WIP: Damask 3.0.2 for StdEnv/2020

.gitignore

@@ -1,13 +1,26 @@
-.pydevproject
-.project
-LICENSE_HEADER
-*.pyc
-*.pyo
-*.nja
-build/
-dist/
-*egg-info/
-*.swp
-*.ropeproject/
-eb-*.log
-/MANIFEST
+# Ignore all
+*
+
+# Unignore all dirs
+!*/
+
+# Unignore some extensions
+!*.eb
+!*.py
+!*.txt
+!*.xml
+!*.patch
+!*.patch.gz
+!*.md
+!**/README
+
+# Unignore specific files
+!.gitignore
+!LICENSE
+!MANIFEST.in
+!README.rst
+!RELEASE_NOTES
+!setup.cfg
+!test/**
+!.pre-commit-config.yaml
+!checksums.json

RELEASE_NOTES

@@ -3,8 +3,131 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html.
 
-The latest version of easybuild-easyconfig provides 14,449 easyconfig files, for 2,667 different software packages,
-incl. 36 different (compiler) toolchains.
+The latest version of easybuild-easyconfig provides 15,020 easyconfig files, for 2,736 different software packages,
+incl. 37 different (compiler) toolchains.
+
+
+v4.6.0 (July 8th 2022)
+----------------------
+
+feature release
+
+- added easyconfigs for foss/2022a, intel/2022a common toolchains (#15755)
+- add easyconfig for gfbf/2022a toolchain (#15653, #15755)
+  - see also https://docs.easybuild.io/en/latest/Common-toolchains.html
+- added example easyconfig files for 24 new software packages:
+  - BLT (#15624), category_encoders (#15638), fio (#10321), FSON (#15721), G-PhoCS (#7619), GCTA (#15649),
+    Gibbs2 (#15702), InterProScan_data (#15717), Jorg (#15346), libopus (#15682), Minipolish (#15713),
+    mm-common (#15764), MONA (#15696), NetPyNE (#15606), pfind (#15685), regionmask (#15786), samplot (#15686),
+    SISSO (#15766), sklearn-pandas (#15637), STAR-CCM+ (#7398), SWIPE (#6795), topaz (#15739),
+    uncertainty-calibration (#15612), Virtuoso-opensource (#14102)
+- added additional easyconfigs for various supported software packages, including:
+  - AlphaFold 2.2.2, Arriba 2.3.0, Arrow 8.0.0, Bracken 2.7, CellRanger 7.0.0, Clp 1.17.7, CoinUtils 2.11.6,
+    cppy 1.2.1, deal.II 9.3.3, double-conversion 3.2.0, Doxygen 1.9.4, FLAC 1.3.4, fmt 7.1.1, FSL 6.0.5.1, GDAL 3.5.0,
+    gdbm 1.21, geopandas 0.11.0, GEOS 3.10.3, Ghostscript 9.56.1, GLibmm 2.66.4, Groovy 4.0.3, GULP 6.1, h5py 3.7.0,
+    HDF5 1.13.1, hifiasm 0.16.1, IGMPlot 2.6.9b, ImageMagick 7.1.0-37, InterProScan 5.55-88.0, IRkernel 1.3,
+    jemalloc 5.3.0, JsonCpp 1.9.5, Julia 1.7.3, Leptonica 1.82.0, libgeotiff 1.7.1, libgit2 1.4.3, libiconv 1.17,
+    libRmath 4.2.0, libsigc++ 2.10.8, libsndfile 1.1.0, libxc 5.2.3, libxml++ 2.42.1, line_profiler 3.5.1,
+    LittleCMS 2.13.1, MaSuRCA 4.0.9, mayavi 4.7.4, MetaEuk 5, mold 1.3.0, NCCL 2.12.12, netCDF 4.9.0, nettle 3.8,
+    networkx 2.8.4, NEURON 7.8.2, NLopt 2.7.1, nodejs 16.15.1, NSPR 4.34, NSS 3.79, nsync 1.25.0, nvtop 2.0.2,
+    Osi 0.108.7, p4est 2.8, parasail 2.5, Pillow 9.1.1, PLUMED 2.8.0, PnetCDF 1.12.3, PRISMS-PF 2.2, PROJ 9.0.0,
+    protobuf 3.19.4, protobuf-python 3.19.4, pyfaidx 0.7.0, PyOpenGL 3.1.6, pyproj 3.3.1, PyTorch 1.11.0, Qhull 2020.2,
+    Qt5 5.15.5, QuantumESPRESSO 7.1, Qwt 6.2.0, R 4.2.1, rasterio 1.2.10, Ray-project 1.13.0, RE2 2022-06-01,
+    redis-py 4.3.3, ReFrame 3.11.2, rioxarray 0.11.1, RNA-SeQC 2.4.2, Schrodinger 2022-2, Shapely 1.8.2, Siesta 4.1.5,
+    SimpleITK 2.1.1.2, SpectrA 1.0.1, TensorFlow 2.7.1, Tk 8.6.12, Tkinter 3.10.4, Transformers 4.20.1,
+    UCX-CUDA 1.12.1, utf8proc 2.7.0, WhatsHap 1.4, WPS 3.9.1, Xvfb 21.1.3
+- minor enhancements, including:
+  - add extensions to R v4.2.0: hypergeo (#15701), rtdists (#15734), geeM (#15810)
+  - add patch for GCCcore 11.3.0 to support using -fuse-ld=mold (#15715)
+  - add patch for porefoam to fix hardcoded mpirun command and take into account $POREFOAM_MPIRUN_CMD (#15730)
+- various bug fixes, including:
+  - switch to Rust 1.60.0 build dependency for bamtofastq, since build of fails with Rust 1.52.1 (#15636)
+  - avoid that pygmo v2.18.0 installs stuff in Python installation directory + add custom sanity check paths to pygmo easyconfigs (#15657)
+  - add patch for Mmg v5.6.0 to remove library CI tests that point to external sources (#15691)
+  - correct configopts in deal.II v9.1.1 easyconfig (#15692)
+  - add missing Python dependency for HPDBSCAN to fix unresolved %(pyshortver)s template (#15694)
+- other changes:
+   - disable flaky GPU test for TensorFlow 2.6.0 (#15824)
+
+
+v4.5.5 (June 8th 2022)
+----------------------
+
+update/bugfix release
+- add candidates for 2022a common toolchains: foss/2022.05 (#15561), intel/2022.05 (#15485)
+- added example easyconfig files for 35 new software packages:
+  - Albumentations (#15302), AMPtk (#15435), arosics (#15249), CellTypist (#15530), detectron2 (#15442),
+    EigenExa (#15234), Fastaq (#15332), FFTW.MPI (#15561), FreeBarcodes (#15350), gcloud (#15443),
+    GST-plugins-bad (#15446), gsutil (#15507), GTK4 (#15447), hector (#15397), i7z (#15236), libde265 (#15395),
+    libheif (#15395), ModelTest-NG (#15448), num2words (#15473), OGDF (#15407), panito (#15314),
+    parameterized (#15481), purge_dups (#15385), redis-py (#15475), ruamel.yaml (#15531), SCGid (#15065),
+    scPred (#15575), slow5tools (#15457), smooth-topk (#15506), SPOTPY (#15326), tmap (#14601), UCC (#14291),
+    Wayland (#11107), XGrafix (#15268), XPLOR-NIH (#15479)
+- added additional easyconfigs for various supported software packages, including:
+  - ABAQUS 2022, Arb 2.22.1, ARGoS 3.0.0, Arriba 2.2.1, astropy 5.0.4, ATK 2.38.0, Autotools 20220317,
+    Bader 1.04, Bazel 4.2.2 + 5.1.1, BDBag 1.6.3, binutils 2.38, biom-format 2.1.12, BLIS 0.9.0, Boost 1.79.0,
+    breseq 0.36.1, bx-python 0.8.13, cairo 1.17.4, CellRanger-ARC 2.0.1, CMake 3.23.1, cryoDRGN 1.0.0,
+    CUDA 11.7.0, cuDNN 8.4.1.50, cURL 7.83.0, DBus 1.14.0, eggnog-mapper 2.1.7, elfutils 0.187,
+    EvidentialGene 2022.01.14, expat 2.4.8, FlexiBLAS 3.2.0, FLINT 2.8.4, fontconfig 2.14.0, freebayes 1.3.6,
+    freeglut 3.2.2, freetype 2.12.1, FriBidi 1.0.12, GCC 9.5.0 + 11.3.0 + GCC 12.1.0, Gdk-Pixbuf 2.42.8,
+    geopandas 0.10.2, git 2.36.0, GLib 2.72.1, GMAP-GSNAP 2021-21-17, Go 1.18.1, GObject-Introspection 1.72.0,
+    Graphene 1.10.8, GST-plugins-base 1.20.2, GStreamer 1.20.2, GTDB-Tk 2.0.0, GTK3 3.24.33, gzip 1.12,
+    HarfBuzz 4.2.1, help2man 1.49.2, hwloc 2.7.1, hypothesis 6.46.7, Hypre 2.24.0, ICU 71.1, IGV 2.12.3,
+    IMB 2021.3, inferCNV 1.10.1, InterProScan 5.52, IQ-TREE 2.2.1, jax 0.3.9, json-c 0.16, LAPACK 3.10.1,
+    libarchive 3.6.1, libdeflate 1.10, libdrm 2.4.110, libedit 20210910, libepoxy 1.5.10, libfabric 1.15.1,
+    libglvnd 1.4.0, libjpeg-turbo 2.1.3, libreadline 8.1.2, librsb 1.3.0.1, librsvg 2.52.8, libtool 2.4.7,
+    libunwind 1.6.2, libxml2 2.9.13, LLVM 14.0.3, LocARNA 1.9.2.3, MACS2 2.2.7.1, magma 2.6.2, Mako 1.2.0,
+    Mathematica 13.0.0, MCL 14.137, MCR R2022a.1, Mesa 22.0.3, Meson 0.62.1, MIRA 5.0rc2, Mmg 5.6.0, mold 1.2.1, 
+    mosdepth 0.3.3, MrBayes 3.2.7a, MultiQC 1.12, MUMPS 5.5.0, muParser 2.3.3, ncurses 6.3, neptune-client 0.16.2, 
+    Nextflow 22.04.0, Nim 1.6.6, NTPoly 2.7.1, OpenMPI 4.1.4, openpyxl 3.0.9, OpenSSL 1.1.1n, OpenStackClient 5.8.0,
+    OSU-Micro-Benchmarks 5.9, pagmo 2.18.0, Pango 1.50.7, parallel-fastq-dump 0.6.7, PCRE2 10.40, Perl 5.34.1,
+    Pillow 9.1.0, PLINK 2.00a3.1, PMIx 4.1.2, PyAMG 4.2.3, pybind11 2.9.2, PyCairo 1.21.0, pygmo 2.18.0,
+    PyGObject 3.42.1, Python 3.10.4, R 4.2.0, RAxML-NG 1.1.0, R-bundle-Bioconductor 3.15, ReFrame 3.11.0,
