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release EasyBuild v4.2.2 #638

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e30b6e1
Add paragraph explaining exts_list options.
kelseymh Apr 17, 2020
ad027b1
Remove modifications under version-specific. Start adding section on…
kelseymh Apr 21, 2020
85a105f
Expand new 'Module extensions' section with example code and cross-re…
kelseymh Apr 22, 2020
fdd50c3
Clean up formatting of new 'Module extensions'
kelseymh Apr 23, 2020
544c236
Update exts_list to be explicit about options.
kelseymh Apr 25, 2020
0a97a7d
Improve description of exts_list options, and how they differ from ma…
kelseymh Apr 25, 2020
3a4d12c
Fix literal quoting in Module Extensions section.
kelseymh Apr 25, 2020
b9701ae
Add section explaining how to use self.cfg in an EasyBlock, for issue…
kelseymh Apr 25, 2020
a88fda3
Merge upstream branch 'develop' into 3266_exts_list_options
kelseymh May 8, 2020
91b9697
Expand explanation of self.cfg[] vs. local self.variable usage.
kelseymh May 8, 2020
bf4df40
Use proper version number in 'pyCAP' example of downloading extension…
kelseymh May 8, 2020
06b015e
Use version-number with exaple of exts_list git_config.
kelseymh May 8, 2020
b27ba3a
Merge upstream 'develop' from easybuilders into 3266_exts_list_options
kelseymh May 27, 2020
6cfd6f8
Updated extensions section to reflect PR #3294 using 'sources', not '…
kelseymh Jun 9, 2020
03b3ee9
Fix misspelling of 'preferred'.
kelseymh Jun 9, 2020
25ff2e2
Per @ocaisa, add 'namd' to Codespell 'ignore-words-list'.
kelseymh Jun 9, 2020
ba320e2
Add 'namd' to igore-words-list for Travis CI as well, per @ocaisa.
kelseymh Jun 9, 2020
fb06f79
Improve explanation of using self.cfg['key'] vs. self.key; replace Ea…
kelseymh Jun 22, 2020
2407c0b
Merge pull request #617 from kelseymh/3266_exts_list_options
Jun 22, 2020
cbeee49
Clarify use of easyblock 'properties' (look like data member names) w…
kelseymh Jul 3, 2020
2feaae8
Merge pull request #634 from kelseymh/Improvements_to_PR617
boegel Jul 4, 2020
1889b6c
Updated Davide Vanzo affiliation and email
vanzod Jul 7, 2020
c65a705
Merge pull request #635 from vanzod/dv_ms_email
boegel Jul 7, 2020
c75d131
update release notes for EasyBuild v4.2.2
migueldiascosta Jul 8, 2020
1023f01
auto-update docs for EasyBuild v4.2.2
boegel Jul 8, 2020
206bffe
Merge pull request #636 from migueldiascosta/eb422
boegel Jul 8, 2020
627666b
Merge pull request #637 from boegel/eb422_auto_update_docs
migueldiascosta Jul 8, 2020
928282f
bump version to 4.2.2
migueldiascosta Jul 8, 2020
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update release notes for EasyBuild v4.2.2
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migueldiascosta committed Jul 8, 2020

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ob-stripe Olivier Bellone
commit c75d13191818655c11684007001ef101e75a0734
1 change: 1 addition & 0 deletions docs/Changelog.rst
Original file line number Diff line number Diff line change
@@ -5,6 +5,7 @@ Changelog for EasyBuild documentation

(for EasyBuild release notes, see :ref:`release_notes`)

* **release 20200708.01** (`July 8th 2020`): update release notes for EasyBuild v4.2.2 (see :ref:`release_notes_eb422`)
* **release 20200520.01** (`May 20th 2020`): update release notes for EasyBuild v4.2.1 (see :ref:`release_notes_eb421`)
* **release 20200414.01** (`Apr 14th 2020`):

135 changes: 132 additions & 3 deletions docs/Release_notes.rst
Original file line number Diff line number Diff line change
@@ -3,12 +3,141 @@
EasyBuild release notes
=======================

The latest version of EasyBuild provides support for building and installing **1,978** different software packages,
including 31 different (compiler) toolchains. It contains 219 software-specific easyblocks and 37 generic easyblocks,
alongside 9,894 easyconfig files.
The latest version of EasyBuild provides support for building and installing **2,013** different software packages,
including 31 different (compiler) toolchains. It contains 222 software-specific easyblocks and 37 generic easyblocks,
alongside 10,147 easyconfig files.

.. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 <eb4_changes_overview>`.

.. _release_notes_eb422:

EasyBuild v4.2.2 (July 8th 2020)
--------------------------------

bugfix/update release

**framework**

* various enhancements, including:

* add support for using ``sources`` and ``git_config`` for extensions in ``exts_list`` (`#3294 <https://github.com/easybuilders/easybuild-framework/pull/3294>`_)
* add support for software minver template (like ``%(pyminver)s``, etc.) (`#3344 <https://github.com/easybuilders/easybuild-framework/pull/3344>`_, `#3345 <https://github.com/easybuilders/easybuild-framework/pull/3345>`_)
* add support for updating dictionary or tuple easyconfig parameters with ``self.cfg.update`` (`#3356 <https://github.com/easybuilders/easybuild-framework/pull/3356>`_)

* various bug fixes, including:

* fix crash in ``--avail-easyconfig-constants`` when using ``--output-format=rst`` + ensure sorted output (`#3341 <https://github.com/easybuilders/easybuild-framework/pull/3341>`_)
* always take into account ``builddependencies`` when generating template values, also when we're not iterating over ``builddependencies`` (`#3346 <https://github.com/easybuilders/easybuild-framework/pull/3346>`_)
* fix running command as ``easybuild`` user in generated Singularity definition file (`#3347 <https://github.com/easybuilders/easybuild-framework/pull/3347>`_)
* allow ignoring ``versionsuffix`` in ``--try-update-deps`` (`#3350 <https://github.com/easybuilders/easybuild-framework/pull/3350>`_, `#3353 <https://github.com/easybuilders/easybuild-framework/pull/3353>`_)
* retain order of paths when generating ``prepend_path`` statements for module file (don't sort them alphabetically) (`#3367 <https://github.com/easybuilders/easybuild-framework/pull/3367>`_)
* also put easyblocks used by extensions in ``reprod`` directory (`#3375 <https://github.com/easybuilders/easybuild-framework/pull/3375>`_)
* also copy template values in ``EasyConfig.copy`` method to ensure they are defined when installing extensions (`#3377 <https://github.com/easybuilders/easybuild-framework/pull/3377>`_)
* skip lines that start with ``module-version`` when determining whether a module exists in ``ModulesTool.exist`` (`#3379 <https://github.com/easybuilders/easybuild-framework/pull/3379>`_)

**easyblocks**

* 3 new software-specific easyblocks:

* LLVM (`#2065 <https://github.com/easybuilders/easybuild-easyblocks/pull/2065>`_), Scipion (`#1847 <https://github.com/easybuilders/easybuild-easyblocks/pull/1847>`_), XALT (`#1942 <https://github.com/easybuilders/easybuild-easyblocks/pull/1942>`_)

* minor enhancements, including:

* use ``wclean -platform`` instead of ``wcleanPlatform`` for OpenFOAM v2006 & newer (`#2088 <https://github.com/easybuilders/easybuild-easyblocks/pull/2088>`_)

* various bug fixes, including:

* only build OpenCV with IPP support on x86_64 systems (`#2056 <https://github.com/easybuilders/easybuild-easyblocks/pull/2056>`_)
* make sure ``CFLAGS`` and ``MYCFLAGS`` are used in Lua easyblock (`#2062 <https://github.com/easybuilders/easybuild-easyblocks/pull/2062>`_)
* also accept ``exist_lic`` as valid value for ``license_file`` in IntelBase easyblock (`#2067 <https://github.com/easybuilders/easybuild-easyblocks/pull/2067>`_)
* fix minor bug in shared libs handling and correctly setup SuiteSparse variables in Trilinos easyblock (`#2071 <https://github.com/easybuilders/easybuild-easyblocks/pull/2071>`_)
* make sure ``PythonBundle`` uses correct ``python`` command in extensions filter + also add ``lib64/python*/site-packages`` to ``$PYTHONPATH`` (if it exists) (`#2075 <https://github.com/easybuilders/easybuild-easyblocks/pull/2075>`_, `#2081 <https://github.com/easybuilders/easybuild-easyblocks/pull/2081>`_)
* fix build environment for WRF by patching shebang in compile script (`#2079 <https://github.com/easybuilders/easybuild-easyblocks/pull/2079>`_)
* fix order of ``intel64/lib`` paths in generated module for impi (and drop ``intel64/lib/release_mt``) (`#2080 <https://github.com/easybuilders/easybuild-easyblocks/pull/2080>`_)
* set ``$XDG_CACHE_HOME`` to avoid abuse of ``$HOME/.cache/pip`` when installing DOLFIN (`#2082 <https://github.com/easybuilders/easybuild-easyblocks/pull/2082>`_)
* make VMD easyblock Python 3 compatible (`#2083 <https://github.com/easybuilders/easybuild-easyblocks/pull/2083>`_)
* rename include-fixed subdirectory in GCC installation to avoid problems after OS upgrade (`#2087 <https://github.com/easybuilders/easybuild-easyblocks/pull/2087>`_, `#2093 <https://github.com/easybuilders/easybuild-easyblocks/pull/2093>`_, `#2094 <https://github.com/easybuilders/easybuild-easyblocks/pull/2094>`_)
* use glob pattern to determine name of Mathematica installation script (`#2089 <https://github.com/easybuilders/easybuild-easyblocks/pull/2089>`_)
* use ``mpirun`` for sanity check commands in LAMMPS easyblock (`#2096 <https://github.com/easybuilders/easybuild-easyblocks/pull/2096>`_)

