Merge pull request #10385 from migueldiascosta/eb420

bump version and update release notes for EasyBuild v4.2.0

RELEASE_NOTES

@@ -3,9 +3,116 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
-The latest version of easybuild-easyconfig provides 8,964 easyconfig files, for 1,798 different software packages,
+The latest version of easybuild-easyconfig provides 9,462 easyconfig files, for 1,912 different software packages,
 incl. 31 different (compiler) toolchains.
 
+v4.2.0 (April 14th 2020)
+------------------------
+
+feature release
+
+- added example easyconfig files for 114 new software packages:
+  - ABRA2 (#10272), ABRicate (#10310), ADIOS (#10036), aNCI (#9929), any2fasta (#10310), apex (#10269),
+    archspec (#9898), ArviZ (#10366), autopep8 (#9626), BAMSurgeon (#10330), BatMeth2 (#10323),
+    BiG-SCAPE (#10352), BinSanity (#10001), Bonito (#10269), BSMAPz (#10283), BSseeker2 (#10039),
+    BUStools (#9838), Cbc (#10052), Cgl (#10048), CGmapTools (#10288), Clp (#10033), CoinUtils (#9937),
+    dtcwt (#9695), ELSI (#9857), EnsEMBLCoreAPI (#8734), fastq-pair (#9894), FigureGen (#10076), Fiona (#10321),
+    FuSeq (#10004), GenomeTools (#9797), GraphMap2 (#10299), GRASP (#9896), Groovy (#9809), gsport (#9821),
+    gubbins (#9689), igv-reports (#9977), inferCNV (#9686), iVar (#10291), joypy (#10212), JupyterLab (#9752),
+    kma (#10259), LAMMPS (#10371), lancet (#10271), libBigWig (#10006), libGridXC (#9858), libPSML (#5859),
+    LtrDetector (#10343), manta (#5104), medImgProc (#10228), MedPy (#9748), Mini-XML (#10036), mkl_fft (#9887),
+    Monocle3 (#9825), MoreRONN (#10255), motionSegmentation (#10228), NanoComp (#10212), NanoFilt (#10212),
+    nanoget (#10212), nanomath (#10212), NanoPlot (#10212), ngspice (#9922), ntEdit (#9836), ntHits (#9833),
+    occt (#9939), OCNet (#9955), OpenAI-Gym (#10347), OpenPIV (#9959), OpenPyXL (#10115), orca (#9518),
+    Osi (#10361), PartitionFinder (#9983), pauvre (#10212), polymake (#9904), pretty-yaml (#10041)),
+    PRSice (#9988), pycodestyle (#9626), pydot (#9899), pygraphviz (#9969), pylift (#10051), PyMC3 (#10279),
+    pyparsing (#9983), PyRe (#10095), python-weka-wrapper3 (#9704), PyTorch-Geometric (#9995), qcat (#10244),
+    RAxML-NG (#9990), Ray (#10302), rclone (#7934), Red (#9856), rstanarm (#9964), scikit-build (#9762),
+    scVelo (#9805), SECAPR (#9721), segmentation-models (#10211), SentencePiece (#10192), SEPP (#10047),
+    Shapely (#10309), Singular (#10030), SLATEC (#7529), spatialreg (#9767), split-seq (#9749), spoa (#9705),
+    SSN (#9955), STEAK (#10337), stpipeline (#9736), SVG (#9905), Togl (#9868), torchtext (#10193),
+    units (#9682), UQTk (#10279), WildMagic (#10044), Winnowmap (#10005), xtb (#9993), Zip (#9972)
+- added additional easyconfigs for various supported software packages, including:
+  - ABySS 2.1.5, Arrow 0.16.0, BCFtools 1.10.2, BEDTools 2.29.2, BUSCO 4.0.5, BerkeleyGW 2.1.0, binutils 2.34,
+    CVXPY 1.0.28, CharLS 2.1.0, CheckM 1.1.2, Clang 10.0.0, CppUnit 1.15.1, canu 1.9, cutadapt 2.8,
+    DIAMOND 0.9.30, davix 0.7.5, ELPA 2019.11.001, FastANI 1.3, FastQC 0.11.9, Ferret 7.5.0, GATK 4.1.4.1,
+    GCCcore 9.3.0, GDB 9.1, GMAP-GSNAP-2019-09-12, GObject-Introspection 1.63.1,  GPAW 20.1.0, GROMACS 2020,
+    GTDB-Tk 1.0.2, GTK+ 3.24.13, Go 1.14.1, Gradle 6.1.1, GraphicsMagick 1.3.34, Graphviz 2.42.2, Gurobi 9.0.1,
+    gSOAP 2.8.100, gnuplot 5.2.8, gtest 1.10.0, HDDM 0.7.5, HTSlib 1.10.2, HarfBuzz 2.6.4, Horovod 0.19.1,
+    Hypre 2.18.2, IGV 2.8.0, IQ-TREE 1.6.12, IRkernel 1.1, iccifort 2020.0.166, igraph 0.8.0, impi 2019.6.166,
+    ispc 1.12.0, Java 13(.0.2), Julia 1.4.0, Keras 2.3.1, Kraken2 2.0.8-beta, kim-api 2.1.3, LAST 1045,
+    LASTZ 1.04.03, LLVM 9.0.1 + 10.0.0, LMfit 0.9.14, LS-PrePost 4.7.8, likwid 5.0.1, MAFFT 7.453,
+    MATLAB 2019b, MMseqs2 10, Maven 3.6.3, Meson 0.53.1, MethylDackel 0.5.0, Mono 6.8.0.105, medaka 0.12.0,
+    Nextflow 20.01.0, ncdf4 1.17, netcdf4-python 1.5.3, nodejs 12.16.1, numba 0.47.0, numexpr 2.7.1,
+    Octave 5.1.0, OpenBLAS 0.3.8, OpenBabel 3.0.0, OpenCV 4.2.0, OpenFOAM-Extend 4.1-20191120, OrthoFinder 2.3.11,
+    PETSc 3.12.4, PGI 19.10, PMIx 2.2.1, Pango 1.44.7, PyTables 3.6.1, PyTorch 1.4.0, parasail 2.4.1,
+    pydicom 1.4.2, pyproj 2.4.2, Qhull 2019.1, QuantumESPRESSO 6.5, R-bundle-Bioconductor 3.10, RDKit 2019.09.3
+    Racon 1.4.10, ReFrame 2.21, Ruby 2.7.1, rjags 4-9, rpy2 3.2.6, SLEPc 3.12.2, SPAdes 3.14.0,
+    SPAdes 3.14.0, STAR-Fusion 1.8.1, STAR 2.7.3a, Seaborn 0.10.0, SeqAn 1.4.2, Seurat 3.1.2, SimpleElastix 1.1.0,
+    SimpleITK 1.2.4, Stacks 2.5, Stata 16, StringTie 2.1.0, scikit-optimize 0.7.4, statsmodels 0.11.0,
+    TensorFlow 1.15.2 + 2.0.1, Tkinter 2.7.16, Trim_Galore 0.6.5, Trimmomatic 0.39, Trinity 2.10.0, tbb 2020.2,
+    tqdm 4.41.1, XCrySDen 1.6.2, XGBoost 0.90, xarray 0.15.1, xmlf90 1.5.4,
+- minor enhancements, including:
+  - add easyconfig for Java 11.0.6 on ppc64le and alter the Java 11 wrapper to support both x86_64 and ppc64le (#9371)
+  - add additional extensions for R: HiddenMarkov (#9685), lmerTest (#9853), VSURF + Rborist (#10355)
+  - change Mesa 19.1.7 + 19.2.1 easyconfigs to use custom easyblock for Mesa (#9764)
+  - build shared libs and install header files for Ghostscript (#9785)
+  - add MUMPS as dependency in PETSc 3.12.4 easyconfigs (#9880, #9891)
+  - add Perl extensions: Term::ReadLine::Gnu (#9901), URI::Escape and Set::IntervalTree (#10049)
+  - add dat directory to aNCI (#9929)
+  - add patch to create a symlink from libsvm.so.$(SHVER) to libsvm.so in LIBSVM easyconfigs (#10045)
+  - build SUNDIALS with 'pic' (#10278)
+  - add BSgenome.Hsapiens.UCSC.hg38 + MEDIPS extensions to R-bundle-Bioconductor v3.10 (#10298)
+  - fix checksums for mkl-dnn and tbb extensions (moved to oneAPI repo) in PyTorch easyconfigs (#10367)
+  - update Java/1.8 wrapper to Java/1.8.0_241.eb (#10305)
+- various bug fixes, including:
+  - use CMake for building double-conversion (#9659)
+  - update recent libdrm easyconfigs to use custom easyblock & avoid hardcoded x86-specific sanity check (#9694)
+  - add alternate checksum for OpenMolcas 18.09 (#9701)
+  - use Github to download releases for MariaDB-connector-c (#9702)
+  - add -DOMPI_SKIP_MPICXX in configopts for MathGL, to avoid using mpicxx during build (#9703)
+  - make installing independent of build folder in pybind11 easyconfig (#9738)
+  - add Lua as a dependency to gnuplot (#9773)
+  - stick to http:// source URLS for ISL in GCCcore easyconfigs, since https:// doesn't work (#9784)
+  - add alternative checksums for farver/fracdiff/pkgmaker/rngtools/doRNG/cobs extensions in R 3.6.2 easyconfigs (#9789)
+  - add patch for OpenBLAS 0.3.4 w/ GCC/8.2.0-2.31.1 to fix broken tests (#9865)
+  - revert removal of AVX512 vmovd with 64-bit operands in binutils 2.32 easyconfigs (#9866)
+  - fix inline asm in dscal: mark x, x1 as clobbered, in OpenBLAS 0.3.8 (#9867)
+  - add missing sanity_check_commands to cutadapt v1.18 and v2.7 easyconfigs (#9869)
+  - don't overwrite configopts in BLAST+ easyconfigs, append to it (#9875)
+  - add alternate checksum for LaplacesDemon in R 3.6.x easyconfigs (#9879, #10382)
+  - fix redefining of preconfigopts in OpenCV easyconfigs (#9895)
+  - use symlinks for terminfo files instead of hard links in ncurses 6.1 easyconfigs (#9912)
+  - fix NCIPLOT build flags (#9915)
+  - add missing patch to iccifort libxc easyconfigs (#9918)
+  - use checkout@v2 in GitHub Actions to fix broken re-triggered tests (#9925)
+  - re-enable building utils in Siesta 4.1-MaX-1.0 release (#9936)
+  - fix homepage and source URLs in SLEPc easyconfigs by using https (#9943)
+  - fix source URLs for rgeos after source tarball was moved to CRAN archive (#9954)
+  - add dependencies on Python 3 and SciPy-bundle in Trinity v2.9.1 easyconfig (#9957)
+  - patch GCC lisanitizer for glibc 2.31 (#9966)
+  - add Zip as build dependency for recent Bazel versions (#9972)
+  - fix checksums in Jellyfish v2.3.0 easyconfigs (#9997)
+  - fix source URLs for ParMGridGen easyconfigs (#10019)
+  - disable unintended Octave support in all libsndfile easyconfigs (#10027)
+  - fix sources for LS-PrePost 4.6 (#10236)
+  - security update for vsc-mympirun 4.1.9 (#10185)
+  - configure libwebp to also install libwebpmux (#10274)
+  - ensure that CVS easyconfigs are included in source tarball produced by 'python setup.py sdist' (#10326)
+  - fix undefined reference error due to libxc 4.3.4 built with CMake (#10356)
+  - fix source_urls for tbb: use (new) official 'oneapi-src' GitHub repository (#10361)
+  - add missing build dependency on pkg-config in GObject-Introspection 1.63.1 w/ Python 3.7.4 easyconfig (#10380)
+  - update checksums and homepage in tbb easyconfigs (#10285)
+- other changes:
+  - use new custom easyblock in recent CMake easyconfigs (#9871, #9923)
+  - add check for redefined easyconfig parameters in easyconfig tests (#9876)
+  - use M4-1.4.18.eb for test installation in easyconfigs test suite (#9926)
+  - use https in homepage/source_urls of zlib-1.2.11.eb (#10018)
+  - add -GCCcore-9.2.0 versionsuffix for intel/2020.00 components (#10083)
+  - add checksum of new tbb 2019_U9 source tarball, next to original one + update homepage (#10237)
+  - add comment informing about manually setting Gallium drivers in easyconfigs for Mesa v19.1.7 and v19.2.1 (#10276)
+
+
 v4.1.1 (January 16th 2020)
 --------------------------
 

setup.py

@@ -44,7 +44,7 @@
 # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like
 #   UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0'
 # This causes problems further up the dependency chain...
-VERSION = '4.1.2.dev0'
+VERSION = '4.2.0'
 
 MAJ_VER = VERSION.split('.')[0]
 MAJMIN_VER = '.'.join(VERSION.split('.')[0:2])