+    RNA-Bloom 1.4.3, rnaQUAST 2.2.2, Rust 1.60.0, Sambamba 0.8.2, SAMtools 1.15.1, ScaLAPACK 2.2.0,
+    SciPy-bundle 2022.05, SeqKit 2.2.0, Shapely 1.8.1.post1, SpaceRanger 1.3.1, Spack 0.17.2, Spark 3.2.1,
+    SQLite 3.38.3, StringTie 2.2.1, SUMO 1.12.0, SuperLU 5.3.0, tbl2asn 20220427, Tcl 8.6.12, TCLAP 1.2.5,
+    tcsh 6.24.01, texlive 20220321, ToFu 1.5.0, UCX 1.12.1, util-linux 2.38, VEP 105, ViennaRNA 2.5.0,
+    vsc-mympirun 5.2.11, worker 1.6.13, X11 2022050, YAXT 0.9.2.1, Z3 4.8.16, Zip 3.0, zlib 1.2.12, zstd 1.5.2
+- minor enhancements, including:
+  - use OpenSSL wrapper dependency for CMake 3.18.4 with system toolchain (#15227)
+  - also build BLIS backend for FlexiBLAS v3.0.4 with GCC/10.3.0 (#15347)
+  - add extensions to R v4.1.2 + v4.2.0 easyconfigs:
+    - Hmsc (#15393), MonteCarlo + RhpcBLASctl (#15438), chkptstanr (#15540), chkptstanr + MLmetrics + renv (#15573)
+  - add extensions to R-bundle-Bioconductor 3.14 easyconfig: DNABarcodes (#15405)
+  - use redist source_urls for cuDNN > 7.5 (#15411)
+  - add download_instructions to Java 1.8 > 200 (#15412)
+  - update Arrow to use EasyBuild-provided versions of some dependencies and enable all compression codecs (#15512)
+  - add csh -> tcsh symlink in recent tcsh easyconfigs (#15571)
+  - allow external tools to be located elsewhere for ETE (#15578)
+  - add additional sanity check commands for IQ-TREE v2.2.1 (#15596)
+- various bug fixes, including:
+  - fix source URL for freetype 2.6.5 with foss/2016b (#14204)
+  - fix installation of easybuild-easyconfigs with setuptools>=61 by explicitly declaring there are no Python packages (#15206)
+  - use x.py to boostrap Rust so that build options are properly passed through (#15211)
+  - fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (#15280, #15615)
+  - add hwloc dependency to tbb v2021.4.0 (#15294)
+  - tweak find command used in preconfigopts in easyconfig for pkg-config v0.29.2 with system toolchain to avoid descending into other filesystems (#15313)
+  - remove pkg-config use from SeqLib configure patch (avoids problem due to faulty autoconf macro) (#15316)
+  - update source URL for isl in GCCcore easyconfigs (#15320)
+  - update source URLs for YAXT 0.9.x to fix download (#15323)
+  - define $HHLIB as path to HH-suite installation directory, required by Perl scripts (#15324)
+  - add missing parallel and tbl2asn dependencies for prokka 1.14.5 (#15360, #15381)
+  - add missing dependencies for libheif (libpng, libjpeg-turbo) (#15408)
+  - switch to configuring build of libheif with CMake so libde265 dependency is picked up (#15408)
+  - disable use of -ftree-vectorize for OpenFOAM v2112 with foss/2021b (#15495)
+  - add patch for OpenMPI 4.1.1 to support building using --with-cuda=internal (#15528, #15589)
+  - add patch to fix support for external PMIx v3.1 in OpenMPI v3.1.3 (#15566)
+  - also build shared library + fix $PYTHONPATH for gmsh 4.9.0 (#15579)
+  - add patch for GLib 2.68.2 to fix use of close_range (#15594)
+  - fix download of thrift 0.12.0 for Arrow 0.16.0 (#15597)
+  - add Bison and flex build dependencies to SCOTCH 6.1.x (#15618)
+  - add alternative checksums for class, nnet, spatial extensions in R v4.2.0 easyconfig (#15619)
+  - add missing dependencies + switch to non-static build for Arriba v2.1.0 (#15623)
+- other changes:
+  - add R dependency to vcflib 1.0.3, and move from GCC/11.2.0 to foss/2021b toochain (#15216)
+  - update fallback version for OpenSSL 1.1 wrapper to v1.1.1o (#15592)
+  - install sklearn meta-package with scikit-learn v1.0.1 (#15613)
+  - switch from pkg-config to pkgconf as build dependency for OpenSSL wrapper easyconfigs (#15616, #15617)
 
 
 v4.5.4 (March 31st 2022)

easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-9.3.0.eb

@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = '4ti2'
+version = '1.6.9'
+
+homepage = 'https://4ti2.github.io/'
+description = "A software package for algebraic, geometric and combinatorial problems on linear spaces"
+
+toolchain = {'name': 'GCC', 'version': '9.3.0'}
+
+source_urls = ['https://github.com/%(name)s/%(name)s/archive/']
+sources = ['Release_%s.tar.gz' % version.replace('.', '_')]
+checksums = ['7b1015718102d8cd4dc2de64f69094fdba0bc69a1878ada5960979b171ff89e4']
+
+builddependencies = [
+    ('Autotools', '20180311'),
+]
+
+dependencies = [
+    ('GMP', '6.2.0'),
+    ('GLPK', '4.65'),
+]
+
+preconfigopts = "./autogen.sh && "
+
+sanity_check_paths = {
+    'files': ['bin/4ti2gmp', 'bin/4ti2int32', 'bin/4ti2int64'],
+    'dirs': ['include/%(name)s', 'lib', 'share/%(name)s'],
+}
+
+moduleclass = 'math'

easybuild/easyconfigs/__archive__/__archive__/i/ictce-5.2.0.eb

@@ -0,0 +1,21 @@
+easyblock = "Toolchain"
+
+name = 'ictce'
+version = '5.2.0'
+deprecated = "ictce toolchains are deprecated"
+
+homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
+description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI &
+ Intel MKL."""
+
+toolchain = SYSTEM
+
+compver = '2013.2.146'
+dependencies = [
+    ('icc', compver),
+    ('ifort', compver),
+    ('impi', '4.1.0.030', '', ('iccifort', compver)),
+    ('imkl', '11.0.2.146', '', ('iimpi', version)),
+]
+
+moduleclass = 'toolchain'

easybuild/easyconfigs/__archive__/__archive__/i/ictce-5.3.0.eb

@@ -0,0 +1,22 @@
+easyblock = "Toolchain"
+
+name = 'ictce'
+version = '5.3.0'
+deprecated = "ictce toolchains are deprecated"
+
+homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
+description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI &
+ Intel MKL."""
+
+toolchain = SYSTEM
+
+compsuffix = '.3.163'
+compver = '2013' + compsuffix
+dependencies = [
+    ('icc', compver),
+    ('ifort', compver),
+    ('impi', '4.1.0.030', '', ('iccifort', compver)),
+    ('imkl', '11.0' + compsuffix, '', ('iimpi', version)),
+]
+
+moduleclass = 'toolchain'

easybuild/easyconfigs/__archive__/__archive__/i/ictce-5.4.0.eb

@@ -0,0 +1,23 @@
+easyblock = "Toolchain"
+
+name = 'ictce'
+version = '5.4.0'
+deprecated = "ictce toolchains are deprecated"
+
+homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
+description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI &
+ Intel MKL."""
+
+toolchain = SYSTEM
+
+compsuffix = '.4.183'
+compver = '2013' + compsuffix
+
+dependencies = [
+    ('icc', compver),
+    ('ifort', compver),
+    ('impi', '4.1.0.030', '', ('iccifort', compver)),
+    ('imkl', '11.0' + compsuffix, '', ('iimpi', version)),
+]
+
+moduleclass = 'toolchain'

easybuild/easyconfigs/__archive__/__archive__/i/ictce-5.5.0.eb

@@ -0,0 +1,22 @@
+easyblock = "Toolchain"
+
+name = 'ictce'
+version = '5.5.0'
+deprecated = "ictce toolchains are deprecated"
+
+homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
+description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI &
+ Intel MKL."""
+
+toolchain = SYSTEM
+
+compsuffix = '.5.192'
+compver = '2013' + compsuffix
+dependencies = [
+    ('icc', compver),
+    ('ifort', compver),
+    ('impi', '4.1.1.036', '', ('iccifort', compver)),
+    ('imkl', '11.0' + compsuffix, '', ('iimpi', version)),
+]
+
+moduleclass = 'toolchain'

easybuild/easyconfigs/__archive__/__archive__/i/ictce-6.1.5.eb

@@ -0,0 +1,23 @@
+easyblock = "Toolchain"
+
+name = 'ictce'
+version = '6.1.5'
+deprecated = "ictce toolchains are deprecated"
+
+homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
+description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI &
+ Intel MKL."""
+
+toolchain = SYSTEM
+
+suff = '1.106'
+compver = '2013_sp1.%s' % suff
+
+dependencies = [
+    ('icc', compver),
+    ('ifort', compver),
+    ('impi', '4.1.3.045', '', ('iccifort', compver)),
+    ('imkl', '11.1.%s' % suff, '', ('iimpi', version)),
+]
+
+moduleclass = 'toolchain'

easybuild/easyconfigs/__archive__/__archive__/i/ictce-6.2.5.eb

@@ -0,0 +1,23 @@
+easyblock = "Toolchain"
+
+name = 'ictce'
+version = '6.2.5'
+deprecated = "ictce toolchains are deprecated"
+
+homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
+description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI &
+ Intel MKL."""
+
+toolchain = SYSTEM
+
+suff = '2.144'
+compver = '2013_sp1.%s' % suff
+
+dependencies = [
+    ('icc', compver),
+    ('ifort', compver),
+    ('impi', '4.1.3.049', '', ('iccifort', compver)),
+    ('imkl', '11.1.%s' % suff, '', ('iimpi', version)),
+]
+
+moduleclass = 'toolchain'

easybuild/easyconfigs/__archive__/__archive__/i/ictce-7.1.2.eb

@@ -0,0 +1,23 @@
+easyblock = "Toolchain"
+
+name = 'ictce'
+version = '7.1.2'
+deprecated = "ictce toolchains are deprecated"
+
+homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
+description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI &
+ Intel MKL."""
+
+toolchain = SYSTEM
+
+suff = '0.090'
+compver = '2015.%s' % suff
+
+dependencies = [                                         # version/released
+    ('icc', compver),                                    # Jul 28th 2014
+    ('ifort', compver),                                  # Jul 28th 2014
+    ('impi', '5.0.1.035', '', ('iccifort', compver)),    # Aug 26th 2014
+    ('imkl', '11.2.%s' % suff, '', ('iimpi', version)),  # Aug 26th 2014
+]
+
+moduleclass = 'toolchain'

easybuild/easyconfigs/__archive__/__archive__/i/ictce-7.3.5.eb

@@ -0,0 +1,23 @@
+easyblock = "Toolchain"
+
+name = 'ictce'
+version = '7.3.5'
+deprecated = "ictce toolchains are deprecated"
+
+homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
+description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI &
+ Intel MKL."""
+
+toolchain = SYSTEM
+
+suff = '3.187'
+compver = '2015.%s' % suff
+
+dependencies = [                                         # version/released
+    ('icc', compver),                                    # Apr 13th 2015
+    ('ifort', compver),                                  # Apr 13th 2015
+    ('impi', '5.0.3.048', '', ('iccifort', compver)),    # Feb 10th 2015
+    ('imkl', '11.2.%s' % suff, '', ('iimpi', version)),  # Apr 13th 2015
+]
+
+moduleclass = 'toolchain'