyconfigs for R versions 3.4.3 & 3.4.4 (`#6118 `_) * include pkg-config as build dep in recent R easyconfigs (required for at least nloptr) (`#6122 `_) * remove Intel-specific workaround for '``undefined symbol: __stack_chk_guard``' issue from Python 3.6.4 foss/2018a easyconfig (`#6130 `_) * add configopt ``--without-matlab``/``octave`` to all NLopt easyconfigs (`#6132 `_) * also consider ``lib64`` in ``sanity_check_paths`` for Bison 3.0.4 (`#6170 `_) * don't use libyaml built with dummy as dep for PyYAML (`#6208 `_) * add missing pkg-config build dep in recent GObject-Introspection, GLib & cairo easyconfigs (`#6216 `_) * don't include (ancient version of) ``Time::HiRes`` as Perl extension, since it's a core Perl module (`#6225 `_) * this fixes problems with the installation of BioPerl and proovread * add missing XML-LibXML dependency in recent BioPerl easyconfigs (`#6226 `_) * add ``--without-ada`` configure option in recent ncurses easyconfigs (`#6228 `_) * add patch for snaphu to fix segmentation fault due to use of short integer (`#6230 `_) .. _release_notes_eb353: EasyBuild v3.5.3 (March 7th 2018) --------------------------------- bugfix/update release **framework** * various enhancements, including: * re-enable testing against environment modules, bump Lmod to 7.7.16 (`#2425 `_) * print which hook is being executed in the command line output (`#2427 `_) * various bug fixes, including: * fix order in result of gen_list_easyblocks and gen_easyblocks_overview_rst (`#2421 `_) * fix target account for branch pushed when using ``--new-pr`` (`#2426 `_) **easyblocks** * minor enhancements, including: * make GROMACS easyblock select build type based on value for '``debug``' in '``toolchainopts``' (`#1374 `_) * re-enable testing against environment modules, bump Lmod to 7.7.16 (`#1376 `_) * enhance Gurobi easyblock to support installing Python bindings (`#1378 `_) **easyconfigs** * added example easyconfig files for 2 new software packages: * CNVkit and hmmlearn (`#5954 `_) * added additional easyconfigs for various supported software packages, including: * matplotlib 2.1.2, TensorFlow 1.6.0 * minor enhancements, including: * re-enable testing against environment modules, bump Lmod to 7.7.16 (`#5944 `_) * add cghFLasso extension to R 3.4.3 easyconfigs (`#5953 `_) * add '``Math::CDF``' extension to recent Perl modules (`#5957 `_) * various bug fixes, including: * add missing ``--enable-ld-version-script`` configure option for LibTIFF 4.0.9 built with ``GCCcore/6.4.0`` (`#5945 `_) * hard disable UCX support in recent OpenMPI versions, to dance around bug in OpenMPI configure script (`#5949 `_) .. _release_notes_eb352: EasyBuild v3.5.2 (March 2nd 2018) --------------------------------- bugfix/update release **framework** * various enhancements, including: * add functionality to skip devel module with naming scheme (`#2374 `_) * add pagination support in ``clean_gists.py`` (`#2379 `_) * allow basic compiler modulenames to be specified as keys in ``--optarch`` (`#2387 `_) * initial set of OHPC module meta data for EasyBuild (`#2392 `_) * allow different target account in ``post_comment_in_issue`` (`#2399 `_) * declare support for RPATH linking stable (`#2409 `_) * various bug fixes, including: * update bootstrap script to be compatible with Modules v4 (`#2390 `_) * avoid fatal error when determining glibc version on non-glibc Linux system (e.g. Alphine Linux) (`#2398 `_) * exclude location of RPATH wrappers from ``$PATH`` to avoid fork bomb (`#2410 `_) * fix target account for ``--update-pr`` in case it's different from GitHub account being used to push branch (`#2419 `_) **easyblocks** * new software-specific easyblocks for COMSOL (`#1317 `_), Stata (`#1241 `_) and TensorFlow (`#1287 `_, `#1361 `_) * enhance GCC easyblock to support building generically (via '``generic``' easyconfig parameter or ``--optarch=GENERIC``) (`#1336 `_) * minor enhancements, including: * make GROMACS easyblock aware of building for KNL via ``--optarch=MIC-AVX512`` (`#1360 `_) * unset ``$PERL_MM_OPT`` and ``$PERL_MB_OPT`` when installing Perl modules to avoid problems (`#1362 `_) * add custom '``use_pip_for_deps``' easyconfig parameter to ``PythonPackage`` easyblock (`#1366 `_) * add support for '``default_component_specs``' easyconfig parameter in ``Bundle`` easyblock (`#1369 `_) * various bug fixes, including: * fix logic in icc easyblock w.r.t. location of debugger libraries (libipt library for gdb) (`#1224 `_) * fix Tkinter easyblock to install Tkinter 3.x (`#1347 `_) * let impi modules also update ``$MANPATH`` (`#1354 `_) * enhance Octave extension filter to avoid false positives (`#1355 `_) * make CUDA easyblock aware of '``preinstallopts``' easyconfig parameter (`#1367 `_) * fix handling of per-component (checksums for) patches in ``Bundle`` easyblock (`#1369 `_) **easyconfigs** * added example easyconfig files for 24 new software packages: * AMPL-MP (`#5800 `_), AmberTools (`#5632 `_), bcolz (`#5864 `_), detonate (`#5709 `_), dropEst (`#5734 `_), EvidentialGene (`#5627 `_), faceswap (`#5825 `_), fineSTRUCTURE (`#5663 `_), Gradle (`#5828 `_), gbs2ploidy (`#5877 `_), HIPS (`#5725 `_), Ipopt (`#5800 `_), libMemcached (`#5804 `_), MEGAHIT (`#5748 `_), Mmg (`#5807 `_), methylpy (`#5874 `_), pstoedit (`#5884 `_), python-igraph (`#5905 `_), RNAcode (`#5854 `_), Seq-Gen (`#5695 `_), Stata (`#5102 `_), scikit-allel (`#5864 `_), TetGen (`#5681 `_), zarr (`#5864 `_) * added new easyconfigs for existing toolchains: giolf/2018a (`#5777 `_), goolfc/2017b (`#5768 `_), iomkl/2018a (`#5878 `_) * added additional easyconfigs for various supported software packages, including: * CP2K 5.1, IPython 6.2.1, OpenFOAM v1712, Perl 5.26.1, Python 3.6.4, TensorFlow 1.5.0, X11 20180131 * minor enhancements, including: * add ``feather`` and ``tidyverse`` as extensions for R 3.4.3 (`#5693 `_) * build recent PLUMED versions with all modules enabled (`#5696 `_) * add MAST/splatter/scDD to Bioconductor 3.6 bundle (`#5704 `_) * add ``dummies`` as extension for R 3.4.3 + ``monocle``/``scde``/``ROTS`` (+ deps) to Bioconductor 3.6 bundle (`#5724 `_) * include ``io`` and ``statistics`` extensions to Octave 4.2.1 easyconfigs (`#5798 `_) * switch to using TensorFlow as backend for recent versions of Keras (`#5821 `_) * various bug fixes, including: * using the correct binutils in jemalloc 5.0.1 easyconfig using ``GCCcore/6.4.0`` (`#5659 `_) * fix source URLs for MPC (`#5662 `_) * add Tkinter as dependency for ASE & matplotlib using Python 3.6.3 (`#5658 `_) * fix versions for updated extensions in Bioconductor 3.6 bundle (`#5704 `_, `#5724 `_, `#5880 `_) * fix missing M4 build dependency in nettle easyconfigs (`#5722 `_) * fix homepage for OpenFOAM 4.x & 5.x, should be ``openfoam.org`` (`#5422 `_, `#5780 `_) * add matplotlib, cairo & PyCairo dependencies for graph-tool 2.26 + enhance sanity check (`#5787 `_) * fix hardcoded version in scikit-image easyconfigs (`#5822 `_) * fix pkgconfig moduleclass, '``data``' doesn't make much sense (`#5817 `_) * add sanity check in recent matplotlib easyconfigs to ensure that Tkinter is available (`#5689 `_, `#5896 `_) * correct MPI path when building ABINIT with '``foss``' toolchain (`#5760 `_) * patch Hyperopt to make it work with networkx 2.0 (`#5642 `_) * add Tkinter sanity check to ASE easyconfigs (`#5691 `_, `#5909 `_) * include autotools as build dep in git easyconfigs (`#5718 `_) * fix sanity check paths for Debian OS in JasPer easyconfigs (`#5897 `_) * fix source_urls for recent versions of ABINIT (`#5908 `_) * add patch for recent GDAL easyconfigs using ``intel`` toolchain to fix icc get stuck on compiling ``ceos.c`` (`#5915 `_) * add explicit zlib dependency in Tkinter 2.x and 3.x (`#5797 `_, `#5926 `_) * fix source URLs & homepage in Singularity easyconfigs (`#5927 `_) * fix installation of TensorFlow 1.3 via binary wheel after introducing TensorFlow easyblock (`#5938 `_) .. _release_notes_eb351: EasyBuild v3.5.1 (January 16th 2018) ------------------------------------ bugfix/update release **framework** * various enhancements, including: * add definition of ``giolfc`` toolchain (`#2359 `_) * add support for Environment Modules 4 (`#2365 `_) * various bug fixes, including: * install SQLAlchemy < 1.2.0 with Python 2.6 in Travis config (`#2367 `_) * make code in ``easybuild/tools/job/gc3pie.py`` forward-compatible with GC3Pie 2.5 (`#2373 `_) **easyblocks** * minor enhancements, including: * auto-detect default build target for Clang (`#1115 `_) * build GROMACS for target architecture based on ``--optarch`` (`#1163 `_) * ensure correct $PYTHONPATH for recent OpenBabel versions (`#1219 `_) * enhance Amber easyblock with support for OpenBLAS and better Intel MPI support (`#1305 `_) * also support only installing AmberTools through Amber easyblock (`#1305 `_) * also pick locations for CUPTI headers & libraries in CUDA easyblock (`#1306 `_) * update patching out of sanitizer tests for recent Clang versions (>=5.0) (`#1327 `_) * update known questions for Qt5 to support installing recent versions (`#1328 `_) * update BamTools easyblock for v2.5.0 (`#1332 `_, `#1337 `_) * disable ``libfox`` target if external module found in QuantumESPRESSO easyblock (`#1333 `_) * add support for linking Octave with multi-threaded BLAS/LAPACK library (`#1340 `_) * support ``install_target`` in PythonPackage + deprecate ``use_easy_install`` & ``use_setup_py_develop`` (`#1341 `_, `#1342 `_) * various bug fixes, including: * make RubyGem easyblock use ``$GEM_*`` environment variables except if as extension of Ruby itself (`#1247 `_) * move initialisation in ``SystemCompiler`` & ``SystemMPI`` easyblocks to the prepare step (`#1282 `_) * enable skipping sanitizer tests by default in Clang easyblock, they can't be relied on (`#1329 `_) * fix quotes when using ``$ORIGIN`` in ``RPATH`` locations for DOLFIN (`#1338 `_) * fix sanity check for shared libraries in Trilinos easyblock (`#1339 `_) **easyconfigs** * added easyconfigs for ``foss/2018a`` and ``intel/2018a`` common toolchains (`#5577 `_), (`#5578 `_) * added example easyconfig files for 26 new software packages: * BeautifulSoup (`#5601 `_), Calendrical (`#5588 `_), ChimPipe (`#5560 `_), crb-blast (`#5124 `_)), dammit (`#5125 `_), deepTools (`#5536 `_), FastQ_Screen (`#5404 `_), FoX (`#5496 `_), GffCompare (`#5581 `_), GlimmerHMM (`#5559 `_), LocARNA (`#5548 `_), MapSplice (`#5566 `_), MariaDB-connector-c (`#5557 `_), NextGenMap (`#5430 `_), nd2reader (`#5545 `_), PIMS (`#5545 `_), Pysolar (`#5585 `_), phono3py (`#5551 `_), preseq (`#5569 `_), proovread (`#5513 `_), QUAST (`#5610 `_), RNA-SeQC (`#5589 `_), RNAclust (`#5607 `_), Ragout (`#5608 `_), SOAPfuse (`#5417 `_), TransDecoder (`#5125 `_) * added additional easyconfigs for various supported software packages, including: * BLAST+ 2.7.1, BamTools 2.5.0, Boost 1.66.0, Clang 5.0.0, dask 0.16.0, FFmpeg 3.4.1, GROMACS 2016.4, HDF5 1.8.20, matplotlib 2.1.1, PLUMED 2.4.0, Pillow 5.0.0, Qt5 5.9.3, QuantumESPRESSO 6.2, Ruby 2.5.0, Rust 1.22.1 * minor enhancements, including: * include ``gomms`` in list of extensions for R 3.4.3 (`#5547 `_) * clean up BamTools easyconfigs to rely on updated easyblock + add SHA256 checksums (`#5575 `_) * add ``Time::HiRes`` to recent Perl versions (`#5616 `_) * add ``DNAcopy`` & ``dupRadar`` extensions to bundle for Bioconductor 3.6 (`#5587 `_, `#5618 `_) * switch to using ``install_target`` rather than now deprecated ``use_easy_install`` and ``use_setup_py_develop`` (`#5625 `_) * various bug fixes, including: * avoid auto-downloading of parcel in gdc-client 1.3.0 easyconfig (`#5523 `_) * fix permissions on ``make_raw_alos.pl`` script in ROI_PAC installation (`#5546 `_) * remove erroneous patch for Intel compiler support in Perl 5.26.0 easyconfig built with ``GCCcore/6.4.0`` (`#5561 `_) * include ``HWxtest`` as extension to fix issue with ``diveRsity`` in R 3.4.3 easyconfig file (`#5570 `_) * add pkg-config as build dependency for fontconfig, harfbuzz, gnuplot, pango (`#5580 `_) * fix versions of updated extensions in BioConductor bundle (`#5587 `_, `#5618 `_) * add missing libpng dependency in ROOT 6.10.08 easyconfigs (`#5595 `_) * fix option passed to configure in M4 (`#5606 `_) * rename SIBELia to Sibelia (`#5603 `_) * add patch for binutils 2.26 to fix compatibility with GCC 6.x (`#5611 `_) * fix for dependencies was set twice in OpenMPI 3.0.0 easyconfig (`#5619 `_) * fix download URL in comment of Kent tools easyconfigs (`#5633 `_) * add SHA256 checksums to various easyconfigs (`#5635 `_, `#5636 `_, `#5639 `_) * add ``rdma-core-devel`` to OS dependencies for OpenMPI 3.0.0 (`#5648 `_) .. _release_notes_eb350: EasyBuild v3.5.0 (December 15th 2017) ------------------------------------- feature release **framework** * add support for implementing pre- and post-step hooks (`#2343 `_) * documentation available at http://easybuild.readthedocs.io/en/latest/Hooks.html * various enhancements, including: * add support for foss-like toolchain with Spectrum MPI: ``gsolf`` (`#2329 `_) * add support for ``--preview-pr`` (`#2331 `_, `#2337 `_, `#2348 `_) * see also http://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html#previewing-easyconfig-pull-requests-preview-pr * flesh out ``find_extension`` function, hoist dict with extract commands into a constant (`#2336 `_) * add support for using ``self.start_dir`` rather than using ``self.cfg['start_dir']`` (`#2339 `_) * add support for '``exts_default_options``' easyconfig parameter (`#2345 `_, `#2346 `_) * allow use of '``start_dir``' easyconfig parameter in extensions (`#2353 `_) * various bug fixes, including: * fix typo in '``giolf``' toolchain definition (`#2327 `_) * fix minor issues with ``--inject-checksums`` (`#2333 `_) * fix error message when '``gv``' Python package is not available (`#2340 `_) * install paramiko version < 2.4.0 for Python 2.6 in Travis config (`#2344 `_) * disable broken log rotation, avoid duplicate logging of output of executed commands under '``--debug``' (`#2347 `_) * also include $ORIGIN and absolute paths to '``lib``' and '``lib64``' subdirectories in RPATH locations (`#2358 `_) * fix repo references in ``install-EasyBuild-develop.sh`` script (`#2360 `_) **easyblocks** * new software-specific easyblock for Bazel (`#1286 `_) and Octave (`#1304 `_) * new generic easyblock for installing Octave packages as extensions (`#1304 `_, `#1318 `_) * minor enhancements, including: * remove ``foamExec`` & ``wdot`` from sanity checks, add ``blockMesh`` & ``checkMesh`` + enable logging for recent OpenFOAM versions (`#1205 `_, `#1272 `_) * add exceptions for FFTW/3.3.6 on POWER with GCC 5/6/7 (`#1274 `_) * add support for Spectrum MPI to the ``SystemMPI`` easyblock (`#1275 `_) * allow skipping of steps for ``Bundle`` components + fix issues with templates & formatting of error message (`#1278 `_) * update HPCG easyblock for v3.0 by changing configure syntax (`#1284 `_) * correctly configure for BLAS/LAPACK in R easyblock & check configure output (`#1292 `_, `#1300 `_) * make R easyblock set configure options for dependencies (`#1297 `_, `#1303 `_) * allow tuning of build command in ``PythonPackage`` via custom '``buildcmd``' easyconfig parameter (`#1299 `_) * set default Java encoding to ``UTF8`` when installing Trinity (`#1302 `_) * also define ``$CUDA_ROOT`` in generated module for CUDA (`#1234 `_) * make the ScaLAPACK easyblock capable of building in parallel (`#1288 `_, `#1321 `_, `#1324 `_) * various bug fixes, including: * avoid changing ``$CPATH``, ``$LD_LIBRARY_PATH`` an ``$LIBRARY_PATH`` in generated modules for Intel Advisor, Inspector, and VTune (`#1229 `_) * fix check for Intel MKL in PSI easyblock (`#1273 `_) * fix missing space in fftw easyblock (`#1277 `_) * fix use of FFTW on top of Intel MKL in CP2K easyblock (`#1281 `_) * fix wrong sanity check for Boost when using Python 3.x (`#1283 `_) * pick up per-component checksums in ``Bundle`` generic easyblock (`#1285 `_) * correctly pass down optimization flags in CP2K easyblock (`#1293 `_) **easyconfigs** * added example easyconfig files for 39 new software packages: * AmberMini (`#5476 `_), arrow (`#5416 `_), bat (`#5416 `_), CIRCexplorer (`#5356 `_), CIRCexplorer2 (`#5470 `_), CIRI (`#5358 `_), FALCON (`#5265 `_), FastaIndex (`#5465 `_), find_circ (`#5348 `_), future (`#5236 `_), GapCloser (`#5465 `_), glibc (`#5428 `_), GRNBoost (`#5373 `_), HDFView (`#5391 `_), Horovod (`#5239 `_), HPDBSCAN (`#5371 `_), Hyperopt (`#5455 `_), IntelClusterChecker (`#4970 `_), ITK (`#5434 `_), LAST (`#5465 `_), MDTraj (`#5317 `_), Meson (`#5228 `_), mkl-dnn (`#5319 `_, `#5362 `_), Ninja (`#5228 `_), OpenKIM-API (`#5479 `_), ParmEd (`#5476 `_), PCRaster (`#5386 `_), piSvM (`#5308 `_), piSvM-JSC (`#5316 `_), PTESFinder (`#5359 `_), pybedtools (`#5347 `_), pymbar (`#5476 `_), pyScaf (`#5465 `_), QIIME2 (`#5355 `_), QTLtools (`#5361 `_), Redundans (`#5465 `_), Rmath (`#5361 `_), sbt (`#5373 `_), SNAP (`#5465 `_) * added new easyconfigs for existing toolchains: ``intel/2017.09`` (`#5303 `_), ``intel/2018.00`` (`#5129 `_), ``intel/2018.01`` (`#5345 `_) * added additional easyconfigs for various supported software packages, including: * CGAL 4.11, CMake 3.10.0, Caffe 1.0, FFTW 3.3.7, GATE 8.0, gnuplot 5.2.2, HPCG 3.0, HTSlib 1.6, Keras 2.1.2, LLVM 5.0.0, Mesa 17.2.5, mpi4py 3.0.0, netCDF 4.5.0, OpenFOAM 5.0, ParaView 5.4.1, R 3.4.3, Ruby 2.4.2, Rust 1.21.0, SCons 3.0.1, Szip 2.1.1, Theano 1.0.0, VTK 8.0.1, X11 20171023 * minor enhancements, including: * add SHA256 checksums to Autoconf (`#5304 `_), Automake (`#5305 `_), libtool (`#5306 `_) and M4 (`#5307 `_) easyconfigs * avoid hardcoding extension versions in worker easyconfig, include '``perl``' as OS dep (`#5324 `_) * enable building ScaLAPACK in parallel with enhanced ScaLAPACK easyblock (`#5331 `_) * include ``RInside`` extension in R 3.4.0 easyconfig (`#5354 `_) * clean up configure options that are now handled by R easyblock (`#5478 `_, `#5485 `_) * update Octave easyconfigs to use Octave easyblock, add extensions for latest Octave versions (`#5484 `_, `#5503 `_, `#5507 `_) * add ``Log4perl`` extension to Perl 5.26.0 easyconfigs (`#5511 `_) * various bug fixes, including: * add missing extensions required by MultiQC & stick to networkx 1.11 (`#5240 `_) * disable ``optarch`` when using Intel compilers and enable tests in all libxc easyconfigs (`#5256 `_, `#5257 `_) * avoid downloads when installing matplotlib 2.1.0 w/ Python 2.7.14 (`#5267 `_) * fix ``$CPATH`` in recent libffi easyconfigs + enhance sanity check & add checksum (`#5271 `_) * use Github source URL, run ``autogen.sh`` + include Autotools build dep for numactl (`#5286 `_, `#5296 `_, `#5297 `_, `#5299 `_, `#5302 `_) * add hwloc to GROMACS dependencies (`#5295 `_) * fix ``source_urls`` (& ``sources`` spec) for GATE (`#5367 `_) * consistently add Autotools build dep in recent netCDF easyconfigs (`#5394 `_) * fix check in test suite for binutils build dep when ``GCCcore`` used as toolchain (`#5436 `_) * libdap 3.19.1 checksum changed (`#5473 `_) * disable new rfkill feature in easyconfig for util-linux 2.31 since it requires a recent kernel (`#5480 `_) * add missing PROJ dependency in recent GDAL easyconfigs (`#5481 `_) * fix name in TensorFlow easyconfigs (was 'TensorFlow') (`#5495 `_) * fix checksum for Szip 2.1.1 (`#5517 `_) * fix order of extensions for FSLeyes, add missing MarkupSafe (dep for Jinja2) (`#5520 `_) .. _release_notes_eb341: EasyBuild v3.4.1 (October 17th 2017) ------------------------------------ bugfix/update release **framework** * various enhancements, including: * improve trace output for executed commands + drop requirement for ``--experimental`` for ``--trace`` (`#2306 `_) * add ``giolf`` toolchain definition: GCC, IntelMPI, OpenBLAS, (Sca)LAPACK and FFTW (`#2310 `_) * add support for ``--force-download`` and ``--ignore-checksums`` (`#2313 `_, `#2314 `_) * flesh out ``pypi_source_urls`` from ``derive_alt_pypi_url`` (`#2319 `_) * various bug fixes, including: * also check for use of ``--rebuild`` next to ``--force`` to skip sanity check with ``--module-only`` (`#2307 `_) * ensure ``$TMPDIR`` is set to a short path for OpenMPI v2.x (`#2311 `_) * guard '``module load``' commands in generated modules under ``--recursive-unload`` to avoid load storms (`#2316 `_) * correctly deal with use of special characters in description & co (`#2320 `_) * fix incorrect ``FFT_INC_DIR`` for Intel MKL (`#2323 `_) **easyblocks** * add generic '``SystemMPI``' easyblock (`#1106 `_, `#1261 `_, `#1262 `_) * add software-specific easyblock for SAS (`#1263 `_) * minor enhancements, including: * run '``wcleanAll``' or '``wcleanPlatform -all``' before building OpenFOAM (`#780 `_, `#1258 `_) * enhance generic '``SystemCompiler``' easyblock (`#1106 `_) * clean up ``--trace`` output for Python & Python packages (`#1248 `_) * update Intel MPI easyblock to support 2018.* versions (`#1253 `_) * add support for Intel MPI and Intel MKL to ScaLAPACK easyblock (`#1255 `_) * enhance GCC easyblock to also put symlinks in place for ``cc``/``c++``/``f77``/``f95`` commands (`#1256 `_) * various bug fixes, including: * allow that '``gcc -print-multiarch``' fails in icc easyblock (`#1249 `_) * fix prefix subdirectory for older versions of icc (in particular 2011.3.174) (`#1250 `_) * use ``remove_file`` rather than ``os.remove`` in generic ``IntelBase`` easyblock to correctly deal with broken symlinks (`#1251 `_) * fix sanity check for MXNet easyblock + correctly detect unpacked source directory (`#1257 `_) * avoid building CP2K twice due to incorrect attempt at running '``make clean``' first (`#1266 `_) **easyconfigs** * added easyconfigs for new toolchain ``giolf/2017b`` (`#5140 `_) * added example easyconfig files for 13 new software packages: * ASAP3 (`#5200 `_), Albacore (`#5153 `_), CatMAP (`#5225 `_), DLCpar (`#5209 `_), FSLeyes (`#5192 `_), IQ-TREE (`#3695 `_), NEST (`#5515 `_), nanonet (`#5149 `_), OMA (`#5211 `_), , oxford_asl (`#5193 `_), QEMU (`#5220 `_), REMORA (`#5159 `_), SAS (`#5208 `_), supermagic (`#5187 `_) * added additional easyconfigs for various supported software packages, including: * Anaconda2/3 4.4.0, Blender 2.79, Boost 1.65.1, CMake 3.9.4, FFmpeg 3.3.4, GCC 5.5.0, h5py 2.7.1, Keras 2.0.8, matplotlib 2.1.0, mympingpong 0.8.0, OpenCV 3.3.0, OpenFOAM-Extend 4.0, OpenMPI 2.1.2 + 3.0.0, Pillow 4.3.0, Python 2.7.14 + 3.6.3, SAMtools 1.6, scikit-image 0.13.0, scikit-learn 0.19.0, Tensorflow 1.3.0, vsc-mympirun 4.0.2 * minor enhancements, including: * add ``xkeyboard-config`` component in X11 bundle (`#5066 `_) * clean up use of ``wcleanAll`` in OpenFOAM-Extend easyconfigs, now handled by OpenFOAM easyblock (`#5131 `_) * also install ``run_rcorrector.pl`` with Rcorrector (`#5135 `_) * add SHA256 checksum to PyCUDA easyconfig (`#5154 `_) * fix/improve description in HDF5 easyconfigs (`#5182 `_) * include heatmap3 extension for R 3.4.0 (`#5185 `_) * add ComplexHeatmap to Bioconductor 3.5 bundle + dep pkgs in R 3.4.0 easyconfig (`#5195 `_) * various bug fixes, including: * fix source URLs for AUGUSTUS 3.2.3 (`#5119 `_) * fix building Bison 2.5 on systems with recent glibc (`#5130 `_) * also consider ``rdma-core-devel`` as alternative to ``libibverbs-devel`` OS dependency (`#5132 `_) * consistently use empty toolchain version in icc & ifort easyconfigs to ensure that GCC(core) dep is loaded during installation (`#5133 `_, `#5134 `_) * add patches for Boost 1.64.0 to fix known issues (`#5148 `_) * remove PyCUDA easyconfig for ``intel/2017a``, doesn't work due to incompatibility between GCC 6.3.0 & CUDA 8 (`#5156 `_) * add missing Perl extensions in easyconfig for Worker 1.6.7 (`#5157 `_) * fix checksums for packages that download from ``github.com/x/y/archive`` (`#5162 `_) * add missing libpng dependency to g2lib-1.4.0 easyconfig using intel-2017a (`#5196 `_) * fix source_urls for Szip 2.1 & include SHA256 checksum (`#5206 `_) * remove unneeded ``--with-fft-incs`` configure option for ABINIT (`#5207 `_) * disable optarch for libjpeg-turbo 1.5.1 built with ``intel/2017a`` (`#5214 `_) * update ``$R_LIBS`` in plotly easyconfig (`#5215 `_) * include NLopt as a dependency in R easyconfigs that include ``nloptr`` as extension (`#5217 `_) .. _release_notes_eb340: EasyBuild v3.4.0 (September 10th 2017) -------------------------------------- feature release **framework** * various enhancements, including: * add support for backing up modules via ``--backup-modules`` (`#2134 `_) * enabled automatically with ``--module-only`` and ``--skip`` * see also http://easybuild.readthedocs.io/en/latest/Backup_modules.html * add support for ``--search-paths`` to extend list of locations considered by ``--search``/``-S`` (`#2255 `_) * include ``userInGroup`` check in Lua modules when installation is group-restricted (`#2274 `_) * add experimental support for '``eb --trace``' (`#2285 `_) * see also http://easybuild.readthedocs.io/en/latest/Tracing_progress.html * add support for '``eb --inject-checksums``' (`#2286 `_, `#2292 `_, `#2293 `_) * see also http://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html#adding-or-replacing-checksums-using-inject-checksums * add support for ``append_paths`` in module generator (`#2294 `_) * various bug fixes, including: * strip provided GitHub token of spaces in ``--install-github-token`` (`#2270 `_) * remove '``provides``' line from ``setup.py`` (`#2275 `_) * pass down stdin in '``import``' check for extensions during sanity check (`#2276 `_) * make sure location to 'eb' installed during stage 1 is included in ``$PATH`` during stage 2 of bootstrap procedure (`#2281 `_) * make resolve_path robust against ``None`` path being provided (`#2282 `_) * ensure clean error message on easyconfig file parse failure (`#2290 `_) * fix regex to avoid sucking up additional lines prior to module file path in ``modulefile_path`` (`#2291 `_) * fix error message when ``--use-ccache`` is used but ``ccache`` is not available in ``$PATH`` (`#2295 `_) **easyblocks** * minor enhancements, including: * update Siesta easyblock for versions 4.0.1 and 4.1-b3 (`#1218 `_) * updates GAMESS-US easyblock for version 20170420R1 + move ``ddikick.x`` when ``ddi_comm`` is set to '``sockets``' (`#1221 `_) * update MRtrix easyblock for 3.0 & beyond + use ``copy`` function (`#1230 `_) * update ROOT easyblock to support recent versions that require using CMake, add sanity check, clean up/enhance ``make_module*`` (`#1236 `_) * enhance icc easyblock to include multipath include dir in ``$CPATH`` (`#1237 `_, `#1242 `_) * various bug fixes, including: * use ``plumed-patch`` command rather than '``plumed patch``' in GROMACS easyblock (`#1212 `_) * remove '``provides``' line from ``setup.py`` (`#1217 `_) * fixed wrong use of ``build_type`` in ``self.cfg`` in WRF easyblock that resulted in an raised exception (`#1220 `_) * added a call to super ``post_install_step`` in CUDA easyblock (`#1226 `_) * fix ``$MCRROOT`` definition in generated module file under ``--module-only`` in MCR easyblock (`#1228 `_) * fix permissions for directories in SuiteSparse (`#1238 `_) * fix function signature for ``fetch_extension_sources`` in OCaml easyblock (`#1240 `_) **easyconfigs** * added easyconfigs for ``foss/2017b`` and ``intel/2017b`` common toolchains (`#4768 `_), (`#4618 `_) * added new easyconfigs for existing toolchains: * ``iomkl/2017b`` (`#5097 `_) * added example easyconfig files for 31 new software packages: * BAMM (`#4650 `_), BamM (`#4650 `_), bcl2fastq2 (`#4902 `_), CGNS (`#5078 `_), CLAPACK (`#5096 `_), CLISP (`#4926 `_, `#4986 `_), cadaver (`#4873 `_), destiny (`#5009 `_), GroopM (`#4650 `_), Lucene-Geo-Gazetteer (`#5064 `_), libffcall (`#4850 `_), libsigsegv (`#4840 `_), MERCKX (`#5056 `_), minimap2 (`#4991 `_), ncompress (`#4852 `_), OpenNLP (`#5059 `_, `#5061 `_), OpenRefine (`#5058 `_), PHAST (`#5096 `_), PYTHIA (`#5083 `_), ParallelIO (`#5071 `_), PnetCDF (`#5071 `_), plotly (`#5010 `_), QML (`#5101 `_), Quorum (`#5095 `_), Rcorrector (`#5095 `_), SCnorm (`#5008 `_), SOAPdenovo-Trans (`#5095 `_), Shannon (`#5095 `_), Tika (`#5063 `_), UNAFold (`#4997 `_), VERSE (`#4843 `_) * added additional easyconfigs for various supported software packages, including: * Boost 1.65.0, binutils 2.29, GAMESS-US 20170420-R1, GCC(core) 7.2.0, gzip 1.8, HDF5 1.8.19, LLVM 4.0.1, MRtrix 3.0_RC2, Perl 5.26.0, ROOT 6.10.04, Spark 2.2.0 * minor enhancements, including: * add checksums to Perl 5.24.1 easyconfigs (`#4973 `_, `#4992 `_) * add additional extensions for R 3.4.0 and Bioconductor 3.5 bundle (`#5007 `_, `#5028 `_, `#5029 `_, `#5062 `_, `#5079 `_) * also define ``$INCLUDEPATH`` and ``$LIBRARY_PATH`` in Tesla-Deployment-Kit easyconfig (`#5018 `_) * add check to see whether binutils is included as build dep when GCCcore toolchain is used (`#5084 `_) * various bug fixes, including: * added Rmpi patch file for R built with intel toolchains incl. impi 5.x (`#4623 `_) * use single-line description in ``setup.py`` (`#4881 `_) * fix version and source for Seurat + add extensions required by Seurat in R 3.4.0 easyconfig (`#4889 `_) * add zlib as dependency to util-linux easyconfigs (`#4900 `_, `#4998 `_) * use ``modextrapaths`` instead of ``modextravars`` in OpenMM easyconfig (`#4903 `_) * update deprecated PLINK urls (`#4920 `_, `#5006 `_) * fix ``moduleclass`` for Cookiecutter (`#4947 `_) * fix order of OpenMPI dependency in ``iomkl/2016.09*`` easyconfigs, must come after icc/ifort (`#5024 `_) * fix typo in comment in util-linux easyconfigs & add SHA256 checksums (`#5052 `_) * remove superfluous ``$CPATH`` update in GLib 2.44.0 easyconfig (`#5053 `_) * update ncurses to not build a separate libtinfo but provide a soft link instead + force linking to ncurses in libreadline (`#5067 `_, `#5074 `_) * include Autotools as build dep for netCDF (`#5077 `_) * add missing binutils build dep for texinfo (`#5099 `_) .. _release_notes_eb331: EasyBuild v3.3.1 (July 12th 2017) --------------------------------- bugfix/update release **framework** * various enhancements, including: * add support for '``allow_prepend_abs_path``' easyconfig parameter (`#2254 `_) * support for ``--merge-pr`` (`#2266 `_) * various bug fixes, including: * resolve symlinks to location of '``eb``' in ``get_paths_for`` (`#2248 `_) * fall back to checking location relative to '``eb``' location in ``find_eb_script`` (`#2249 `_) * respect ``--suffix-modules-path`` value for user-specific module path extensions (`#2250 `_) * update EasyBuild bootstrap script to download ``distribute`` tarball from http://easybuilders.github.io/easybuild/files (`#2256 `_) * fix default target GitHub account/organisation for ``--new-pr`` & co + fix tests that got broken by migration to github.com/easybuilders (`#2258 `_) * fix checking for new easyconfigs in ``copy_easyconfigs``, pick up specified commit message as PR title if none was provided (`#2259 `_) * get rid of references to ``hpcugent`` after move to github.com/easybuilders (`#2261 `_) * automatically enable ``--ignore-osdeps`` under ``--new-pr`` and ``--update-pr`` (`#2262 `_) **easyblocks** * minor enhancements, including: * enhance HDF5 easyblock: define ``$HDF5_DIR`` & include ``-DMPICH_IGNORE_CXX_SEEK`` in ``$CXXFLAGS`` (`#1200 `_) * consistently pass down (named) arguments in ``prepare_step``, and check for it in the tests (`#1202 `_) * remove no longer supported ``VersionIndependentPythonPackage`` generic easyblock (`#1202 `_) * update ABAQUS easyblock for recent versions, incl. support for installing hotfixes (`#1203 `_) * get rid of references to '``hpcugent``' organisation after move to github.com/easybuilders (`#1206 `_) * make Boost easyblock fully aware of ``(pre)configopts``, ``(pre)buildopts`` and ``(pre)installopts`` (`#1207 `_) * drop check for '``ipython``' in sanity check of Anaconda easyblock, to also support Miniconda (`#1210 `_) **easyconfigs** * added example easyconfig files for 6 new software packages: * FastME (`#4811 `_), geopy (`#4821 `_), Miniconda2 (`#4841 `_), ngmlr (`#4818 `_), OpenCoarrays (`#4799 `_), Seurat (`#4832 `_) * added additional easyconfigs for various supported software packages, including: * ABAQUS 2017, GCC(core) 6.4.0, Keras 2.0.5, NCBI-Toolkit 18.0.0, numpy 1.13.0, Tensorflow 1.2.0 * minor enhancements, including: * add ``SVG`` and ``Statistics::Basic`` to recent Perl versions (`#4796 `_) * remove ``buildopts`` from HDF5 easyconfigs, taken care of by updated HDF5 easyblock now (`#4779 `_) * include ``joblib`` as extension in recent Python easyconfigs (`#4805 `_) * changed moduleclass in mpi4py to better reflect what it is and to not confuse HMNS (`#4807 `_) * get rid of references to '``hpcugent``' organisation after move to github.com/easybuilders (`#4815 `_, `#4837 `_) * add ``Rtsne`` as extension to R 3.4.0 (`#4831 `_) * various bug fixes, including: * use ``PYPI_SOURCE`` as source URL in Tensorflow easyconfigs (`#4786 `_) * fix ``homepage`` for skewer (`#4791 `_) * sync/fix ``source_urls`` & ``homepage`` in HDF5 easyconfigs (`#4800 `_) * fix ``ubsan`` error blocking build of GCCcore 6.1.0, 6.2.0, 6.3.0 with system GCC 7.1 (`#4813 `_) .. _release_notes_eb330: EasyBuild v3.3.0 (June 26th 2017) --------------------------------- feature release **framework** * various enhancements, including: * clean up easyconfigs that are copied for inclusion in pull request (`#2197 `_, `#2227 `_) * use devel logging where relevant in ``easybuild.tools.toolchain`` (`#2198 `_) * check exit code for executed ``module`` commands (`#2200 `_) * also copy patches to installation directory & easyconfigs archive along with easyconfig file (`#2202 `_, `#2241 `_) * add support for SHA256 checksums (`#2215 `_) * also auto-detect whether provided checksum is MD5 or SHA256 based on length (if not checksum type is specified) * add support for ``--enforce-checksums``, to require availability of checksums for sources/patches * see http://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html#source-files-patches-and-checksums * add support for renaming sources on download (`#2223 `_) * also involves deprecating use of 2-tuple elements in list of sources, see http://easybuild.readthedocs.io/en/latest/Deprecated-functionality.html#depr-sources-2-element-tuple * add support for ``--detect-loaded-modules`` (`#2228 `_) * give extensions access to ``module_generator`` of parent (`#2229 `_) * pass down additional arguments to ``copy_dir`` down to ``shutil.copytree`` (`#2230 `_) * avoid reloading already loaded modules that extend ``$MODULEPATH`` (`#2232 `_) * various bug fixes, including: * make sure test account & accompanying token is used in tests for ``github.py`` (`#2220 `_, `#2224 `_) * only use MPD for old versions of Intel MPI (<4.1) in ``mpi_cmd_for`` (`#2221 `_) * escape dots in package filename to ensure correct match in ``derive_alt_pypi_url`` (`#2225 `_) * fix ``GNU_SOURCE`` template by adding missing ``/gnu/`` (`#2235 `_) * catch exception ``shutil.Error`` in ``copy_file`` (`#2239 `_) * report full error and traceback on unhandled exception in test report (`#2240 `_) * fix ``--set-default-module`` flag (`#2243 `_) **easyblocks** * added easyblocks for MXNet (`#1135 `_), Tkinter(`#1184 `_) * minor enhancements, including: * enhance sanity check for NCL (`#1169 `_, `#1179 `_) * enable building of shared FFTW libraries (`#1180 `_) * include update statements for ``$CPATH`` and ``$*LIBRARY_PATH`` in generated module in numpy easyblock (`#1183 `_) * stop using deprecated '``copytree``' function from ``easybuild.tools.filetools`` (`#1185 `_) * update SAMtools easyblock for v0.1.17 (`#1189 `_) * update MATLAB easyblock for 2016b & 2017a versions (adjust permissions and change dir) (`#1182 `_, `#1197 `_) * consider ``$EB_*_LICENSE_SERVER(_PORT)`` in MATLAB and ANSYS easyblocks (`#1195 `_) * add ``omp_num_threads`` custom parameter in CP2K easyblock to allow defining ``$OMP_NUM_THREADS`` during testing (`#1196 `_) * various bug fixes, including: * fix Siesta easyblock to enable and verify parallel build (`#1186 `_) * fix bug in alias definition in impi easyblock for ``mpigxx``, ``mpiicpc`` and ``mpiifort`` (`#1192 `_) **easyconfigs** * enable automatic style checks in easyconfig tests (`#2506 `_) * added example easyconfig files for 28 new software packages: * ada (`#4594 `_), Aspera-CLI (`#4635 `_), AUGUSTUS (`#4624 `_), ada (`#4594 `_), Bio-SamTools (`#4637 `_), Bpipe (`#4590 `_), BUSCO (`#4624 `_), CNVnator (`#4649 `_), davix (`#4755 `_), EricScript (`#4594 `_), FUNWAVE-TVD (`#4743 `_), gmpy2 (`#4609 `_), gSOAP (`#4755 `_), libsndfile (`#4628 `_), lpsolve (`#4264 `_), LUMPY (`#4682 `_), MaSuRCA (`#4706 `_), modred (`#4729 `_), MXNet (`#4765 `_), NRGLjubljana (`#4651 `_), OrfM (`#4703 `_), Perl4-CoreLibs (`#4670 `_), prodigal (`#4468 `_), pydlpoly (`#4756 `_), SeqAn (`#4603 `_), sharutils (`#4745 `_), Spyder (`#4627 `_), Tkinter (`#4620 `_), VariantMetaCaller (`#4632 `_) * added new easyconfigs for existing toolchains: * ``gimkl/2017a`` (`#4646 `_) * added additional easyconfigs for various supported software packages, including: * ABINIT 8.2.2, BLAST+ 2.6.0, Bowtie2 2.3.2, FFmpeg 3.3.1, NCL 6.4.0, Rust 1.18.0, SAMtools 1.5, VTK 7.1.1 * minor enhancements, including: * use '``git diff --name-only``' and ``$TRAVIS_COMMIT_RANGE`` in Travis config to get list of changed files (`#4606 `_, `#4619 `_) * add tuneR, seewave, soundecology, vcfR extensions for R 3.4.0 (+ libsndfile as dep) (`#4628 `_, `#4680 `_, `#4747 `_) * also copy ``README`` for GapFiller (`#4631 `_) * enable inclusion of version symbol by using ``--enable-ld-version-script`` configure option for LibTIFF (`#4639 `_) * add SHA256 checksums for libpciaccess to discriminate from old tarballs that required running ``autogen.sh`` (`#4688 `_) * fix ``NE_GLOBAL_DIR`` path for ne by also specifying ``PREFIX`` in ``buildopts`` (`#4698 `_) * more (trivial) style fixes (`#4761 `_) * avoid use of ``import`` in ANSYS & MATLAB easyconfigs (`#4762 `_) * set ``$OMP_NUM_THREADS`` during CP2K test step via dedicated easyconfig parameter (`#4763 `_) * avoid use of '``import``' in BFAST easyconfigs, just strip of '``a``' from version (`#4764 `_) * add the docopt module to all Python 2017a easyconfigs (`#4770 `_) * stop using deprecated 2-element tuple format in sources, use equivalent dict format instead (`#4774 `_) * various bug fixes, including: * fix typo in statsmodels source url (``/sources/`` -> ``/source/``) (`#4612 `_) * add location to ``DotLib.pm`` to ``$PERL5LIB`` for SSPACE_Basic (`#4638 `_) * add missing ``/gnu/`` in ftpmirror.gnu.org ``source_urls``, or use ``GNU_SOURCE`` where possible (`#4653 `_) * consistently use ``--with-harfbuzz=no`` configure option in freetype easyconfigs (`#4668 `_) * use ``--with-x=yes`` in R easyconfigs that include X11 as a dependency (`#4701 `_) * remove '``4.0``' in tbb description (`#4707 `_) * add lib sanity check paths for Debian compatibility in nettle (`#4722 `_) * fix source URLs for HDF5 (`#4749 `_) .. _release_notes_eb321: EasyBuild v3.2.1 (May 12th 2017) -------------------------------- bugfix/update release **framework** * various enhancements, including: * make hardcoded max ratio for failures in ``adjust_permissions`` configurable (`#2213 `_) * allow ``https://`` on direct download in sources (`#2214 `_) * various bug fixes, including: * bump version bootstrap script to sync with latest update (`#2208 `_) * fix crash during module generation when '``%``' character is used in description (`#2209 `_) **easyblocks** * added easyblock for Siesta (`#1105 `_) * minor enhancements, including: * enhance GROMACS easyblock to build with PLUMED support (`#1121 `_) * enhance NAMD easyblock: add OpenMP support, update for recent NAMD versions (2.12), fix compatibility with Tcl versions other than 8.5 (`#1173 `_) **easyconfigs** * added example easyconfig files for 12 new software packages: * AdapterRemoval (`#4509 `_), blasr_libcpp (`#4566 `_), canu (`#4473 `_), enchant (`#4567 `_), hunspell (`#4567 `_), memkind (`#4544 `_), NLTK (`#4565 `_), pbbam (`#4566 `_), pbdagcon (`#4566 `_), pyenchant (`#4567 `_), Siesta (`#4562 `_), xarray (`#4556 `_) * added new easyconfigs for existing toolchains: * goolfc 2017.01 (`#4577 `_) * added additional easyconfigs for various supported software packages, including: * HDF5 1.10.1, NAMD 2.12, OpenFOAM 4.1, pandas 0.20.1, ParaView 5.2.0, R 3.4.0, R-bundle-Bioconductor 3.5, Tensorflow 1.1.0 * minor enhancements, including: * update source URLs in libpciaccess easyconfigs (`#3960 `_) * enable use of double precision floating point in METIS 5.1.0 ``foss/2016a`` easyconfig (`#4555 `_) .. _release_notes_eb320: EasyBuild v3.2.0 (May 5th 2017) ------------------------------- feature release **framework** * various enhancements, including: * add support for marking installed module file as new default version using ``--set-default-module`` (`#2110 `_) * additional easyconfig parameters for documentation: ``docpaths``, ``examples``, ``site_contacts``, ``upstream_contacts``, ``usage`` (`#2113 `_) * add support for ``--allow-use-as-root-and-accept-consequences`` (`#2123 `_) * enable extraction of patches from compressed files before applying them (`#2128 `_) * alphabetically sort functions and methods in ``module_generator`` module (`#2132 `_) * introduce function ``ensure_iterable_license_specs`` (`#2157 `_) * bump Travis config to use Lmod 7.4 (`#2176 `_) * implement ``copy_dir`` function in ``filetools`` (`#2177 `_) * clarify error message when no software-specific easyblock was found (`#2178 `_) * make ``log.deprecated`` more verbose by also printing deprecation warnings to stderr (`#2179 `_) * add ``copy`` function to ``filetools`` for easy copying of lists of files/directories (`#2180 `_) * add support for ``--verify-easyconfig-filenames`` (`#2185 `_) * add support for ``--package-tool-options`` (`#2187 `_) * take into account inline trailing comments in ``fetch_parameters_from_easyconfig`` (`#2192 `_) * add support for customising easyconfig parameters on a per-extension basis (`#2194 `_) * perform sanity check after stage 2 of EasyBuild bootstrap script, module file should be in place (`#2199 `_) * change order in which module commands are checked, consider Lmod first (`#2201 `_) * various bug fixes, including: * fix use of compiler-specific ``--optarch`` value in combination with ``--job`` (`#2183 `_) * call ``run_all_steps`` in regtest mode rather than running steps individually (`#2203 `_) **easyblocks** * added easyblocks for Doris (`#1154 `_, `#1161 `_), VMD (`#1148 `_) and WRF-Fire (`#1153 `_, `#1159 `_) * minor enhancements, including: * update ``IntelBase``, PGI and TotalView easyblocks to allow list of license files/servers via '``license_file``' easyconfig parameter (`#1129 `_) * update Bowtie2 easyblock to set correct build options, copy more files, extend sanity check (`#1146 `_) * added the option to build Boost with multi-threading support (`#1147 `_) * allow libpng as OS dependency for WPS (`#1150 `_) * extend Boost ``TIME_UTC`` patch to Boost versions <= 1.49.0 (`#1152 `_) * enhance Python sanity check to check for Tkinter support if Tk is included as a dependency (`#1156 `_, `#1158 `_) * add support to install Python extensions without unpacking (`#1166 `_) * enhance TBB easyblock to also support building open source versions (`#1168 `_) * various bug fixes, including: * update FFTW easyblock: ``--enable-avx-128-fma`` depends on the ``fma4`` CPU feature (AMD), not ``fma`` (`#1142 `_) * fix problems when ``usempi`` not defined in toolchain in NAMD easyblock (`#1162 `_) **easyconfigs** * added example easyconfig files for 34 new software packages: * ACTC (`#4386 `_), atomate (`#4484 `_), BreakDancer (`#4455 `_), bx-python (`#4486 `_), ClusterShell (`#4432 `_), custodian (`#4484 `_), DFTB+ (`#4398 `_), Doris (`#4404 `_), ED2 (`#4402 `_), FireWorks (`#4484 `_), GETORB (`#4414 `_), GapFiller (`#4462 `_), IPy (`#4450 `_), imbalanced-learn (`#4373 `_), ipyrad (`#4507 `_), libiconv (`#4499 `_), MultiQC (`#3564 `_), NLopt (`#1750 `_), Node-RED (`#4542 `_), PyCUDA (`#4523 `_), pymatgen-db (`#4484 `_), QuTiP (`#4371 `_), ROI_PAC (`#4414 `_), Rascaf (`#4459 `_), RepastHPC (`#4395 `_), rootpy (`#4242 `_), SSPACE_Basic (`#4461 `_), Sambamba (`#4442 `_), Spack (`#4431 `_), SpiceyPy (`#4406 `_), StaMPS (`#4454 `_), samblaster (`#4435 `_), VMD (`#4391 `_), WRF-Fire (`#4403 `_) * added additional easyconfigs for various supported software packages, including: * BamTools 2.4.1, Boost 1.64.0, GCC 7.1.0, IPython 5.3.0, LLVM 4.0.0, Mesa 17.0.2, Octave 4.2.1, OpenMPI 2.1.0, PETSc 3.7.5, PGI 17.3, Perl 5.24.1, Python 2.7.13 + 3.6.1 (incl. numpy 1.12.1, scipy 0.19.0), R 3.3.3, SuiteSparse 4.5.5 * various enhancements, including: * sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock (`#4380 `_) * use ``pl2`` source tarball for FFTW 3.3.6 which already includes patch for ``F03`` interface (`#4529 `_) * various bug fixes, including: * add missing XZ dep in easyconfig for libunwind 1.1 w/ ``GCC/4.9.2``, sync ``sanity_check_paths`` across libunwind easyconfigs (`#4369 `_) * use '``use_fma4``' rather than deprecated '``use_fma``' easyconfig parameter in FFTW easyconfigs using ``intel`` toolchain (`#4384 `_) * fix ``pkgconfig`` patch for Qhull (`#4451 `_) * also use patch for METIS 5.1.0 to enable use of doubles in easyconfig for ``foss/2016b`` (`#4467 `_) * add dependency NLopt for R extension ``nloptr`` (`#4481 `_) * fix issue with ``configparser`` and ``backports`` namespace blocking inclusion of ``nbconvert`` with IPython (`#4504 `_) * change source_urls of pycrypto to encrypted ``https://pypi.python.org/...`` (`#4505 `_) * fix sources spec for HMMER 3.1b2 + minor style fixes + better sanity check (`#4531 `_) * also build IMB-IO in IMB 4.1 easyconfig using ``foss/2016a`` (`#4539 `_) .. _release_notes_eb312: EasyBuild v3.1.2 (March 20th 2017) ---------------------------------- bugfix/update release **framework** * fix broken packaging support by fixing ``run_cmd`` bug with ``shell=False`` (`#2153 `_) * minor enhancements, including: * implement ``change_dir`` function in ``filetools`` module (`#2155 `_) * use ``checker_state`` in trailing whitespace style check + add dedicated test (`#2160 `_, `#2169 `_) * consider both ``pycodestyle`` and ``pep8`` Python modules in style checks (`#2161 `_) * make bootstrap script aware various modules-related ``$EASYBUILD_*`` environment variables (`#2170 `_) * various bug fixes, including: * interpret statements that extend ``$MODULEPATH`` in ``modpath_extensions_for`` method (`#2104 `_) * also fixes inclusion of superfluous load statements in modules installed in user HMNS module tree (cfr. `#2172 `_) * take into account that ``$PATH`` or ``$PYTHONPATH`` may be empty when running tests (`#2149 `_) * handle duplicates in ``--include-*`` (`#2151 `_) * exclude dependencies of dependencies that extend ``$MODULEPATH`` (`#2152 `_) * add ``ld.bfd`` to RPATH wrappers (`#2156 `_) * fix ``test_vsc_location``, ``vsc.__file__`` may not be available when ``vsc`` is installed as a namespace package (`#2159 `_) * fix reported problems with scripts & docs tests (`#2164 `_) * fix ``--try-software-version`` using non-greedy matching + lookahead assertion, add test for ``tweak_one`` (`#2166 `_) * avoid creating empty modulefile directories when using ``modaltsoftname`` (`#2168 `_) * fix ``fftw_libs`` for MKL without interface libraries (`#2171 `_) **easyblocks** * add easyblock for QScintilla (`#1127 `_) * minor enhancements, including: * auto-disable quad precision on POWER and ARM in FFTW (`#1102 `_, `#1138 `_) * allow "download install" for PETSc (`#1114 `_) * modify Trinity sanity check for versions 2.3 and above (`#1133 `_) * make unpacking Python extensions optional (`#1134 `_) * update SAMtools easyblock for version 1.4 (`#1139 `_) * various bug fixes, including: * reduce number of environment variables in ``icc`` and ``ifort`` modules (`#1126 `_, `#1143 `_) * also run tests with Tcl module syntax, Lua is the default in EasyBuild v3.x (`#1128 `_) * rename member variable to avoid conflict with member of base class in PGI (`#1137 `_) * don't set ``$FPATH`` environment variable in multiple easyblocks (`#1140 `_) **easyconfigs** * add patch to FFTW 3.3.6 easyconfigs to fix MPI F03 interface (`#4334 `_) * note that this warrants rebuilding FFTW that is a part of ``foss/2017a`` * added example easyconfig files for 14 new software packages: * DBG2OLC (`#4281 `_), disambiguate (`#4125 `_), fqtrim (`#4280 `_), GFOLD (`#4293 `_), Kaiju (`#4349 `_), LSMS (`#4335 `_), L_RNA_scaffolder (`#4282 `_), PileOMeth (`#4289 `_), psycopg2 (`#4319 `_), QGIS (`#4307 `_, `#4332 `_), QJson (`#4305 `_), QScintilla (`#4306 `_, `#4313 `_), sketchmap (`#4360 `_), snaphu (`#4362 `_) * added additional easyconfigs for various supported software packages, including GROMACS 2016.3, PGI 17.1, SAMtools 1.4 * various enhancements, including: * fix style in several easyconfigs (`#4267 `_-`#4271 `_, `#4274 `_, `#4275 `_, `#4277 `_, `#4279 `_, `#4286 `_-`#4288 `_, `#4318 `_) * various bug fixes, including: * correctly set ``$PYTHONPATH`` in ROOT easyconfigs (`#4239 `_, `#4331 `_) * correct libjpeg turbo references in GDAL (`#4276 `_) * make sure that HDF5 provided via EasyBuild is used in BLASR easyconfigs (`#4278 `_) * fix issues with miRDeep2 installation (`#4291 `_, `#4301 `_, `#4316 `_) * also run tests with Tcl module syntax, Lua is the default in EasyBuild v3.x (`#4315 `_) * fix PostgreSQL homepage + minor style fixes (`#4318 `_) * detect use of '``$root``', which is not compatible with module files in Lua syntax (`#4330 `_) * fix ``homepage``/``source_urls`` for ViennaRNA (`#4338 `_) * pass down ``$FFLAGS`` via ``FLAGS_OPT`` in SWASH easyconfigs (`#4341 `_) * remove ``include/GL/wglext.h`` from Mesa sanity check (`#4354 `_) * rename ``S.A.G.E.`` to ``SAGE``, can't have directories with trailing dot in Windows (`#4368 `_) .. _release_notes_eb311: EasyBuild v3.1.1 (March 7th 2017) --------------------------------- bugfix/update release **framework** * minor enhancements, including: * print more useful error message when no compiler-specific ``optarch`` flag is defined (`#1950 `_) * add ``ec`` parameter to ``expand_toolchain_load()`` (`#2103 `_) * clarify unstable/closed PR warning message (`#2129 `_) * various bug fixes, including: * ensure that ``$EBEXTSLIST*`` is also included in generated module under ``--module-only`` (`#2112 `_) * fix formatting issues in generated documentation for ``--list-software`` and ``--avail-easyconfig-licenses`` (`#2121 `_) * fix problem with backticks in description breaking '``fpm``' packaging command (`#2124 `_) * replace ``--enable-new-dtags`` with ``--disable-new-dtags`` instead of removing it in RPATH wrapper script (`#2131 `_) * only perform ``is_short_modname_for`` sanity check in ``det_short_module_name`` if ``modaltsoftname`` is available (`#2138 `_) * fix logic in ``make_module_dep`` w.r.t. excluding loads for toolchain & toolchain components (`#2140 `_) * skip ``test_check_style`` if ``pep8`` is not available (`#2142 `_) **easyblocks** * minor enhancements, including: * change the sanity check for MCR 2016b since the directory structure has changed (`#1096 `_) * update NWChem easyblock for version 6.6.x and to handle different versions of OpenMPI for older versions (`#1104 `_) * allow per-component ``source_urls`` with templating in ``Bundle`` easyblock (`#1108 `_) * add slib to ``$LD_LIBRARY_PATH`` for itac (`#1112 `_) * consider both ``lib`` and ``lib64`` in CGAL sanity check (`#1113 `_) * add support for installing Intel tools that do not require license at installation time (`#1117 `_) * required for Intel MPI and Intel MKL version 2017.2.174 * remove ``prefix_opt`` as custom easyconfig parameter for Qt easyblock (`#1120 `_) * various bug fixes, including: * use '``-prefix ``' rather than '``--prefix=``' for ``configure`` in Qt (`#1109 `_) * fix indentation problem in PETSc easyblock (`#1111 `_) **easyconfigs** * added example easyconfig files for 16 new software packages: * Caffe (`#3667 `_), DIAMOND (`#4107 `_), fmt (`#4131 `_), googletest (`#4132 `_), igraph (`#4172 `_), MEGA (`#4202 `_), meRanTK (`#4175 `_), meshio (`#4178 `_), miRDeep2 (`#4229 `_, `#4255 `_), OOMPA (`#4211 `_), PBSuite (`#4224 `_, `#4230 `_), randfold (`#4217 `_), skewer (`#4246 `_), Smoldyn (`#4110 `_), SpiecEasi (`#4215 `_), stress (`#4180 `_) * added additional easyconfigs for various supported software packages, including: * binutils 2.28, Cantera 2.3.0, CGAL 4.9, GMP 6.1.2, IPython 5.2.2, JasPer 2.0.10, NWChem 6.6, matplotlib 2.0.0, PCRE 8.40, Qt5 5.8.0, Vim 8.0, X11 bundle v20170129, VTK 7.1.0, Yade 2017.01a * added new easyconfigs for existing toolchains: * ``iomkl/2017a`` (`#4216 `_), ``intel/2017.02`` (`#4248 `_) * various enhancements, including: * fix style in several easyconfigs (`#4174 `_, `#4176 `_, `#4190 `_, `#4233 `_) * add sanity check command to Yade easyconfig to make sure that '``import yade``' works, include bzip2 as dep (`#4193 `_) * add ``PDF::API2`` extension to Perl 5.24.0 easyconfigs + sync ``exts_list`` (`#4221 `_) * various bug fixes, including: * add Bison and gettext as build deps for X11 (`#4111 `_) * clean up dependencies in libdrm (`#4113 `_) * make sure Ghostscript picks up external libraries (`#4118 `_) * fix ippicv source download and library install for OpenCV v3.1.0 (`#4126 `_) * fix software name for OrthoMCL + modernise OrthoMCL easyconfigs (`#4134 `_, `#4135 `_) * get rid of backticks in gettext descriptions, causes problems when packaging with FPM (`#4146 `_) * remove duplicate sources specification in OpenMPI (`#4150 `_) * fix definition of ``buildopts``/``installopts`` in Cantera easyconfig (`#4133 `_, `#4164 `_, `#4177 `_) * use ``http://`` rather than ``ftp://`` source URLs in CFITSIO easyconfigs (`#4167 `_) * add patch for XZ 5.2.2 to include ``5.1.2alpha`` symbols required by '``rpm``' command on CentOS 7.x (`#4179 `_) * add patch for Boost v1.61-1.63 to fix problem with ``make_array``/``array_wrapper`` in Boost serialization library (`#4192 `_) * set ``CMAKE_PREFIX_PATH`` to ncurses install directory in CMake easyconfigs (`#4196 `_) * switch to ``lowopt=True`` for libxc v2.2.* and v3.* (`#4199 `_) * remove custom ``sanity_check_paths``, since it's identical to that used by the R easyblock (`#4200 `_) * fix ``version`` (& ``homepage``) in ea-utils easyconfigs (`#4205 `_) * remove ``--with-threads`` configure option in OpenMPI-2.* (`#4213 `_) * fix check for Szip library in configure script for netCDF 4.1.3 (`#4226 `_) * fix ``source_urls`` in several easyconfigs, including: * bsoft, cutadapt, EMBOSS, GnuTLS, ImageMagick, LibTIFF, Mercurial, netCDF, netCDF-Fortran, pigz, ROOT and Subversion (`#4227 `_) .. _release_notes_eb310: EasyBuild v3.1.0 (February 3rd 2017) ------------------------------------ feature release **framework** * various enhancements, including: * ARM: GCC optimal/generic architecture compiler flags (`#1974 `_) * add support for ``--check-style`` to check style in easyconfig files (`#1618 `_, `#2038 `_) * add ``HOME`` and ``USER`` from env to available cfg file constants (`#2063 `_) * ``--optarch`` can now be specified on a toolchain basis (`#2071 `_) * implement ``get_cpu_features`` function in systemtools (`#2074 `_, `#2078 `_) * support use of ``linalg`` without MPI, add ``iimkl`` toolchain definition (`#2082 `_) * spoof HTTP request header with empty agent (`#2083 `_) * exclude dependencies of dependencies that extend $MODULEPATH in make_module_dep (`#2091 `_) * various bug fixes, including: * make ``fetch_github_token`` more robust against ``RuntimeError`` from ``keyring`` (`#2070 `_) * POWER: Fix ``--optarch=GENERIC`` for GCC (`#2073 `_) * fix docstring in toolchain class (`#2075 `_) * skip test cases involving ``.yeb`` if ``PyYAML`` is not installed, silence test in options subsuite (`#2081 `_) * fix traceback with '``eb --check-github``' if ``GitPython`` is not installed (`#2085 `_) * fix regex for determining list of patched files in GitHub diff (`#2088 `_) * modify robot so that it only appends dependencies of tweaked easyconfigs (`#2090 `_) * escape metacharacters in paths passed to ``re.compile`` in ``dry_run_set_dirs`` (`#2098 `_) * fix broken error message in ``get_toolchain_hierarchy`` + dedicated test case (`#2099 `_) **easyblocks** * new easyblock for FFTW (`#1083 `_) * various enhancements, including: * update sanity check for flex 2.6.3, no more ``libfl_pic.a`` library (`#1077 `_) * cleanup build before proceeding with full Boost (`#1080 `_) * update CP2K easyblock: copy data dir, support version 4.1, support ELPA, fix psmp build with foss toolchain (`#996 `_, `#1020 `_, `#1043 `_, `#1084 `_) * add sanity check support for OpenSSL 1.1 (`#1087 `_) * support the latest changes in Inspector 2017 (`#1047 `_) * update NEURON easyblock to support the lack of ``hoc_ed`` in 7.4 (`#987 `_) * add support for WPS 3.8 (`#1079 `_) * also consider ``setuptools`` in ``EasyBuildMeta`` easyblock (`#1093 `_) * various bug fixes, including: * (correctly) define ``$ROSETTA3_DB`` in Rosetta easyblock (`#1092 `_) **easyconfigs** * added easyconfigs for ``foss/2017a`` and ``intel/2017a`` common toolchains (`#3968 `_, `#3969 `_) * added example easyconfig files for 16 new software packages: * ack (`#3983 `_), cclib (`#4065 `_), ConnectomeWorkbench (`#3411 `_), GroIMP (`#3994 `_), hyperspy (`#3991 `_), I-TASSER (`#1216 `_), ImageJ (`#4023 `_, `#4062 `_), libconfig (`#4051 `_), libspatialindex (`#4002 `_), mahotas (`#3990 `_), Minia (`#3949 `_), muParser (`#4007 `_), NetLogo (`#3941 `_), QIIME (`#3868 `_), QwtPolar (`#4019 `_), Tensorflow (`#4084 `_, `#4095 `_) * added additional easyconfigs for various supported software packages, including: * Boost 1.62.0 + 1.63.0, CP2K 4.1, GSL 2.3, PLUMED 2.3.0, Qt5 5.7.1, WRF 3.8, WPS 3.8, Yade 2016.06a, zlib 1.2.11 * various enhancements, including: * update FFTW 3.3.5 easyconfigs to use FFTW easyblock & enable running of tests (`#3985 `_) * add FME extensions (+ deps) in R 3.3.1 easyconfigs (`#4063 `_) * various bug fixes, including: * add libxml2 dependency on HDF5 (`#3759 `_) * remove unnecessary dependency in libmatheval (`#3988 `_) * fix permissions on SWASH binaries (`#4003 `_) * add conda-forge channel to perl-app-cpanminus (`#4012 `_) * add missing deps (libpthread-stubs, libpciaccess) to libdrm 2.4.70 (`#4032 `_) * modloadmsg style fixes in multiple easyconfigs (`#4035 `_) * include X11 as dep for Molden (`#4082 `_) * remove incorrect definition for $ROSETTA3_DB, now (correctly) defined via Rosetta easyblock (`#4083 `_) * fix source URLs for several easyconfigs, including: * arpack-ng 3.1.3 + 3.1.5 (`#4050 `_), ChIP-Seq 1.5-1 (`#4050 `_), Ghostscript 9.10, 9.14 + 9.16 (`#4050 `_), Git 1.7.12, 1.8.2 + 1.8.3.1 (`#4050 `_), HBase 1.0.2 (`#4043 `_), libevent 2.0.22 (`#4037 `_), libsodium 1.0.3 (`#4046 `_), lynx 2.8.7 (`#4050 `_), Maven 3.2.2 and 3.3.3 (`#4039 `_), MEME 4.8.0 (`#4050 `_), PCC 20131024 (`#4044 `_), S-Lang 2.3.0 (`#4045 `_), Spark 1.3.0 (`#4041 `_), splitRef 0.0.2 (`#4040 `_) .. _release_notes_eb302: EasyBuild v3.0.2 (December 22nd 2016) ------------------------------------- bugfix release **framework** * various bug fixes, including: * also skip dependencies of dependencies marked as external module in get_toolchain_hierarchy (`#2042 `_) * disable verbose setvar in modules.py (`#2044 `_) * force copying of easyconfigs in --new-pr/--update-pr, even when combined with -x (`#2045 `_) * fix verification of filename for easyconfigs used to resolve deps (`#2051 `_) * skip RPATH sanity check when toolchain did not use RPATH wrappers (`#2052 `_) * check whether file-like paths are readable before reading them in systemtools module (`#2065 `_) * various small enhancements, including: * add 'rpath' toolchain option to selectively disable use of RPATH wrappers (`#2047 `_) **easyblocks** * various enhancements, including: * enhance DL_POLY_Classic easyblock to support building with Plumed support (REVIEW) (`#829 `_) * make the Allinea easyblock search for the templates in the easyconfig paths (`#1025 `_) * make FortranPythonPackage aware of (pre)buildopts (`#1065 `_) * update sanity check for Mono to support recent versions (`#1069 `_) * fix Eigen sanity check for latest version 3.3.1 (`#1074 `_) * various bug fixes, including: * skip RPATH sanity check for binary installations (`#1056 `_) * pass CXXFLAGS and LDFLAGS to Boost bjam (`#1064 `_) * make pip ignore already installed versions of the package being installed (`#1066 `_) * don't pass empty string as custom installopts for numpy in test_step (`#1067 `_) * make the Rosetta EasyBlock work in --module-only mode (`#1073 `_) **easyconfigs** * added example easyconfig files for 13 new software packages: * CryptoMiniSat (`#3952 `_), MATSim (`#3902 `_), Molcas (`#2084 `_), ne (`#3376 `_), psmc (`#3910 `_), PyCogent (`#3897 `_), PyNAST (`#3897 `_), RASPA2 (`#3903 `_, `#3946 `_), SimPEG (`#3876 `_), SolexaQA++ (`#3892 `_), taco (`#3882 `_), UCLUST (`#3896 `_), USPEX (`#3767 `_) * added additional easyconfigs for various supported software packages, including: * Mono 4.6.2.7, PGI 16.10, ROOT 6.08.02 * various enhancements, including: * trivial style fixes (`#3878 `_, `#3893 `_, `#3895 `_) * various bug fixes, including: * add X11 develop libs to ncview easyconfig (`#3881 `_) * fix source_urls in pkg-config easyconfigs (`#3907 `_) * install numpy/scipy as .egg to ensure shadowing of numpy/scipy in parent Python installation (`#3921 `_) * fix broken source URL + homepage for Infernal (`#3928 `_) * fix test that verifies dumped easyconfig, take into account that dumped dependencies may include hardcoded dependency (`#3932 `_) * include libGLU as dependency in freeglut easyconfigs with recent Mesa (`#3936 `_) * add patch for FreeSurfer to fix issue with MATLAB 2013 (`#3954 `_) .. _release_notes_eb301: EasyBuild v3.0.1 (November 30th 2016) ------------------------------------- bugfix release **framework** * important changes * always use Intel-specific MPI compiler wrappers (``mpiicc``, ``mpiicpc``, ``mpiifort``) for toolchains using both Intel compilers and Intel MPI (`#2005 `_) * various small enhancements, including: * use ``setvar`` in ``modules.py`` to define environment variables (`#2011 `_) * include output of ``sanity_check_commands`` in the build log (`#2020 `_) * various bug fixes, including: * fix testing of bootstrap script in Travis config (`#2003 `_) * use correct module syntax in bootstrap script if Lmod is not used (i.e. Tcl) (`#2007 `_) * fix packaging issue with non-Python scripts in easybuild/scripts (`#2015 `_) * fixes issue where RPATH wrapper template script (``rpath_wrapper_template.sh.in``) was not included in the v3.0.0 release * make tests more robust against running headless (`#2016 `_) * avoid rewrapping already wrapped compiler/linker command with RPATH wrapper script (`#2022 `_) * fix ``log.error`` traceback due to '``raise EasyBuildError``' involving a '``%s``' in error message (`#2024 `_) * make sure '``modules_tool``' attribute is also defined for extensions (`#2026 `_) * only dump easyconfig with modified deps due to ``--minimal-toolchains`` to 'reprod' subdir of install dir (`#2028 `_) * avoid appending '``-h'`` to sanity check commands specified as a string (`#2030 `_) * fix bug in ``list_software_rst``: always include version suffix regardless of value (`#2032 `_) **easyblocks** * various enhancements, including: * update SAMtools easyblock for recent versions (`#1048 `_) * various bugfixes, including: * fix QuantumESPRESSO easyblock to handle gipaw correctly (`#1041 `_) * always specify name of serial Fortran compiler to ALADIN, it already knows to use MPI wrapper commands (`#1050 `_) **easyconfigs** * added example easyconfig files for 7 new software packages: * Cookiecutter (`#3827 `_), ETE (`#3857 `_), findhap (`#3860 `_), graphviz (Python bindings, `#3826 `_), LoFreq (`#3856 `_), PhyloBayes-MPI (`#3859 `_), XGBoost (`#3849 `_) * added additional easyconfigs for various supported software packages * various enhancements, including: * add ``ipywidgets`` and ``widgetsnbextension`` extensions to IPython 5.1.0 easyconfigs (`#3818 `_, `#3823 `_) * run dadi test suite as a sanity check command (`#3858 `_) * various bug fixes, including: * fix incorrect descriptions for ifort (`#3817 `_) * fix ``modulename`` for Jinja2 and Pygments (`#3823 `_) * fix download URL in BLAST 2.2.26 easyconfig (`#3861 `_) .. _release_notes_eb300: EasyBuild v3.0.0 (November 16th 2016) ------------------------------------- feature release **framework** * backward-incompatible changes: * make robot always consider subtoolchains, even without ``--minimal-toolchains`` (but in reverse order) (`#1973 `_) * clean up behaviour that was deprecated for EasyBuild v3.0 (`#1978 `_) * change *default* config to use ``Lmod``/``Lua`` for modules tool/syntax, ``GC3Pie`` as job backend (`#1985 `_) * the minimal required version of Lmod was bumped to 5.8 (`#1985 `_) * major new features: * (experimental) support for RPATH linking via ``--rpath`` (`#1942 `_) * see http://easybuild.readthedocs.org/en/latest/RPATH-support.html * add support for ``--consider-archived-easyconfigs`` (`#1972 `_) * see http://easybuild.readthedocs.org/en/latest/Archived-easyconfigs.html * stabilize ``--new-pr`` and ``--update-pr`` (`#1979 `_) * see http://easybuild.readthedocs.org/en/latest/Integration_with_GitHub.html * various other small enhancements, including: * add support for '``devel``' log level (`#1815 `_) * make ``remove_file`` aware of ``--extended-dry-run`` + add dedicated unit test (`#1932 `_) * add support for filtering out setting/updating particular environment variables from generated modules (`#1943 `_) * see ``--filter-env-vars`` * clean up output of EasyBuild bootstrap script & add version (`#1944 `_) * improved ARM platform/CPU detection (`#1953 `_) * use '``0``' as letter dir for funky software names that don't start with a letter, e.g., ``3to2`` (`#1954 `_) * make bootstrap script aware of ``vsc-install`` for offline installation (`#1955 `_) * add support for ``blas_family()`` and ``lapack_family()`` methods in ``Toolchain`` instances (`#1961 `_) * make ``copy_file`` dry-run aware (`#1963 `_) * reorganise test easyconfigs to match structure in easyconfigs repo (`#1970 `_) * add a toolchain compiler option for enforcing IEEE-754 conformance (`#1975 `_) * support for ``intelcuda`` compiler toolchain (`#1976 `_) * check that each glob pattern matches at least one file ``expand_glob_paths`` (important for ``--include-*``) (`#1980 `_) * enhance bootstrap to auto-skip stage 0 in case a suitable setuptools is already available (`#1946 `_, `#1984 `_) * simplify ``GC3Pie`` version check (`#1987 `_) * include suggestion on how to change configuration w.r.t. modules tool/syntax (`#1989 `_) * various bug fixes, including: * fix test for ``find_easybuild_easyconfig`` (`#1931 `_) * remove existing module file under ``--force``/``--rebuild`` (`#1933 `_) * fix combining ``--search`` and ``--try-*`` (`#1937 `_) * fix appending to existing ``buildstats`` in ``FileRepository.add_easyconfig`` (`#1948 `_) * fix handling of iterate easyconfig parameters, restore them during cleanup (`#1949 `_) * fix filtering loads for (hidden) build deps from generated module (`#1959 `_) * handle multi-flag compiler options on all types of options (`#1966 `_) * fix ``--list-software`` by making ``letter_dir_for`` function aware of '``*``' wildcard name (`#1969 `_) * skip dependencies of toolchain marked as external modules when determining module hierarchy (`#1977 `_) * bump page limit in ``fetch_latest_commit_sha``, spit out more meaningful error if too many branches were encountered (`#1981 `_) * fix CUDA-related issues in ``HierarchicalMNS`` (`#1986 `_) **easyblocks** * backwards incompatible changes: * remove deprecated GenomeAnalysisTK/GATK easyblock (`#1001 `_) * remove deprecated '``get_netcdf_module_set_cmds``' function from netCDF easyblock (`#1015 `_) * remove deprecated '``get_blas_lib``' function from LAPACK easyblock (`#1016 `_) * remove ``QLogicMPI`` easyblock (`#1023 `_) * new easyblock for installing Anaconda (`#950 `_) * add generic easyblock for Conda installations (`#950 `_) * various enhancements, including: * enable use of ``GCCcore`` as toolchain for Clang, fail if no GCC prefix is found (`#1002 `_) * also build Boost MPI library in parallel (`#1005 `_, `#1038 `_) * enhance g2clib easyblock to allow to install 1.6.0 or higher (`#1006 `_) * update QuantumESPRESSO easyblock to support packaging changes in 6.0 (`#1007 `_) * add support to ``Scons`` generic easyblock to provide argument to specify installation prefix (`#1008 `_) * update ``IntelBase`` and imkl easyblocks to handle the 2017 versions of compilers/imkl (`#1012 `_) * leverage ``toolchain.linalg`` functionality in ScaLAPACK easyblock, use ``copy_file`` (`#1014 `_) * allow netCDF-C++4 to be used with ESMF (`#1019 `_) * update Advisor easyblock to support latest versions (`#1021 `_) * update CBLAS easyblock to build with ``foss`` toolchain (`#1024 `_) * update Gurobi easyblock to use ``copy_file`` (`#1028 `_) * add support for giving ``/lib`` preference over ``/lib64`` & co in GCC installation (`#1030 `_, `#1035 `_) * enable installation of ``libiberty`` by default for binutils (`#1030 `_) * avoid CMake fiddling with the RPATHs injected by EasyBuild via ``--rpath`` in CMakeMake and METIS easyblocks (`#1031 `_, `#1034 `_) * simplify scipy sanity check to make it more robust w.r.t. version updates (`#1037 `_) * various bug fixes, including: * make sure '``None``' doesn't appear in modules generated with ``--module-only`` (`#998 `_) * fix ATLAS easyblock for non-x86 systems (`#1003 `_) * fix '``usempi``' and '``with_mpi``' usage to allow for a serial build of Amber 16 (`#1013 `_) * add both ``lib/python2.7/site-packages/{,wx-3.0-gtk2}`` to ``$PYTHONPATH`` for wxPython (`#1018 `_) * only hard inject RPATH for ``/usr/lib*`` directories when building binutils with ``dummy`` toolchain (`#1026 `_) * make HDF5 easyblock handle ``--filter-deps`` correctly (`#1027 `_) * update Travis config w.r.t. changes framework config defaults and required Lmod version (`#1029 `_) * be more patient when running Mathematica Q&A installer (`#1036 `_) **easyconfigs** * backwards incompatible changes: * archive easyconfigs using old inactive toolchains * see `#3725 `_, `#3728 `_, `#3729 `_, `#3730 `_, `#3731 `_, `#3732 `_, `#3733 `_, `#3735 `_, `#3736 `_, `#3737 `_, `#3738 `_ * only taken into account by EasyBuild if ``--consider-archived-easyconfigs`` is enabled * no easyconfigs available outside of archive for QLogicMPI + 15 toolchains: * ``ClangGCC``, ``cgmpich``, ``cgmpolf``, ``cgmvapich2``, ``cgmvolf``, ``cgompi``, ``cgoolf``, ``gmacml``, ``goalf``, ``gpsmpi``, ``gpsolf``, ``iiqmpi``, ``intel-para``, ``ipsmpi``, ``iqacml`` * fix name in PyTables easyconfigs (was 'pyTables') (`#3785 `_) * added example easyconfig files for 32 new software packages: * 3to2 (`#3655 `_), Anaconda2 (`#3337 `_), Anaconda3 (`#3337 `_), ART (`#3724 `_), atools (`#3631 `_), awscli (`#3645 `_), behave (`#3751 `_), Blosc (`#3785 `_), bokeh (`#3790 `_), Cantera (`#3655 `_), Cargo (`#3764 `_), dadi v1.7.0, distributed (`#3786 `_), ea-utils (`#3634 `_), Elk (`#3644 `_), FGSL (`#3638 `_), gencore_variant_detection (`#3337 `_), help2man (`#3768 `_), lbzip2 (`#3791 `_), Log-Log4perl (`#3574 `_), Minimac2 (`#3783 `_), mypy (`#3694 `_), OBITools (`#3573 `_), perl-app-cpanminus (`#3337 `_), PGDSpider (`#3625 `_), prokka (`#3755 `_), Reads2snp (`#3609 `_), spglib-python (`#3620 `_), SUNDIALS (`#3654 `_, `#3655 `_), SelEstim (`#3626 `_), XMLStarlet (`#3797 `_), x265 (`#3090 `_) * added easyconfigs for new '``intelcuda``' toolchain (`#3750 `_) * added new easyconfigs for existing toolchains: * ``goolfc/2016.08`` (`#3796 `_), ``goolfc/2016.10`` (`#3666 `_, `#3775 `_), ``intel/2017.00`` (`#3543 `_), ``intel/2017.01`` (`#3757 `_), ``iomkl/2016.09-GCC-4.9.3-2.25`` (`#3680 `_), ``iomkl/2016.09-GCC-5.4.0-2.26`` (`#3772 `_) * added additional easyconfigs for various supported software packages, including: * Advisor 2017 update 1, Amber 16, ATLAS 3.10.2, GROMACS 2016, Octave 4.0.3, OpenFOAM 3.0.1, PyTables 3.3.0, QuantumESPRESSO 6.0, Rust v1.12.1 * various other enhancements, including: * STREAM builds using ~56GiB and ~111GiB (`#3670 `_) * various bug fixes, including: * fix source spec in VASP easyconfig, ensure static linking with Intel MKL (`#3381 `_) * fix source URL in GCCcore 6.2.0 easyconfig (`#3608 `_) * correct STAMP dependency in i-cisTarget, must be 1.3 (`#3613 `_) * consistently specify to use ``-fgnu89-inline`` flag in M4 1.4.17 easyconfigs (`#3623 `_) * fix source URLs for Cython (`#3636 `_) * add Bison as build dep and M4 as runtime dep for flex 2.6.0 (`#3656 `_) * enable parallel building of flex 2.6.0 (`#3630 `_) * add zlib and bzip2 dependencies to X11 bundle (`#3662 `_) * use '``letter_dir_for``' function rather than just grabbing 1st letter of software name in easyconfigs tests (`#3664 `_) * add patch to fix typo in GRIT 2.0.5 (`#3675 `_) * fix typo in patch for WRF 3.8.0 (`#3702 `_) * use ``$CC``, ``$CXX`` rather than ``$I_MPI_CC``, ``$I_MPI_CXX`` in patch for OpenFOAM 4.0 (`#3703 `_) * patch FLTK to fix '``undefined symbol``' issue when building Octave (`#3704 `_) * include Pillow as a proper dep for scikit-image rather than as extension, since it has deps itself (`#3723 `_) * update Travis config w.r.t. changes framework config defaults and required Lmod version (`#3773 `_) * don't limit parallellism to 4 in recent GCC easyconfigs (`#3776 `_, `#3777 `_, `#3778 `_) * include M4 as dependency in flex 2.5.39 easyconfigs + fix consistency issues (`#3782 `_) * consistently apply patch for ncurses 6.0 (`#3792 `_) * eliminate dependency on ``mpi-mic-rt`` in ifort (`#3793 `_) * include Autotools as build dependency in all beagle-lib and MrBayes easyconfigs (`#3794 `_) * make OpenBLAS use the LAPACK version specified in the easyconfig (v0.2.18 & v0.2.19) (`#3795 `_) * include original download URL for ISL source tarball in GCC easyconfigs (`#3798 `_) * disable installing ``libiberty`` for binutils built with intel toolchain (`#3802 `_) .. _release_notes_eb290: EasyBuild v2.9.0 (September 23rd 2016) -------------------------------------- feature release **framework** * note: vsc-base 2.5.4 or more recent is now required * various small enhancements, including: * change option ``--color`` choices to auto/always/never (`#1701 `_, `#1898 `_, `#1911 `_) * add support for '``hidden``' easyconfig parameter (`#1837 `_) * add support for using ``ccache`` and ``f90cache`` compiler caching tools (`#1844 `_, `#1912 `_) * see ``--use-ccache`` and ``--use-f90cache`` * update Cray metadata for 16.06 CrayPE release (`#1851 `_) * also include patch files in ``--new-pr`` and ``--update-pr`` (`#1852 `_) * handle deleted files in ``--new-pr`` (`#1853 `_) * add support for ``--install-latest-eb-release`` (`#1861 `_) * add support for hiding toolchains, see ``--hide-toolchains`` and '``hidden``' key in '``toolchain``' spec (`#1871 `_) * add template for GitHub source URL (`#1872 `_) * add support for combining ``--new-pr``/``--update-pr`` and ``--robot`` (`#1881 `_) * add support for ``--list-software`` and ``--list-installed-software`` (`#1883 `_, `#1910 `_, `#1917 `_) * print message on which extension is being installed, incl. progress counter (`#1886 `_, `#1914 `_) * add support for ``--github-org`` to specify GitHub organisation rather than GitHub user (`#1894 `_) * add support for running Lmod in debug mode (`#1895 `_) * avoid needless use of deepcopy, speed up support for templating in easyconfigs (`#1897 `_) * convert ``all_dependencies`` to a property in ``EasyConfig`` class (`#1909 `_) * add support for ``--mpi-cmd-template`` (`#1918 `_) * add support for ``--disable-mpi-tests`` (`#1920 `_) * various bug fixes, including: * merge with develop when using ``--from-pr`` (`#1838 `_, `#1867 `_) * ensure ``--new-pr`` doesn't open empty pull requests (`#1846 `_) * better error handling for outdated ``GitPython`` module in ``--check-github`` (`#1847 `_) * fix formatting for generated easyblocks documentation (`#1860 `_) * make sure the robot ignores filtered dependencies when creating toolchain cache (`#1862 `_) * honor ``--filter-deps`` under ``--minimal-toolchains`` (`#1863 `_) * correct format for '``param``' and '``author``' tags in docstrings (`#1866 `_) * ignore failing bootstrap test in Travis config file (`#1870 `_) * make sure all output of executed command is included in generated temporary log file (`#1873 `_, `#1874 `_) * ensure ``--show_hidden`` is used in the correct location for '``avail``' with Lmod (`#1875 `_) * make sure ``self.path`` is passed down in copy method of ``EasyConfig`` object (`#1884 `_) * take into account possible multi-line modloadmsg in ``ModuleGeneratorLua`` (`#1885 `_) * fix extracting ``.bz2`` source files (`#1889 `_) * don't resolve path to Lmod command (`#1892 `_) * fix skipping of stage 0 in bootstrap script (`#1893 `_) * fix function signature of ``log.deprecated`` compared to ``fancylogger.deprecated`` (`#1896 `_, `#1899 `_) * apply patch to Tcl/C environment modules tool for Tcl 8.6 support in Travis config (`#1901 `_) * fix combining ``--extended-dry-run`` with ``--from-pr`` (`#1902 `_) * also template dict keys (`#1904 `_) * don't pass '``--try-*``' command-line options to EB instance running within job script (`#1908 `_) * add workaround for incorrectly passing command line arguments with ``--job`` (`#1915 `_) * fix issues with ``--module-only`` (`#1919 `_, `#1924 `_, `#1925 `_) * correctly deal with specified start_dir * do not remove installation directory when build-in-installdir is enabled * make sure '``which``' function returns path to a file (`#1921 `_) * fix ``:param:``, ``:return:`` tags in docstrings & add test for it (`#1923 `_) **easyblocks** * new easyblocks for 6 software packages that require customized support: * cppcheck (`#983 `_), HEALPix (`#982 `_), IMOD (`#847 `_), IronPython (`#321 `_), Mono (`#321 `_), MyMediaLite (`#321 `_) * various enhancements, including: * extend OpenFoam-Extend sanity check for decomp libraries (`#784 `_) * enhance Java easyblock to support installing Java 6.x (`#940 `_) * make QuantumESPRESSO easyblock aware of multithreaded FFT (`#954 `_) * extend PSI easyblock to use PCMSolver and CheMPS2 (`#967 `_) * make Boost easyblock add definition for ``$BOOST_ROOT`` to generated module file (`#976 `_) * add support to Bundle easyblock to install list of components (`#980 `_) * enhance & clean up libxml2 easyblock to also enable installing without Python bindings (`#984 `_) * update Libint easyblock for Libint 2.1.x (`#985 `_) * update sanity check for OpenFOAM to support OpenFOAM 4.x (`#986 `_) * make easyblocks that run MPI tests aware of '``mpi_tests``' build option (`#993 `_) * various bug fixes, including: * fix compatibility of OpenFOAM easyblock with ``--module-only`` (`#784 `_) * fix testing of ``--module-only`` compatibility for OpenFOAM and IMOD easyblocks (`#784 `_) * add '``include/libxml2``' to ``$CPATH`` in libxml2 easyblock (`#981 `_) * fix compatibility of IntelBase generic easyblock with ``--module-only`` (`#994 `_) * make sure correct config script is used for Tcl/Tk deps of R (`#995 `_) **easyconfigs** * added example easyconfig files for 88 new software packages: * ADMIXTURE (`#3359 `_), angsd (`#3593 `_), ASHS (`#3429 `_), AutoDock (`#3465 `_), AutoGrid (`#3466 `_), BayeScan (`#2748 `_, `#3356 `_), BayPass (`#3451 `_), Bazel (`#3379 `_), Blender (`#3553 `_, `#3558 `_), bwakit (`#3567 `_), BXH_XCEDE_TOOLS (`#3410 `_), CastXML (`#3403 `_), CHASE (`#3304 `_), configparser (`#3368 `_, `#3424 `_), configurable-http-proxy (`#3380 `_), cppcheck (`#3508 `_), CRPropa (`#779 `_), DicomBrowser (`#3432 `_), DMTCP (`#3422 `_), entrypoints (`#3368 `_, `#3424 `_), f90cache (`#3570 `_), fastPHASE (`#3343 `_), fastQValidator (`#3192 `_), FFindex (`#1135 `_), FragGeneScan (`#1198 `_), gdc-client (`#3399 `_), gflags (`#3417 `_), glog (`#3417 `_), GRIT (`#3561 `_), H5hut (`#3431 `_), HAPGEN2 (`#3344 `_), HEALPix (`#779 `_), IMOD (`#1187 `_, `#3347 `_), IronPython (`#607 `_), jhbuild (`#3476 `_), jupyterhub (`#3380 `_), Keras (`#3581 `_), khmer (`#1158 `_), LeadIT (`#3345 `_, `#3599 `_), LevelDB (`#3417 `_), libbitmask (`#3481 `_), libcpuset (`#3481 `_), LMDB (`#3417 `_), log4cplus (`#1136 `_), MACH (`#3346 `_), Mako (`#3460 `_), Maq (`#3428 `_), MetaGeneAnnotator (`#3307 `_), Metal (`#3324 `_), Mono (`#607 `_), MyMediaLite (`#607 `_), nco (`#2575 `_), nose-parameterized (`#3579 `_), OpenEXR (`#3553 `_), OpenImageIO (`#3553 `_), path.py (`#3368 `_, `#3424 `_), PCRE2 (`#3325 `_), pftoolsV3 (`#3317 `_), PHASE (`#3385 `_), PLAST (`#3288 `_), PLINKSEQ (`#3402 `_), POV-Ray (`#3551 `_), ProbABEL (`#3108 `_), prompt-toolkit (`#3368 `_, `#3424 `_), protobuf-python (`#3563 `_), PSORTb (`#3317 `_), py (`#3403 `_, `#3482 `_), pygccxml (`#3403 `_, `#3482 `_), pyGIMLi (`#3403 `_, `#3482 `_), pyplusplus (`#3403 `_, `#3482 `_), PyQt5 (`#3533 `_), Pyro4 (`#3527 `_), pytest (`#3403 `_, `#3482 `_), QCA (`#3595 `_), RDMC (`#1137 `_), S.A.G.E. (`#3427 `_), SDL2 (`#3551 `_), SHORE (`#3531 `_), SimVascular (`#3555 `_), SortMeRNA (`#3326 `_), SUMACLUST (`#3316 `_), SUMATRA (`#3316 `_), Text-CSV (`#3323 `_), Triangle (`#3403 `_), VEGAS (`#3457 `_), VirSorter (`#3307 `_), wcwidth (`#3368 `_, `#3424 `_), X11 (`#3340 `_) * added new easyconfigs for existing toolchains: * CrayGNU + CrayIntel 2016.06 (`#3377 `_) * foss 2016.07 (`#3517 `_) + 2016.09 (`#3523 `_) * iomkl 2016.07 (`#3458 `_) * pomkl 2016.09 (`#3516 `_) * added additional easyconfigs for various supported software packages, including: * FFTW 3.3.5, GCC 4.9.4 + 6.2.0, GROMACS 5.1.4, IPython 5.1.0, LLVM 3.9.0, Mesa 12.0.1, OpenCV 3.1.0, OpenFOAM 4.0, OpenMPI 2.0.1, ParaView 5.1.2, PGI 16.7, QuantumESPRESSO 5.4.0, Qt5 5.7.0, R-bundle-Bioconductor 3.3, VTK 7.0.0, Yade 2016.06a * various enhancements, including: * adjust PSI4 easyconfigs for updated easyblock (`#3312 `_) * clean up libxml2 easyconfigs according to updated libxml2 easyblock (`#3479 `_, `#3509 `_) * significantly speed up verifying of dumped easyconfig by resorting to 'shallow' parsing (`#3520 `_) * include sanity checks for all MATIO config files (`#3528 `_) * remove ``--with-tcl-config``/``--with-tk-config`` from R easyconfig, already done in R easyblock (`#3580 `_) * various bug fixes, including: * disable testing in all ParaView 4.4.0 easyconfigs, required download is too much of a PITA (`#3178 `_) * add SQLite as dep to GDAL 2.1.0 easyconfigs (`#3342 `_) * add zlib/SQLite/LibTIFF as dep to R 3.3.1 easyconfigs (`#3342 `_) * add bzip2 as a dependency of freetype (`#3464 `_) * specify correct MPI target in FDS easyconfigs (`#3488 `_) * add tcsh as OS dep in NAMD easyconfigs (`#3491 `_) * statically link ncurses/libreadline in Lua easyconfig with '``dummy``' toolchain (`#3545 `_) * add M4 as dep for flex 2.6.x (`#3542 `_, `#3550 `_) * add bzip2 and libxcb dependencies to FFmpeg 3.x easyconfigs (`#3548 `_) * make sure & check that Graphviz does not install Tcl bindings in Tcl install prefix (`#3556 `_) * add missing patches for extensions in Python 3.x easyconfigs (`#3557 `_) * add missing XZ dependency to libxml2 2.9.4 easyconfigs, change gettext dep of XZ to build-only dep (`#3568 `_) * enable running of tests for HPCG (`#3578 `_) * fix ``buildopts`` in tabix easyconfigs (`#3584 `_) .. _release_notes_eb282: EasyBuild v2.8.2 (July 13th 2016) --------------------------------- bugfix release **framework** * various small enhancements, including: * add support for rst output for ``--list-*`` and ``--avail-*`` (`#1339 `_) * add support for '``eb --check-conflicts``' (`#1747 `_, `#1807 `_, `#1833 `_) * ensure nice error message when non-existing path is passed to ``apply_regex_substitutions`` (`#1788 `_) * add check for module output, empty stdout is a sign of trouble with Lmod (`#1793 `_) * add multi-threaded FFT to toolchain (`#1802 `_) * avoid special characters like '[', ']' in path to temporary directory (`#1808 `_) * add support for ``--zip-logs`` (`#1820 `_) * add support for ``--extra-modules`` (`#1821 `_) * add type conversion for 'checksums' and 'patches' parameter in .yeb easyconfigs (`#1826 `_, `#1840 `_) * add support for filtering tests by name (`#1828 `_) * add support for ``--avail-toolchain-opts`` (`#1830 `_, `#1839 `_) * use absolute path for robot and easyconfig files (`#1834 `_) * add backup URL for tarballs hosted on SourceForge in ``install_eb_dep.sh`` script (`#1843 `_) * various bug fixes, including: * fix installation of Lua in ``install_eb_dep.sh`` script (`#1789 `_) * fix OpenMP flag for Cray compiler wrappers (`#1794 `_) * only reset ``$MODULEPATH`` before loading a module if environment was reset (`#1795 `_) * include vsc-install as dependency in ``setup.py`` (`#1805 `_) * cache ``$PATH`` & ``$PYTHONPATH`` in test setUp, restore them in tests where '``eb``' is used (`#1806 `_) * don't reset ``$MODULEPATH`` in stage 2 of bootstrap script, support forced installation during stage 2 (`#1810 `_) * fix issue with templates defined by deps being required while still parsing deps (`#1812 `_) * skip unneeded unuse/use commands on tail of ``$MODULEPATH`` in ``check_module_path`` (`#1813 `_) * fix auto-convert for all ``*dependencies`` params in ``.yeb`` easyconfigs, ensure version is a string (`#1818 `_) * fix ``keyring`` version in Travis config (`#1819 `_) * fix dumping of ``.yeb`` easyconfig files in easyconfigs archive (`#1822 `_) * fix format of supported easyconfig templates in help output (`#1825 `_) * stick to ``pydot`` 1.1.0 for Python 2.6 in Travis config (`#1827 `_) **easyblocks** * new easyblocks for 5 software packages that require customized support: * Amber (`#958 `_), Extrae (`#955 `_), Gurobi (`#962 `_), Paraver (`#956 `_), Tau (`#887 `_) * various enhancements, including: * add support for building & installing old GROMACS versions (`#569 `_, `#960 `_) * add support for building Boost with Cray toolchain (`#849 `_) * libxsmm support for CP2K (`#942 `_) * pick up specified components for imkl (`#943 `_) * add support for building GROMACS with double precision (`#946 `_, `#960 `_) * add support for building GROMACS with CUDA support and using dynamic libraries using ``Cray`` toolchains (`#951 `_, `#960 `_) * also install vsc-install in ``EasyBuildMeta`` easyblock, if tarball is provided (`#957 `_) * enhance PSI easyblock to support PSI4 1.0 (`#965 `_) * various bug fixes, including: * also install scripts with MRtrix 0.3.14 (`#941 `_) * enhance Qt easyblock to support Qt3 (`#944 `_) * create '``release``' symlink in MRtrix install dir (`#947 `_) * fix ``make_installdir`` in Inspector & VTune easyblocks (`#952 `_) * make ``Binary`` and ``MakeCp`` easyblocks aware of '``keepsymlinks``' (`#959 `_) * correctly define ``$G4*`` environment variables in Geant4 easyblock (`#961 `_, `#970 `_) * prepend tmp install path to ``$PYTHONPATH`` in numpy test step, move to build dir when removing '``numpy``' subdir (`#963 `_) * correct full path to ALADIN config file & patch it to use right Fortran compiler flags (`#964 `_) * ensure correct compiler command/flags are used for SAMtools (`#966 `_) **easyconfigs** * added example easyconfig files for 54 new software packages: * Amber (`#3200 `_), Bullet (`#3175 `_), CONTRAlign (`#690 `_), Cluster-Buster (`#3191 `_), damageproto (`#3222 `_, `#3308 `_), DCA++ (`#3219 `_), EIGENSOFT (`#3147 `_, `#3163 `_), Extrae (`#507 `_), fdstools (`#3237 `_), ffnet (`#3273 `_), GP2C (`#3257 `_), Gurobi (`#3239 `_), gc (`#3202 `_, `#3261 `_), gputools (`#546 `_), IMa2p (`#3300 `_), IOzone (`#3253 `_), i-cisTarget (`#3191 `_, `#3194 `_), icmake (`#3243 `_), io_lib (`#3255 `_), Kent_tools (`#3191 `_), libcmaes (`#3256 `_), libpsortb (`#3259 `_), libxsmm (`#3099 `_), MEGACC (`#3263 `_), MM-align (`#1428 `_), MOSAIK (`#880 `_), MView (`#1345 `_), MySQL-python (`#3172 `_, `#3189 `_), magma (`#3219 `_), mrFAST (`#862 `_), mrsFAST (`#862 `_), mysqlclient (`#3172 `_, `#3232 `_), NTL (`#3183 `_), PARI-GP (`#3257 `_), Paraver (`#508 `_), psutil (`#3171 `_, `#3231 `_), PSI4 (`#3293 `_), Qwt (`#3157 `_), RMBlast (`#3142 `_), STAMP (`#3191 `_), Seqmagick (`#3264 `_), splitRef (`#946 `_), TAU (`#509 `_), TRF (`#3141 `_), TVB (`#3053 `_, `#3247 `_, `#3251 `_), TVB-deps (`#3053 `_, `#3247 `_, `#3251 `_), tvb-data (`#3053 `_, `#3247 `_, `#3251 `_), tvb-framework (`#3053 `_, `#3247 `_, `#3251 `_), tvb-library (`#3053 `_, `#3247 `_, `#3251 `_), VampirTrace (`#509 `_), Voro++ (`#3174 `_), wheel (`#3235 `_), wxPropertyGrid (`#508 `_), xonsh (`#3159 `_) * added easyconfigs for update of common toolchains: ``foss/2016b`` (`#3271 `_), ``intel/2016b`` (`#3270 `_) * added new easyconfigs for existing toolchains: ``CrayGNU/2016.03`` & ``CrayGNU/2016.04`` (`#3291 `_), ``foss/2016.06`` (`#3184 `_), ``intel/2016.03-GCC-5.4`` (`#3185 `_) * added additional easyconfigs for various supported software packages, including: * Boost 1.61.0, GCC 5.4.0, GROMACS 3.3.3, HDF5 1.8.17, netCDF 4.4.1, numpy 1.11.0, Perl 5.24.0, PETSc 3.7.2, Python 2.7.12, Python 3.5.2, Qt 3.3.8, R 3.3.1 * various enhancements, including: * use ``check_conflicts`` function in easyconfigs tests (`#2981 `_) * also include vsc-install in list of sources for recent EasyBuild easyconfigs, to support offline installation (`#3203 `_) * enable building of ``libmysqld.*`` in MariaDB easyconfigs (`#3230 `_) * add ALDEx2, phyloseq to bundles for Bioconductor 3.2 (`#3211 `_, `#3241 `_) * add biom, geepack, lubridate, pim to list of R 3.2.3 extensions (`#3186 `_, `#3211 `_, `#3275 `_) * various bug fixes, including: * add patch for Boost 1.60.0 to fix bug resulting in ``TypeError`` (`#3162 `_) * add fftw dependency to CP2K 2.6.0 easyconfigs using CrayGNU (`#3176 `_) * fix location of ``libelf.h``, only (also) installed as ``include/libelf.h`` is there's no ``/usr/include/libelf.h`` (`#3201 `_) * fix software name for Guile & GnuTLS (was 'guile' & 'gnutls') (`#3207 `_) * added missing space in Geant4 configopts to specify ``-DGEANT4_INSTALL_DATA`` (`#3209 `_) * fix Cython download URL in Python 2.7.11 easyconfigs (`#3212 `_) * add missing build deps for X stack in easyconfigs using ``foss/2016a`` or ``intel/2016a`` (`#3222 `_, `#3308 `_) * fix overruling of exts_list in Perl 5.22.2 easyconfig (`#3224 `_) * add missing dependency on GMP in R 3.2.3 easyconfigs (`#3226 `_) * don't hard specify toolchain for binutils build dep in likwid easyconfig, since it matches parent toolchain (`#3240 `_) * fix ``homepage`` & ``source_urls`` in HMMER easyconfigs (`#3246 `_) * stick to ``pydot`` 1.1.0 for Python 2.6 in Travis config (`#3282 `_) * add ``python-dev(el)`` to OS deps in GC3Pie easyconfigs (`#3310 `_) .. _release_notes_eb281: EasyBuild v2.8.1 (May 30th 2016) -------------------------------- bugfix release **framework** * various bug fixes, including: * fix error message on missing module command in bootstrap script (`#1772 `_) * expand '``~``' in paths specified to ``--include-*`` (`#1774 `_) * break after deleting cache entry to avoid attempt to delete cache entry again (`#1776 `_) * avoid changing ``$MODULEPATH`` when prepending with symlink of path already at head of ``$MODULEPATH`` (`#1777 `_) * filter out duplicates in ``find_flexlm_license`` (`#1779 `_) * stick with GitPython < 2.0 with Py2.6 in Travis configuration (`#1781 `_) * don't use ``LooseVersion`` to define ``version_major``/``version_minor`` (`#1783 `_) **easyblocks** * various enhancements, including: * update MRtrix easyblock for version 0.3.14 (`#932 `_) * update Inspector easyblock for recent versions (`#934 `_) * update VTune easyblock for recent versions (`#935 `_) * add debug message to IntelBase easyblock w.r.t. switching to 'exist_lic' (`#936 `_) **easyconfigs** * added example easyconfig files for 13 new software packages: * drFAST (`#906 `_), git-lfs (`#2478 `_), grabix (`#3127 `_), JWM (`#3007 `_), libcroco (`#3007 `_), librsvg (`#3007 `_), MaCH (`#3136 `_), mayavi (`#3106 `_), OpenMM (`#2762 `_), Pysam (`#3080 `_), SeqPrep (`#3097 `_), vt (`#3128 `_), wkhtmltopdf (`#3098 `_) * added new easyconfigs for existing toolchains: ``intel/2016.03-GCC-4.9`` (`#3088 `_) * added additional easyconfigs for various supported software packages, including: * Boost 1.61.0, ESMF 7.0.0, Inspector 2016 update 3, IPython 4.2, netCDF-C++4 4.3.0, netCDF-Fortran 4.4.4, Perl 5.22.2, VTune 2016 update 3 * various bug fixes, including: * apply libreadline patch to fix bug triggering segmentation fault (`#3086 `_) .. _release_notes_eb280: EasyBuild v2.8.0 (May 18th 2016) -------------------------------- feature + bugfix release **framework** * significant speedup improvements of EasyBuild itself, thanks to: * stop creating ``ModulesTool`` instances over and over again (`#1735 `_) * cache result of '``module avail``' calls (`#1742 `_) * add support for using PGI as toolchain compiler (`#1342 `_, `#1664 `_, `#1759 `_, `#1761 `_, `#1764 `_) * incl. new toolchain definitions ``pompi`` and ``pomkl`` (`#1724 `_) * add test configuration for Travis (`#1733 `_, `#1737 `_, `#1743 `_, `#1767 `_) * various other enhancements, including: * add ``get_total_memory()`` function in ``systemtools`` module (`#1623 `_) * ignore ``__init__.py`` files in ``--include-*`` (`#1704 `_) * use ``-fopenmp`` rather than ``-openmp`` for Intel compilers, since ``-openmp`` is deprecated (`#1718 `_) * add modules to metadata for Cray modules (`#1721 `_) * make sure user write permissions are set after failed removal attempt of installation directory (`#1722 `_) * escape special characters in software name in ``find_related_easyconfigs`` (`#1726 `_) * add support for ``CrayPGI`` compiler toolchain (`#1729 `_) * ensure read permission to all installed files for everybody (unless other options specify otherwise) (`#1731 `_) * also consider ``$LMOD_CMD`` in bootstrap script (`#1736 `_) * translate PyPI download URL to alternate URL with a hash (`#1749 `_) * make ``get_software_libdir`` compatible with ``-x`` (`#1750 `_) * set ``$LMOD_REDIRECT`` to '``no``' when initialising Lmod (`#1755 `_) * add test for broken modules tool setup affecting '``module use``' (`#1758 `_) * various bug fixes, including: * isolate '``options``' tests from easyblocks other than the ones included in the tests (`#1699 `_) * don't run '``module purge``' in tests, since EasyBuild may be made available through a module (`#1702 `_) * avoid rehandling ``--include-*`` options over and over again during ``--show-config`` (`#1705 `_) * remove useless ``test_cwd`` (`#1706 `_) * fix bootstrap script: make sure setuptools installed in stage0 is still available at end of stage1 (`#1727 `_) * forcibly create target branch in ``--update-pr`` (`#1728 `_) * remove check whether '``easybuild``' is being imported from dir that contains ``easybuild/__init__.py`` (`#1730 `_) * (re)install vsc-base during stage1 using ``--always-copy`` in bootstrap script, if needed (`#1732 `_) * use ``os.path.realpath`` in ``test_wrong_modulepath`` to avoid symlinked path breaking the test (`#1740 `_) * unset ``$PYTHONPATH`` in before tested bootstrapped EasyBuild module (`#1743 `_) * take into account that paths in modulepath may be symlinks in ``test_module_caches`` (`#1745 `_) * change to install dir rather than buildpath in sanity check of extension, latter may not exist (`#1746 `_, `#1748 `_) * only load modules using short module names (`#1754 `_) * (re)load modules for build deps in extensions_step (`#1762 `_) * fix ``modpath_extensions_for method``: take into account modules in Lua syntax (`#1766 `_) * fix broken link to VSC website in license headers (`#1768 `_) **easyblocks** * add test configuration for Travis (`#895 `_, `#897 `_, `#900 `_, `#926 `_) * new easyblocks for 4 software packages that require customized support: * binutils (`#907 `_), libQGLViewer (`#890 `_), SuperLU (`#860 `_), wxPython (`#883 `_) * various other enhancements, including: * update SuiteSparse easyblock for version >= 4.5 (`#863 `_) * enhance imkl easyblock to install on top of PGI (`#866 `_, `#916 `_) * enable runtime logging of install cmd in ``IntelBase`` (`#874 `_) * enhance Qt easyblock to support installing with ``dummy`` toolchain (`#881 `_) * delete libnuma symbolic links in PGI installation directory (`#888 `_) * enhance PDT easyblock to support installing with ``dummy`` toolchain (`#894 `_) * add support for building Clang with OpenMP support (`#898 `_) * update Score-P easyblock for additional compilers, MPI libraries & dependencies (`#889 `_) * drop deprecated '``testrb``' from sanity check in Ruby easyblock (`#901 `_) * enhance WRF easyblock to support versions >= 3.7 (`#902 `_) * update QuantumESPRESSO easyblock for version 5.3.0 (`#904 `_) * add support in PythonPackage easyblock to use '``setup.py develop``' (`#905 `_) * update Qt easyblock for Qt 5.6.0 (`#908 `_) * extend bzip2 easyblock to also build dynamic libraries (`#910 `_) * make threading an explicit option rather than relying on MPI library in SCOTCH easyblock (`#914 `_) * update PGI easyblock to install siterc file so PGI picks up ``$LIBRARY_PATH`` (`#919 `_) * enhance sanity check paths for compiler commands in PGI easyblock (`#919 `_) * also filter out ``-ldl`` from $LIBBLAS & co for Intel MKL in numpy easyblock (`#920 `_) * define ``$MIC_LD_LIBRARY_PATH`` for impi (`#925 `_) * various bug fixes, including: * don't hardcode Python version in ``test_make_module_pythonpackage`` (`#876 `_) * make PythonPackage easyblock compatible with ``--module-only`` (`#884 `_, `#906 `_) * remove check whether '``easybuild``' is being imported from dir that contains ``easybuild/__init__.py`` (`#891 `_) * fix passing compiler configure option in PDT easyblock (`#894 `_) * fix bug in Score-P easyblock w.r.t. ``--with-libbfd`` (`#889 `_) * fix extension filter for Ruby (`#901 `_) * fix ``ACTIVATION_TYPES`` list in IntelBase + minor style change (`#913 `_) * correctly define ``$MIC_LD_LIBRARY_PATH`` in imkl 11.3.x and newer (`#915 `_) * fix broken link to VSC website in license headers (`#927 `_) **easyconfigs** * added example easyconfig files for 69 new software packages: * ALPS (`#2888 `_), annovar (`#3010 `_), BayeScEnv (`#2765 `_), BayesAss (`#2870 `_), BerkeleyGW (`#2925 `_), Blitz++ (`#2784 `_, `#3004 `_), bam-readcount (`#2850 `_), Commet (`#2938 `_), CrossTalkZ (`#2939 `_), cuDNN (`#2882 `_), DBus (`#2855 `_), DFT-D3 (`#2107 `_), DIAL (`#3056 `_), dask (`#2885 `_), dbus-glib (`#2855 `_), FFLAS-FFPACK (`#2793 `_), FLAC (`#2824 `_), FLANN (`#3015 `_, `#3029 `_), FLEUR (`#3043 `_), GConf (`#2855 `_), GROMOS++ (`#1297 `_), GST-plugins-base (`#2855 `_), GStreamer (`#2855 `_), GTOOL (`#2805 `_), Givaro (`#2793 `_), gdist (`#2935 `_), gromosXX (`#1297 `_), HISAT2 (`#2809 `_), i-PI (`#2940 `_), Kraken (`#3037 `_, `#3041 `_), LAME (`#2823 `_), LASTZ (`#3002 `_), LinBox (`#2793 `_), Loki (`#2839 `_), libQGLViewer (`#2923 `_, `#3008 `_), libXxf86vm (`#2855 `_), MDSplus (`#2787 `_, `#2838 `_, `#3027 `_), MRIcron (`#2831 `_), Mawk (`#2732 `_), minieigen (`#2839 `_), mpmath (`#3058 `_), NBO (`#3047 `_, 3048), NGS (`#2803 `_), NGS-Python (`#2810 `_), ncbi-vdb (`#2808 `_), OptiX (`#2795 `_), PCL (`#3024 `_), PEAR (`#2731 `_), PLplot (`#2990 `_), Postgres-XL (`#2891 `_), PyGTS (`#2969 `_), RSeQC (`#2788 `_), Rust (`#2920 `_, `#2943 `_), rainbow (`#2730 `_), SHAPEIT (`#2806 `_), SIONlib (`#2908 `_), Saxon-HE (`#2773 `_), Singularity (`#2901 `_), SoX (`#2825 `_), Subread (`#2790 `_), SuperLU (`#2665 `_), travis (`#2953 `_), VASP (`#2950 `_), Wannier90 (`#2906 `_, `#3042 `_), wget (`#3041 `_), wxPython (`#2855 `_), xf86vidmodeproto (`#2855 `_), Yade (`#2839 `_), Yambo (`#2932 `_) * add test configuration for Travis (`#2942 `_, `#2944 `_, `#2954 `_, `#3061 `_) * added easyconfigs for new PGI-based toolchains * ``pomkl/2016.03`` (`#2899 `_, `#2900 `_, `#3046 `_), ``pomkl/2016.04`` (`#3044 `_), ``CrayPGI/2016.04`` (`#2927 `_) * added new easyconfigs for existing toolchains: * ``foss/2016.04`` (`#3013 `_), ``intel/2016.02-GCC-5.3`` (`#2523 `_), ``intel/2016.03-GCC-5.3`` (`#3009 `_) * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * incl. CGAL 4.8, Clang 3.8.0, icc/ifort 2016.2.181 & 2016.3.210, imkl 11.3.2.181 & 11.3.3.210, impi 5.1.3.181, LLVM 3.8.0, OpenCV 2.4.12, pandas 0.18.0, Qt 5.6.0, Scalasca 2.3, Score-P 2.0.1, SuiteSparse 4.5.2, WRF 3.8 * various other enhancements, including: * enhance ORCA easyconfig for compatibility with SLURM (`#1819 `_) * enable ``-fPIC`` in GraphicsMagick easyconfig, required by Octave (`#2764 `_) * clean up binutils easyconfigs to use binutils easyblock (`#3006 `_) * add ``include/GraphicsMagick`` to ``$CPATH`` in GraphicsMagick easyconfigs (`#3034 `_) * update SuiteSparse easyconfigs according to updated SuiteSparse easyblock (`#3050 `_) * various bug fixes, including: * fix Perl extensions download urls (`#2738 `_) * add Autoconf as build dep for ``GCCcore`` (`#2772 `_) * fix versions of extensions in Bioconductor 3.2 bundles (`#2769 `_) * fix (build) deps for ``intel/2016a`` easyconfigs of cairo, libXext, libXrender (`#2785 `_, `#2874 `_) * use '``env``' wherever preconfig/build/installopts is used to set environmental variables (`#2807 `_, `#2811 `_, `#2812 `_) * add zlib as explicit dep in Tk easyconfigs (`#2815 `_) * consistently specify to use ``-fgnu89-inline`` flag in M4 1.4.17 easyconfigs (`#2774 `_, `#2779 `_, `#2816 `_) * fix homepage and description in Pygments easyconfigs (`#2822 `_) * include pkg-config as build dependencies for libXau, libXdmcp, libxcb (`#2827 `_) * consistently use ``XORG_*_SOURCE`` constants (`#2829 `_, `#2830 `_, `#2848 `_) * update source URLs in ScientificPython easyconfig files (`#2847 `_) * add checksums in SuiteSparse easyconfigs (`#2849 `_) * fix build deps for GObject-Introspection (`#2852 `_) * correctly specify Perl location in git easyconfig (`#2866 `_) * fix bitstring 3.1.3 download URL in Python easyconfigs, source tarball on PyPI disappeared (`#2880 `_) * fix Perl dependency in worker easyconfigs, it requires non-standard Perl modules (`#2884 `_) * add XZ as dependency in Python 3.5.1 easyconfigs, required for lzma (`#2887 `_) * fix download URL for packmol (`#2902 `_) * drop ``usempi`` toolchain in numexpr easyconfigs, not needed (`#2937 `_) * fix use of ``resolve_dependencies`` in tests according to changes in framework (`#2952 `_) * add dependency extensions for MarkupSafe and jsonscheme in IPython 3.2.3 easyconfigs (`#2967 `_) * add patch for matplotlib 1.5.1 to fix Tcl/Tk library paths being used (`#2971 `_) * add xproto build dependency for makedepend v1.0.5 (`#2982 `_) * disable parallel build for Doxygen (`#2986 `_) * fix source URLs for ``FreezeThaw`` and ``Tie::Function`` extensions for Perl v5.22.1 (`#2988 `_) * add ``sed`` command in worker easyconfig files to fix module_path in conf/worker.conf (`#2997 `_, `#3000 `_) * drop toolchainopts from Eigen easyconfigs, since it is headers-only (`#3025 `_) * clean up dummy bzip2 easyconfig, define buildopts rather than defining ``$CC`` and ``$CFLAGS`` via ``os.environ`` (`#3036 `_) * use ``%(pyshortver)s`` template rather than hardcoding 2.7 in VTK easyconfigs (`#3052 `_) * correct install location of OpenCV Python bindings (`#3054 `_) * include XZ as dependency for libunwind (`#3055 `_) * add patch to fix broken OpenSSL tests due to expired certificates (`#3057 `_) * fix broken link to VSC website in license headers (`#3062 `_) .. _release_notes_eb270: EasyBuild v2.7.0 (March 20th 2016) ---------------------------------- feature + bugfix release **framework** * stabilize Cray support * enable '``dynamic``' toolchain option by default for ``Cray*`` toolchains (`#1581 `_) * remove FFTW from the Cray toolchains definition (`#1585 `_) * add external modules metadata for Cray systems (`#1638 `_) * fix independency of Cray toolchains w.r.t. toolchain build environment (`#1641 `_, `#1647 `_) * remove requirement to use ``--experimental`` for Cray toolchains (`#1663 `_) * enable Python optimization mode in '``eb``' (`#1357 `_) * improved GitHub integration * improve error handling on git commands + better logging for ``--new-pr``/``--update-pr`` (`#1590 `_) * use ``git`` rather than ``https`` in ``--new-pr``/``--update-pr`` (`#1602 `_) * add ``-u`` as shorthand for ``--upload-test-report`` (`#1605 `_) * fix ``--from-pr`` for PRs that include renamed/deleted files (`#1615 `_) * add support for ``--install-github-token`` and ``--check-github`` (`#1616 `_) * fix ``fetch_easyconfigs_from_pr`` w.r.t. duplicate files in PRs (`#1628 `_) * various other enhancements, including: * add support for ``--search-filename`` and ``--terse`` (`#1577 `_) * support complete bash completion (`#1580 `_) * add support for ``%(*ver)s`` and ``%(*shortver)s`` templates (`#1595 `_, `#1604 `_) * incl. ``%(javaver)s``, ``%(javashortver)s``, ``%(perlver)s``, ``%(perlshortver)s``, ``%(pyver)s``, ``%(pyshortver)s``, ``%(rver)s``, ``%(rshortver)s`` * define ``HOME`` constant that can be used in easyconfig files (`#1607 `_) * implement support for generating '``swap``' statements in module files (`#1609 `_) * add support for ``--show-config`` (`#1611 `_, `#1620 `_) * simplified support for ``--minimal-toolchains`` (`#1614 `_, `#1619 `_, `#1622 `_, `#1625 `_, `#1646 `_) * add support for ``--dump-env-script`` (`#1624 `_) * enhance ModulesTool.exist to also recognize partial module names (`#1630 `_) * improve error message for toolchain definition errors (`#1631 `_) * make default is_short_modname_for check less strict to support versionless external modules as deps (`#1632 `_) * mention hostname in comment made by ``--upload-test-report`` (`#1635 `_) * support providing additional relative path for prefix in external module metadata (`#1637 `_) * add ``ThematicModuleNamingScheme`` (`#1645 `_) * enhance logging format: remove logger name, mention location instead (`#1649 `_, `#1654 `_) * update kernel versions for SLES12 (`#1659 `_) * raise ``EasyBuildError`` rather than ``ImportError`` in ``only_if_module_is_available`` decorator (`#1662 `_) * various bug fixes, including: * fix Lmod spider output in generated modules (`#1583 `_) * correctly define '``easybuild``' namespaces (`#1593 `_, `#1666 `_, `#1680 `_) * this change requires that the ``setuptools`` Python package is available (at runtime) * using custom easyblocks by adding them in the Python search path (``$PYTHONPATH``) may require adjustments, i.e. also using ``pkg_resources.declare_namespace`` in the ``__init__.py`` files; *we highly recommend to use* ``--include-easyblocks`` *instead*, see http://easybuild.readthedocs.org/en/latest/Including_additional_Python_modules.html * note: this has the side-effect of not being able anymore to reliably use '``eb``' in the parent directory of the easybuild-framework repository (`#1667 `_) * fix template for ``savannah.gnu.org`` source URL (`#1601 `_) * stop running '``module purge``', only restore environment (`#1608 `_) * fix license headers: Hercules foundation is now FWO (`#1629 `_) * avoid that ``fancylogger`` tries to import ``mpi4py`` to determine MPI rank (`#1648 `_) * fix error in tests when '``file``' backend is not available in Python keyring (`#1650 `_) * update develop install script (`#1651 `_) * handle allowed system deps during ``prepare_step`` rather than during parsing of easyconfig (`#1652 `_) * add function to find FlexLM licenses: ``find_flexlm_license`` (`#1633 `_, `#1653 `_) * fix availability check for external modules with partial module name (`#1634 `_, `#1643 `_) * fix bootstrap script to ensure ``setuptools`` is also installed (`#1655 `_) * fix issue in bootstrap script with ``vsc-base`` being picked up from the OS (`#1656 `_) * fix bootstrap script for environment where '``python``' is Python 3.x (`#1660 `_) * remove ``--experimental`` for tests related to ``--package`` (`#1665 `_) * ensure path to setuptools is included in ``$PYTHONPATH`` being used to test scripts (`#1671 `_) * sanitize environment before initializing easyblocks (`#1676 `_) * remove ``reload`` statements in ``include.py``, since they are not required and break ``--include-toolchains`` (`#1679 `_) **easyblocks** * new easyblocks for 6 software packages that require customized support: * ADF (`#826 `_), MPICH (`#844 `_, `#852 `_, `#868 `_), mutil (`#859 `_), pplacer (`#835 `_), psmpi (`#852 `_), SNPhylo (`#865 `_) * various other enhancements, including: * implement support for '``use_pip``' in PythonPackage easyblock (`#719 `_, `#831 `_) * add support in CUDA easyblock to install wrappers for host compilers (`#758 `_) * update sanity check for picard version 1.124 and above (`#796 `_) * use '``module swap``' for all components in ``CrayToolchain`` (`#823 `_) * update PSI4 easyblock to cope with changed name of PSI4 data dir (`#824 `_) * use ``find_flexlm_license`` function and avoid defining ``$CPATH`` in PGI easyblock (`#837 `_) * use ``find_flexlm_license`` function in ``IntelBase`` generic easyblock (`#839 `_) * add unit test to check module file generated by ``PythonPackage`` easyblock (`#841 `_) * rework MVAPICH2 easyblock on top of new MPICH easyblock (`#844 `_) * add CUDA support in CP2K easyblock (`#850 `_) * also define ``$LD`` in ``buildopts`` for GATE (`#855 `_) * use ``find_flexlm_license`` function in TotalView easyblock (`#839 `_) * enhance ``MakeCp`` easyblock to also support renaming of files while copying them (`#859 `_) * hunt for usable '``python``' command in ``PythonPackage`` easyblock when system Python is used (`#861 `_) * add sanity check in ``easybuild/__init__.py`` w.r.t. current working dir (`#869 `_) * change suffix of original file to ``.easybuild`` when using ``fileinput`` in impi easyblock (`#870 `_) * various bug fixes, including: * make sure Python unicode settings match that of the system Python (`#817 `_) * remove FFTW related statements in HPL easyblock, since HPL doesn't require FFTW at all (`#822 `_) * use ``pkg_resources.declare_namespace`` rather than ``pkgutil.extend_path`` to declare '``easybuild``' namespaces (`#827 `_) * fix license headers: Hercules foundation is now FWO (`#836 `_) * fix check for non-empty lib dirs in ``PythonPackage`` easyblock (`#840 `_) * consider all Python lib dirs in sanity check for libxml2 (`#842 `_) * correctly handle deprecated configure options (``--with-hwloc``/``--enable-mpe``) in MVAPICH2 easyblock (`#853 `_) * use correct configure option for checkpoint/restart in MVAPICH2 easyblock (`#854 `_) * ensure list of Python lib dirs always has a '``lib/...``' entry (`#858 `_) * check whether ``rpm``/``rpmrebuild`` commands are available using '``which``', rather than checking for OS deps (`#864 `_) * fix ``test_step`` in UFC easyblock (`#872 `_) **easyconfigs** * added example easyconfig files for 63 new software packages: * ATSAS (`#616 `_, `#2587 `_), astropy (`#2724 `_, `#2727 `_), attr (`#2706 `_), BamUtil (`#2654 `_), BBMap (`#2322 `_), BH (`#2508 `_), CheMPS2 (`#2445 `_), CosmoloPy (`#2723 `_, `#2727 `_), csvkit (`#2639 `_), Firefox (`#2648 `_), FreeXL (`#2422 `_), GL2PS (`#2667 `_), Glade (`#2631 `_), htop (`#2538 `_), IGV (`#2019 `_), IGVTools (`#2019 `_), ImageMagick (`#2438 `_), jModelTest (`#2529 `_), KEALib (`#2420 `_), libcerf (`#2656 `_), libgcrypt (`#2201 `_), libglade (`#2631 `_), libgpg-error (`#2201 `_), libspatialite (`#2431 `_), LittleCMS (`#2438 `_), MAST (`#2542 `_), MLC (`#2577 `_), MPJ-Express (`#2529 `_), mutil (`#2201 `_), neon (`#758 `_), NextClip (`#2544 `_), npstat (`#2686 `_, `#2703 `_), Octopus (`#2643 `_), QuickFF (`#2721 `_), p4vasp (`#2328 `_), PCMSolver (`#2445 `_), PFFT (`#2643 `_), PHYLIP (`#2694 `_), pkgconfig (`#2475 `_, `#2476 `_), Platypus (`#2618 `_), pplacer (`#1056 `_), PRINSEQ (`#2437 `_, `#2444 `_, `#2585 `_), PyFFmpeg (`#2501 `_, `#2519 `_), PyGObject (`#2443 `_), PyGTK (`#2443 `_), PyOpenGL (`#2628 `_), pyringe (`#2533 `_), qrupdate (`#2675 `_), rgeos (`#2635 `_), rpmrebuild (`#2402 `_), shift (`#2201 `_), SNAPE-pooled (`#2688 `_), SNPhylo (`#2701 `_), sratoolkit (`#2715 `_), STAR-Fusion (`#2463 `_), statsmodels (`#2719 `_), StringTie (`#2527 `_), synchronicity (`#2508 `_), testpath (`#2461 `_), USEARCH (`#2537 `_), VarScan (`#2464 `_), vsc-install (`#2165 `_), Whoosh (`#2725 `_), xprop (`#2645 `_) * added new easyconfigs for existing toolchains: * ``intel/2016.02-GCC-4.9`` (`#2620 `_), ``gmpolf/2016a`` & ``gmvolf/2016a`` (`#2589 `_) * stable Cray-specific easyconfigs * delete deprecated Cray toolchains and easyconfig files (`#2400 `_) * don't hardcode ``PrgEnv`` version, remove ``craype`` and ``fftw`` components in Cray toolchains (`#2554 `_) * remove ``-XC`` versionsuffix for stable definitions for ``Cray*`` toolchains (`#2714 `_) * support for various software packages with ``CrayGNU`` and ``CrayIntel`` toolchains: CP2K, GROMACS, WRF * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including BWA 0.7.13, CMake 3.4.3, GATE 7.2, GROMACS 5.1.2, Mesa 11.1.2, netCDF 4.4.0, Perl 5.22.1, Python 3.5.1, R 3.2.3, R-bundle-Bioconductor 3.2, scipy 0.17.0, SuiteSparse 4.5.1 * various other enhancements, including: * copy ``contrib`` dir in Velvet easyconfigs so scripts are also available (`#2456 `_) * redefine matplotlib 1.5.1 easyconfig as a bundle, also include ``cycler`` extension (dep for matplotlib) (`#2470 `_) * add bitstring extension to Python 2.7.11 easyconfigs (`#2471 `_) * enable building of MetaVelvet in Velvet 1.2.10 easyconfigs (`#2473 `_) * add custom sanity check for libjpeg-turbo (`#2480 `_) * add Velvet easyconfigs that include BioPerl dependency, so VelvetOptimizer can use it (`#2495 `_, `#2729 `_, `#2733 `_) * add source URL in RAxML 7.2.6 easyconfigs (`#2536 `_) * update MPICH easyconfigs to use new MPICH easyblock (`#2589 `_) * free libX11 & co from unneeded Python dependency/versionsuffix (`#2549 `_, `#2563 `_, `#2605 `_, `#2664 `_) * add '``--enable-utf --enable-unicode-properties``' configure options in PCRE easyconfigs (`#2561 `_) * required for latest R versions * add HCsnip, metagenomeSeq in Bioconductor 3.1 bundles (`#2553 `_, `#2578 `_) * add additional extensions in R 3.2.x easyconfigs that are required for extra Bioconductor extensions (`#2547 `_, `#2556 `_) * update psmpi easyconfig files to use the new psmpi easyblock (`#2619 `_) * add easyconfig for Python 2.7.11 on top of X11-enabled Tk (`#2614 `_, `#2621 `_) * add virtualenv as extension in Python 2.7.11 easyconfigs (`#2660 `_) * various bug fixes, including: * fix software name for GTK+ (was 'gtk+'), PyCairo (was 'pycairo') and Gdk-Pixbuf (was 'gdk-pixbuf') (`#2468 `_) * don't hardcode ``CC``/``CXX`` in OpenMPI easyconfigs (`#2472 `_) * remove Google Code source URL for mpi4py (`#2474 `_) * rename ffmpeg to FFmpeg (`#2425 `_, `#2481 `_) * use available easyblock for flex (`#2486 `_) * fix determining list of easyconfigs in unit test suite, don't assume locations are correct (`#2530 `_) * fix specifying DB dependency in DB_File easyconfigs (`#2539 `_) * remove hard-coded ``-xSSE4.2`` for numpy/scipy with Intel compilers (`#2546 `_) * fix license headers: Hercules foundation is now FWO (`#2550 `_) * add ``--with-zlib`` configure argument in libxml easyconfigs (`#2555 `_) * don't hardcode ``optarch=True`` in xextproto/xtrans easyconfigs (`#2601 `_) * change toolchain version to '' in easyconfigs that use ``dummy`` toolchain and include dependencies (`#2612 `_) * GLib doesn't require libxml2 with Python bindings (`#2632 `_) * add patch file to imkl 10.2.6.038 32-bit easyconfig to fix installer not being able to deal with '``--``' in build path (`#2634 `_) * add missing 'pkgconfig' dependency for h5py (`#2476 `_, `#2650 `_) * correct software name in FastQC easyconfigs (was 'fastqc'), use '``dummy``' toolchain for all FastQC version (`#2657 `_, `#2666 `_) * add missing libxml2 dependencies in GLib easyconfigs (`#2658 `_) * fix Xerces-C++ download location (`#2668 `_) * enable ``XML::Bare`` extension in all Perl easyconfigs (`#2672 `_) * update dead link for SuiteSparse (`#2679 `_) * remove custom ``exts_filter`` in easyconfigs used ``PythonPackage`` easyblock (`#2683 `_, `#2685 `_) * add M4 as build dep for binutils & flex (`#2681 `_) * add missing dependencies in Python 3.5.x easyconfigs: SQLite, Tk, GMP (`#2704 `_) * fix (OS) deps, add checksums, remove parameter definition with default values in MVAPICH2 easyconfigs (`#2707 `_) * style cleanup in various easyconfigs (`#2378 `_, `#2387 `_, `#2395 `_, `#2396 `_, `#2488 `_-`#2493 `_, `#2496 `_-`#2500 `_, `#2502 `_-`#2504 `_, `#2602 `_) * working towards automated style review of pull requests .. _release_notes_eb260: EasyBuild v2.6.0 (January 26th 2016) ------------------------------------ feature + bugfix release **framework** * add (experimental) support for opening/updating (easyconfigs) pull requests (``--new-pr``, ``--update-pr``) (`#1528 `_) * sanitize environment before each installation by undefining ``$PYTHON*`` (`#1569 `_, `#1572 `_) * various other enhancements, including: * allow user-local modules with hierarchical naming schemes (``--subdir-user-modules``) (`#1472 `_) * enhance ``--extended-dry-run`` output to include paths for requirements in ``make_module_req`` (`#1520 `_) * rewrite read_file to use '``with``' (`#1534 `_) * add support for ``eb --last-log`` (`#1541 `_) * support using fixed install dir scheme (``--fixed-installdir-naming-scheme``) (`#1546 `_) * add edge attributes for build dependencies in ``--dep-graph`` output (`#1548 `_) * check whether dependencies marked as external module are hidden (`#1552 `_) * implement support for ``--modules-header`` (`#1558 `_) * add support to specify '``else``' body for conditional statements in modules (`#1559 `_) * add extra test for ``--include-easyblocks`` for generic easyblocks (`#1562 `_) * allow user to define the default compiler optimization level (``--default-opt-level``) (`#1565 `_) * make ``toolchain.get_variable`` more robust w.r.t. dummy toolchain (`#1566 `_) * various bug fixes, including: * fix missing '``yaml``' module check in tests (`#1525 `_) * fix 'develop' install script (`#1529 `_) * correctly quote FPM option values in packagin support (`#1530 `_) * correctly handle '``.``' in software name w.r.t. ``$EB*`` environment variables (`#1538 `_) * exclude logs and test reports from packages (`#1544 `_) * also pass down ``--job-cores`` for ``pbs_python`` job backend (`#1547 `_) * skip dependencies marked as external modules when packaging (`#1550 `_) * fix syntax for ``set_alias`` statement in Lua syntax (`#1554 `_) * handle the case of all 'offline' nodes correctly for ``--job`` (`#1560 `_) * fix ``test_modules_tool_stateless`` unit test for stateless ModulesTool with Lmod as modules tool (`#1570 `_) **easyblocks** * add generic easyblock for Cray toolchains (`#766 `_) * new easyblocks for 2 software packages that require customized support: * EggLib (`#811 `_), PGI (`#658 `_) * various other enhancements, including: * update BamTools easyblock for versions 2.3.x and newer: some shared libraries are now static) (`#785 `_) * don't hardcode ``.so``, use ``get_shared_lib_ext`` instead (`#789 `_, `#790 `_, `#791 `_, `#793 `_, `#794 `_, `#803 `_, `#815 `_) * enhance CPLEX easyblock by adding more subdirs to ``$PATH``, define ``$LD_LIBRARY`` and ``$CPLEXDIR`` (`#797 `_) * make sanity check for netcdf4-python work with both egg and non-egg installs (`#799 `_) * update sanity check in PETSc/SLEPc easyblocks for v3.6.x (`#800 `_) * update Trinity easyblock for 2.x versions (`#802 `_) * update DOLFIN easyblock for v1.6.0 (`#804 `_) * check for ``libkokkoscore.a`` rather than ``libkokkos.a`` for Trilinos 12.x (`#805 `_) * add an option to skip the sanitizer tests of Clang (`#806 `_) * update Molpro easyblock to support binary installs and 2015 version (`#807 `_) * make ``ConfigureMake`` more robust w.r.t. custom easyconfig parameters (`#810 `_) * various bug fixes, including: * add back support for Eigen 2.x in Eigen easyblock (`#798 `_) * fix for vsc-base being picked up from OS in EasyBuildMeta easyblock (`#813 `_) * remove ``setuptools.pth`` if it includes absolute paths after installing EasyBuild (`#813 `_) **easyconfigs** * add easyconfigs for ``foss/2016a`` and ``intel/2016`` common toolchains (`#2310 `_, `#2311 `_, `#2339 `_, `#2363 `_) * incl. easyconfigs for Boost, CMake, Python, Perl using these toolchains * added example easyconfig files for 21 new software packages: * BLASR (`#922 `_), BioKanga (`#2247 `_), BoltzTraP (`#2365 `_), basemap (`#2221 `_), CppUnit (`#2271 `_), EggLib (`#2335 `_), FLASH (`#2281 `_), GLM (`#2288 `_), hub (`#2249 `_), MACS2 (`#1983 `_), MotEvo (`#843 `_), numba (`#2243 `_), PGI (`#1833 `_, `#2367 `_), PLY (`#2305 `_), PaStiX (`#2319 `_, `#2326 `_), patchelf (`#2327 `_), pip (`#2284 `_), RSEM (`#2316 `_), RcppArmadillo (`#2289 `_), SCDE (`#2289 `_), slepc4py (`#2318 `_) * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including BamTools 2.4.0, Boost 1.60.0, Clang 3.7.1, DOLFIN/FFC/FIAT/Instant/UFL 1.6.0, GATE 7.0, GCC 5.3.0, LLVM 3.7.1, pandas 0.17.1, PETSc 3.6.3, SAMtools 1.3, scipy 0.16.1, SLEPc 3.6.2, Trilinos 12.4.2, Trinity 2.1.1, VTK 6.3.0 * various other enhancements, including: * added new ``Cray*`` toolchain versions with pinned dependency versions (`#2222 `_) * don't hardcode ``.so``, use ``SHLIB_EXT`` constant instead (`#2245 `_) * add custom sanity check in GEOS easyconfigs (`#2285 `_) * various bug fixes, including: * add Autotools (M4) as a build dependency in GMP v6.x easyconfigs (`#2096 `_) * remove argparse from list of extensions in Python 3.2+ easyconfigs, since it became part of stdlib (`#2323 `_) * various style fixes, including: * get rid of tabs (`#2302 `_) * remove trailing whitespace (`#2341 `_) .. _release_notes_eb250: EasyBuild v2.5.0 (December 17th 2015) ------------------------------------- feature + bugfix release **framework** * add support for IBM XL compilers on Power7 and PowerPC (BlueGene) (`#1470 `_) * add support for generic compilation using ``--optarch=GENERIC`` (`#1471 `_) * see also :ref:`controlling_compiler_optimization_flags` * update experimental support for ``.yeb`` easyconfigs (`#1515 `_) * support clean way to specify toolchain + dependencies in ``.yeb`` easyconfigs * various other enhancements, including: * add support for '``whatis``' easyconfig parameter (`#1271 `_) * add support for SLES 12 and kernel 3.12.x (`#1412 `_) * add GCCcore toolchain definition (`#1451 `_) * use '``diff --git``' lines to determine patched files in pull request with ``--from-pr`` (`#1460 `_) * add proper option parser to bootstrap script (`#1468 `_) * add ``get_gcc_version()`` function in systemtools module (`#1496 `_) * don't load fake module in sanity_check_step during a dry run (`#1499 `_) * allow string values to be passed in ``make_module_req`` by hoisting them into a list (`#1502 `_) * add support for listing build dependencies as hidden dependencies (`#1503 `_) * also consider ``lib32/pkgconfig`` and ``lib64/pkgconfig`` for ``$PKG_CONFIG_PATH`` (`#1505 `_) * add support to ``make_module_dep`` to specify module to unload before loading a dependency module (`#1506 `_) * add support to ``make_module_extra`` to specify alternative root/version for ``$EBROOT``/``$EBVERSION`` (`#1508 `_) * packaging support is no longer considered experimental (`#1510 `_) * various bug fixes, including: * also consider ``lib64`` in sanity check performed during EasyBuild bootstrap (`#1464 `_) * also add description/homepage to packages created with FPM (`#1469 `_) * fix develop setup script to install EasyBuild-develop module in subdirectory (`#1480 `_) * don't create a whole set of temporary '``minimal-easyconfigs``' subdirs with ``--minimal-toolchains`` (`#1484 `_) * only keep polling if exit code is ``None`` in ``run_cmd_qa``, to correctly deal with negative exit codes (`#1486 `_) * fix bootstrap script for missing sys_platform by using newer distribute 0.6.49 in stage 0 (`#1490 `_) * make sure that extra custom easyconfig parameters are known for extensions (`#1498 `_) * add missing import for ``EasyBuildError`` in ``easybuild/toolchains/linalg/libsci.py`` (`#1512 `_) * isolate tests from possible system-wide configuration files (`#1513 `_) * only use ``glob`` in ``make_module_req`` on non-empty strings (`#1519 `_) * this fixes the problem where ``$CUDA_HOME`` and ``$CUDA_PATH`` are not defined in module files for CUDA **easyblocks** * update easyblocks for Intel tools to support 2016 versions (`#691 `_, `#745 `_, `#756 `_, `#777 `_) * IntelBase easyblock has been enhanced to support specifying which components to install * new easyblocks for 3 software packages that require customized support: * Intel Advisor (`#767 `_), DIRAC (`#778 `_), MRtrix (`#772 `_) * various other enhancements, including: * update numpy and SuiteSparse easyblock to use scikit-umfpack (`#718 `_) * add an option to allow removal of the ``-Dusethreads`` flag in Perl easyblock (`#724 `_) * update Doxygen easyblock for 1.10.x (CMake) (`#734 `_) * update sanity check in Qt easyblock for Qt 5.x (`#740 `_) * add support for multilib build of GCC on PowerPC (`#741 `_) * add support to OpenFOAM and SCOTCH easyblocks to support 64-bit integers, via 'i8' toolchain option (`#744 `_) * fix sanity check to support numpy 1.10 (dropped _dotblas.so) (`#757 `_, `#761 `_, `#762 `_) * update IPP easyblock for v9.x (`#759 `_) * cleaner output for PythonPackage under dry run, make numpy easyblock dry-run aware (`#760 `_, `#671 `_) * add support for using netCDF-Fortran as dependency in ALADIN easyblock (`#764 `_) * add support for tbb 4.4.x in tbb easyblock (`#769 `_) * add support for specifying altroot/altversion in Bundle easyblock (`#773 `_) * update OpenFOAM easyblock for OpenFOAM-Extend 3.2 + use apply_regex_substitutions (`#770 `_) * various bug fixes, including: * fix module path extension of system compiler in HMNS setup (`#742 `_) * only restore ``$PYTHONPATH`` if it was defined in EasyBuildMeta easyblock (`#743 `_) * make sure ``$PYTHONPATH`` is defined correctly in module file for Python packages created with ``--module-only`` (`#748 `_) * fix WRF easyblock to produce correct module under ``--module-only --force`` (`#746 `_, `#752 `_) * don't hardcode '``openPBS``' in GATE easyblock, use value for ``default_platform`` easyconfig parameter (`#753 `_) * avoid adding lib subdirs to ``$*LIBRARY_PATH`` if no libraries are there in ``PythonPackage`` easyblock (`#755 `_) * fix installing Python bindings for libxml2 to correct installation prefix (`#765 `_) **easyconfigs** * add GCCcore easyconfig that can be used as base for all compilers (without getting in the way) (`#2214 `_) * along with easyconfig for ``GCC/4.9.3-2.25``: bundle of GCCcore 4.9.3 and binutils 2.25 * intended to replace the GNU toolchain * added example easyconfig files for 39 new software packages: * DIRAC (`#2212 `_), GeoIP (`#2172 `_, `#2185 `_), GeoIP-C (`#2172 `_, `#2185 `_), graph-tool (`#1591 `_), gtkglext (`#2217 `_), Intel Advisor (`#2210 `_), InterProScan (`#2225 `_, `#2227 `_, `#2234 `_), intltool (`#2136 `_), kallisto (`#2173 `_), LibUUID (`#1930 `_), LuaJIT (`#2153 `_), libXcursor (`#2136 `_), libXrandr (`#2136 `_), libXtst (`#2143 `_), libdap (`#1930 `_), libtasn1 (`#2208 `_), libxkbcommon (`#2136 `_), MRtrix (`#2217 `_, `#2218 `_), MultiNest (`#2166 `_, `#2168 `_), Nipype (`#2150 `_), PPfold (`#2183 `_, `#2187 `_), p11-kit (`#2208 `_), pangox-compat (`#2217 `_), Qt5 (`#2136 `_), randrproto (`#2136 `_), rhdf5 (`#2175 `_), Stampy (`#2180 `_, `#2182 `_), scikit-umfpack (`#2061 `_), scp (Python pkg) (`#2196 `_), sleuth (`#2175 `_), traits (`#2150 `_), vincent (`#2169 `_, `#2185 `_), XKeyboardConfig (`#2136 `_), xcb-util (`#2136 `_), xcb-util-image (`#2136 `_), xcb-util-keysyms (`#2136 `_), xcb-util-renderutil (`#2136 `_), xcb-util-wm (`#2136 `_), zlibbioc (`#2175 `_) * added new easyconfigs for existing toolchains: ``intel/2015.08`` (`#2194 `_), ``intel/2016.00`` (`#2209 `_), ``intel/2016.01`` (`#2219 `_), ``iomkl/2015.03`` (`#2155 `_) * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including CMake 3.4.1, HDF5 1.8.16, netCDF 4.3.3.1, netCDF-Fortran 4.4.2, numpy 1.10.1, Octave 4.0.0, OpenFOAM 3.0.0, OpenFOAM-Extend 3.2, Python 2.7.11 * various other enhancements, including: * add tidyr to R 3.2.1 easyconfigs (`#2174 `_) * enable C++ support in MIGRATE-N (`#2178 `_) * also installed shared libraries for AMD and UMFPACK in SuiteSparse (`#2061 `_) * fix software name for ParaView (was: Paraview) (`#2132 `_) * enable building of shared libraries for binutils (`#2133 `_) * harden binutils built with dummy toolchain by linking to system libraries via ``RPATH`` (`#2228 `_) * enhance easyconfig unit tests to check that each easyconfig file is in the right subdirectory (`#2232 `_) * various bug fixes, including: * fix ALADIN patch file to not use relative paths, and adjust list of ALADIN sources accordingly ((`#2207 `_), (`#2213 `_)) * rename patch files for OpenFOAM to be in line with other patches (`#2226 `_) * fix typo in bzip2 source URLs (`#2204 `_) * force linking of ncurses in libreadline (`#2206 `_) * enable ``-fPIC`` in all zlib 1.2.8 easyconfigs (`#2220 `_) * move Net-LibIDN/SRA-Toolkit/bbftpPRO/o2scl easyconfigs to right location (`#2232 `_) * restrict parallel build in OpenFOAM-Extend easyconfigs via '``maxparallel``', not '``parallel``' (`#2233 `_) .. _release_notes_eb240: EasyBuild v2.4.0 (November 10th 2015) ------------------------------------- feature + bugfix release **framework** * add support for ``--extended-dry-run``/``-x`` (`#1388 `_, `#1450 `_, `#1453 `_, `#1455 `_) * detailed documentation is available at :ref:`extended_dry_run` * fix checking of sanity check paths w.r.t. discriminating between files and directories (`#1436 `_) * this impacts several easyconfig files where ``sanity_check_paths`` was not 100% correct * make '``eb``' script aware of Python v3.x, fall back to using ``python2`` if required (`#1411 `_) * add experimental support for parsing .yeb easyconfig files in YAML syntax (`#1447 `_, `#1448 `_, `#1449 `_) * see also :ref:`easyconfig_yeb_format` * add experimental support for resolving dependencies with minimal toolchains (`#1306 `_) * see also :ref:`minimal_toolchains` * various other enhancements, including: * refactor ``extract_cmd`` function to get rid of if/elif/else spaghetti blob (`#1382 `_) * add support for ``--review-pr`` (`#1383 `_) * add ``apply_regex_substitutions`` function to perform runtime patching from easyblocks (`#1388 `_, `#1458 `_) * add support for specifying alternate name to be part of generated module name (`#1389 `_) * via '``modaltsoftname``' easyconfig parameter * support overriding # used cores via ``--parallel`` (`#1393 `_) * also define ``$FC`` and ``$FCFLAGS`` in build environment (`#1394 `_) * add support extracting for ``.tar.Z`` files (`#1396 `_) * include easybuild/scripts in installation (`#1397 `_) * ignore hidden directories in find_base_dir (`#1413 `_, `#1415 `_) * add ``only_if_module_is_available`` decorator function to guard functionality that uses optional dependencies (`#1416 `_) * give easyblocks the possibility to choose ``maxhits`` for ``run_cmd_qa`` (`#1417 `_) * use class name (string) rather than License instances as values for software license constants (`#1418 `_) * support controlling recursive unloading of dependencies via '``recursive_module_unload``' easyconfig parameter (`#1425 `_) * implement basic support for type checking of easyconfig parameters (`#1427 `_) * support auto-converting to expected value type for easyconfig parameters (enabled by default) (`#1428 `_, `#1437 `_) * add support for ``--rebuild`` command line option, alternative for ``--force`` which doesn't imply ``--ignore-osdeps`` (`#1435 `_) * add support for Mercurial easyconfig repository (`#979 `_, `#1446 `_) * add dedicated class for psmpi toolchain MPI component, and use it in gpsmpi and ipsmpi toolchains (`#1454 `_) * various bug fixes, including: * fix extracting of comments from an easyconfig file that includes 'tail' comments (`#1381 `_) * fix dev version to follow PEP-440, as required by recent setuptools versions (`#1403 `_) * required to avoid that setuptools transforms the version itself * see also https://www.python.org/dev/peps/pep-0440/#developmental-releases * allow ``get_cpu_speed`` to return ``None`` if CPU freq could not be determined (`#1421 `_) * relax ``sanity_check_paths`` in EasyBuild bootstrap script to deal with possible zipped .egg (`#1422 `_) * use empty list as default value for src/patches in Extension class (`#1434 `_) * skip symlinked files in ``adjust_permissions`` function (`#1439 `_) * fix HierarchicalMNS to always use full version number (`#1440 `_) **easyblocks** * 3 new generic easyblocks: OCamlPackage (`#467 `_), SCons (`#689 `_, `#700 `_), Waf (`#722 `_) * new easyblocks for 2 software packages that require customized support: * OCaml (`#467 `_), Samcef (`#678 `_) * various other enhancements, including: * add support for installing OpenFOAM with external METIS, CGAL and Paraview (`#497 `_) * update netCDF easyblock updated for netCDF v4.3.3.1 (`#674 `_) * update Rosetta easyblock for recent Rosetta versions (`#677 `_) * make unpacked source dir detection in easyblock for VSC-tools a little bit more flexible (`#679 `_) * add support for building with Plumed support enabled in CP2K easyblock (`#681 `_) * update Go easyblock for Go v1.5 (`#683 `_) * use ``apply_regex_substitutions`` function in WRF easyblock (`#685 `_) * update MUMPS easyblock for 5.x (`#686 `_) * implement runtime patching of ``$WM_*`` and compiler variables for OpenFOAM (`#688 `_) * specify sequential compiler to use in compiler command that gets injected in OpenFOAM easyblock (`#692 `_) * make ``PythonPackage`` and WRF easyblocks dry-run aware (`#696 `_) * see also :ref:`extended_dry_run_guidelines_easyblocks` * add support in ``PythonPackage`` for installing with ``easy_install`` + installing zipped eggs (`#698 `_, `#711 `_, `#715 `_) * update Bowtie easyblock for recent Bowtie versions (`#707 `_) * update CUDA easyblock for CUDA 7.x(`#708 `_) * also consider ``config/make.sys.in`` for want in QuantumESRESSO easyblock (`#714 `_) * define ``$NWCHEM_LONG_PATH`` if needed in NWChem easyblock (`#720 `_) * remove custom post-install step in PDT easyblock (`#723 `_) * no longer needed now that ``adjust_permissions`` functions ignores symlinks * use ``$LIBS`` in HPL easyblock (`#727 `_, `#736 `_) * various bug fixes, including: * also define ``$MCRROOT`` for MCR in module (`#687 `_) * add missing '``super``' call in ``configure_step`` of easyblock for python-meep (`#694 `_) * only prepend existing non-empty paths to ``$PYTHONPATH`` in ``PythonPackage`` easyblock (`#697 `_) * fix extra_options definition in ``CMakePythonPackage`` easyblock (`#698 `_) * fix dev version to follow PEP-440, as required by recent setuptools versions (`#702 `_, `#703 `_, `#704 `_) * required to avoid that setuptools transforms the version itself * see also https://www.python.org/dev/peps/pep-0440/#developmental-releases * consider both ``lib`` and ``lib64`` in sanity check paths for flex (`#705 `_) * also copy signature file and don't copy CMake files in Eigen easyblock (`#709 `_) * fix directory names in ``make_module_req_guess`` of ANSYS easyblock (`#713 `_) * fix imports for ``set_tmpdir`` in easyblock unit tests after function was moved in EasyBuild framework (`#726 `_) * use ``--with-tcltk*`` configure options for Python to point to ensure Tcl/Tk deps are picked up (`#729 `_) * fix order of subdirs for QuantumESPRESSO binaries (`#730 `_) * correctly handle having both ``$FC``/``$FCFLAGS`` and ``$F90``/``$F90FLAGS`` defined when building MVAPICH2 (`#732 `_) * fix OpenSSL sanity check paths: lib/engines is a directory (`#731 `_, `#733 `_) * fix sanity check paths for netcdf-python (`#735 `_) **easyconfigs** * added example easyconfig files for 45 new software packages: * animation (`#2007 `_), ANSYS CFD (`#1969 `_), ANTLR (`#1191 `_, `#1980 `_), APR (`#1970 `_), APR-util (`#1970 `_), Aspera Connect (`#2005 `_), ChIP-Seq (`#2119 `_), deap (`#2082 `_), DISCOVARdenovo (`#1932 `_), FastQC (`#1984 `_), fontsproto (`#1618 `_, `#2038 `_), GraphicsMagick (`#2007 `_), HBase (`#1990 `_), ISIS (`#1972 `_), libedit (`#293 `_), libfontenc (`#1618 `_, `#2038 `_), libGLU (`#1627 `_), libXdamage (`#1618 `_, `#2038 `_), libXfont (`#1618 `_, `#2038 `_), LLVM (`#1620 `_, `#1989 `_, `#2031 `_), MIGRATE-N (`#1944 `_), MIRA (`#1938 `_), mympingpong (`#2049 `_), MySQLdb (`#2011 `_), NCO (`#1191 `_, `#1980 `_), NIPY (`#2064 `_), Nilearn (`#2064 `_), NiBabel (`#2064 `_), PBZIP2 (`#1038 `_), PIL (`#2062 `_), PhyloCSF (`#2018 `_), pycairo (`#2085 `_), pydicom (`#2063 `_), Salmon (`#2051 `_), Samcef (`#1941 `_), scikit-image (`#1974 `_, `#2006 `_), Serf (`#1970 `_), SSAHA2 (`#1039 `_), Subversion (`#1970 `_), SWASH (`#2059 `_), time (`#1954 `_), Trim_Galore (`#1984 `_), Trimmomatic (`#1987 `_), WEKA (`#1986 `_), x264 (`#2017 `_) * added new easyconfigs for existing toolchains: ``gimkl/2.11.5`` (`#2093 `_) * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including Clang + LLVM 3.7.0, CMake 3.3.2, CUDA 7.5.18, hanythingondemand v3.0.1, Mesa 11.0.2, mpi4py v2.0.0, ncurses 6.0, OpenFOAM 2.4.0, Paraview 4.4.0, Python 3.5.0, QuantumESPRESSO v5.2.1 * various other enhancements, including: * enable '``pic``' toolchain option in libxml2 easyconfigs (`#1993 `_) * extend list of R libraries included in R v3.2.1 easyconfigs (`#2042 `_, `#2046 `_, `#2067 `_, `#2072 `_) * add Rsubread in Bioconductor easyconfigs (`#1971 `_) * various bug fixes, including: * fix software name for ``BEEF`` (was '``libbeef``') (`#1679 `_) * add patch to install ``qhull.pc`` (pkgconfig) file with Qhull (`#1975 `_) * don't enable experimental nouveau API in libdrm easyconfigs (`#1994 `_) * fix dev version to follow PEP-440, as required by recent setuptools versions (`#1997 `_) * required to avoid that setuptools transforms the version itself * see also https://www.python.org/dev/peps/pep-0440/#developmental-releases * correct homepage in Cufflinks easyconfigs (`#2060 `_) * fix imports for ``set_tmpdir`` in easyblock unit tests after function was moved in EasyBuild framework (`#2097 `_) * add patch for Tk 8.6.4 to fix problem with ``tk.tcl`` not being found (`#2102 `_) * don't use ``%(version)s`` template in toolchain version, causes problems with HierarchicalMNS (`#2104 `_) * fix sanity check paths in several easyconfig (`#2109 `_, `#2120 `_, `#2121 `_, `#2125 `_) * required because of bug fix in ``sanity_check_step`` implementation * CVXOPT, h5py, LIBSVM, libunistring, MDP, monty, PhyloCSF, Pyke, pandas, pycosat, pyhull, pymatgen, python-dateutils, Seaborn, Theano, XML-LibXML, XML-Simple .. _release_notes_eb230: EasyBuild v2.3.0 (September 2nd 2015) ------------------------------------- feature + bugfix release **framework** * requires vsc-base v2.2.4 or more recent (`#1343 `_) * required for ``mk_rst_table`` function in ``vsc.utils.docs`` * various other enhancements, including: * add support for generating documentation for (generic) easyblocks in ``.rst`` format (`#1317 `_) * preserve comments in easyconfig file in ``EasyConfig.dump()`` method (`#1327 `_) * add ``--cleanup-tmpdir`` option (`#1365 `_) * enables to preserve the used temporary directory via ``--disable-cleanup-tmpdir`` * enhance ``EasyConfig.dump()`` to reformat dumped easyconfig according to style guidelines (`#1345 `_) * add support for extracting ``.iso`` files using 7z (p7zip) (`#1375 `_) * various bug fixes, including: * correctly deal with special characters in template strings in ``EasyConfig.dump()`` method (`#1323 `_) * rework ``easybuild.tools.module_generator`` module to avoid keeping state w.r.t. fake modules (`#1348 `_) * fix dumping of hidden deps (`#1354 `_) * fix use of ``--job`` with hidden dependencies: include ``--hidden`` in submitted job script when needed (`#1356 `_) * fix ``ActiveMNS.det_full_module_name()`` for external modules (`#1360 `_) * fix ``EasyConfig.all_dependencies`` definition, fix tracking of job dependencies (`#1359 `_, `#1361 `_) * fix ``ModulesTool.exist()`` for hidden Lua module files (`#1364 `_) * only call ``EasyBlock.sanity_check_step`` for non-extensions (`#1366 `_) * this results in significant speedup when installing easyconfigs with lots of extensions, but also results in checking the default sanity check paths if none were defined for extensions installed as a module * fix using module naming schemes that were included via ``--include-module-naming-schemes`` (`#1370 `_) **easyblocks** * new easyblocks for 2 software packages that require customized support: * MCR (`#623 `_), Molpro (`#665 `_) * various other enhancements, including: * enhance BWA easyblock to also install man pages (`#650 `_) * enhance tbb easyblock to consider lib dirs in order and also define ``$CPATH``, ``$LIBRARY_PATH``, ``$TBBROOT`` (#653, #654) * call ``PythonPackage.configure_step`` in ``ConfigureMakePythonPackage.configure_step`` (`#668 `_) * add '``foldx3b6``' as possible binary name in FoldX easyblock (`#671 `_) * enhance/cleanup MATLAB easyblock (`#672 `_) * move preparing of '``intel``' subdir in ``$HOME`` to ``configure_step`` in ``IntelBase`` easyblock (`#673 `_) * various bug fixes, including: * add missing super call in ``post_install_step`` of imkl easyblock (`#648 `_, `#660 `_) * fix regex used to correct ``I_MPI_ROOT`` in impi ``mpivars.sh`` scripts (`#662 `_) * fix regex used to patch ``.mk`` file in configure step of SuiteSparse easyblock (`#666 `_) * correctly specify installation prefix via ``$GEM_HOME`` in ``RubyGem`` easyblock (`#667 `_) * add custom sanity check in scipy easyblock (`#669 `_) * specify to always use the bfd linker for OpenFOAM, to stay away from using ``ld.gold`` (`#670 `_) **easyconfigs** * added example easyconfig files for 19 new software packages: * ATK (`#1780 `_), Atkmm (`#1780 `_), cairomm (`#1780 `_), GLibmm (`#1780 `_), GlobalArrays (`#1868 `_), gdk-pixbuf (`#1780 `_), gtk+ (`#1780 `_), Gtkmm (`#1780 `_), libbeef (`#1827 `_), libsigc++ (`#1780 `_), libsodium (`#1876 `_), MACS (`#1869 `_), MCR (`#1677 `_), Molpro (`#1880 `_), NFFT (`#1921 `_), p7zip (`#1931 `_), Pangomm (`#1780 `_), pygraphviz (`#1861 `_), pycosat (`#1859 `_) * added new easyconfigs for existing toolchains: GNU/4.9.3-2.25 (`#1836 `_), foss/2015b (`#1695 `_), intel/2015b (`#1696 `_) * add easyconfigs using this toolchain for BLAST+ 2.2.31, Boost 1.58.0, CP2K 2.6.1, OpenFOAM 2.3.1, Perl 5.20.2 + 5.22.0 (bare), Python 2.7.10, R 3.2.1 * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including Boost 1.59.0, CP2K 2.6.1, GCC 5.2.0 * various other enhancements, including: * enhance texinfo easyconfig w.r.t. ``texmf``, only use it as a build dependency (`#1840 `_) * enable building of ``ld.gold`` in binutils 2.25 (`#1885 `_) * various bug fixes, including: * fix enabling MPI support for h5py 2.5.0 (`#1825 `_) * fix versions of Bioconductor packages + add a couple extra (`#1828 `_, `#1852 `_, `#1895 `_, `#1917 `_) * put dummy values in place for ``builddir``/``installdir`` templates in easyconfigs unit tests (`#1835 `_) * fix easyconfigs unit tests w.r.t. changes made in framework (`#1853 `_, `#1870 `_, `#1874 `_, `#1875 `_) * add GMP as missing dep in Python 2.7.10 easyconfigs, required for pycrypto extension (`#1858 `_) * specify installation prefix for SIP (`#1888 `_, `#1892 `_) * add custom sanity check paths in various easyconfigs (`#1889 `_, `#1894 `_, `#1897 `_ - `#1909 `_) * required because of fix in EasyBuild framework, causing default sanity check paths to be considered for extensions that are installed as a module * affected easyconfigs include: AnalyzeFMRI, Biggus, bibtexparser, DB_File, DBD-Pg, DBD-SQLite, DBD-mysql, evmix, fmri, FPM, GraphViz, gsl, GSSAPI, MDP, mpi4py, ncdf, ncdf4, netifaces, NetLibIDN, networkx, ordereddict, Parallel-ForkManager, paycheck, PyQuante, Pyke, PyQt, r2py, rjags, runjags, scikit-learn, SOBAcl, vsc-processcontrol, vsc-mympirun-scoop, XML, XML-Dumper, XML-Parser, XML-Twig, YAML-Syck * don't enable '``static``' toolchain option in SuiteSparse 4.4.3 easyconfig (`#1911 `_) * add --exclude unpack options for OpenFOAM 2.3.1 to avoid cyclic symlink causing problems when unpacking (`#1925 `_) .. _release_notes_eb220: EasyBuild v2.2.0 (July 15th 2015) --------------------------------- feature + bugfix release **framework** * add support for using GC3Pie as a backend for ``--job`` (`#1008 `_) * see also :ref:`submitting_jobs` * add support for ``--include-*`` configuration options to include additional easyblocks, toolchains, etc. (`#1301 `_) * see :ref:`including_additional_python_modules` * add (experimental) support for packaging installed software using FPM (`#1224 `_) * see :ref:`packaging_support` * various other enhancements, including: * use https for PyPI URL templates (`#1286 `_) * add GNU toolchain definition (`#1287 `_) * make bootstrap script more robust (`#1289 `_, `#1325 `_): * exclude 'easyblocks' pkg from ``sys.path`` to avoid that ``setup.py`` for easybuild-easyblocks picks up wrong version * undefine ``$EASYBUILD_BOOTSTRAP*`` environment variables, since they do not correspond with known config options * improve error reporting/robustness in ``fix_broken_easyconfigs.py`` script (`#1290 `_) * reset keep toolchain component class 'constants' every time (`#1294 `_) * make ``--strict`` also a build option (`#1295 `_) * fix purging of loaded modules in unit tests' setup method (`#1297 `_) * promote ``MigrateFromEBToHMNS`` to a 'production' MNS (`#1302 `_) * add support for ``--read-only-installdir`` and ``--group-writable-installdir`` configuration options (`#1304 `_) * add support for *not* expanding relative paths in ``prepend_paths`` (`#1310 `_) * enhance ``EasyConfig.dump()`` method to use easyconfig templates where possible (`#1314 `_), `#1319 `_), `#1320 `_), `#1321 `_) * various bug fixes, including: * fix issue with cleaning up (no) logfile if ``--logtostdout``/``-l`` is used (`#1298 `_) * stop making ``ModulesTool`` class a singleton since it causes problems when multilple toolchains are in play (`#1299 `_) * don't modify values of 'paths' list passed as argument to prepend_paths in ``ModuleGenerator`` (`#1300 `_) * fix issue with ``EasyConfig.dump()`` + cleanup (`#1308 `_), `#1311 `_) * re-enable (and fix) accidentally disabled test (`#1316 `_) **easyblocks** * modified easybuild.easyblocks package declaration to support giving preference to custom easyblocks (`#617 `_) * 2 new generic easyblocks: RubyGem (`#565 `_), SystemCompiler (`#633 `_) * new easyblocks for 5 software packages that require customized support: * NEMO (`#564 `_), pbdMPI (`#612 `_), `#620 `_), pbdSLAP (`#620 `_), PDT (`#624 `_), Ruby (`#565 `_) * various other enhancements, including: * update CUDA easyblock for v6.x (`#476 `_) * make METIS easyblock take into account configopts (`#494 `_) * enable building of EOMIP and EOMEA for NWChem versions 6.5 and up (`#508 `_) * make out-of-source build with CMake truly out-of-source (`#615 `_) * add support in Bundle easyblock to run full sanity check (`#627 `_) * also take platform-specific Python lib dirs into account in PythonPackage easyblock (`#628 `_) * fix mpivars scripts in Intel MPI installation for versions where the installation is moved (`#629 `_) * don't restrict ``det_pylibdir`` function to only EasyBuild-provided Python (`#631 `_), `#641 `_) * support snappy and other optional native libs in Hadoop easyblock (`#632 `_), `#638 `_), `#640 `_), `#642 `_) * various bug fixes, including: * fix Xmipp easyblock, use provided ``install.sh`` script (`#630 `_) * update Clang easyblock to disable tests that may fail when unlimited stack size is used (`#622 `_) * fix setting of ``$INTEL_LICENSE_FILE`` for port@server values (`#635 `_) **easyconfigs** * added example easyconfig files for **62** new software packages: * ADF (`#899 `_), AutoDock_Vina (`#808 `_), bibtexparser (`#1726 `_), Biggus (`#1770 `_), Bismark (`#990 `_), blasr (`#1662 `_), BSMAP (`#1171 `_), Check (`#811 `_), Circuitscape (`#1222 `_), CONTRAfold (`#689 `_), cramtools (`#1741 `_), DBD-Pg (`#1066 `_), DendroPy (`#995 `_), EMAN2 (`#1737 `_), ETSF_IO (`#727 `_), eudev (`#1578 `_), fastqc (`#1636 `_), FDS (`#814 `_), `#1617 `_), `#1625 `_), FPM (`#1440 `_), frealign (`#1619 `_), g2log (`#1035 `_), GC3Pie (`#1692 `_), `#1756 `_), `#1768 `_), GenotypeHarmonizer (`#1672 `_), gensim (`#1762 `_), GraphViz (`#1658 `_), hisat (`#1674 `_), IDBA-UD (`#1045 `_), IMa2 (`#828 `_), IMPUTE2 (`#824 `_), JUBE (`#1396 `_), LAMARC (`#760 `_), libXScrnSaver (`#1653 `_), MATIO (`#1004 `_), MuTect (`#1483 `_), ncdf (`#617 `_), NEMO (`#1640 `_), ngspice (`#1116 `_), ordereddict (`#1774 `_), OSU Micro-Benchmarks (`#1777 `_), Parallel-ForkManager (`#847 `_), pBWA (`#1009 `_), PeakSeq (`#1412 `_), Pillow (`#1702 `_), Pindel (`#1126 `_), PLUMED (`#1596 `_), `#1665 `_), PostgreSQL (`#1066 `_), PROJ (`#1006 `_), PyAMG (`#1222 `_), Pyke (`#1776 `_), rpy2 (`#1775 `_), Sailfish (`#1035 `_), SCANMS (`#1386 `_), Seaborn (`#1763 `_), snpEff (`#1680 `_), SOBAcl (`#1658 `_), SPIDER (`#1624 `_), `#1723 `_), STAR (`#1043 `_), `#1676 `_), system GCC (`#1778 `_), tabix (`#1059 `_), tecplot360ex (`#1100 `_), Vampir (`#512 `_), VampirServer (`#512 `_), verifyBamID (`#1675 `_) * added easyconfigs for 4 new software bundles: * R-bundle-Bioconductor (`#1573 `_), `#1795 `_), R-bundle-devtools (`#1621 `_), `#1759 `_), R-bundle-extra (`#1387 `_), `#1759 `_), R-bundle-pbd (`#1659 `_) * added easyconfigs for new GNU toolchain (`#1346 `_), `#1669 `_) * added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including BLAST 2.2.31+, Clang 3.6.1, CUDA 6.x, GCC 4.9.3, GROMACS 5.0.5, HDF5 1.8.15 + 1.8.15-patch1, Python 2.7.10, R 3.2.0 + 3.2.1, WRF 3.6.1 * various other enhancements, including: * update all ncurses easyconfigs to enable ncursesw and use ConfigureMake easyblock (`#1337 `_) * update PDT easyconfigs to use PDT easyblock (`#1687 `_) * add custom ``sanity_check_paths`` in libxml2 easyconfigs (`#1690 `_) * enhance unit tests to also cover EasyConfig.dump() method on all easyconfigs (`#1761 `_) * include snappy as dependency in Hadoop easyconfigs (`#1758 `_), `#1773 `_) * enable SSL support in CMake v3.2.3 easyconfigs (`#1784 `_) * add additional extensions in R easyconfigs (`#1637 `_) * various bug fixes, including: * add patch file required for correct CUDA-aware OpenMPI v1.7.3 build (`#631 `_) * fix issue with OpenMPI dependency in ECore easyconfigs (`#777 `_) * don't run the Bloom tests for Jellyfish, they can randomly fail (`#1016 `_) * fix source URLs in BioPerl easyconfigs (`#1075 `_) * patch out svnversion command in Python 2.5.6 to fix build on recent systems (`#1576 `_) * consistently use https for PyPI URLs in homepage/source_urls (`#1616 `_), `#1722 `_) * include Tcl and Tk as dependencies in R easyconfig (`#1623 `_) * add patch for installing paycheck as Py3 extension (`#1629 `_) * add Perl dependency in git 2.x easyconfigs (`#1631 `_) * fix easyconfig for GMP 6.0.0, don't use 6.0.0a sources (`#1635 `_) * fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs (`#1652 `_) * include Tk as dependency in Python 2.7.9 easyconfigs (`#1654 `_) * include tk-devel is list of OS deps for Python 2.7.9 Cray easyconfigs, make sure '``import Tkinter``' works (`#1655 `_) * drop gpfs versionsuffix and stop using no longer existing ``--enable-gpfs`` configopt for recent HDF5 versions (`#1657 `_) * include missing libxml2 dep in GLib easyconfigs (`#1666 `_) * fix source URLs in Qt easyconfigs (`#1673 `_) * fix source URLs for argparse Python extension (`#1697 `_) * fix source URLs for deap Python extension (`#1699 `_) * fix easyconfigs unit tests after making ModulesTool a non-singleton class (`#1708 `_) * fix names for Xmipp easyconfigs and patches (`#1719 `_) * add patch for Qt 4.8.6 to fix build issue on RHEL6 with intel/2015a (`#1734 `_) * add M4 as build dep for GCC 5.1.0 (`#1735 `_) * fix Bioconductor extension versions in R 3.1.3 easyconfigs (`#1748 `_) * remove custom exts_filter definition from Python 3.4.3 easyconfig (`#1765 `_) * fix source_urls in netCDF easyconfigs (`#1766 `_) * fix source_urls in netCDF-C++ and netCDF-Fortran easyconfigs (`#1767 `_) .. _release_notes_eb211: EasyBuild v2.1.1 (May 18th 2015) -------------------------------- bugfix release **framework** * fix issue with missing load statements when ``--module-only`` is used, don't skip ready/prepare steps (`#1276 `_) * enhance ``--search``: only consider actual filename (not entire path), use regex syntax (`#1281 `_) * various other bug fixes, including: * fix ``generate_software_list.py`` script w.r.t. dependencies marked as external modules (`#1273 `_) * only use ``$LMOD_CMD`` value if ``lmod`` binary can't be found in $PATH (`#1275 `_) * fix location of ``module_only`` build option w.r.t. default value (`#1277 `_) * fix combined use of ``--hide-deps`` and ``hiddendependencies`` (`#1280 `_) * remove log handlers that were added during tests, to ensure effective cleanup of log files (`#1282 `_) * this makes the unit test suite run ~3x faster! * define ``$CRAYPE_LINK_TYPE`` if '``dynamic``' toolchain option is enabled for Cray compiler wrappers (`#1283 `_) **easyblocks** * fix compatibility of easyblocks with ``--module-only`` + dedicated unit test module (`#610 `_) * minor enhancements, including: * update GROMACS easyblock for version 5 (`#513 `_) * various other bug fixes, including: * only check compiler being used if FFTW interfaces are being built in Intel MKL easyblock (`#606 `_) **easyconfigs** * added example easyconfig files for **3** new software packages: * networkx (`#1592 `_), Platanus (`#1597 `_), SaguaroGW (`#1600 `_) * added new easyconfigs for existing toolchains: ``ictce/7.3.5``, ``CrayCCE/5.2.40``, ``CrayGNU/5.2.40``, ``CrayIntel/5.2.40`` * added easyconfigs using ``CrayGNU/5.2.25`` and ``CrayGNU/5.2.40`` toolchains (`#1610 `_, `#1611 `_) * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including Boost 1.58.0, GROMACS 5.0.4, Python 3.4.3 * various bug fixes, including: * enable usempi in GROMACS easyconfig using CrayGNU toolchain (as required by GROMACS easyblock) (`#1590 `_) * use system-provided tcsh when building WRF on Cray systems, to avoid hanging build (`#1595 `_) * only use '``dynamic``' toolchain option, not '``shared``', in easyconfigs using Cray toolchain (`#1609 `_) .. _release_notes_v2.1.0: EasyBuild v2.1.0 (April 30th 2015) ---------------------------------- feature + bugfix release **framework** * requires vsc-base v2.2.0 or more recent * added support for LoggedException (`vsc-base#160 `_, `vsc-base#163 `_, `vsc-base#165 `_, `vsc-base#167 `_) * added support for add_flex action in GeneralOption (`vsc-base#162 `_) * added support to GeneralOption to act on unknown configuration environment variables (`vsc-base#162 `_) * add support for only (re)generating module files: ``--module-only`` (`#1018 `_) * module naming scheme API is enhanced to include det_install_subdir method * see :ref:`module_only` * add support for generating module files in Lua syntax (note: requires Lmod as modules tool) (`#1060 `_, `#1255 `_, `#1256 `_, `#1270 `_) * see ``--module-syntax`` configuration option and :ref:`module_syntax` * deprecate ``log.error`` method in favor of raising ``EasyBuildError`` exception (`#1218 `_) * see :ref:`depr_error_reporting` * add support for using external modules as dependencies, and to provide metadata for external modules (`#1230 `_, `#1265 `_, `#1267 `_) * see :ref:`using_external_modules` * add experimental support for Cray toolchains on top of PrgEnv modules: ``CrayGNU``, ``CrayIntel``, ``CrayCCE`` (`#1234 `_, `#1268 `_) * see https://github.com/easybuilders/easybuild/wiki/EasyBuild-on-Cray * various other enhancements, including: * clear list of checksums when using ``--try-software-version`` (`#1169 `_) * sort the results of searching for files (e.g., ``--search`` output) (`#1214 `_) * enhance test w.r.t. use of templates in cfgfile (`#1217 `_) * define '``%(DEFAULT_REPOSITORYPATH)s``' template for cfgfiles (see ``eb --avail-cfgfile-constants``) (`#1220 `_) * also reset ``$LD_PRELOAD`` when running module commands, in case module defined ``$LD_PRELOAD`` (`#1222 `_) * move location of '``module use``' statements in generated module file (*after* '``module load``' statements) (`#1232 `_) * add support for ``--show-default-configfiles`` (`#1240 `_) * see :ref:`default_configuration_files` * report error on missing configuration files, rather than ignoring them (`#1240 `_) * clean up commit message used in easyconfig git repository (`#1248 `_) * add ``--hide-deps`` configuration option to specify names of software that must be installed as hidden modules (`#1250 `_) * see :ref:`hide_deps` * add support for appending/prepending to ``--robot-paths`` to avoid overwriting default robot search path (`#1252 `_) * see :ref:`robot_search_path_prepend_append` * enable detection of use of unknown ``$EASYBUILD``-prefixed environment variables (`#1253 `_) * see :ref:`configuration_env_vars` * add ``--installpath-modules`` and ``--installpath-software`` configuration options (`#1258 `_) * see :ref:`installpath` * use dedicated subdirectory in temporary directory for each test to ensure better cleanup (`#1260 `_) * get rid of ``$PROFILEREAD`` hack when running commands, not needed anymore (`#1264 `_) * various bug fixes, including: * make bootstrap script robust against having ``vsc-base`` already available in Python search path (`#1212 `_, `#1215 `_) * set default value for unpack_options easyconfig parameter to ``''``, so ``self.cfg.update`` works on it (`#1229 `_) * also copy rotated log files (`#1238 `_) * fix parsing of ``--download-timeout`` value (`#1242 `_) * make ``test_XDG_CONFIG_env_vars`` unit test robust against existing user config file in default location (`#1259 `_) * fix minor robustness issues w.r.t. ``$XDG_CONFIG*`` and ``$PYTHONPATH`` in unit tests (`#1262 `_) * fix issue with handling empty toolchain variables (`#1263 `_) **easyblocks** * replace '``log.error``' with '``raise EasyBuildError``' in all easyblocks (`#588 `_) * one new generic easyblock: ``ConfigureMakePythonPackage`` (`#540 `_) * new easyblocks for 2 software packages that require customized support: * TINKER (`#578 `_), Xmipp (`#581 `_) * various other enhancements, including: * enhance WIEN2k easyblock for recent versions + cleanup (`#486 `_) * define ``$PYTHONNOUSERSITE`` in PythonPackage easyblock so user-installed packages are not picked up (`#577 `_) * add support in CP2K easyblock for building on top of MPICH/MPICH2 (`#579 `_) * enhance Hadoop easyblock to support parallel builds (`#580 `_) * drop ``-noroot`` for recent FLUENT versions, honor ``installopts``, enable ``-debug`` (`#582 `_) * include ``prebuildopts`` in build command for Python packages (`#585 `_) * also install ``rosetta_tools`` subdirectory for Rosetta (`#586 `_) * update SLEPc easyblock for v3.5 + style cleanup (`#593 `_) * minor fix in HPL easyblock w.r.t. checking defined environment variables (`#595 `_) * tweak CP2K easyblock w.r.t. LAPACK/FFTW support (`#596 `_) * minor update to GCC easyblock to support GCC v5.x (`#598 `_) * update sanity check in R easyblock for version 3.2.0 (`#602 `_) * various bug fixes, including: * fix Score-P easyblock for compiler-only toolchains, include Qt as optional dependency (`#552 `_) * fix definition of ``$MKLROOT``, should be set to '``mkl``' subdir of install dir (`#576 `_) * add ``-libmpichf90`` to list of MPI libraries in NWChem easyblock (`#584 `_) * stop using '``$root``' to make easyblocks compatible with module files in Lua syntax (`#590 `_) * also set ``$PYTHONPATH`` before installing Python package in temporary directory in ``test_step`` (`#591 `_) * unset ``buildopts``/``installopts`` before installing Python extensions in Python easyblock (`#597 `_) * allow not including vsc-base sources when installing EasyBuild (gets installed with easybuild-framework) (`#600 `_) * use ``self.initial_environ`` rather than ``self.orig_environ`` in EasyBuildMeta easyblock (`#600 `_) * make GCC easyblock compatible with ``--module-only`` by setting default value for ``self.platform_lib`` in constructor (`#603 `_) **easyconfigs** * added example easyconfig files for **27** new software packages: * AFNI (`#1322 `_, `#1521 `_), BCFtools (`#1492 `_), getdp (`#1518 `_), gmsh (`#1518 `_), gtest (`#1244 `_), hanythingondemand (`#1530 `_), mawk (`#1369 `_), Minimac (`#815 `_), Minimac3 (`#1502 `_), monty (`#1548 `_), Octave (`#1563 `_), pbs_python (`#1530 `_), pigz (`#1036 `_), Pygments (`#1536 `_), pyhull (`#1539 `_), pymatgen (`#1549 `_), PyQt (`#1322 `_, `#1521 `_), Ray (`#1494 `_), requests (`#1536 `_), seqtk (`#1524 `_), SIP (`#1322 `_, `#1521 `_), S-Lang (`#1369 `_), Spark (`#1554 `_), spglib (`#1549 `_), TINKER (`#1465 `_), tmux (`#1369 `_), Xmipp (`#1489 `_) * added easyconfigs for new (Cray-specific) toolchains (`#1538 `_): ``CrayGNU``, ``CrayIntel``, ``CrayCCE`` * initially supported software (using CrayGNU toolchains): CP2K, GROMACS, HPL, Python + numpy/scipy, WRF (`#1558 `_) * see also https://github.com/easybuilders/easybuild/wiki/EasyBuild-on-Cray * added new easyconfigs for existing toolchains: ``goolf/1.5.16``, ``intel/2014.06`` * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3 and v3.2.0, PETSc/SLEPc v3.5.3, WIEN2k v14.1 * various other enhancements, including: * include pbr dependency for lockfile Python extension in Python v2.7.9 easyconfigs + mock/pytz/pandas (`#1462 `_, `#1540 `_) * include SQLite as dependency in Python v2.7.9 easyconfigs (`#1468 `_) * set ``$LD_PRELOAD`` for Hoard and jemalloc (`#1470 `_) * fix homepage in SCOTCH easyconfigs (`#1485 `_) * adding missing six/ecdsa dependencies for dateutil/paramiko Python packages in Python easyconfigs (`#1504 `_, `#1505 `_, `#1506 `_, `#1507 `_, `#1508 `_, `#1509 `_, `#1510 `_) * enable ``pic`` toolchain option in expat easyconfigs (`#1562 `_) * extend list of source URLs for Bioconductor packages in R easyconfigs to include 'release' source URLs (`#1568 `_) * various bug fixes, including: * adding missing zlib dependency in all Tcl easyconfig files (`#1344 `_) * fix homepage in FLUENT easyconfigs (`#1472 `_) * use ``--with-verbs`` rather than deprecated ``--with-openib`` in OpenMPI configure options (`#1511 `_) * stop relying on ``OS_NAME`` constant to specify OS dependencies in OpenMPI easyconfigs (`#1512 `_) * replace use of '``$root``' with '``%(installdir)s``' to ensure compatibility with module files in Lua syntax (`#1532 `_) * stop relying on '``$MKLROOT``' in ROOT easyconfigs (`#1537 `_) * use proper Bundle easyblock for biodeps/PRACE (`#1566 `_) * make source_urls in Cube and Scalasca easyconfigs compatible with --try-software-version (`#1574 `_) * add patch for Cube to fix configure script w.r.t. Qt dependency, add --without-java-reader configure option (`#1574 `_) .. _release_notes_v2.0.0: EasyBuild v2.0.0 (March 6th 2015) --------------------------------- feature + bugfix release **framework** * requires vsc-base v2.0.3 or more recent * avoid deprecation warnings w.r.t. use of ``message`` attribute (`vsc-base#155 `_) * fix typo in log message rendering ``--ignoreconfigfiles`` unusable (`vsc-base#158 `_) * removed functionality that was deprecated for EasyBuild version 2.0 (`#1143 `_) * see :ref:`removed_functionality` * the fix_broken_easyconfigs.py script can be used to update easyconfig files suffering from this (`#1151 `_, `#1206 `_, `#1207 `_) * for more information about this script, see :ref:`fix_broken_easyconfigs_script` * stop including a crippled copy of vsc-base, include vsc-base as a proper dependency instead (`#1160 `_, `#1194 `_) * vsc-base is automatically installed as a dependency for easybuild-framework, if a Python installation tool is used * see :ref:`required_python_packages` * various other enhancements, including: * add support for Linux/POWER systems (`#1044 `_) * major cleanup in ``tools/systemtools.py`` + significantly enhanced tests (`#1044 `_) * add support for '``eb -a rst``', list available easyconfig parameters in ReST format (`#1131 `_) * add support for specifying one or more easyconfigs in combination with ``--from-pr`` (`#1132 `_) * see :ref:`from_pr_specifying_easyconfigs` * define ``__contains__`` in EasyConfig class (`#1155 `_) * restore support for downloading over a proxy (`#1158 `_) * i.e., use ``urllib2`` rather than ``urllib`` * this involved sacrificing the download progress report (which was only visible in the log file) * let ``mpi_family`` return ``None`` if MPI is not supported by a toolchain (`#1164 `_) * include support for specifying system-level configuration files for EasyBuild via ``$XDG_CONFIG_DIRS`` (`#1166 `_) * see :ref:`default_configuration_files` * make unit tests more robust (`#1167 `_, `#1196 `_) * see :ref:`unit_tests` * add hierarchical module naming scheme categorizing modules by ``moduleclass`` (`#1176 `_) * enhance bootstrap script to allow bootstrapping using supplied tarballs (`#1184 `_) * see :ref:`bootstrap_advanced_options` * disable updating of Lmod user cache by default, add configuration option ``--update-modules-tool-cache`` (`#1185 `_) * for now, only the Lmod user cache can be updated using ``--update-modules-tool-cache`` * use available ``which()`` function, rather than running '``which``' via ``run_cmd`` (`#1192 `_) * fix ``install-EasyBuild-develop.sh`` script w.r.t. vsc-base dependency (`#1193 `_) * also consider robot search path when looking for specified easyconfigs (`#1201 `_) * see :ref:`specifying_easyconfigs` * various bug fixes, including: * stop triggering deprecated/no longer support functionality in unit tests (`#1126 `_) * fix ``from_pr`` test by including dummy easyblocks for HPL and ScaLAPACK (`#1133 `_) * escape use of '``%``' in string with command line options with ``--job`` (`#1135 `_) * fix handling specified patch level 0 (+ enhance tests for fetch_patches method) (`#1139 `_) * fix formatting issues in generated easyconfig file obtained via ``--try-X`` (`#1144 `_) * use ``log.error`` in ``tools/toolchain/toolchain.py`` where applicable (`#1145 `_) * stop hardcoding ``/tmp`` in ``mpi_cmd_for`` function (`#1146 `_, `#1200 `_) * correctly determine variable name for ``$EBEXTLIST`` when generating module file (`#1156 `_) * do not ignore exit code of failing postinstall commands (`#1157 `_) * fix rare case in which used easyconfig and copied easyconfig are the same (`#1159 `_) * always filter hidden deps from list of dependencies (`#1161 `_) * fix implementation of ``path_matches`` function in ``tools/filetools.py`` (`#1163 `_) * make sure plain text keyring is used by unit tests (`#1165 `_) * suppress creation of module symlinks for ``HierarchicalMNS`` (`#1173 `_) * sort all lists obtained via ``glob.glob``, since they are in arbitrary order (`#1187 `_) * stop modifying ``$MODULEPATH`` directly in ``setUp``/``tearDown`` of toolchain tests (`#1191 `_) **easyblocks** * one new generic easyblock for installing a bundle of modules: ``Bundle`` (`#550 `_) * and let the ``Toolchain`` generic easyblock derive from ``Bundle`` * new easyblocks for 2 software packages that require customized support: * GAMESS-US (`#470 `_, `#544 `_, `#558 `_), Hadoop (`#563 `_) * various other enhancements, including: * move support for ``staged_install`` from CPLEX easyblock to generic ``Binary`` easyblock (`#502 `_) * fix sanity check in picard easyblock for v1.119 that doesn't include ``sam.jar`` (`#522 `_) * log warning message when unlinking jellyfish symlink fails in Trinity easyblock (`#534 `_) * revamp ``EB_libint2`` easyblock into ``EB_Libint`` that works for both Libint v1x and v2.x (`#536 `_) * update CP2K easyblock for recent versions (no more '``fes``') (`#537 `_) * update SuiteSparse easyblock for recent versions (`#541 `_) * fix easyblock unit tests after dropping support for deprecated behaviour in framework (`#543 `_) * rework PSI easyblock to support future releases (`#545 `_) * enable always generating a 'verbose' Makefile in the generic CMakeMake easyblock (`#546 `_) * remove functionality in (generic) easyblocks that was deprecated for EasyBuild v2.0 (`#547 `_) * enhance generic RPackage easyblock to support installing extensions in a separate prefix (`#551 `_) * deprecate GenomeAnalysisTK easyblock, since it's basically equivalent to Tarball (`#557 `_) * update SAMtools easyblock for v1.2 (`#562 `_) * take ``preconfigopts`` easyconfig parameter into account in ROOT easyblock (`#566 `_) * update easyblock for installing EasyBuild * to support bootstrapping with provided source tarballs (`#559 `_) * to also cover vsc-base dependency, and verify ``easy-install.pth`` (`#567 `_) * update disabling sanitizer tests for Clang 3.6 (`#570 `_) * various bug fixes, including: * fix handling of LTO in GCC easyblock (`#535 `_) * relocate FDTD RPM to fix installation on SL6 (`#538 `_) **easyconfigs** * added example easyconfig files for **29** new software packages: * bsoft (`#1353 `_), Coot (`#1400 `_), Cuby (`#1258 `_), DSRC (`#1242 `_), Exonerate (`#568 `_), fastqz (`#1242 `_), FSA (`#568 `_), fqzcomp (`#1242 `_), GAMESS-US (`#1153 `_, `#1406 `_), Grep (`#1308 `_), Hadoop (`#1418 `_), Hoard (`#1415 `_), IMB (`#1284 `_), ISL (`#1389 `_), jemalloc (`#1416 `_), libdwarf (`#1283 `_), libelf (`#1283 `_), MPC (`#1310 `_), multitail (`#1327 `_), Pmw (`#1403 `_), Quip (`#1242 `_), rCUDA (`#720 `_), SCALCE (`#1242 `_), SMALT (`#568 `_), STREAM (`#1332 `_), worker (`#1307 `_), Xerces-C++ (`#1370 `_), XQilla (`#1370 `_), ZPAQ (`#1242 `_) * added easyconfigs for new (common) toolchains * ``foss/2015a`` (`#1239 `_), ``gompi/1.5.16`` (`#1380 `_), ``gmvolf/1.7.20`` (`#1397 `_), ``goolf/1.7.20`` (`#1294 `_), intel/2015a (`#1238 `_), ``intel/2015.02`` (`#1393 `_), ``iomkl/2015.01`` (`#1325 `_), ``iomkl/2015.02`` (`#1401 `_) * added new software bundle: ``Autotools`` (`#1385 `_) * various other enhancements, including: * don't define ``$LDSHARED`` in zlib easyconfigs (`#1350 `_) * this fixes the long-standing "``no version information available``" issue with zlib * see also `framework#108 `_ * add unit test to check that all ``extra_options`` keys are defined in ``EasyConfig`` instance (`#1378 `_) * add source MD5 checksums in all GCC easyconfigs (`#1391 `_) * speeding up the unit tests by avoiding rereading of same easyconfig file (`#1432 `_) * fix conflict detection in unit tests by considering build deps separately from runtime deps (`#1447 `_) * fix toolchain for Bison build dep in ``MVAPICH2-1.9-iccifort-2011.13.367.eb`` easyconfig (`#1448 `_) * use ``Bundle`` generic easyblock for HPCBIOS bundles and fix ``moduleclass`` (`#1451 `_) * various bug fixes, including: * revert version of Libint dependency to 1.1.4 in CP2K v2.5.1 easyconfig (`#1144 `_) * added Java dependencies to EMBOSS easyconfigs (`#1167 `_) * don't list '``lto``' as a language in GCC easyconfigs (`#1286 `_) * related to the fixes in the GCC easyblock, see `easyblocks#535 `_ * rename libint2 easyconfigs as Libint v2 easyconfigs (`#1287 `_) * fix mpi4py ``source_urls`` in Python easyconfigs (`#1306 `_) * consistently use CLooG 0.18.0 for GCC 4.8 series (`#1392 `_) * rename GenomeAnalysisTk easyconfigs to GATK (`#1399 `_) * include ``openssl-devel`` SLES11 OS dependency in cURL/MySQL/Python easyconfigs (`#1422 `_) * add missing Perl dependency in parallel easyconfigs (`#1430 `_) * correct name in BLAST+ easyconfigs (`#1443 `_) * fix name for sparsehash easyconfigs (`#1452 `_) EasyBuild v1.16.2 (March 6th 2015) ---------------------------------- bugfix release **framework** `(no changes compared to v1.16.1, simple version bump to stay in sync with easybuild-easyblocks)` **easyblocks** * make ``EB_EasyBuildMeta`` easyblock aware of vsc-base to make upgrading to EasyBuild v2.0.0 possible (`#573 `_) **easyconfigs** `(no changes compared to v1.16.1, simple version bump to stay in sync with easybuild-easyblocks)` EasyBuild v1.16.1 (December 19th 2014) -------------------------------------- bugfix release **framework** * fix functionality that is broken with ``--deprecated=2.0`` or with ``$EASYBUILD_DEPRECATED=2.0`` * don't include easyconfig parameters for ``ConfigureMake`` in ``eb -a``, since fallback is deprecated (`#1123 `_) * correctly check software_license value type (`#1124 `_) * fix ``generate_software_list.py`` script w.r.t. deprecated fallback to ``ConfigureMake`` (`#1127 `_) * other bug fixes * fix logging issues in tests, sync with vsc-base v2.0.0 (`#1120 `_) **easyblocks** * fix EasyBuild versions for which ``$EASYBUILD_DEPRECATED=1.0`` is set in EasyBuild sanity check (`#531 `_) **easyconfigs** * set default easyblock to ConfigureMake in TEMPLATE.eb (`#1277 `_) EasyBuild v1.16.0 (December 18th 2014) -------------------------------------- feature + bugfix release **framework** * deprecate automagic fallback to ``ConfigureMake`` easyblock (`#1113 `_) * easyconfigs should specify ``easyblock = 'ConfigureMake'`` instead of relying on the fallback mechanism * **note: automagic fallback to** ``ConfigureMake`` **easyblock will be removed in EasyBuild v2.0** * see also `Automagic fallback to ConfigureMake `_ * stop triggering deprecated functionality, to enable use of ``--deprecated=2.0`` (`#1107 `_, `#1115 `_, `#1119 `_) * see `Deprecated functionality `_ for more information * various other enhancements, including: * add script to clean up gists created via ``--upload-test-report`` (`#958 `_) * also use ``-xHost`` when using Intel compilers on AMD systems (as opposed to ``-msse3``) (`#960 `_) * add Python version check in ``eb`` command (`#1046 `_) * take ``versionprefix`` into account in ``HierarchicalMNS`` module naming scheme (`#1058 `_) * clean up and refactor ``main.py``, move functionality to other modules (`#1059 `_, `#1064 `_, `#1075 `_, `#1087 `_) * add check in ``download_file`` function for HTTP return code + show download progress report (`#1066 `_, `#1090 `_) * include info log message with name and location of used easyblock (`#1069 `_) * add toolchains definitions for ``gpsmpi``, ``gpsolf``, ``impich``, ``intel-para``, ``ipsmpi`` toolchains (`#1072 `_, `#1073 `_) * support for Parastation MPI based toolchains * enforce that ``hiddendependencies`` is a subset of ``dependencies`` (`#1078 `_) * this is done to avoid that site-specific policies w.r.t. hidden modules slip into contributed easyconfigs * enable use of ``--show_hidden`` for ``avail`` subcommand with recent Lmod versions (`#1081 `_) * add ``--robot-paths`` configure option (`#1080 `_, `#1093 `_, `#1095 `_, `#1114 `_) * support use of ``%(DEFAULT_ROBOT_PATHS)s`` template in EasyBuild configuration files (`#1100 `_) * see also `Controlling the robot search path `_ * use ``-xHost`` rather than ``-xHOST``, to match Intel documentation (`#1084 `_) * update and cleanup ``README`` file (`#1085 `_) * deprecate ``self.moduleGenerator`` in favor of ``self.module_generator`` in ``EasyBlock`` (`#1088 `_) * also support ``MPICH`` MPI family in ``mpi_cmd_for`` function (`#1098 `_) * update documentation references to point to http://easybuild.readthedocs.org (`#1102 `_) * check for OS dependencies with *both* ``rpm`` and ``dpkg`` (if available) (`#1111 `_) * various bug fixes, including: * fix picking required software version specified by ``--software-version`` and clean up ``tweak.py`` (`#1062 `_, `#1063 `_) * escape ``$`` characters in module load message specified via ``modloadmsg`` easyconfig parameter) (`#1068 `_) * take available hidden modules into account in dependency resolution (`#1065 `_) * fix hard crash when using patch files with an empty list of sources (`#1070 `_) * fix Intel MKL BLACS library being used for MPICH/MPICH2-based toolchains (`#1072 `_) * fix regular expression in ``fetch_parameter_from_easyconfig_file`` function (`#1096 `_) * don't hardcode queue names when submitting a job (`#1106 `_) * fix affiliation/mail address for Fotis in headers (`#1105 `_) * filter out ``/dev/null`` entries in patch file in ``det_patched_files`` function (`#1108 `_) * fix ``gmpolf`` toolchain definition, to have ``gmpich`` as MPI components (instead of ``gmpich2``) (`#1101 `_) * 'MPICH' refers to MPICH v3.x, while MPICH2 refers to MPICH(2) v2.x (MPICH v1.x is ancient/obsolete) * **note**: this requires to reinstall the ``gmpolf`` module, using the updated easyconfig from `easybuild-easyconfigs#1217 `_ **easyblocks** * new easyblocks for **2** software packages that requires customized support: * Chimera (`#524 `_), GATE (`#518 `_) * fix use of deprecated functionality, enhance unit tests to check for it (`#523 `_) * various other enhancements, including: * update PETSc easyblock for recent versions (v3.5) (`#446 `_) * only include major/minor version numbers for FLUENT subdir (`#480 `_) * factor out 'move after install' code from impi easyblock to ``IntelBase``, use it for itac (`#487 `_) * support custom easyconfig parameters in ``EB_impi`` easyblock to correct behavior of MPI wrapper commands (`#493 `_) * consider both ``lib`` and ``lib64`` in sanity check for GROMACS (`#501 `_) * take ``preinstallopts`` and ``installopts`` into account in ``Binary`` easyblock (`#503 `_) * add sanity check command ``abaqus information=all`` for ABAQUS (`#504 `_) * update and clean up ``README``, refer to http://easybuild.readthedocs.org documentation (`#505 `_, `#516 `_) * rename deprecated ``self.moduleGenerator`` to ``self.module_generator`` (`#506 `_) * see also `easybuild-framework#1088 `_ * check whether specified ``type`` value is a known value (``psmp`` or ``popt``) in CP2K easyblock (`#509 `_) * add support to ``SAMtools`` easyblock for installing recent versions (v1.x) (`#512 `_) * fix version check + sanity check in Geant4 easyblock + style fixes (`#517 `_) * added ``$root/modlib`` to ``$PYTHONPATH`` guesses in Modeller easyblock (`#525 `_) * mark ``license`` custom easyconfig parameter as deprecated in ``IntelBase`` (`#527 `_) * various bug fixes, including: * fix Libxc version check in CP2K easyblock (`#478 `_) * correctly specify ``mkl_libs`` when building *numpy* with GCC and imkl (`#485 `_) * extend noqa for OpenFOAM-Extend in build_step (`#488 `_, `#520 `_) * correctly set ``$LD_LIBRARY_PATH``, ``$LIBRARY_PATH`` and ``$PKG_CONFIG_PATH`` for ``R`` (`#495 `_) * fix default value for ``files_to_copy`` in ``MakeCp`` easyblock (`#500 `_) * treat ``MPICH`` MPI family as MPICH v3.x instead of MPICH v1.x (`#519 `_) * see also `easybuild-framework#1112 `_ * fix affiliation/mail address for Fotis in headers (`#521 `_) * clean up in ``extra_options`` methods, avoid casting return value to ``dict`` or returning via parent (`#528 `_) **easyconfigs** * added example easyconfig files for **39** new software packages: * ANTs (`#1232 `_), BEOPS (`#1264 `_), Chhimera (`#1255 `_), ctffind (`#1249 `_), DBD-SQLite (`#1064 `_), DBD-mysql (`#1063 `_), DIALIGN-TX (`#668 `_), ffmpeg (`#1088 `_), GObject-Introspection (`#1079 `_), GTS (`#1079 `_), Graphviz (`#1079 `_), GraphViz2 (`#1079 `_), grace (`#1131 `_), HarfBuzz (`#1079 `_), HTSlib (`#1161 `_), GSSAPI (`#1048 `_), Kerberos_V5 (`#1048 `_), libevent (`#1063 `_), libXdmcp (`#1129 `_), libXft (`#1017 `_), libXinerama (`#1017 `_), libXrender (`#1017 `_), Maven (`#1094 `_), MySQL (`#1063 `_), Net-LibIDN (`#1060 `_), OpenCV (`#1088 `_), OpenMD (`#1105 `_), Qhull (`#1105 `_), Pango (`#1079 `_), psmpi (`#1245 `_, `#1246 `_), RELION (`#1017 `_), renderproto (`#1017 `_), rjags (`#1125 `_), runjags (`#1125 `_), SPRNG (`#1138 `_, `#1141 `_), xineramaproto (`#1017 `_), XML-Dumper (`#1061 `_), XML-Parser (`#1061 `_), XML-Twig (`#1061 `_) * added easyconfigs for new toolchains * ``intel/2014.10`` & ``intel/2014.11`` (`#1219 `_), ``intel-para/2014.12`` (`#1246 `_), ``gpsolf/2014.12`` (`#1245 `_), ``iompi/6.6.4`` (`#1215 `_) * include ``easyblock = 'ConfigureMake'`` in relevant easyconfigs to deal with deprecation of automagic fallback to ``ConfigureMake`` (`#1248 `_) * see also `easybuild-framework#1113 `_ and `Automagic fallback to ConfigureMake `_ * clean up use of deprecated functionality in existing easyconfigs (`#1252 `_, `#1259 `_) * stop using deprecated ``makeopts``, ``premakeopts`` and ``shared_lib_ext`` * check for use of deprecated functionality in easyconfigs unit tests * see also http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#easyconfig-parameters * various other enhancements, including: * also build ``fftw3_threads`` libraries, and enhance sanity checks (`#1013 `_) * add unit test to verify specified ``sanity_check_paths`` (`#1119 `_) * update and clean up ``README``, refer to http://easybuild.readthedocs.org documentation (`#1184 `_, `#1224 `_) * various bug fixes, including: * fix unit tests w.r.t. changes in framework (`#1146 `_) * remove unnecessary build dependencies for OpenMPI (`#1168 `_) * remove duplicate line in OpenMPI easyconfigs (`#1207 `_) * fix affiliation/mail address for Fotis in headers (`#1237 `_) * fix permissions of easyconfig files for consistency (`#1210 `_) * disable symbol lookup feature in cairo to fix build on SL6 (`#1241 `_) * fix easyconfig ``gmpolf`` toolchain w.r.t. MPICH software name (`#1217 `_) * see also `easybuild-framework#1112 `_ * fix ``source_urls`` for WRF and WPS (`#1225 `_) * fix and clean up GATE easyconfigs (`#1228 `_) * fix broken CLHEP builds by including ``-gcc`` in ``$CXXFLAGS`` (`#1254 `_) * add patch to fix broken test in Go (`#1257 `_) * fix name of GMAP easyconfigs, should be GMAP-GSNAP (`#1268 `_) * fix easyconfig filenames, enhance unit test to check easyconfig filenames (`#1271 `_) EasyBuild v1.15.2 (October 7th 2014) ------------------------------------ bugfix release **framework** * fix ``$MODULEPATH`` extensions for Clang/CUDA, to make ``goolfc``/``cgoolf`` compatible with ``HierarchicalMNS`` (`#1050 `_) * include ``versionsuffix`` in module subdirectory with ``HierarchicalMNS`` (`#1050 `_, `#1055 `_) * fix unit tests which were broken with bash patched for ShellShock bug (`#1051 `_) * add definition of gimpi toolchain, required to make gimkl toolchain compatible with ``HierarchicalMNS`` (`#1052 `_) * don't override ``COMPILER_MODULE_NAME`` obtained from ``ClangGCC`` in Clang-based toolchains (`#1053 `_) * fix wrong code in ``path_to_top_of_module_tree`` function (`#1054 `_) * because of this, load statements for compilers were potentially included in higher-level modules under ``HierarchicalMNS`` **easyblocks** * only disable sanitizer tests for recent Clang versions (`#481 `_, `#482 `_) * pass down installopts to CUDA install command (`#483 `_) **easyconfigs** * disable parallel build for slalib (`#968 `_) * fix compatibility of goolfc with HierarchicalMNS by using GCC toolchain for installing CUDA (`#1106 `_, `#1115 `_) * fix zlib OS dependency spec for Debian in Boost easyconfigs (`#1109 `_) * fix compatibility of gimkl with HierarchicalMNS by using gimpi subtoolchain (`#1110 `_) * make both GCC and Clang first-class members in Clang-based toolchains to fix compatibility with HierarchicalMNS (`#1113 `_) EasyBuild v1.15.1 (September 23rd 2014) --------------------------------------- bugfix release **framework** * take into account that multiple modules may be extending ``$MODULEPATH`` with the same path, when determining path to top of module tree (see `#1047 `_) * this bug caused a load statement for either ``icc`` or ``ifort`` to be included in higher-level modules installed with an Intel-based compiler toolchain, under the ``HierarchicalMNS`` module naming scheme * make ``HierarchicalMNS`` module naming scheme compatible with ``cgoolf`` and ``goolfc`` toolchain (`#1049 `_) * add definition of ``iompi`` (sub)toolchain to make ``iomkl`` toolchain compatible with ``HierarchicalMNS`` (`#1049 `_) **easyblocks** `(no changes compared to v1.15.0, simple version bump to stay in sync with easybuild-framework)` **easyconfigs** * minor bug fixes, including: * use SHLIB_EXT in GMP/MPFR easyconfigs (`#1090 `_) * fix TopHat homepage and source_urls since page moved (`#1092 `_) * make iomkl toolchain compatible with HierarchicalMNS (`#1099 `_) EasyBuild v1.15.0 (September 12th 2014) --------------------------------------- feature + bugfix release **framework** * various other enhancements, including: * fetch extension sources in fetch_step to enhance ``--stop=fetch`` (`#978 `_) * add ``iimpi`` toolchain definition (`#993 `_) * prepend robot path with download location of files when ``--from-pr`` is used (`#995 `_) * add support for excluding module path extensions from generated modules (`#1003 `_) * see ``include_modpath_extensions`` easyconfig parameter * add support for installing hidden modules and using them as dependencies (`#1009 `_, `#1021 `_, `#1023 `_) * see ``--hidden`` and ``hiddendependencies`` easyconfig parameter * stop relying on ``conflict`` statement in module files to determine software name of toolchain components (`#1017 `_, `#1037 `_) * instead, the ``is_short_modname_for`` method defined by the module naming scheme implementation is queried * improve error message generated for a missing easyconfig file (`#1019 `_) * include path where tweaked easyconfigs are placed in robot path (`#1032 `_) * indicate forced builds in ``--dry-run`` output (`#1034 `_) * fix interaction between ``--force`` and ``--try-toolchain --robot`` (`#1035 `_) * add ``--software`` option, disable recursion for ``--try-software(-X)`` (`#1036 `_) * various bug fixes, including: * fix ``HierarchicalMNS`` crashing when MPI library is installed with a dummy toolchain (`#986 `_) * fix list of FFTW wrapper libraries for Intel MKL (`#987 `_) * fix stability of unit tests (`#988 `_, `#1027 `_, `#1033 `_) * make sure ``$SCALAPACK_INC_DIR`` (and ``$SCALAPACK_LIB_DIR``) are defined when using ``imkl`` (`#990 `_) * fix error message on missing FFTW wrapper libs (`#992 `_) * fix duplicate toolchain elements in ``--list-toolchains`` output (`#993 `_) * filter out load statements that extend the ``$MODULEPATH`` to make the module being installed available (`#1016 `_) * fix conflict specification included in module files (`#1017 `_) * avoid ``--from-pr`` crashing hard unless ``--robot`` is used (`#1022 `_) * properly quote GCC version string in archived easyconfig (`#1028 `_) * fix issue with ``--repositorypath`` not honoring ``--prefix`` (`#1031 `_) * sync with latest vsc-base version to fix log order (`#1039 `_) * increase # commits per page for ``--from-pr`` (`#1040 `_) **easyblocks** * added support for **2** new software packages that requires customized support: * Modeller (`#392 `_), NAMD (`#397 `_) * various enhancements, including: * fix locale used for running Perl unit tests (`#425 `_) * fix Rmpi easyblock to correctly configure for Intel MPI (`#435 `_) * add support in generic Rpackage easyblock for handling patches (`#435 `_) * enhance OpenFOAM easyblock: fix building MPI build of Pstream and (pt)scotchDecomp + overall cleanup (`#436 `_) * enhance NWChem easyblock for version 6.3, clean up running of test cases (`#441 `_) * enhance noqa for interactive configuration of Qt build procedure (`#447 `_) * add custom sanity check for R in easyblock (`#449 `_) * make perlmodule take into account ``(pre){config,build,install}opts`` (`#450 `_) * add support for specifying an activation key after installing Mathematica (`#452 `_) * consider both ``lib`` and ``lib64`` directories in netCDF sanity check (`#453 `_) * fix sanity check for ANSYS for v15.0.x (`#458 `_) * fix Trilinos easyblock for recent version (`#462 `_) * enhance impi easyblock to handle install subdir for impi v5.0.1 and future version (`#465 `_, `#472 `_) * include $CFLAGS in linker flags for HPL (`#466 `_) * update sanity test checks for GROMACS 5.x (`#471 `_) * various bug fixes: * fix building of FFTW wrappers for Intel MKL v11.1.x + cleanup of imkl easyblock (`#445 `_) **easyconfigs** * added example easyconfig files for **13** new software packages: * Circos (`#780 `_), DB_File (`#913 `_), Emacs (`#970 `_), evmix (`#1077 `_), GD (`#780 `_), gsl (`#1077 `_), IOR (`#949 `_), JAGS (`#1076 `_), libgd (`#780 `_), MethPipe (`#1070 `_), Modeller (`#825 `_), NAMD (`#835 `_), netCDF-C++4 (`#1015 `_) * added easyconfigs for new toolchains (`#986 `_, `#1051 `_): * gimkl/1.5.9, ictce/7.1.2 * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including Python 2.7.8/3.4.1, Perl 5.20.0, R 3.1.1, NWChem 6.3, OpenFOAM-Extend 3.1, GCC 4.9.1, Clang 3.4.2, ... * various enhancements, including: * make existing ictce/intel toolchains compatible with HierarchicalMNS (`#1069 `_) * this involves installing impi with an iccifort toolchain, and imkl with an iimpi toolchain * various bug fixes, including: * download link for Perl modules changed to use cpan.metapan.org * fix missing MPI-based OpenFOAM libraries (``Pstream``, ``(pt)scotchDecomp``), make sure provided SCOTCH is used (`#957 `_) EasyBuild v1.14.0 (July 9th 2014) --------------------------------- feature + bugfix release **framework** * important changes * required Lmod version bumped to v5.6.3 (`#944 `_) * required due to enhancements and bug fixes in Lmod, e.g. making ``--terse avail`` significantly faster, and correctly handling a ``prepend-path`` statement that includes multiple directories at once * required Tcl/C environment modules version set to 3.2.10 ( * hard requirement due to fixed ``modulecmd`` segmentation fault bug, that only tends manifests itself when making a large amount of changes in the environment (e.g. ``module load ``) * renamed ``EasyBuildModuleNamingScheme`` to ``EasyBuildMNS`` * enhanced custom module naming schemes functionality to support hierarchical module naming schemes (`#953 `_, `#971 `_, `#975 `_) * extended API for custom module naming schemes to allow tweaking different aspects of module naming * see ``easybuild/tools/module_naming_scheme/mns.py`` for abstract ``ModuleNamingScheme`` class * an example hierarchical module naming scheme is included, see ``HierarchicalMNS`` * split up full module names into a module subdirectory part, which becomes part of ``$MODULEPATH``), and a 'short' module name (is exposed to end-users) * example: ``GCC/4.7.2`` in ``Core`` subdir, ``OpenMPI/1.6.5`` in ``Compiler/GCC/4.7.2`` subdir * make ``ModuleNamingScheme`` class a singleton, move it into ``easybuild.tools.module_naming_scheme.mns`` module * implement ``ActiveMNS`` wrapper class for querying active module naming scheme * implement toolchain inspection functions that can be used in a custom module naming scheme * ``det_toolchain_compilers``, ``det_toolchain_mpi`` in ``easybuild.tools.module_naming_scheme.toolchain`` * significant code cleanup & enhanced unit tests * enhance & clean up ``tools/modules.py`` (`#944 `_, `#953 `_, `#963 `_, `#964 `_, `#969 `_) * make ``ModulesTool`` a singleton to avoid repeating module commands over & over again needlessly * use ``module use``, ``module unuse`` rather than fiddling with ``$MODULEPATH`` directly * improve debug logging (include full stdout/stderr output of module commands) * remove deprecated functionality (``add_module``, ``remove_module``, indirect module load) * various other enhancements, including: * added toolchain definitions for 'common' toolchains: ``intel`` and ``foss`` (`#956 `_) * implement caching for easyconfig files, parsed easyconfigs and toolchains (`#953 `_) * enable ``--ignore-osdeps`` implicitly when ``-D``, ``--dry-run`` or ``--dep-graph`` are used (`#953 `_) * flesh out ``use_group`` and ``det_parallelism`` function, include them in ``easybuild.tools.systemtools`` (`#953 `_) * make symlinking of module files part of module naming scheme API (`#973 `_) * list of symlinks paths can be controlled using ``det_module_symlink_paths()`` method * added support for new configuration options: * tweaking compiler flags triggered by ``optarch`` toolchain options using ``--optarch`` (`#949 `_) * filtering out dependencies from easyconfig files using ``--filter-deps`` (`#957 `_) * filtering environment included in test reports with ``--test-report-env-filter`` (`#959 `_) e.g. ``--test-report-env-filter='^SSH|USER|HOSTNAME|UID|.*COOKIE.*'`` * made suffix used for module files install path configurable, using ``--suffix-modules-path`` (`#973 `_) * added support for additional easyconfig parameters: * define aliases in module files (``modaliases``) (`#952 `_) * add print message on module load (``modloadmsg``) and Tcl footer (``modtclfooter``) in module files (`#954 `_, `#974 `_) * various bug fixes, including: * don't try to tweak generated easyconfigs when using ``--try-X`` (`#942 `_) * currently create symlinks to module files modules/all under a custom module naming scheme (`#953 `_) * restore traceback error reporting on hard crashes (`#965 `_) **easyblocks** * added **one** new `generic` easyblock: CmdCp (`#395 `_) * added support for **2** new software packages that requires customized support: * ANSYS (`#398 `_), HPCG (`#408 `_) * various enhancements, including: * updated ABAQUS easyblock so that it works for version 13.2 (`#406 `_) * enhance BLAT easyblock by using ``super``'s ``build_step`` and ``prebuildopts``/``buildopts`` (`#423 `_) * enhance Mothur easyblock to guess correct start dir for recent versions (`#424 `_) * replace use of deprecated (pre)makeopts with (``pre``)``buildopts`` in all easyblocks (`#427 `_) * fix poor mans version of toolchain compiler detection in imkl easyblock (`#429 `_) * various bug fixes: * only check for ``idb`` for older versions of icc (`#426 `_) * fix issues with installing RPMS when ``rpmrebuild`` is required (`#433 `_) * correctly disable parallel build for ATLAS (`#434 `_) * fix sanity check for Intel MPI v5.x (only provides bin64) (`#432 `_) * add ``$MIC_LD_LIBRARY_PATH`` for MKL v11.x (`#437 `_) **easyconfigs** * added example easyconfig files for **17** new software packages: * ANSYS (`#836 `_), Beast (`#912 `_), ELPH (`#910 `_, `#911 `_), FastTree (`#900 `_, `#947 `_), GEM-library (`#858 `_), HPCG (`#853 `_), mdtest (`#925 `_), ncview (`#648 `_), PRANK (`#917 `_), RDP-Classifier (`#903 `_), SDPA (`#955 `_), SIBELia (`#886 `_), SOAPaligner (`#857 `_), SPAdes (`#884 `_), stemming (`#891 `_), WHAM (`#872 `_), YAXT (`#656 `_) * added easyconfigs for new toolchains (`#935 `_, `#944 `_, `#948 `_): * foss/2014b, ictce/6.3.5, intel/2014b * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * various enhancements, including: * replace use of deprecated ``(pre)makeopts`` with ``(pre)buildopts`` in all easyblocks (`#954 `_) * disable running embossupdate on installation of EMBOSS (`#963 `_) * various bug fixes, including: * really enable OpenMP support in FastTree easyconfigs (`#947 `_) * fix easyconfigs unit tests after changes in framework (`#958 `_) EasyBuild v1.13.0 (May 29th 2014) --------------------------------- feature + bugfix release **framework** * make ``--try-X`` command line options work recursively (i.e. collaborate with ``--robot``) (`#922 `_) * EasyBuild will first build a full dependency graph of the specified easyconfigs, and then apply the ``--try`` specifications * the elements of the dependency graph for the used toolchain and its dependencies are left untouched * this makes ``eb foo-1.0-goolf-1.4.10.eb --try-toolchain=ictce,5.5.0 --robot`` also work when ``foo`` has dependencies * caveat: the specified easyconfig files must all use the same toolchain (version) * add support for testing easyconfig pull requests from EasyBuild command line (`#920 `_, `#924 `_, `#925 `_, `#932 `_, `#933 `_, `#938 `_) * add ``--from-pr`` command line option for downloading easyconfig files from pull requests * add ``--upload-test-report`` command line option for uploading a detailed test report to GitHub as a gist * this requires specifying a GitHub username for which a GitHub token is available, using ``--github-user`` * with ``--dump-test-report``, the test report can simply be dumped to file rather than being uploaded to GitHub * see also https://github.com/easybuilders/easybuild/wiki/Review-process-for-contributions#testing-result * the ``makeopts`` and ``premakeopts`` easyconfig parameter are deprecated, and replaced by ``buildopts`` and ``prebuildopts`` (`#918 `_) * both ``makeopts`` and ``premakeopts`` will still be honored in future EasyBuild v1.x versions, but should no longer be used * various other enhancements, including: * add ``--disable-cleanup-builddir`` command line option, to keep the build dir after a (successful) build (`#853 `_) * the build dir is still cleaned up by default for successful builds, i.e. ``--cleanup-builddir`` is the default * also consider lib32 in paths checked for ``$LD_LIBRARY_PATH`` and ``$LIBRARY_PATH`` (`#912 `_) * reorganize support for file/git/svn repositories into ``repository`` package, making it extensible (`#913 `_) * add support for ``postinstallcmds`` easyconfig parameter, to specify commands that need to be run after the install step (`#918 `_) * make ``VERSION=`` part in version of C environment modules tool optional, which is required for older versions (`#930 `_) * various bug fixes, including: * fix small issues in bootstrap script: correctly determine EasyBuild version and make sure modules path exists (`#915 `_) * fix github unit tests (`#916 `_) * disable useless debug logging for unit tests (`#919 `_) * fix unit test for ``--skip`` (`#929 `_) * make sure ``start_dir`` can be set based on location of unpacked first source file (`#931 `_) * the ``vsc`` package shipped with easybuild-framework is synced with vsc-base v1.9.1 (`#935 `_) * fancylogger (used for logging in EasyBuild) is now robust against strings containing UTF8 characters * the ``deprecated`` logging function now does a non-strict version check (rather than an erroneous strict check) * the ``easybuild.tools.agithub`` module is removed, ``vsc.utils.rest`` now provides the required functionality * fix support for unpacking gzipped source files, don't unpack ``.gz`` files in-place in the source directory (`#936 `_) **easyblocks** * added support for **1** new software package that requires customized support: * Go (`#417 `_) * various enhancements, including: * enhance OpenFOAM easyblock so OpenFOAM-Extend fork can be built too + style fixes (`#253 `_, `#416 `_) * enhance CPLEX easyblock by adding support for staged installation (`#372 `_) * include support for ``configure_cmd_prefix`` easyconfig parameter in ConfigureMake generic easyblock (`#393 `_) * enhance GCC easyblock for building v4.9.0 and versions prior to v4.5 (`#396 `_, `#400 `_) * enhance easyblocks for Intel ipp and itac to support recent versions (`#399 `_) * enhance Clang easyblock: install static analyzer (`#402 `_), be more robust against changing source dir names (`#413 `_) * enhance FoldX easyblock, update list of potential FoldX binaries to support recent versions (`#407 `_) * add runtime patching in Boost easyblock to fix build issue with old Boost versions and recent glibc (> 2.15) (`#412 `_) * enhance ``MakeCp`` generic easyblock: use location of 1st unpacked source as fallback base dir for ``files_to_copy`` (`#415 `_) * various bug fixes: * fix installing Mathematica when X forwarding is enabled (make sure ``$DISPLAY`` is unset) (`#391 `_) * fix permissions of installed files in SAMtools easyblock, ensure read/execute for group/other (`#409 `_) * fix implementation of ``det_pylibdir`` function in PythonPackage generic easyblock (`#419 `_, `#420 `_) * determine Python lib dir via ``distutils`` Python, which works cross-OS (as opposed to hardcoding ``lib``) **easyconfigs** * added example easyconfig files for **32** new software packages: * APBS (`#742 `_), BayesTraits (`#770 `_), bc (`#888 `_), BitSeq (`#791 `_), CEM (`#789 `_), CVS (`#888 `_), eXpress (`#786 `_), file (`#888 `_), GEMSTAT (`#861 `_), GMAP (`#594 `_), Go (`#887 `_), iscp (`#602 `_), IsoInfer (`#773 `_), Jellyfish (`#868 `_), less (`#888 `_), libcircle (`#883 `_), mcpp (`#602 `_), MMSEQ (`#795 `_), MUSTANG (`#800 `_), OpenFOAM-Extend (`#437 `_), popt (`#759 `_), pscom (`#759 `_), psmpi2 (`#759 `_), QuadProg++ (`#773 `_), rSeq (`#771 `_), RSEQtools (`#870 `_), Ruby (`#873 `_), segemehl (`#792 `_), SOAPec (`#879 `_), SOAPdenovo2 (`#874 `_), SRA-Toolkit (`#793 `_), texinfo (`#888 `_) * added easyconfig for new toolchain goolfc/1.4.10 * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * e.g., older versions of Boost (1.47.0), GCC (4.1-4.4), & recent versions of Clang, GCC, Lmod, etc. * various enhancements, including: * add OpenSSL dependency for cURL, to enable HTTPS support (`#881 `_) * also install esl-X binaries for HMMER (`#889 `_) * various bug fixes, including: * properly pass down compiler flags for ParMGridGen (`#437 `_) * specify proper make options for PLINK, fixing the build on SL6 (`#594 `_, `#772 `_) * fix netloc version (0.5 rather than 0.5beta) (`#707 `_) * remove Windows-style line ending in netCDF patch file (`#796 `_) * bump version of OpenSSL dep for BOINC (`#882 `_) EasyBuild v1.12.1 (April 25th 2014) ----------------------------------- bugfix release **framework** * return to original directory after executing a command in a subdir (`#908 `_) * fix bootstrap with Lmod, fix issue with module function check and Lmod (`#911 `_) **easyblocks** `(no changes compared to v1.12.0, simple version bump to stay in sync with easybuild-framework)` **easyconfigs** `(no changes compared to v1.12.0, simple version bump to stay in sync with easybuild-framework)` EasyBuild v1.12.0 (April 4th 2014) ---------------------------------- feature + bugfix release **framework** * various enhancements, including: * completed support for custom module naming schemes (`#879 `_, `#904 `_) * a fully parsed easyconfig file is now passed to the ``det_full_module_name`` function * this does require that an easyconfig file matching the dependency specification is available * added more features to better support using a shared install target with multiple users (`#902 `_, `#903 `_, `#904 `_) * further development on support for new easyconfig format (v2.0) (`#844 `_, `#848 `_) * not considered stable yet, so still requires using ``--experimental`` * enhanced bootstrap script to also support Lmod and ``modulecmd.tcl`` module tools (`#869 `_) * added support to ``run_cmd_qa`` function to supply a list of answers (`#887 `_) * detect mismatch between definition of ``module`` function and selected modules tool (`#871 `_) * allowing mismatch now requires ``--allow-modules-tool-mismatch``; an empty ``module`` function is simply ignored * provide lib64 fallback option for directories in default sanity check paths (`#896 `_) * add support for adding JAR files to ``$CLASSPATH`` (`#898 `_) * enhanced and cleaned up unit tests (`#877 `_, `#880 `_, `#884 `_, `#899 `_, `#901 `_) * code cleanup and refactoring * get rid of global variable for configuration settings in ``config.py``, use singleton instead (`#874 `_, `#888 `_, `#890 `_, `#892 `_) * track build options via singleton in ``config.py`` rather than passing them around all over (`#886 `_, `#889 `_) * avoid parsing easyconfig files multiple times by passing a parsed easyconfig to the easyblock (`#891 `_) * deprecate list of tuples return type of ``extra_options`` static method (`#893 `_, `#894 `_) * move OS dependency check to ``systemtools.py`` module (`#895 `_) * bug fixes, including: * fix linking with ``-lcudart`` if CUDA is part of the toolchain, should also include ``-lrt`` (`#882 `_) **easyblocks** * various enhancements, including: * also run ``Perl Build build`` for Perl modules (usually not required, but sometimes it is) (`#380 `_) * added glob support in generic makecp block (`#367 `_, `#384 `_) * enhance sanity check in GCC easyblock such that it also passes/works on OpenSuSE (`#365 `_) * add multilib support in GCC easyblock (`#379 `_) * various bug fixes: * Clang: disable sanitizer tests when vmem limit is set (`#366 `_) * make sure all libraries are installed for recent Intel MKL versions (`#375 `_) * fix appending Intel MPI include directories to ``$CPATH`` (`#371 `_) * statically link readline/ncurses libraries in Python and NWChem easyblocks (`#370 `_, `#383 `_, `#385 `_) * fix easyblock unit tests after changes in framework (`#376 `_, `#377 `_, `#378 `_) **easyconfigs** * added example easyconfig files for **6** new software packages: * CLooG (`#653 `_), ELPA (`#738 `_), LIBSVM (`#788 `_), netaddr (`#753 `_), netifcas (`#753 `_), slalib-c (`#750 `_) * added easyconfigs for new toolchains: * ClangGCC/1.3.0 (`#653 `_), goolf/1.4.10-no-OFED (`#749 `_), goolf/1.5.14(-no-OFED) (`#764 `_, `#767 `_), ictce/6.2.5 (`#726 `_), iomkl (`#747 `_) * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * various enhancements, including: * tweak BOINC easyconfig to make use of ``glob`` support available for ``files_to_copy`` (`#781 `_) * enable ``-fPIC`` for libreadline, so it can be linked into shared libs (e.g. ``libpython2.x.so``) (`#798 `_) * various bug fixes, including: * fix Qt source_urls (`#756 `_) * enable ``-fPIC`` in ncurses 5.9 ictce/5.2.0 easyconfig, just like in the others (`#801 `_) * fix unit tests after changes to framework (`#763 `_, `#766 `_, `#769 `_) EasyBuild v1.11.1 (February 28th 2014) -------------------------------------- bugfix release **framework** * various bug fixes, including: * fix hard crash when ``$LMOD_CMD`` specified full path to lmod binary, but ``spider`` binary is not in ``$PATH`` (`#861 `_, `#873 `_) * fix bug in initialisation of repositories, causing problems when a repository subdirectory is specified (`#852 `_) * avoid long wait when dependency resolution fails if ``--robot`` is not specified (`#875 `_) **easyblocks** `(no changes compared to v1.11.0, simple version bump to stay in sync with easybuild-framework)` **easyconfigs** `(no changes compared to v1.11.0, simple version bump to stay in sync with easybuild-framework)` EasyBuild v1.11.0 (February 16th 2014) -------------------------------------- feature + bugfix release **framework** * various enhancements, including: * add checksum support for extensions (`#807 `_) * make checksum functionality more memory efficient by reading in blocks (`#836 `_) * rewrite of dependency solving for speed and better reporting of missing dependencies (`#806 `_, `#818 `_) * refactoring of ``main.py`` (`#815 `_, `#828 `_) * function/method signatures to pass down build options * move functions from main.py into easybuild.framework.X or easybuild.tools * provide better build statistics (`#824 `_) * add --experimental, ``--deprecated`` and ``--oldstyleconfig`` command line options (`#838 `_) * with ``--experimental``, new but incomplete (or partially broken) features are enabled * with ``--deprecated``, removed of deprecated functionality can be tested (anything deprecated will fail hard) * with ``--disable-oldstyleconfig``, support for the old style configuration is disabled * define ``$LIBRARY_PATH`` in generated module files (`#832 `_) * more constants for source URLs (e.g. for downloads from bitbucket) (`#831 `_) * prefer ``$XDG_CONFIG_HOME`` and ``~/.config/easybuild`` over ``~/.easybuild`` for configuration files (`#820 `_) * add support for specifying footers to be appended to generated module files (`#808 `_) * see ``--modules-footer`` command line option * track version of modules tool + cleanup of ``modules.py`` (`#839 `_) * move actual ``run_cmd`` and ``run_cmd_qa`` implementations from ``tools.filetools`` into ``tools.run`` (`#842 `_, `#843 `_) * add support for generating modules that support recursive unloading (`#830 `_) * see ``--recursive-module-unload`` command line option * add flexibility support for specifying OS dependencies (`#846 `_) * alternatives can be specified, e.g. (``openssl-devel``, ``libssl-dev``) * initial (incomplete) support for easyconfig files in new format (v2.0) (`#810 `_, `#826 `_, `#827 `_, `#841 `_) * requires ``--experimental`` to be able to experiment with format v2 easyconfig files * various bug fixes, including: * fix problems with use of new-style configuration file (`#821 `_) * fix removal of old build directories, unless ``cleanupoldbuild`` easyconfig parameter is set (`#809 `_) * fix support for different types of repository path specifications (`#814 `_) * fix unit tests sensitive to ``$MODULEPATH`` and available easyblocks (`#845 `_) **easyblocks** * added **one** new `generic` easyblock: ``VSCPythonPackage`` (`#348 `_) * added support for **1** new software package that requires customized support: * netcdf4-python (`#347 `_) * various enhancements, including: * add support for installing recent tbb versions (`#341 `_) * use ``makeopts`` in the build step of the generic ``PythonPackage`` easyblock (`#352 `_) * define the ``$CMAKE_INCLUDE_PATH`` and ``$CMAKE_LIBRARY_PATH`` in the generic ``CMakeMake`` easyblock (`#351 `_, `#360 `_) * update Clang easyblock to support v3.4 (`#346 `_) * make sure Python is built with SSL support, adjust Python easyblock to pick up OpenSSL dep (`#359 `_) * note: providing OpenSSL via an OS package is still recommended, such that security updates are picked up * add support for recent netCDF versions (`#347 `_) * update SuiteSparse easyblock for new versions, and clean it up a bit (`#350 `_) * various bug fixes: * fix name of ``VersionIndependentPythonPackage`` easyblock, deprecate ``VersionIndependendPythonPackage`` easyblock (`#348 `_) * fix detection of machine architecture in FSL easyblock (`#353 `_) * fix bug in NWChem easyblock w.r.t. creating local dummy ``.nwchem`` file (`#360 `_) * make sure ``$LIBRARY_PATH`` is set for Intel compilers and Intel MPI, fix 64-bit specific paths (`#360 `_) **easyconfigs** * added example easyconfig files for **30** new software packages: * argtable (`#669 `_), Clustal-Omega (`#669 `_), Coreutils (`#582 `_), GMT (`#560 `_), gperftools (`#596 `_), grep (`#582 `_), h4toh5 (`#597 `_), libunwind (`#596 `_), Lmod (`#600 `_, `#692 `_), Lua (`#600 `_, `#692 `_), MAFFT (`#654 `_), Molekel (`#597 `_), NEdit (`#597 `_), netcdf4-python (`#660 `_), nodejs (`#678 `_), OCaml (`#704 `_), patch (`#582 `_), PhyML (`#664 `_), PRACE Common Production Environment (`#599 `_), protobuf (`#680 `_), python-dateutil (`#438 `_), sed (`#582 `_), sickle (`#651 `_), Tesla-Deployment-Kit (`#489 `_), TREE-PUZZLE (`#662 `_), VCFtools (`#626 `_), Vim (`#665 `_), vsc-mympirun-scoop (`#661 `_), vsc-processcontrol (`#661 `_), XZ (`#582 `_) * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * OpenSSL with ictce toolchain (`#703 `_) * various enhancements, including: * using more constants and templates (`#613 `_, `#615 `_) * specify OS dependency for SSL support, with OpenSSL dependency as fallback (`#703 `_) * various bug fixes, including: * fix unit tests after (internal) framework API changes (`#667 `_, `#672 `_) * fix homepage in vsc-mympirun easyconfig file (`#681 `_) * align OpenMPI easyconfigs (`#650 `_) * add additional source URL in Qt easyconfigs (`#676 `_) * specify correct $PATH specification and define ``$CHPL_HOME`` for Chapel (`#683 `_) EasyBuild v1.10.0 (December 24th 2013) -------------------------------------- feature + bugfix release **framework** * various enhancements, including: * set unique default temporary directory, add ``--tmpdir`` command line option (`#695 `_) * add support for computing and verifying source/patch file checksums (`#774 `_, `#777 `_, `#779 `_, `#801 `_, `#802 `_) * cfr. ``checksums`` easyconfig parameter * add support for `eb --confighelp`, which prints out an example configuration file (`#775 `_) * add initial support for ``eb`` tab completion in bash shells (`#775 `_, `#797 `_, `#798 `_) * see also https://github.com/easybuilders/easybuild/wiki/Setting-up-tab-completion-for-bash * note: may be quite slow for now * enhancements for using Lmod as modules tool (`#780 `_, `#795 `_, `#796 `_): * ignore Lmod spider cache by setting ``$LMOD_IGNORE_CACHE`` (requires Lmod 5.2) * bump required Lmod version to v5.2 * get rid of slow workaround for detecting module directories (only required for older Lmod versions) * fix version parsing for Lmod release candidates (rc) * improve integration with `lmod spider` by adding ``Description: `` prefix to ``module-whatis`` field of module * add ``--dry-short-short``/``-D`` and ``--search-short``/``-S`` command line options (`#781 `_) * add toolchain definition for 'gompic', intended for using with CUDA-aware OpenMPI (`#783 `_) * add support for specifying multiple robot paths (`#786 `_) * add various source URL constants, add support for ``%(nameletter)s`` and ``%(nameletterlower)s`` templates (`#793 `_) * add ``buildininstalldir`` easyconfig parameter (`#794 `_) * add ``--ignore-osdeps`` command line option (`#799 `_, `#802 `_) * various bug fixes, including: * enable ``-mt_mpi`` compiler flag if both ``usempi`` and ``openmp`` toolchain options are enabled (`#771 `_) * only use ``libmkl_solver*`` libraries for Intel MKL versions prior to 10.3 (`#776 `_) * fix toolchain support for recent Intel tools (`#785 `_) * code style fixes in ``main.py`` to adhere more to PEP8 (`#789 `_) * make sure ``easyblock`` easyconfig parameter is listed in ``eb -a`` (`#791 `_) * fix error that may pop up when using ``skipsteps=source`` (`#792 `_) **easyblocks** * added **one** new `generic` easyblock: ``VersionIndependendPythonPackage`` (`#329 `_, `#334 `_) * added support for **2** new software packages that require customized support: * Charmm (`#318 `_), GROMACS (`#335 `_, `#339 `_) * various enhancements, including: * fix support for recent SAMtools version (>= 0.1.19) (`#320 `_) * fix support for recent Intel tools (icc, ifort, imkl, impi) (`#325 `_, `#327 `_, `#338 `_) * enhance generic easyblock for installing RPMs (`#332 `_) * pick up ``preinstallopts`` in generic ``PythonPackage`` easyblock (`#334 `_) * enhance CP2K easyblock (libxc support, new versions) + style cleanup (`#336 `_) * various bug fixes: * use unwanted env var functionality to unset ``$MKLROOT`` rather than failing with an error (`#273 `_) * always include ``-w`` flag for preprocessor to suppress warnings that may break QuantumESPRESSO configure (`#317 `_) * link with multithreaded LAPACK libs for ESMF (`#319 `_) * extend ``noqanda`` list of patterns in CUDA easyblock (`#328 `_, `#337 `_) * add ``import _ctypes`` to Python sanity check commands to capture a common build issue (`#329 `_) * bug fixes in generic ``IntelBase`` easyblock (`#331 `_, `#333 `_, `#335 `_) * remove broken symlink ``$HOME/intel`` if present * fix use of gettempdir to obtain a common (user-specific) tmp dir to symlink ``$HOME/intel`` to * fix build of recent scipy versions with GCC-based toolchain (`#334 `_) * fix use of gettempdir to obtain common (user-specific) tmp dir for ``$HOME/.nwchemrc`` symlink (`#340 `_, `#342 `_) * extend ``noqanda`` list in Qt easyblock (`#342 `_) **easyconfigs** * added example easyconfig files for **18** new software packages: * BEDTools (`#579 `_, `#632 `_, `#635 `_), CAP3 (`#548 `_), CHARMM (`#584 `_), cutadapt (`#620 `_), ErlangOTP (`#556 `_, `#630 `_), Ghostscript (`#547 `_, `#632 `_), HTSeq (`#554 `_, `#632 `_), Jansson (`#545 `_), libjpeg-turbo (`#574 `_), Molden (`#566 `_), netloc (`#545 `_), o2scl (`#633 `_), packmol (`#566 `_), PP (`#405 `_), qtop (`#500 `_), TAMkin (`#566 `_), vsc-base (`#621 `_), vsc-mympirun (`#621 `_) * added easyconfigs for new toolchains (`#545 `_, `#609 `_, `#629 `_): * gcccuda/2.6.10, gompic/2.6.10, goolfc/2.6.10, ictce/6.0.5, ictce/6.1.5 * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * new versions of icc, ifort, imkl, impi (`#609 `_, `#629 `_) * large collection of ictce/5.3.0 easyconfigs (`#627 `_) * various enhancements, including: * extended list of Python packages as extensions to Python (`#625 `_) * add MPI-enabled version of GROMACS + easyconfigs using ictce (`#606 `_, `#636 `_) * clean up templating of ``source_urls`` (`#637 `_) * various bug fixes, including: * provide alternative download URL for Mesa (`#532 `_) * add Python versionsuffix in OpenBabel filenames (`#566 `_) * apply no-gets patch in all M4 v1.4.16 easyconfigs (`#623 `_) * fix patching of Python w.r.t. ``libffi``/``_ctypes`` issues (`#625 `_, `#642 `_) * bug fixes in GROMACS easyconfigs (`#606 `_) * change versionsuffix for non-MPI GROMACS easyconfigs to ``-mt`` * stop using 'CMakeMake' easyblock for GROMACS now that there's a dedicated GROMACS easyblock, which correctly specifies building against external BLAS/LAPACK libraries * fix Qt dependency for CGAL (`#642 `_) * fix libctl, libmatheval, Meep, PSI build issues caused by full paths in ``guile-config``/``python-config`` shebang (`#642 `_) * make sure HDF easyconfigs specify dedicated ``include/hdf`` include dir (`#642 `_) * this is required to avoid build issues with NCL, because HDF ships it's own ``netcdf.h`` * this also triggered removal of patch files for NCL that rewrote ``include/hdf`` to ``include`` * fix WPS v3.5.1 patch file after upstream source tarball was changed, supply checksum for verification (`#642 `_) EasyBuild v1.9.0 (November 17th 2013) ------------------------------------- feature + bugfix release **framework** * add support for Tcl environment modules (``modulecmd.tcl``) (`#728 `_, `#729 `_, `#739 `_) * special care was taken to make sure also the DEISA variant of ``modulecmd.tcl`` can be used * code refactoring to prepare for supporting two formats for easyconfig files (`#693 `_, `#750 `_) * this prepares the codebase for supporting easyconfig format v2.0 * some initial work on adding support for the new easyconfig format is included, but it's by no means complete yet * the current easyconfig format (now dubbed v1.0) is still the default and only supported format, for now * for more details, see https://github.com/easybuilders/easybuild/wiki/Easyconfig-format-two * various other enhancements, including: * include a full version of vsc-base (see the ``vsc`` subdirectory) (`#740 `_) * this is a first step towards switching to using vsc-base as a proper dependency * implement get_avail_core_count function in systemtools module that takes cpusets and co into account (`#700 `_) * the ``get_core_count`` function is now deprecated * add ``impmkl`` toolchain definition (`#736 `_) * make regtest more robust: put holds on jobs without dependencies, release holds once all jobs are submitted (`#751 `_) * add support for specifying multiple alternatives for sanity check paths (`#753 `_) * add ``get_software_libdir`` function to modules.py (along with unit tests) (`#758 `_) * add support for more file extensions and constants w.r.t. sources (`#738 `_, `#760 `_, `#761 `_) * add MPICH2 support in ``mpi_cmd_for`` function (`#761 `_) * various bug fixes, including: * fix checking of OS dependencies on Debian/Ubuntu that have ``rpm`` command available (`#732 `_) * make unit tests more robust w.r.t. non-writeable ``/tmp`` and loaded modules prior to starting unit tests (`#752 `_, `#756 `_) * also call ``EasyBlock``'s sanity check in ``ExtensionEasyblock`` if paths/commands are specified in easyconfig (`#757 `_) * set compiler family for dummy compiler, add definition of toolchain constant for dummy (`#759 `_) * other * add build status badges for master/develop branches to ``README`` (`#742 `_) * add scripts for installing EasyBuild develop version or setting up git development environment (`#730 `_, `#755 `_) **easyblocks** * added support for **8** new software packages that require customized support: * Allinea DDT/MAP (`#279 `_), ARB (`#291 `_), GenomeAnalysisTK (`#278 `_), OpenBabel (`#305 `_, `#309 `_), picard (`#278 `_), PyQuante (`#297 `_), Scalasca v1.x (`#304 `_), Score-P (`#304 `_) * the Score-P easyblock is also used for Cube 4.x, LWM2, OTF2, and Scalasca v2.x * various enhancements, including: * add support building ScaLAPACK on top of MPICH2, required for gmpolf toolchain (`#274 `_) * add support to ConfigureMake easyblock to customize configure ``--prefix`` option (`#287 `_) * add support for specifying install command in Binary easyblock (`#288 `_) * enhance CMakeMake easyblock to specify srcdir via easyconfig parameter, and to perform out-of-source builds (`#303 `_) * various bug fixes: * use correct configure flag for Szip in HDF5 easyblocks, should be ``--with-szlib`` (`#286 `_, `#301 `_) * add support for serial HDF5 builds (`#290 `_, `#301 `_) * enhance robustness of Qt easyblock w.r.t. interactive configure (`#295 `_, `#302 `_) * enhance support for picking up license specification via environment variables (`#298 `_, `#307 `_) * extend list of values for ``$CPATH`` in libint2 easyblock (`#300 `_) * fix ``extra_options`` ``super`` call in Clang easyblock (`#306 `_) * add support in Boost easyblock to specify toolset in easyconfig file (`#308 `_) * other: * add build status badges for master/develop branches to README (`#289 `_) **easyconfigs** * added example easyconfig files for **58** new software packages: * Allinea (`#468 `_), ARB + dependencies (`#396 `_, `#493 `_, `#495 `_), arpack-ng (`#451 `_, `#481 `_), CDO (`#484 `_, `#521 `_), Cube (`#505 `_), ed (`#503 `_), FLTK (`#503 `_), GenomeAnalysisTK (`#467 `_), GIMPS (`#527 `_), GTI (`#511 `_), IPython (`#485 `_, `#519 `_), LWM2 (`#510 `_), MPICH2 (`#460 `_), MUST (`#511 `_), ncdf (`#496 `_, `#522 `_), OPARI2 (`#505 `_), OpenBabel (`#504 `_, `#524 `_), OTF (`#505 `_), OTF2 (`#505 `_), PandaSEQ (`#475 `_), ParaView (`#498 `_, `#514 `_), ParFlow (`#483 `_, `#520 `_), PCC (`#486 `_, `#528 `_), PDT (`#505 `_), picard (`#467 `_), PnMPI (`#511 `_), PyQuante (`#499 `_, `#523 `_), pysqlite (`#519 `_), Scalasca (`#505 `_), Score-P (`#505 `_), SDCC (`#486 `_, `#528 `_), Silo (`#483 `_, `#520 `_), Stride (`#503 `_), SURF (`#503 `_), TCC (`#486 `_, `#528 `_) * ARB dependencies (23): fixesproto, imake, inputproto, kbproto, libICE, libSM, libX11, libXau, libXaw, libXext, libXfixes, libXi, libXmu, libXp, libXpm, libXt, lynx, motif, printproto, Sablotron, xbitmaps, xextproto, xtrans * added easyconfigs for new gmpich2/1.4.8, gmpolf/1.4.8 and goolf/1.6.10 toolchains (`#460 `_, `#525 `_, `#530 `_) * added additional easyconfigs for various software packages (list too long to include here) * version updates, different toolchains, ... * various bug fixes, including: * enable building of shared libraries for MPICH (`#482 `_) * fix HDF configure option for Szip, should be ``--with-szlib`` (`#533 `_) * for HDF5, this issue is fixed in the HDF5 easyblock * other * add build status badges for master/develop branches to README (`#490 `_) EasyBuild v1.8.2 (October 18th 2013) ------------------------------------ bugfix release **framework** * fix regular expression used for obtaining list of modules from ``module avail`` (`#724 `_) * modules marked as default were being hidden from EasyBuild, causing problems when they are used as dependency **easyblocks** * fix installing of EasyBuild with a loaded EasyBuild module (`#280 `_) * this is important to make upgrading to the latest EasyBuild version possible with a bootstrapped EasyBuild **easyconfigs** * port thread pool patch to PSI 4.0b4 and include it to avoid hanging tests (`#471 `_) EasyBuild v1.8.1 (October 14th 2013) ------------------------------------ bugfix release * various bug fixes, including: * fix bugs in regtest procedure (`#713 `_) * force 2nd and 3rd attempt of build in case 1st attempt failed * fix copying of install log to install directory (`#716 `_) * only create first source path if multiple paths are specified (`#718 `_) * detect failed PBS job submission by checking obtained job ID for ``None`` value (`#713 `_, `#717 `_, `#719 `_, `#720 `_) **easyblocks** * various bug fixes: * fix problems in PSI easyblock causing build to fail (`#270 `_) * fix issues with running NWChem test cases, fail early in case broken symlink is present (`#275 `_) **easyconfigs** * added additional easyconfigs for various software packages (`#457 `_): * Boost, bzip2, libreadline, ncurses, PSI, Python, zlib * various bug fixes, including: * fix faulty easyconfig file names for HPCBIOS_Math, MUSCLE, XML-LibXML and YAML-Syck (`#459 `_, `#462 `_) * stop (re)specifying default maximum ratio for failed tests in NWChem easyconfig (`#457 `_) EasyBuild v1.8.0 (October 4th 2013) ----------------------------------- feature + bugfix release **framework** * add support for using alternative module naming schemes (`#679 `_, `#696 `_, `#705 `_, `#706 `_, `#707 `_) * see https://github.com/easybuilders/easybuild/wiki/Using-a-custom-module-naming-scheme for documentation * module naming scheme classes that derive from the 'abstract' ``ModuleNamingScheme`` class can be provided to EasyBuild * the Python module providing the class must be available in the ``easybuild.tools.module_naming_scheme`` namespace * a function named ``det_full_module_name`` must be implemented, that determines the module name in the form of an string based on the supplied dictionary(-like) argument * the active module naming scheme is determined by EasyBuild configuration option ``--module-naming-scheme`` * for now, only the ``name``/``version``/``versionsuffix``/``toolchain`` easyconfig parameters are guaranteed to be provided * consistently providing all easyconfig parameters (i.e., also for dependencies) requires more work (see `#687 `_) * implementing this involved a number of intrusive changes: * the API of the modules.py module needed to be changed, breaking backward compatibility * the function for which the signatures were modified are considered to be internal to the framework, so this should have very minor impact w.r.t. easyblocks not included with EasyBuild * affected functions include: ``available``, ``exists``, ``show``, ``modulefile_path``, ``dependencies_for`` * the format for specifying dependencies was extended, to allow for specifying a custom toolchain * this allows to fix inaccurate dependency specifications, for example: ``('OpenMPI', '1.6.4-GCC-4.7.2')" to "('OpenMPI', '1.6.4', '', ('GCC', '4.7.2'))`` * see also `easyconfigs#431 `_ * the recommended version for Lmod was bumped to v5.1.5 * using earlier 5.x version still works, but may be very slow when 'available' is used, due to bugs and a missing feature in Lmod versions prior to v5.1.5 on which we rely * various other enhancements, including: * only (try to) change group id if it is different from what is wanted (`#685 `_) * added toy build unit test (`#688 `_) * support for specifying a list of source paths in EasyBuild configuration (`#690 `_, `#702 `_) * add function to determine CPU clock speed in ``systemtools.py`` (`#694 `_, `#699 `_) * various bug fixes, including: * avoid importing toolchain modules over and over again to make toolchain constants available in toolchain module (`#679 `) * only change the group id if current gid is different from what we want in ``adjust_permissions`` function (`#685 `) * restore original environment after running 'module purge' (`#698 `) * important sidenote: this results in resetting the entire environment, and has impact on the sanity check step; * any environment variables that are set before the EasyBlock.sanity_check_step method fires, are no longer there when the sanity check commands are run (cfr. `easyblocks#268 `_) **easyblocks** * added **one** new `generic` easyblock: ``BinariesTarball`` (`#255 `_) * added support for **5** new software packages that require customized support: * DB (`#226 `_), FDTD Solutions (`#239 `_), FoldX (`#256 `_), Mathematica (`#240 `_), MUMPS (`#262 `_) * various enhancements, including: * support optionally running configure in generic ``MakeCp`` easyblock (`#252 `_) * enhanced Clang easyblock to support building Clang 3.3 (`#248 `_) * add support for ``$INTEL_LICENSE_FILE`` specifying multiple paths (`#251 `_) * enhanced ATLAS easyblock to support building ATLAS 3.10.1 (`#258 `_) * various bug fixes: * add zlib lib dir in link path dirs for WPS (`#249 `_) * stop using deprecated ``add_module`` function in imkl easyblock (`#250 `_) * fixed PSI easyblock w.r.t. support for building plugins (`#254 `_, `#269 `_) * move OS check for Clang to ``check_readiness_step``, to allow a build job to be submitted from SL5 (`#263 `_, `#264 `_) * enable verbose build for DOLFIN, to allow for proper debugging if the build fails (`#265 `_) * make sure ``$LDFLAGS`` and ``$INSTANT_*_DIR`` env vars are set for DOLFIN sanity check commands (`#268 `_) * this is required after resetting the environment after running module purge (see framework release notes) * don't try to load module in LAPACK test-only build (`#264 `_, `#266 `_) **easyconfigs** * added example easyconfig files for **9** new software packages: * BOINC (`#436 `_), DB (`#343 `_, `#449 `_), fastahack (`#374 `_), FDTD Solutions (`#387 `_), FoldX (`#440 `_, `#442 `_), Mathematica (`#394 `_), Mesquite (`#447 `_), MUMPS (`#447 `_), ParMGridGen (`#447 `_) * added additional easyconfigs for goalf, gompi, ClangGCC, cgmvapich2, cgmvolf toolchains (`#350 `_, `#441 `_) * added additional easyconfigs for various software packages: * ATLAS, Bison, bzip2, Clang, CMake, cURL, EasyBuild, expat, FFTW, GDB, gettext, git, HPL, LAPACK, libreadline, M4, METIS, MVAPICH2, Mercurial, ncurses, OpenBLAS, OpenMPI, ParMETIS, Python, ScaLAPACK, SCOTCH, Valgrind, zlib * various 'bug' fixes, including: * fix source URL for lockfile in Python easyconfigs (`#428 `_) * correct dependency specifications w.r.t. versionsuffix and toolchain (`#431 `_) * this is required to support building the affected easyconfigs with a custom module naming scheme * correct PSI patch file to avoid errors w.r.t. memcpy not being in scope (`#446 `_) * fix gettext build with adding ``--without-emacs`` configure options, add gettext as dependency for a2ps (`#448 `_) * exclude EMACS support in a2ps because of build failures (`#452 `_) EasyBuild v1.7.0 (September 2nd 2013) ------------------------------------- feature + bugfix release **framework** * various enhancements, including: * also search for patch files in directory where easyconfig file is located (`#667 `_) * reduce false positives in reporting of possible errors messages (`#669 `_) * make module update ``$ACLOCAL`` if a share/aclocal subdir is found (`#670 `_) * add ``unwanted_env_vars`` easyconfig parameter to list environment variables to unset during install procedure (`#673 `_) * add support for updating list easyconfig values (next to string values) (`#676 `_) * add ``--dry-run`` command line option which prints installation overview for specified easyconfig files (`#677 `_) * various bug fixes, including: * ensure that all extensions are listed in ``$EBEXTSLISTX`` set by module, also when using ``--skip`` (`#671 `_) * report reason for failed sanity check for extensions (`#672 `_, `#678 `_) * fix ``--list-toolchains`` command line option (`#675 `_) **easyblocks** * added support for **3** new software packages that require customized support: * Libint2 (`#236 `_), Qt (`#210 `_), Rosetta (`#218 `_) * various enhancements, including: * allow building OpenFOAM without 3rd party tools (`#230 `_) * also add sitelib path to ``$PERL5LIB``, refactor code to add generic ``get_site_suffix`` function (`#232 `_, `#233 `_) * support building imkl FFT wrappers using MVAPICH2 MPI library (`#234 `_) * remove libnpp from CUDA sanity check to support installing CUDA v5.5 (`#238 `_) * pick up ``$INTEL_LICENSE_FILE`` for Intel tools, if it is set (`#243 `_) * note: gets preference over ``license_file`` easyconfig parameter * various bug fixes: * call WRF build script with '``tcsh