**easyconfigs**

* added easyconfigs for 2 new toolchains:

* golf/2020a (`#10672 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10672>`_)

* intel/2020.06, based on intel/2020a but with impi 2018 update 5 (`#10864 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10864>`_)

* added example easyconfig files for 36 new software packages:

* AmrPlusPlus (`#9919 <https://github.com/easybuilders/easybuild-easyconfigs/pull/9919>`_), arrow (`#10882 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10882>`_), attrdict (`#10827 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10827>`_), Cartopy (`#10685 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10685>`_), dm-tree (`#10775 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10775>`_), dotNET-SDK (`#10661 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10661>`_),
FLAIR (`#10860 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10860>`_), fastqsplitter (`#10706 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10706>`_), GLFW (`#10709 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10709>`_), git-extras (`#10440 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10440>`_), hl7apy (`#10728 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10728>`_), hyperopt (`#10735 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10735>`_),
IgBLAST (`#10889 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10889>`_), IntelDAAL (`#9848 <https://github.com/easybuilders/easybuild-easyconfigs/pull/9848>`_), ichorCNA (`#10595 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10595>`_), MARS (`#10691 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10691>`_), MITObim (`#10897 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10897>`_), MUST (`#10849 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10849>`_),
mhcnuggets (`#9743 <https://github.com/easybuilders/easybuild-easyconfigs/pull/9743>`_), PAUP (`#10830 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10830>`_), Percolator (`#10665 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10665>`_), PyBerny (`#10885 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10885>`_), poetry (`#10884 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10884>`_), pycocotools (`#10806 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10806>`_),
python-hl7 (`#10673 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10673>`_), SHAPEIT4 (`#10814 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10814>`_), SYMPHONY (`#10058 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10058>`_), SunPy (`#10676 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10676>`_), sdsl-lite (`#10691 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10691>`_),
TEtranscripts (`#10909 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10909>`_, `#10921 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10921>`_), Tombo (`#10646 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10646>`_), tensorboardX (`#10774 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10774>`_), Unidecode (`#10828 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10828>`_), WHAM (`#10736 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10736>`_), XALT (`#9792 <https://github.com/easybuilders/easybuild-easyconfigs/pull/9792>`_),
Xvfb (`#10512 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10512>`_)

* added additional easyconfigs for various supported software packages, including:

* Armadillo 9.900.1, astropy 4.0.1, BLAST+ 2.10.1, BioPerl 1.7.7, Blitz++ 1.0.2,
Bonito 0.2.0, bokeh 2.0.2, CFITSIO 3.48, CGAL 4.14.3, CLHEP 2.4.1.3, cutadapt 2.10,
dask 2.18.1, Elk 6.3.2, GATE 9.0, GLM 0.9.9.8, GRASS 7.8.3, Geant4 10.6,
geopandas 0.8.0, giflib 5.2.1, HDF5 1.12.0, HISAT2 2.2.0, Hadoop 2.10.0,
IPython 7.15.0, inferCNV 1.2.1, Julia 1.4.2, LibSoup 2.70.0, MATIO 1.5.17,
MRtrix 3.0.0, Mathematica 12.1.1 MultiQC 1.9, NGS 2.10.5, NiBabel 3.1.0,
Nipype 1.4.2, ncbi-vdb 20.10.7, numba 0.50.0, OpenBabel 3.1.1, OpenFOAM v2006,
PDT 3.25.1, PRSice 2.3.1, ParaView 5.8.0, ParmEd 3.2.0, PyQt5 5.13.2,
Pysam 0.16.0.1, parallel 20200522, plotly.py 4.8.1, pybedtools 0.8.1,
ROOT 6.20.04, ReFrame 3.0, Roary 3.13.0, rjags 4-10, rstudio 1.3.959,
SPAdes 3.14.1, SRA-Toolkit 2.10.8, Saxon-HE 9.9.1.7, Seaborn 0.10.1,
Seurat 3.1.5, SimPEG 0.14.1, Spark 2.4.5, StringTie 2.1.3, scikit-allel 1.2.1,
scikit-learn 0.23.1, snpEff 4.3t, Valgrind 3.16.1, VarScan 2.4.4,
vsc-mympirun 5.1.0, WebKitGTK+ 2.27.4, wxPython 4.0.7.post2, zarr 2.4.0

* minor enhancements, including:

* add extensions to R 4.0.0 easyconfig: drgee + stdReg (`#10833 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10833>`_), copCAR (`#10911 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10911>`_), ngspatial (`#10913 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10913>`_), drugCombo (`#10914 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10914>`_)
* add extensions to R-bundle-Bioconductor 3.11 easyconfig: BSgenome.Cfamiliaris.UCSC.canFam3 (`#10840 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10840>`_), SingleR (`#10904 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10904>`_)
* include extra extension and support for MPI in MAFFT v7.453 and v7.470 (`#10853 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10853>`_)
* add Array::Transpose to Perl (`#10878 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10878>`_)

* various bug fixes, including:

* fix dependencies and configuration of CoinUtils ecosystem (`#10450 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10450>`_)
* fix Togl configure patch so that it completely ignores ``TCL_SRC_DIR`` and ``TK_SRC_DIR`` (`#10662 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10662>`_)
* change Xerces-C++ to official CMakeMake build (fixes missing links to curl) (`#10664 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10664>`_)
* add ``-fPIC`` to ``toolchainopts`` in easyconfig for Lua 5.3.5 with system toolchain (`#10671 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10671>`_)
* remove hardcoded X86 target in LLVM easyconfigs (`#10677 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10677>`_)
* switch to https ``homepage`` and ``source_urls`` in libGLU easyconfigs (`#10686 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10686>`_)
* add patch for h5py 2.10.0 to avoid triggering ``MPI_Init`` at import (`#10687 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10687>`_)
* add alternative checksum for pkgmaker, doRNG, cobs extension in R 3.6.0 easyconfigs (`#10692 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10692>`_)
* update UDUNITS ``source_urls`` to https sources (`#10693 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10693>`_)
* add missing M4 to netCDF-Fortran easyconfigs using 2020a toolchain (#10695, `#10697 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10697>`_)
* add Rgraphviz patch to R-bundle-Bioconductor easyconfigs (`#10710 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10710>`_)
* add M4 builddependency to SuiteSparse 2019b easyconfigs (`#10720 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10720>`_)
* make sure WHAM is built with correct compiler (`#10736 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10736>`_)
* define ``MAX_JOBS`` in easyconfigs of PyTorch from v1.1.0 to v1.4.0 (`#10772 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10772>`_)
* add dm-tree and lz4 as dependencies to Ray v0.8.4 (`#10775 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10775>`_)
* fix source URL in recent ant easyconfigs (`#10790 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10790>`_)
* bump versions of GO.gb/org.Hs.eg.db/PFAM.db extensions in Bioconductor 3.11 bundle, since sources for old versions have disappeared (`#10791 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10791>`_)
* add patch to Armadillo easyconfigs using the foss toolchain to prevent it from picking up MKL if installed system-wide (`#10812 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10812>`_)
* add missing kerneltree extension in FLAIR easyconfig (`#10860 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10860>`_)
* fix source URLs in Eigen 3.2.* (`#10872 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10872>`_) and 3.3.* (`#10869 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10869>`_) easyconfigs
* refer to issue in GitHub repo in configparser patch, since Bitbucket repo is disappearing (`#10873 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10873>`_)
* switch to github.com source URL for MetaPhlAn (`#10874 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10874>`_)
* switch to GitHub sources for ScientificPython 2.9.4 (`#10875 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10875>`_)
* switch to GitHub source URL for HPDBSCAN (`#10876 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10876>`_)
* download x265 3.2/3.3 sources from ``bitbucket.org/multicoreware/x265_git`` (`#10905 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10905>`_)
* fix download URL for libatomic in gc 7.6.12 easyconfigs (`#10915 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10915>`_)
* fix ``sanity_check_paths`` in CFITSIO-3.48-GCCcore-9.3.0.eb easyconfig (`#10917 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10917>`_)
* add missing dependencies for geopandas 0.7.0 (`#10923 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10923>`_)

* other changes:

* rename OpenPyXL 2.6.4 easyconfig to openpyxl (`#10916 <https://github.com/easybuilders/easybuild-easyconfigs/pull/10916>`_)


.. _release_notes_eb421:

EasyBuild v4.2.1 (May 20th 2020)
4 changes: 2 additions & 2 deletions docs/conf.py
Original file line number Diff line number Diff line change
@@ -41,9 +41,9 @@
# other places throughout the built documents.
#
# The short X.Y version.
version = '4.2.1' # this is meant to reference the version of EasyBuild
version = '4.2.2' # this is meant to reference the version of EasyBuild
# The full version, including alpha/beta/rc tags.
release = '20200520.0' # this is meant to reference the version of the documentation itself
release = '20200708.0' # this is meant to reference the version of the documentation itself

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used: