From 1b40e63d4c674f3cbc65010a58569b912972f324 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Dec 2019 19:59:00 +0100 Subject: [PATCH] move note on concise overview of changes in EasyBuild v4.0 to top of release notes (+ strip trailing whitespace) --- docs/Release_notes.rst | 50 +++++++++++++++++++++--------------------- 1 file changed, 25 insertions(+), 25 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 252cf30f..d4b180e2 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -7,6 +7,8 @@ The latest version of EasyBuild provides support for building and installing **1 including 31 different (compiler) toolchains. It contains 211 software-specific easyblocks and 36 generic easyblocks, alongside 8,748 easyconfig files. +.. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. + .. _release_notes_eb410: EasyBuild v4.1.0 (December 4th 2019) @@ -279,8 +281,6 @@ EasyBuild v4.0.0 (September 20th 2019) feature release (incl. backwards-incompatible changes) -.. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. - **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 `_) @@ -1364,14 +1364,14 @@ bugfix/update release - 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 `_) @@ -1382,25 +1382,25 @@ bugfix/update release - 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 `_) @@ -1408,7 +1408,7 @@ bugfix/update release - 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 `_) @@ -1432,7 +1432,7 @@ bugfix/update release - 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 `_) @@ -1458,7 +1458,7 @@ feature release - 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 `_) @@ -1647,7 +1647,7 @@ bugfix/update release * 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 `_) @@ -1660,20 +1660,20 @@ bugfix/update release * 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 `_), @@ -1681,30 +1681,30 @@ bugfix/update release 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 `_) + * 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 `_) @@ -1718,7 +1718,7 @@ bugfix/update release * 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 `_) @@ -2014,7 +2014,7 @@ bugfix/update release * 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 `_) @@ -3031,7 +3031,7 @@ feature release * 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 `_), + 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: