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RELEASE_NOTES
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This file contains a description of the major changes to the easybuild-easyconfigs EasyBuild package.
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 18,752 easyconfig files, for 3,369 different software packages,
incl. 40 different (compiler) toolchains.
v4.9.0 (30 December 2023)
-------------------------
feature release
- added easyconfigs for foss/2023b (#19449) and intel/2023b (#19450) common toolchains
- added example easyconfig files for 77 new software packages:
- AICSImageIO (#19315), ANTIC (#19203), BiasAdjustCXX (#19341), BOPTEST (#19295), BRiAl (#19208), castor (#19176),
CellBender (#19296), cliquer (#19210, #19323), CPMD (#19387), cppyy (#19204), CUDD (#19208), datalad (#18675),
Demystify (#17990), dftd4 (#19223), dialog (#17696), DIA-NN (#19454), dynesty (#19091), ebGSEA (#19447),
ECL (#19211), eclib (#19209), epct (#19298), EUKulele (#19217), FACE (#14840), fastml (#19357), forbear (#14840),
fplll (#19371), fpylll (#19371), ftfy (#19353), Gdspy (#19458), GFF3-toolkit (#19071), giac (#19323), GMP-ECM (#19323),
HepMC (#19139), hic-straw (#19309), HPCC (#18892), iced (#19309), IML (#19201), iperf (#19259), jedi (#19269),
jedi-language-server (#19269), jupyter-rsession-proxy (#19311), lcalc (#19329), libaed2 (#14840),
LoopTools (#19397), m4ri (#19208), m4rie (#19208), MDI (#19417), mdust (#19106), MitoHiFi (#19263), MPFI (#19323),
multicharge (#19221), OMERO.insight (#19337), OMERO.py (#19338), PFFT (#19255), primecount (#19370),
primecountpy (#19370), PyAV (#19359), pycubescd (#19302), pylipid (#19428), PySINDy (#19306),
pythermalcomfort (#19285), PyTorchVideo (#19359), R-bundle-CRAN (#19170), Restrander (#19232), scikit-lego (#19064),
scrublet (#19215), SEACells (#18724), simanneal (#19347), Simstrat (#14840), solo (#19216), SPEI (#19441),
SUPPA (#19181, #19275), SYMMETRICA (#19328), Triton (#19381), vaeda (#19214), VSCode (#19418), waLBerla (#18932)
- added additional easyconfigs for various supported software packages, including:
- ANTs 2.5.0, Arriba 2.4.0, Arrow 14.0.1, at-spi2-core 2.50.0, Autoconf-archive 2023.02.20, awscli 2.15.2,
Blender 3.6.5 + 4.0.1, Boost 1.83.0, boto3 1.28.70, Bracken 2.9, BUStools 0.43.1, cairo 1.18.0, cairomm 1.16.2,
CASTEP 23.1, cddlib 0.94m, cdo-bindings 1.6.0, CellRanger 7.2.0, CoCoALib 0.99818, COMSOL 6.2.0.290, Coreutils 9.1,
cryptography 41.0.5, CubeLib 4.8.2, CubeWriter 4.8.2, CUDA 12.3.0, CVXPY 1.3.0, cysignals 1.11.2, DBus 1.15.8,
dftd4 3.4.0, E-ANTIC 1.3.0, elfutils 0.190, f90wrap 0.2.11, FastQC 0.12.1, Ferret 7.6.0, FFLAS-FFPACK 2.5.0,
ffnvcodec 12.1.14.0, FPM 1.15.1, FriBidi 1.0.13, gap 4.12.2, git-lfs 3.4.0, GitPython 3.1.40, Givaro 4.2.0,
GLib 2.78.1, glog 0.6.0, GObject-Introspection 1.78.1, gperftools 2.13, GPyTorch 1.10, GROMACS 2023.3,
HarfBuzz 8.2.2, HiC-Pro 3.1.0, hifiasm 0.19.7, hypothesis 6.90.0, ICU 74.1, imageio 2.33.1, imkl 2024.0.0,
impi 2021.11.0, intel-compilers 2024.0.0, IPython 8.17.2, ITK 5.3.0, Kent_tools 457, KyotoCabinet 1.2.80,
LHAPDF 6.5.4, libfdf 0.5.0, libjxl 0.8.2, LinBox 1.7.0, lrslib 7.2, lxml 4.9.3, magma 2.7.2, maturin 1.3.1,
MEME 5.5.4, meson-python 0.15.0, Miniconda3 23.9.0, Mmg 5.7.2, Molden 7.3, mrcfile 1.4.3, nanoflann 1.5.0,
nauty 2.8.6, Nextflow 23.10.0, nodejs 20.9.0, Normaliz 3.10.1, NSS 3.94, NWChem 7.2.2, Oases 20180312, Pango 1.51.0,
Parallel-Hashmap 1.36, parameterized 0.9.0, phonopy 2.20.0, pigz 2.8, pmt 1.2.0, poetry 1.6.1, PostgreSQL 16.1,
pplpy 0.8.9, PyCairo 1.25.1, pypmt 1.2.0, PyQt5 5.15.7, pytest 7.4.2, pytest-xdist 3.3.1,
Python-bundle-PyPI 2023.10, PyTorch 2.1.2, R 4.3.2, RASPA2 2.0.47, SBCL 2.3.11, SCENIC 1.3.0, scikit-image 0.22.0,
SciPy-bundle 2023.11, SDL2 2.28.5, setuptools-rust 1.8.0, Seurat 4.4.0, SimpleITK 2.3.1, Singular 4.3.2p10,
Spark 3.5.0, STAR 2.7.11a, STAR-CCM+ 2310, strace 6.6, SuiteSparse 7.1.0, tbb 2021.11.0, TOML-Fortran 0.4.1,
TRAVIS-Analyzer 220729, UCX-CUDA 1.15.0, VirSorter 1.0.6, virtualenv 20.24.6, VSEARCH 2.25.0, VTK 9.3.0,
wandb 0.16.1, XGBoost 2.0.2, xprop 1.2.6, xtb 6.6.1, Xvfb 21.1.9, xxd 9.0.2112
- minor enhancements, including:
- add sanity check commands for recent GDB versions (#19102)
- add aarch64 and ppc64le checksums to NVHPC 23.7 (#19249)
- allow Python version of Z3 to be used as a dependency (#19354)
- various bug fixes, including:
- use `CargoPythonBundle` generic easyblock for timm to install required Rust packages in a controlled way (#18332)
- add alternate checksum for OpenImageIO v2.4.14.0 (#19090)
- only set flag `--enable-asmjit` for PLUMED when installing on `x86_64` (#19110)
- ensure right Python version is used in DP3, WSClean and dependencies by specifying `-DPython3_EXECUTABLE` CMake option (#19119)
- add patch to work around potential crash in PyTorch 1.13.1 caused by GCC 12 compiler bug (#19133)
- add patch to fix detection of newer Intel CPUs in OpenBLAS 0.3.20 through 0.3.23 (#19141)
- remove outdated `--disable-docs` configure option from FriBidi-1.0.12 (#19147)
- add libiconv dependency to gettext 0.22 (#19155)
- fix OpenBLAS 0.3.20+ on newer Intel CPUs (#19159)
- only use ScaFaCos as dependency for LAMMPS 23Jun2022 on `x86_64` (#19164)
- add patch to fix regression in GCC 12.x on AVX512 systems (#19180)
- add pkgconf build dependency to libGLU (#19186)
- sidestep some build issues with CUDA-Samples 12.1 (#19189)
- make Pillow easyconfigs aware of sysroot template (#19226, #19267)
- fix possible error/crash in NCCL on x86 due to cpuid (#19231)
- reduce timestep to fix sanity check commands in LAMMPS 23Jun2022 (#19246)
- add patch for GCC 12.x to fix miscompiling C++ code causing double-free in case of exceptions (#19253)
- replace format tag with explicit extension name in Optuna v3.0.3 (#19256)
- enhance easyconfigs for gnuplot 5.4.x to make sure that Lua dependency is always used (#19261)
- patch setup.py for grpcio extension in TensorFlow 2.13.0 easyconfigs to take into account alternate sysroot (#19268)
- avoid indirect dependency on old CMake version built with GCCcore/10.2.0 via Catch2 build dependency using system toolchain in recent pybind11 easyconfigs (#19270)
- use existing patch in pybind11 2.6.2 and 2.7.1 to fix failing test due to extra whitespace (#19279)
- change toolchain in `json-fortran` easyconfigs to `GCC`, since it includes Fortran modules (#19283)
- remove Unicode character in description of SMRT-Link easyconfigs (#19312)
- don't use `%(namelower)s` template in extension name in IPython v8.14.0 easyconfig (#19330)
- add patch to fix `[cz]asums` in OpenBLAS 0.3.24 (#19331)
- fix failing tokenizers with `CargoPythonPackage` easyblock (#19333)
- define `$GTKDOCIZE` as '`echo`' before generating configure script for new HarfBuzz versions (#19339)
- fix PAPI test step hanging on some systems (#19372)
- compile LERC test binary in `postinstallcmds` to fix sanity check error when RPATH linking is enabled (#19386)
- use `GCC` toolchain in `kim-api`, since it includes Fortran modules (#19399, #19401, #19402, #19403, #19404, #19405)
- fix wrong handling of floats in z3-solver (#19414)
- Fix numpy build on Sapphire Rapids CPUs in SciPy-bundle-2023.07-gfbf-2023a (#19419, #19425)
- allow ITK legacy code and Python wrappers in ITK v5.2.1 (#19431)
- link to xxHash library provided via EasyBuild in python-xxhash v3.2.0 (#19432)
- include MPFR 4.1.0 patch in MPFR 4.2.0 easyconfigs to fix failing tsprintf test with glibc >= 2.37 (#19438)
- skip `Test::Sys::Info` test that expects `/etc/fstab` in Perl-bundle-CPAN (#19440)
- exclude `cdp*` CUDA samples that fail to build on aarch64 in CUDA-Samples v12.1 (#19451)
- other changes:
- let SuiteSparse easyblock set `CMAKE_OPTIONS` for SuiteSparse v7.1.0 (#19177)
- add versionsuffix `-param` to easyconfig for ReaxFF 2.0 (#19307)
- use `LooseVersion` from `easybuild.tools` (#19376)
v4.8.2 (29 October 2023)
------------------------
update/bugfix release
- added example easyconfig files for 48 new software packages:
- ALL (#18971), anadama2 (#18688), AOFlagger (#19010), bases2fastq (#18866), BgeeCall (#18784),
biobakery-workflows (#18688), BMTK (#18863), CIRIquant (#18815), Clair3 (#18748), CLEAR (#16357),
cpio (#14728), DP3 (#19010), EveryBeam (#19010), fasta-reader (#18936), git-annex (#18673), GSD (#6453),
imutils (#18920), Jblob (#18478), Jmol (#18988), kneaddata (#18688), libbaseencode (#12319),
libcotp (#12319), MACS3 (#18354), Mashtree (#19019), mpath (#5029), MUSCLE3 (#18287), plotutils (#16196),
ProBiS (#18830), PyMC (#10399), PyPy (#18847), PyTensor (#18928), Qt6 (#18683), QuickTree (#19019),
Raptor (#18919), RCall (#18933), ResistanceGA (#18933), scCODA (#18949), scikit-build-core (#18777),
segmentation-models-pytorch (#18930), SNAP-ESA (#19031), SNAP-ESA-python (#19031), starparser (#18965),
synapseclient (#19016), uncertainties (#18923), WSClean (#19010), XBeach (#18849), XOOPIC (#15269),
zeus-mcmc (#19033)
- added additional easyconfigs for various supported software packages, including:
- alleleCount 4.3.0, Amber 22.4, ant 1.10.14, ArviZ 0.16.1, ASAP3 3.13.2, biobambam2 2.0.185, BLAST+ 2.14.1,
bokeh 3.2.2, Brotli 1.1.0, Cantera 3.0.0, CapnProto 1.0.1, casacore 3.5.0, Catch2 2.13.9, CGAL 5.6,
Chemaxon-Marvin 23.9, CMake 3.27.6, code-server 4.16.1, Coot 0.9.8.92, CSBDeep 0.7.4, CUDA-Samples 12.1.1,
CuPy 12.1.0, cURL 8.3.0, dask 2023.9.2, DL_POLY_4 5.1.0, DoubletFinder 2.0.3-20230131, Doxygen 1.9.8, dxpy 0.345.0,
EDirect 20.5.20231006, FastANI 1.34, FastME 2.1.6.3, Flask 2.3.3, Flye 2.9.2, fmt 10.1.0, foss/2023.09,
freetype 2.13.2, GDAL 3.7.1, GDRCopy 2.4, git 2.42.0, GMP 6.3.0, Go 1.21.1, googletest 1.14.0, GPAW 23.9.1,
groff 1.23.0, GTDB-Tk 2.3.2, GTK4 4.13.1, gzip 1.13, harmony 0.1.0, HDF 4.2.16, HighFive 2.7.1, Highway 1.0.7,
HMMER 3.4, hmmlearn 0.3.0, Imath 3.1.9, Inspector 2023.2.0, intel/2023.07, IsoSeq 4.0.0, itac 2021.10.0,
JupyterNotebook 7.0.3, libarchive 3.7.2, libcint 5.4.0, libdeflate 1.19, libdrm 2.4.117, libglvnd 1.7.0,
libjpeg-turbo 3.0.1, libmaus2 2.0.813, libpng 1.6.40, libsigc++ 2.12.1, libsodium 1.0.19, LibTIFF 4.6.0,
libwebp 1.3.2, libxc 6.2.2, line_profiler 4.1.1, LMDB 0.9.31, MAFFT 7.520, makeinfo 7.1, MATLAB 2023b,
MEGAN 6.25.3, Mesa 23.1.9, Meson 1.2.3, mold 2.3.1, MPFR 4.2.1, msgpack-c 6.0.0, nanopolish 0.14.0,
NBO 7.0.10, netcdf4-python 1.6.4, OpenBLAS 0.3.24, OpenCV 4.8.1, OpenEXR 3.2.0, OpenMolcas 23.06, OpenMPI 4.1.6,
openslide-python 1.3.1, OrthoFinder 2.5.5, OSU-Micro-Benchmarks 7.2, ParaView 5.11.2, Perl-bundle-CPAN 5.38.0,
PETSc 3.19.2, PMIx 4.2.6, poppler 23.09.0, preCICE 2.5.0, pretty-yaml 23.9.5, PyCairo 1.25.0, pyEGA3 5.0.2,
PyGObject 3.46.0, pygraphviz 1.11, pytest-rerunfailures 12.0, Python 3.11.5, PyTorch 2.0.1, PyTorch-bundle 1.13.1,
PyTorch-Ignite 0.4.12, PyYAML 6.0.1, RagTag 2.1.0, rapidcsv 8.62, rasterstats 0.19.0, RAxML-NG 1.2.0,
RDFlib 7.0.0, RDKit 2023.03.3, ReFrame 4.3.3, RMBlast 2.14.0, ruamel.yaml 0.17.32, Rust 1.73.0, scikit-learn 1.3.1,
SCons 4.5.2, SHAP 0.42.1, SignalP 6.0h, SMRT-Link 12.0.0.177059, spglib-python 2.1.0, SQLite 3.43.1,
TensorRT 8.6.1, texlive 20230313, Tkinter 3.11.5, UCX 1.15.0, VBZ-Compression 1.0.3, VCFtools 0.1.16,
VTune 2023.2.0, X11 20231019, x264 20231019, xarray 2023.9.0, XlsxWriter 3.1.3, xtb 6.6.0, ZeroMQ 4.3.5
- minor enhancements, including:
- also run easyconfigs test suite with Python 3.11 (#18009)
- don't disable building of third and fourth derivates in libxc 6.1.0 (#18467)
- add easyconfigs cache file to `.gitignore` (#18797)
- add patch to improve CUDA 11 compatibility of `GCCcore/12.2.0` and `GCCcore/12.3.0` (#18854)
- also build Python bindings for ITK 5.2.1 with `foss/2022a` (#18922)
- add ridge extension to R 4.2.2 (#18924)
- add MSstatsLiP (#19009)and escape (#19027) to Bioconductor 3.16 bundle
- add patches to build Qt5 5.15.10 with Python 3 instead of Python 2.7 (#19045)
- various bug fixes, including:
- rename ACT to Artemis (#18382)
- backport lchown patch to PMIx 3.1.x + 3.2.x (#18759)
- also copy scripts directory for Clair3 (#18783)
- rename isoseq3 after download for IsoSeq 3.8.2 + fix permissions (#18785)
- add missing required extensions + fix wrong version of extensions in recent Perl easyconfigs (#18789)
- add patch for OpenBLAS 0.3.23 to fix hanging tests (#18790)
- add patch to fix Open MPI 4.1.5 with PMIx >= 4.2.3 (#18833)
- fix permission issues when copying xvfb-run script in Xvfb easyconfigs (#18834)
- statically link Boost 1.75 in Cufflinks v20190706 installed with `GCC/11.2.0`, so Boost can be changed to build dependency (#18843)
- add missing required PyPy dependency for Clair3, also copy preprocess and shared subdirectories, and enhance sanity check for provided libclair3 Python package (#18847)
- add patch to fix build of util-linux 2.39 on CentOS 7 (#18855)
- add patch to fix finding of tk.tcl for Tk 8.6.13 (#18864)
- add patch to fix issue with automatic detection of NeoverseV1 CPU architecture in OpenBLAS v0.3.20 (#18870)
- fix source URL for segemehl 0.3.4 (#18878)
- avoid use of hardcoded paths for Pillow by using `--disable-platform-guessing` option (#18881)
- add patch to disable flaky DDRGES3 LAPACK test in OpenBLAS 0.3.23 + 0.3.24 (#18887)
- add alternate checksum for NCCL v2.18.3 (#18906)
- add missing dependencies for MONAI to support extras required by MONAI-Label (#18921)
- make sure Python dependency included for ESPResSo is actually used by specifying `-DPYTHON_EXECUTABLE` (#18963)
- only add tbb as dependency in recent LAMMPS easyconfigs when installing on x86_64 (#19000)
- detect the correct Python for vcflib (#19001)
- fix invalid pointer access in UCX 1.11-1.14 (#19023)
- disable threadedmpi in recent SCOTCH easyconfigs using gompi toolchain (#19024)
- add missing GSL dependency for casacore 3.4.0 (#19042)
- fix pybind11 incompatibility with some CUDA versions and add Catch2 dependency for tests (#19047)
- enable `-fPIC` in easyconfig for libwebp 1.3.2 (#19098)
- other changes:
- remove 'cstd': 'c++17' as that's the default in GCC 11 (#18941, #18942, #18943, #18944, #18945, #18946)
- rename CVS to ConcurrentVersionsSystem, to avoid problems with recent setuptools versions (#18985)
- use sysroot template in wget easyconfigs to define PKG_CONFIG_PATH (#19080)
v4.8.1 (11 September 2023)
--------------------------
update/bugfix release
- added example easyconfig files for 83 new software packages:
- ALAMODE (#18733), AMRFinderPlus (#18559), Ax (#68), bcrypt (#18208), bench (#18656), BgeeDB (#18743),
Boost.Python-NumPy (#18505), CatBoost (#18591), centerline (#18273), cffi (#7105), ChIPseeker (#18662),
connected-components-3d (#18289), cryptography (#8495), CVglasso (#18657), DiffBind (#18663), drmaa-python (#18614),
e3nn (#18304), flit (#18208), GAPPadder (#18692), GenerativeModels (#18451), geosphere (#18659), gffutils (#18331),
gkmSVM (#18660), hampel (#18409), hatchling (#18208), HDF-EOS2 (#18297), Hybpiper (#18414), inih (#18516),
IsoformSwitchAnalyzeR (#18664), IsoQuant (#18331), Jupyter-bundle (#18634), JupyterNotebook (#18735, #18735),
leafcutter (#18615), libleidenalg (#18548), LIBSVM-Python (#18455), libvori (#18379), maturin (#18405),
meboot (#18658), mgen (#18402), Mikado (#18614), NanoCaller (#18726), nbclassic (#18617), ncolor (#7146),
nose3 (#18234), novaSTA (#18601), Omnipose (#18402), Optax (#18610), paramiko (#1504), Parsl (#18408),
peakdetect (#18402), PICRUSt2 (#18333, #18459), Platypus-Opt (#18291), PortMidi (#18252), pv (#16439),
py-c3d (#18409), pygame (#18252), pyodbc (#18334), Python-bundle-PyPI (#18208), qforce (#18456),
RFdiffusion (#18304), Rhodium (#18291), ruptures (#18306), Sabre (#18342), scGSVA (#18401), scib-metrics (#18734),
scikit-plot (#18377), SDL2_mixer (#18252), SDL2_ttf (#18252), segment-anything (#18290), sentinelsat (#18367),
setuptools-rust (#18208), slurm-drmaa (#18614), SuAVE-biomat (#18678), T-Coffee (#17916),
tensorflow-compression (#18676), torchvf (#18637), tornado (#18511), tseriesEntropy (#18661), TXR (#18665),
unifdef (#18427), UniFrac (#18407), virtualenv (#2660), WFA2 (#18636)
- added additional easyconfigs for various supported software packages, including:
- ABINIT 9.10.3, Advisor 2023.2.0, aiohttp 3.8.5, AMD-uProf 4.1.424, Anaconda3 2023.07-2, anndata 0.9.2,
APR 1.7.4, APR-util 1.6.3, Arcade-Learning-Envionment 0.8.1, archspec 0.2.1, Armadillo 12.6.2, arpack-ng 3.9.0,
assimp 5.2.5, BAGEL 1.2.2, bam-readcount 1.0.1, Bazel 6.3.1, BCFtools 1.18, BeautifulSoup 4.12.2, BEDTools 2.31.0,
biom-format 2.1.15, bokeh 3.2.1, Boost 1.82.0, cairo 1.17.8, c-ares 1.19.1, ccache 4.8.3, CDO 2.2.2, CFITSIO 4.3.0,
Cgl 0.60.7, CharLS 2.4.2, cicero 1.3.8, Clang 16.0.6, Clp 1.17.8, Cluster-Buster 20200507, CoinUtils 2.11.9,
conan 1.60.2, configurable-http-proxy 4.5.5, coverage 7.2.7, CP2K 2023.1, CubeLib 4.8.1, CubeWriter 4.8.1,
CUDA 12.2.2, dask 2023.7.1, dcm2niix 1.0.20230411, Delly 1.1.6, dill 0.3.7, ecBuild 3.8.0, ecCodes 2.31.0,
ELPA 2023.05.001, exiv2 0.28.0, expecttest 0.1.5, fastparquet 2023.4.0, FFmpeg 6.0, ffnvcodec 12.0.16.0,
flatbuffers 23.5.26, flatbuffers-python 23.5.26, FreeSurfer 7.4.1, fsom 20151117, gc 8.2.4, GCC 13.2.0, GDB 13.2,
GEOS 3.12.0, gettext 0.22, GHC 9.2.2, Ghostscript 10.01.2, GLib 2.77.1, gmpy2 2.1.5, gnuplot 5.4.8,
GObject-Introspection 1.76.1, gperftools 2.12, Graphviz 8.1.0, gRPC 1.57.0, GST-plugins-base 1.22.5,
GStreamer 1.22.5, GTK3 3.24.37, GTK4 4.11.3, h4toh5 2.2.5, h5netcdf 1.2.0, h5py 3.9.0, hiredis 1.2.0,
Horovod 0.28.1, htop 3.2.2, HTSlib 1.18, hwloc 2.9.2, Hydra 1.3.2, hypothesis 6.82.0, Hypre 2.29.0, ICU 73.2,
igraph 0.10.6, iimkl/2023a, imageio 2.31.1, ImageMagick 7.1.1-15, inferCNV 1.14.2, IPython 8.14.0, ISL 0.26,
Julia 1.9.3, JupyterLab 4.0.5, jupyter-resource-usage 1.0.0, kma 1.4.12a, KMC 3.2.2, leidenalg 0.10.1,
libdrm 2.4.115, libdwarf 0.7.0, libfabric 1.19.0, libgit2 1.7.1, libGLU 9.0.3, libsndfile 1.2.2, libwpe 1.14.1,
libxml2 2.11.5, LittleCMS 2.15, LLVM 16.0.6, Lua 5.4.6, MACS2 2.2.9.1, magma 2.7.1, mahotas 1.4.13, makeinfo 7.0.3,
Mamba 23.1.0, matplotlib 3.7.2, medaka 1.8.1 + 1.9.1, Mercurial 6.4.5, Mesa 23.1.4, meson-python 0.13.2,
Miniconda3 23.5.2, Monocle3 1.3.1, MPC 1.3.1, MRtrix 3.0.4, MUMPS 5.6.1, MXNet 1.9.1, napari 0.4.18, ncdu 1.18,
netCDF 4.9.2, netCDF-Fortran 4.6.1, nettle 3.9.1, networkx 3.1, nodejs 18.17.1, nsync 1.26.0, NVHPC 23.7,
OpenAI-Gym 0.26.2, OpenCV 4.8.0, OpenFOAM 11, OpenImageIO 2.4.14.0, Osi 0.108.8, OTF2 3.0.3, Pango 1.50.14,
PAPI 7.0.1, parallel 20230722, Perl 5.38.0, Pillow 10.0.0, Pillow-SIMD 9.5.0, Pint 0.22, pkgconf 2.0.3,
plotly.py 5.16.0, PLUMED 2.9.0, pocl 4.0, poetry 1.5.1, protobuf 24.0, protobuf-python 4.24.0, psutil 5.9.5,
PuLP 2.7.0, pyBigWig 0.3.22, pybind11 2.11.1, PyCairo 1.24.0, PyGObject 3.44.1, Pylint 2.17.4, pyproj 3.6.0,
pyro-ppl 1.8.4, python-igraph 0.10.6, PyZMQ 25.1.1, QIIME2 2023.5.1, Qt5 5.15.10, QuantumESPRESSO 7.2,
rclone 1.63.1, RE2 2023-08-01, re2c 3.1, RegTools 1.0.0, RnBeads 2.14.0, RTG-Tools 3.12.1, SAMtools 1.18,
Scalene 1.5.26, scikit-build 0.17.6, scikit-image 0.21.0, SciPy-bundle 2023.07, Score-P 8.1, SCOTCH 7.0.3,
SDL2 2.28.2, SDL2_image 2.6.3, setuptools 64.0.3, SeuratWrappers 20221022, snakemake 7.32.3, SpaceRanger 2.1.0,
SpiecEasi 1.1.1, Stack 2.11.1, STAR 2.7.11a, SUNDIALS 6.6.0, SWIG 4.1.1, sympy 1.12, tabixpp 1.1.2, tbb 2021.10.0,
tbl2asn 20230713, tcsh 6.24.10, TensorFlow 2.13.0, tensorflow-probability 0.19.0, Tk 8.6.13, Tkinter 3.11.3,
tqdm 4.66.1, unixODBC 2.3.11, Valgrind 3.21.0, vcflib 1.0.9, VirtualGL 3.1, VisPy 0.12.2, Wayland 1.22.0,
WebKitGTK+ 2.40.4, wpebackend-fdo 1.14.1, wxPython 4.2.1, Xvfb 21.1.8, xxd 9.0.1696, XZ 5.4.4, Yambo 5.1.2,
Z3 4.12.2, zarr 2.16.0
- minor enhancements, including:
- add extensions to recent R-bundle-Bioconductors easyconfigs: UCell (#18281), decoupleR (#18399, #18552), RnBeads (#18682)
- add extensions to recent R easyconfigs: tabletools (#18510), flextables (#18719)
- add test for easyconfig file permissions (#18647)
- simplify build and install options for Ghostscript (#18750)
- various bug fixes, including:
- set `$JULIA_DEPOT_PATH` in Julia easyconfigs with default value (#17976)
- remove superflous dependencies from Horovod easyconfig on top of PyTorch (#18262)
- disable building documentation for libsigc++ 2.10.x (#18301)
- use MCR dependency in FreeSurfer 7.3.2 and 7.4.0 (#18303)
- add `hpctestlib` to the `$PYTHONPATH` in ReFrame 4.2.0 easyconfig (#18320)
- fix installation of Python bindings for recent Arrow easyconfigs by adding `--no-build-isolation` to `pip install` command (#18348, #18432, #18440, #18441)
- add/fix patches for PyTorch 1.13.1 w/ foss/2022a (#18371)
- add missing nbclassic extension to jupyter-server 1.21.0 (#18389)
- Fix batchspawner for JupyterHub 3.0 (#18390)
- fix compiler flags and toolchain options for ScaLAPACK 2.1.0 + 2.2.0 (#18396, #18397)
- add patch to fix CUDA race condition problem for Score-P v8.0 (#18411)
- add `-DABSL_PROPAGATE_CXX_STD=ON` to recent Abseil easyconfigs (required for PyTorch) (#18413)
- add missing patches for PyTorch 1.12.0 w/ foss/2022a (#18430)
- fix regression in GCC 12.1 + 12.2 with wrong warnings (#18434)
- add patch for LIBSVM 3.30 to pass `$CFLAGS` + `$LDFLAGS` and run tests (#18454)
- add patch for Automake 1.16.5 to fix help2man error (#18468)
- consistently use ON/OFF for -DBUILD_SHARED_LIBS (#18484)
- add missing patches for PyTorch 1.12.0 w/ `foss/2022a` + CUDA 11.7.0 (#18491)
- add patches to fix PyTorch 1.12.1 + 1.13.1 on POWER on POWER (#18489, #18490, #18492, #18493, #18494, #18500)
- add patch to fix flaky `test_jit_legacy` test for PyTorch 1.13.1 (#18500)
- add alternative checksum for Extrae v4.0.4 (#18564)
- remove appending of `$__EGL_VENDOR_LIBRARY_DIRS` in recent Mesa easyconfigs, since Mesa easyblock now appends to it (#18630)
- correct `dirs` in `sanity_check_paths` in template easyconfig (#18635)
- set `$MUJOCO_PY_FORCE_CPU` to avoid that mujoco-py checks for nvidia-smi and aborts installation because `/usr/lib/nvidia` is not in `$LD_LIBRARY_PATH` (#18641)
- fix sanity check for ccache by setting `LC_ALL=C` (#18677)
- make Autoconf a build dep for tRNAscan-SE + add missing Perl dependency (#18680)
- strip out hardcoded `-march=native` used by RapidJSON 1.1.0 (#18725)
- disable detection of Dbus broker for `at-spi2-core` (#18727)
- make sure that 'moduleclass' is set in all easyconfig files (and is not set to default `base` moduleclass) (#18739)
- add patch for MPFR 4.1.0 to fix failing tsprintf test with glibc >= 2.37 (#18746)
- add patch for PMIx 4.x to use `lchown` so links are not followed (#18755)
- other changes:
- update Java/11 wrapper to Java/11.0.20 (#18435)
- use custom easyblock for recent sympy easyconfigs to prevent test failures (#18428)
- use GCC/12.2.0 toolchain for GSL 2.7, remove easyconfig for GSL 2.7 with GCCcore/12.2.0 (#18501)
- disable wx support in gnuplot 5.4.6 (#18648, #18691)
- filter out template + archived easyconfigs when determining changed easyconfigs in PRs (#18753)
v4.8.0 (7 Jul 2023)
--------------------
feature release
- added easyconfigs for foss/2023a (#18264) and intel/2023a (#18275) common toolchains
- added example easyconfig files for 76 new software packages:
- 3d-dna (#9258), affinity (#18051), AIMAll (#13153), alleleIntegrator (#17923), AlphaPulldown (#17774),
ASCAT (#17923), ASF-SearchAPI (#18179), ATAT (#18213), AutoDockSuite (#9678), axel (#10961), BayesPrism (#17885),
BGC-Bayesian-genomic-clines (#18005), CalculiX-CrunchiX (#16805), CASA (#18055), cctbx-base (#17774),
Circuitscape (#16720), CppHeaderParser (#18272), CuCLARK (#9482), cuteSV (#18077), DALI (#18204), DaliLite (#17989),
DEICODE (#18181), dm-haiku (#18013), dominate (#18086), dx-toolkit (#18232), easel (#18156), ecFlow (#15719),
EDirect (#17479), FragPipe (#18161), GEM (#18120), gemelli (#18120), GLIMPSE (#18163), GRIDSS (#18170),
HOOMD-blue (#18224), KerasTuner (#18197), LayoutParser (#18220), LISFLOOD-FP (#18194), LuaRocks (#18073),
mannkendall (#18043), MOB-suite (#16798), molecularGSM (#13150), MONAI-Label (#18180), MView (#18198),
NanoStat (#18201), oxDNA (#18175 + #18214), pastml (#15336), pbipa (#18229), Perl-bundle-CPAN (#17970), PheWeb (#10951),
plinkliftover (#18136), pmt (#18052), PyBioLib (#18124), Pychopper (#10344), pydicom-seg (#18180),
pyMannKendall (#18044), pypmt (#18045), python-mujoco (#18253), pytorch-CycleGAN-pix2pix (#18086),
PyTorch-Image-Models (#18220), PyWBGT (#17980), Safetensors (#18220), Sniffles (#18048), strace (#14381),
Structure_threader (#18219), subset-bam (#18032), SVclone (#18084), SVIM (#18071), Tapenade (#18109),
TensorFlow-Graphics (#17465), timm (#17787), Trinotate (#18124), Ultralytics (#17894), visdom (#18086),
wrapt (#18125), xclip (#17055), xdotool (#17055)
- added additional easyconfigs for various supported software packages, including:
- AGAT 1.1.0, alleleCount 4.2.1, AMS 2023.101, ANSYS 2023R1, BayesTraits 3.0.2, Bismark 0.24.1, BLAST+ 2.14.0,
boto3 1.26.163, Bowtie2 2.5.1, BUSCO 5.4.7, Cellpose 2.2.2, CHERAB 1.4.0, CmdStanR 0.5.2, CNVkit 0.9.10,
corner 2.2.2, CUDA 12.1.1 + 12.2.0, cuDNN 8.9.2.26, cutadapt 4.4, cuTENSOR 1.7.0.1, CVXOPT 1.3.1, Dalton 2020.1,
datamash 1.8, deepTools 3.5.2, DIAMOND 2.1.8, DMTCP 3.0.0, dorado 0.3.0 + 0.3.1, dtcmp 1.1.4, duplex-tools 0.3.3,
elastix 5.0.0, Emacs 28.2, emcee 3.1.4, Extrae 4.0.4, fastp 0.23.4, FlexiBLAS 3.3.1, fontconfig 2.14.2,
FreeSurfer 7.4.0, freetype 2.13.0, GATK 4.4.0.0, GBprocesS 4.0.0.post1, GCC 11.4.0, GCTA 1.94.1, GDRCopy 2.3.1,
Geant4 11.1.2, Geant4-data 11.1, GetOrganelle 1.7.7.0, git 2.41.0, GMAP-GSNAP 2023-04-20, GROMACS 2023.1,
hifiasm 0.19.5, Horovod 0.25.0, hwloc 2.9.1, InterProScan 5.62, IQ-TREE 2.2.2.3, ITSTool 2.0.7, JAGS 4.3.2,
Julia 1.9.0, libfabric 1.18.0, libheif 1.16.2, libjxl 0.8.1, LibLZF 3.6, LMfit 1.2.1, LSD2 2.4.1, LuaJIT 2.1.0,
lwgrp 1.0.5, MAGeCK 0.5.9.5, MATLAB 2023a, MaxQuant 2.4.2.0.eb, MCR R2022a.5, meshio 5.3.4, Meson 1.1.1,
minimap2 2.26, MMseqs2 14-7e284, mpifileutils 0.11.1, MuJoCo 2.2.2, nanomath 1.3.0, ncbi-vdb 3.0.5, NCCL 2.18.3,
Nextflow 23.04.2, ngspice 39, ont-fast5-api 4.1.1, OpenBLAS 0.3.23, OpenMPI 4.1.5, openpyxl 3.1.2,
OSU-Micro-Benchmarks 7.1-1, parasail 2.6.2, Paraver 4.11.1, ParaView 5.11.1, patchelf 0.18.0, Perl 5.36.1,
PMIx 4.2.4, POT 0.9.0, PSI4 1.7, psutil 5.9.4, psycopg2 2.9.6, PyCalib 20230531, pycocotools 2.0.6,
pyfaidx 0.7.2.1, pyiron 0.3.0, PyQtGraph 0.13.3, Pysam 0.21.0, pySCENIC 0.12.1, pyspoa 0.0.9, Python 3.11.3,
python-parasail 1.3.4, PyTorch 1.13.1, rasterio 1.3.8, regionmask 0.10.0, Ruby 3.2.2, Rust 1.70.0, ScaFaCoS 1.0.4,
seqtk 1.4, SRA-Toolkit 3.0.5, statsmodels 0.14.0, strace 5.14, Subversion 1.14.2, SUNDIALS 6.5.1, tidymodels 1.1.0,
tokenizers 0.13.3, torchaudio 0.12.0, TransDecoder 5.5.0, Transformers 4.29.2 + 4.30.2, UCC 1.2.0, UCC-CUDA 1.2.0,
UCX 1.14.1, UCX-CUDA 1.14.1, util-linux 2.39, VASP 6.3.2, VTK 9.2.6, WhatsHap 1.7, X11 20230603, xarray 2023.4.2,
XlsxWriter 3.1.2, XML-LibXML 2.0208, xorg-macros 1.20.0, zlib-ng 2.0.7
- minor enhancements, including:
- add CI check for -DCMAKE_BUILD_TYPE, should use build_type instead (#14008)
- enhance sanity check for recent LibTIFF easyconfigs (#17975)
- update JupyterLab v3.5.0 to set `$JUPYTERLAB_SETTINGS_DIR` and `$JUPYTERLAB_WORKSPACES_DIR` on loading of module (#17982)
- use custom easyblock for Rust 1.65.0 (#18174) and Rust 1.70.0 (#18167)
- update easyconfig for Nextflow 23.04.2 to use `install_cmds` (#18173)
- add extra packages to recent R easyconfigs (#18029, #18063, #18122, #18195, #18245)
- add extra packages to recent R-bundle-Bioconductor easyconfigs (#18196, #18246)
- various bug fixes, including:
- add patches to fix TensorFlow 2.7.1 on POWER (#16795)
- fix patches + extensions in easyconfig for TensorFlow 2.8.4 w/ foss/2021b (#17058)
- stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2 (#17998)
- add pkgconfig as build dependency for nodejs , required for finding ICU dependency (#18007)
- fix exec permissions for all binaries & scripts of L_RNA_scaffolder 20190530 (#18030)
- update SUNDIALS dependency for Cantera v2.6.0 to v6.5.1 + add missing dependencies (#18041)
- fix --sanity-check-only for MAGeCK v0.5.9.4 (#18047)
- enable building static libs and check for libexslt.* in libxslt (#18064)
- add -pthread flag for dorado (#18072)
- add missing patch files for Qt5 5.15.2 to fix build problems with glibc 2.34 (#18087)
- add missing pkgconf build dependency for XML-LibXML v2.0208 (#18159)
- update homepage for NWChem 7.x (#18184)
- update homepage for SUNDIALS 5.x and 6.x (#18186)
- add missing source_urls for SimpleITK (#18212)
- use patch files for Qt5 v5.17.7 to fix compatiblity with glibc 2.34 (#18230)
- fix incorrect version for GMAP-GSNAP 2021-12-17 (was 2021-21-17) (#18231)
- fix CUDA build of recent TensorFlow easyconfigs when using compiler symlinks (#18235)
- use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2 (#18236)
- update source_urls for Velvet 1.2.10 (#18237)
- use upstream patch for symbol compatibility in XZ 5.2.5 (#18250)
- update source url for pkgconf (#18271)
- other changes:
- stop running easyconfig unit tests with Python 2.7 (#18006)
- fix toolchain for networkx-3.0 (foss/2022b -> gfbf/2022b) (#18061)
- remove unused PyTorch patch (#18062)
- allow multiple dependency variants of ncbi-vdb for SRA-TOolkit per easyconfigs generation, as long as versions match (#18098)
- bump OpenSSL 1.1 wrapper fallback to 1.1.1u (#18188)
- remove default `separate_build_dir = True` and `build_type = 'Release'` from double-conversion (#18222)
- remove default `separate_build_dir = True` and `CMAKE_BUILD_TYPE=Release` from MariaDB (#18223)
- remove incorrect '-Dgallium-drivers=swrast' configure option in ROOT easyconfigs (#18260)
- change base compiler for intel/2023.03 to GCCcore/12.3.0 (required to use it as intel/2023a) (#18263)
v4.7.2 (27 May 2023)
--------------------
update/bugfix release
- added easyconfigs for intel/2023.03 (#17676)
- added example easyconfig files for 89 new software packages:
- AGeNT (#17864), anndata (#17677), Annocript (#17910), avro-cpp (#17527), batchgenerators (#17833),
BoltzTraP2 (#17742), Braindecode (#17913), build (#17776), casacore (#15499), Casanovo (#17735, #17736),
CASPR (#17606), CellChat (#17856), CellOracle (#17507), CLIP (#17782), CodingQuarry (#17682), ColabFold (#17751),
CopyKAT (#17646), CPC2 (#17849), cppzmq (#17601), dask-labextension (#17882), DIALOGUE (#17696), DiCE-ML (#17591),
ESPResSo (#17709), Evcxr-REPL (#17831), EZC3D (#17832), funannotate (#17588), FunGAP (#17652), GATB-Core (#17635),
GenMap (#17746), GimmeMotifs (#17507), GLI (#17793), GOBNILP (#17639), h5netcdf (#17835), HD-BET (#17833),
HTSplotter (#17369, #17586), ipympl (#17613), IsoSeq (#17791), KrakenUniq (#17569), LIANA (#17928),
libWallModelledLES (#17480), LoRDEC (#17635), M3GNet (#17555), mandrake (#17394), mctc-lib (#16760), MOABB (#17913),
MRPRESSO (#17925), ont-guppy (#17477, #17828), OptaDOS (#17777), PALEOMIX (#17912), PGPLOT (#15496),
PICI-LIGGGHTS (#17710), pod5-file-format (#17776), powerlaw (#17647), pp-sketchlib (#17397),
py3Dmol (#17752), pytesseract (#17898), pytest-cpp (#17966), pytest-flakefinder (#17966), Python-bundle (#17626),
python-xxhash (#17844), PyTorch-bundle (#17540), qnorm (#17507), R-MXM (#17667), R-transport (#17642, #17968),
Raven (#15833), ReaxFF (#17780), ripunzip (#17959), RPostgreSQL (#17739), rustworkx (#17857), Scalene (#16472),
sceasy (#17677), SCIP (#17639), Simple-DFTD3 (#16760), SMAP (#17672), SoPlex (#17639), SoupX (#17851),
spektral (#15551), synthcity (#17623), sysbench (#17643), tantan (#17681), thirdorder (#17703), TOPAS (#17553),
Triplexator (#17866), tRNAscan-SE (#17680, #17800), turbinesFoam (#17917), unicore-uftp (#17665), vispr (#17606),
WCSLIB (#15497), ZIMPL (#17639)
- added additional easyconfigs for various supported software packages, including:
- Abseil v20230125.2, AlphaFold v2.3.1 + v2.3.4, Arrow v11.0.0, arrow-R v11.0.0.3, astropy v5.2.2, awscli v2.11.21,
Bismark v0.24.0, biom-format v2.1.14, Blender v3.5.0, Blosc2 v2.8.0, Bottleneck v1.3.7, breseq v0.38.1,
bwa-meth v0.2.6, buildenv default for foss/2022b + CUDA 12.0.0, Cantera v2.6.0, CapnProto v0.10.3, CASTEP v22.11,
Clang v15.0.5, CLHEP v2.4.6.4, CMake v3.26.3, CMSeq v1.0.4, coverage v7.2.3, CP2K v9.1 + v2022.1, CPLEX v22.1.1,
CREST v2.11.2, cURL v8.0.1, CuPy v11.4.0, DBus v1.15.4, DBG2OLC v20200724, dlb v3.3.1, double-conversion v3.3.0,
Doxygen v1.9.7, expat v2.5.0, FASTA v36.3.8i, FHI-aims v221103, fio v3.34, Fiona v1.9.2, Flask v2.2.3, fmt v10.0.0,
freeglut v3.4.0, FUSE v3.14.1, GapFiller v2.1.2, GCC 12.3.0 + 13.1.0, GDCM v3.0.21, GitPython v3.1.31, Go v1.20.4,
googletest v1.13.0, gpustat v1.1, Guile v3.0.9, Gurobi v10.0.1, Harminv v1.4.2, Highway v1.0.4, IgBlast v1.21.0,
Imath v3.1.7, infercnvpy v0.4.2, IQ-TREE v2.2.2.3, jax v0.3.25, jupyterlmod v4.0.3, Kalign v3.3.5,
L_RNA_scaffolder v20190530, libaio v0.3.113, libarchive v3.6.2, libctl v4.5.1, libdeflate v1.8, libgcrypt v1.10.1,
libGridXC v1.1.0, libjpeg-turbo v2.1.5.1, libmaus2 v2.0.499, libopus v1.4, libpng v1.6.39, libPSML v1.1.12,
libRmath v4.2.1, libsigc++ v3.4.0, LibTIFF v4.5.0, libunistring v1.1, libxc v6.1.0, libxml2 v2.11.4,
libxslt v1.1.38, lifelines v0.27.4, lxml v4.9.2, make v4.4.1, MariaDB v10.11.2, Meep v1.26.0, MetaPhlAn v4.0.6,
mold v1.11.0, MPB v1.11.1, muParser v2.3.4, NAG v7.1, NAGfor v7.1, nano v7.2, NASM v2.16.01, ncurses v6.4,
netcdf4-python v1.6.3, networkx v2.8.8, NSS v3.89.1, numexpr v2.8.4, nvtop v3.0.1, OpenEXR v3.1.7, OpenMM v8.0.0,
Pandoc v3.1.2, ParaView v5.11.0, PCRE2 v10.42, PhyloPhlAn v3.0.3, phyx v1.3, picard v3.0.0, Pint v0.20.1,
pkgconf v1.9.5, PostgreSQL v15.2, PROJ v9.2.0, Proteinortho v6.2.3, protobuf v23.0, protobuf-python v4.23.0,
pydantic v1.10.4, pyFFTW v0.13.1, PyGEOS v0.14, Pyomo v6.5.0, pyparsing v3.0.9, pyperf v2.6.0, pyproj v3.5.0,
pytest v7.2.2, PYTHIA v8.309, Qtconsole v5.4.0, R-bundle-Bioconductor v3.16, R-tesseract v5.1.0, RE2 v2023-03-01,
ReFrame v4.2.0, RepeatMasker v4.1.5, RevBayes v1.2.1, rgdal v1.6-6, rioxarray v0.14.0, rocm-smi v5.4.4,
ROOT v6.26.10, Rtree v1.0.1, scib v1.1.3, scikit-build v0.17.2, Seaborn v0.12.2, SHAP v0.41.0, Shapely v2.0.1,
ShengBTE v1.5.0, SLiM v4.0.1, snappy v1.1.10, spdlog v1.11.0, spglib v2.0.2, spglib-python v2.0.2, SQLite v3.42.0,
Subread v2.0.4, Tcl v8.6.13, tcsh v6.24.05, torchtext v0.14.1, trimesh v3.21.5, UCC-CUDA v1.1.0, utf8proc v2.8.0,
Vim v9.0.1434, vsc-mympirun v5.3.1, WRF v4.4.1, xmlf90 v1.5.6, xxHash v0.8.1, XZ v5.4.2, zsh v5.9, zstd v1.5.5
- minor enhancements, including:
- add local::lib extension to Perl 5.34.0 (#17679)
- install shared libraries for tesseract (#17721)
- add additional extensions to recent R easyconfigs: word2vec, tau, quanteda, ... (#17738)
- add extensions to R-bundle-Bioconductor 3.15: deepSNV (#17852)
- add extensions to R 4.2.x: dlm (#17640), PMA + unikn + ppcor (#17695), tvem (#17729), epitools (#17852)
- various bug fixes, including:
- add patch for UCC 1.1.0 for multiple component paths (#17255)
- fix configure step for ELSI 2.5.0+ (#17288)
- switch bamtofastq to Cargo easyblock (#17595)
- add missing OpenJPEG dependency for recent GDAL versions (#17599)
- fix CodAn bin/* executable permissions for all users #(#17607)
- upgrade traitlets, ipywidgets, and widgetsnbextension + downgrade jupyterlab_widgets extensions in IPython v8.5.0 to fix known issues (#17612)
- add patch for GPAW-22.8.0 with 2022a toolchain to make test tolerance a bit less strict (#17618)
- add alternative checksum for MONAI 1.0.1 (#17628)
- fix paths to Perl modules in MAKER v3.01.04 (#17629)
- add missing dependencies and add patch for fix incorrect ids for BRAKER v2.1.6 (#17631)
- explicitely disable mpi/python in Boost (intel-compilers/2021.4.0) (#17638)
- remove LLVM build dependency from TensorFlow easyconfigs (#17641)
- update easyconfig for Longshot 0.4.5 to use Cargo easyblock (#17666)
- fix homepage in ELPA easyconfigs (due to switch to new domain) (#17697)
- add patch for scipy 1.10.1 extension in SciPy-bundle 2023.02 to fix broken test (#17713)
- use CUDA variant of OpenMM 7.5.1 as dependency for AlphaFold 2.3.0 (#17717)
- exclude flaky test_optim for PyTorch 1.12.1 + make excluded tests for PyTorch 1.12.1 consistent (#17726, #17730, #17731, #17737)
- add missing PCRE dependency for InterProScan 5.55-88.0 (#17762)
- fix building Python bindings of DGL, requires static libs (#17764)
- only use QEF gitlab source url for QuantumESPRESSO itself (#17766)
- add egg file to OpenCV 4.6.0 python package for pip + pkgconfig file (#17779)
- fix broken source URL for AOCC 4.0.0 (#17794)
- specify source_urls inside exts_default_options in Seurat easyconfigs to ensure correct name expansion for the archived packages (#17830)
- add Doxygen build dependency to X11 (#17842)
- FLINT needs BLAS so move it up from GCC level (#17868)
- fix broken tarball links for ispc 1.6, 1.10, and 1.12 easyconfigs (#17875)
- add dependency on PycURL to JupyterHub-3.0.0-GCCcore-11.3.0.eb (#17887)
- add historical repo paths to install cmd for old versions of texlive (#17893)
- add missing FastTreeMP binary for FastTree (#17897)
- add checksum for arm64 source tarball for Go 1.18.3 (#17903)
- add patch to fix test_quantization in PyTorch 1.12.1 (#17908)
- add make 4.3 as build dependency for recent OpenBLAS versions (#17924)
- other changes:
- bump versions in Java wrappers to latest builds that include ppc64le: Java/8.362, Java/11.0.8, Java/17.0.6 (#17775)
- move Arb and polymake to gfbf/foss since FLINT is now at gfbf/foss (#17869)
v4.7.1 (March 20th 2023)
------------------------
update/bugfix release
- added example easyconfig files for 99 new software packages:
- astro-tulips (#17263), BA3-SNPS-autotune (#17248), BayesAss3-SNPs (#17247), Block (#27), CatLearn (#14940),
CDFlib (#17133), Cellpose (#13703), CheckM-Database (#17462), chemprop (#17261), cimfomfa (#17268), conan (#17326),
cooler (#17328), crossguid (#16207), cuSPARSELt (#17141), cython-blis (#17544), DBCSR (#17170), dclone (#17225),
DensPart (#17473), Deprecated (#1248), DLPack (#17311), DMLC-Core (#17311), dorado (#17195), duplex-tools (#17497),
eQuilibrator (#16812), fastai (#16985), fastjet (#17367), fastjet-contrib (#17377), ffnvcodec (#17271),
finder (#1917), flowFDA (#17495), gbasis (#17473), genomepy (#17506), Giotto-Suite (#17207), GKeyll (#16044),
GraphDB (#17280), graphviz-python (#17352), grid (#17473), GUSHR (#16905), Health-GPS (#17434), HepMC3 (#17341),
HiCMatrix (#17330), Inferelator (#17223), iodata (#17473), irodsfs (#17486), jupyter-contrib-nbextensions (#17270),
jupyterlab-lmod (#16563), jupyterlmod (#16563), kb-python (#17260), kineto (#17194), KMCP (#17267),
krbalancing (#17325), Lace (#954), LASSO-Python (#17510), libemf (#16188), loomR (#14518), MAKER (#17345),
methylartist (#17264), nanoflann (#17311), netMHCII (#9741), NEXUS-CL (#17350), nichenetr (#17524),
Parallel-Hashmap (#17311), pdsh (#17139), Perseus (#17210), PfamScan (#17530), Phenoflow (#17495), PIRATE (#17275),
PLAMS (#17473), plot1cell (#17498), pybinding (#17137), pyperf (#17063), pyslim (#17150),
pytest-rerunfailures (#17295), pytest-shard (#17295), python-louvain (#17207), PyTorch-Ignite (#15491),
PyVCF3 (#17519), R2jags (#17226), rapidcsv (#16211), rapidNJ (#17399), Rivet (#17380), rmarkdown (#17189),
scArches (#17069), scHiCExplorer (#17334), scib (#17142), SeaView (#17385), silhouetteRank (#17207),
siscone (#17342), smfishHmrf (#17207), sparse-neighbors-search (#17329), SpatialDE (#17207), sradownloader (#17188),
stardist (#17215), Strainberry (#17522), toil (#17098), vConTACT2 (#17372), VirSorter2 (#17371),
vitessce-python (#17472), vitessceR (#17525), YODA (#17343)
- added additional easyconfigs for various supported software packages, including:
- AlphaFold 2.3.0, Anaconda3 2022.10, angsd 0.940, archspec 0.2.0, Armadillo 11.4.3, AUGUSTUS 3.5.0, bcbio-gff 0.7.0,
BCFtools 1.17, beagle-lib 4.0.0, Beast 2.7.3, BeautifulSoup 4.11.1, Biopython 1.81, BLAT 3.7, Blender 3.4.1,
Blosc2 2.6.1, Boost 1.81.0, Bottleneck 1.3.6, BUSCO 5.4.5, bx-python 0.9.0, CatMAP 20220519, CellRanger 7.1.0,
Cereal 1.3.2, CFITSIO 4.2.0, CheckM 1.2.2, code-server 4.9.1, configurable-http-proxy 4.5.3, csvkit 1.1.0, 4.8,
CUDA 12.1.0, cuDNN 8.8.0.121, cwltool 3.1.20221008225030, Cython 0.29.33, DGL 0.9.1, DIAMOND 2.1.0, dill 0.3.6,
DIRAC 23.0, dm-tree 0.1.8, dRep 3.4.2, eggnog-mapper 2.1.10, elfutils 0.189, ELPA 2022.05.001, epiScanpy 0.4.0,
FabIO 0.14.0, FastQ_Screen 0.14.0, FFmpeg 5.1.2, FLAC 1.4.2, flatbuffers 23.1.4, FLINT 2.9.0, GDAL 2.4.4,
GDAL 3.6.2, GDGraph 1.56, GEOS 3.11.1, GMAP-GSNAP 2023-02-17, gmsh 4.11.1, gnuplot 5.4.6, GOATOOLS 1.3.1,
googletest 1.12.1, GPyTorch 1.9.1, Greenlet 2.0.2, GST-plugins-base 1.22.1, GStreamer 1.22.1, GTDB-Tk 2.1.1,
h5py 3.8.0, HDBSCAN 0.8.29, HDF5 1.14.0, HiCExplorer 3.7.2, Highway 1.0.3, HTSlib 1.17, hypothesis 6.68.2,
Hypre 2.27.0, igraph 0.10.3, IGV 2.16.0, IJulia 1.24.0, Imath 3.1.6, imbalanced-learn 0.10.1, imkl 2023.0.0,
imkl-FFTW 2023.0.0, impi 2021.8.0, intel-compilers 2023.0.0, IRkernel 1.3.2, JAGS 4.3.1, jax 0.4.4, Julia 1.8.5,
JupyterHub 3.0.0, jupyter-matlab-proxy 0.5.0, jupyter-resource-usage 0.6.3, jupyter-server-proxy 3.2.2,
Kent_tools 442, leidenalg 0.9.1, LERC 4.0.0, libcerf 2.3, libgit2 1.5.0, libnsl 2.0.0, libsndfile 1.2.0,
libtirpc 1.3.3, libxslt 1.1.37, Longshot 0.4.5, MAFFT 7.505, Maple 2022.1, MaSuRCA 4.1.0, Mathematica 13.1.0,
MATIO 1.5.23, MATLAB 2022a + 2022a-r3 + 2022b, matplotlib 3.7.0, MaxQuant 2.2.0.0, MCL 22.282, MDAnalysis 2.4.2,
Miniconda3 22.11.1, mm-common 1.0.5, MPFR 4.2.0, mpi4py 3.1.4, mpmath 1.2.1, msprime 1.2.0, MultiQC 1.14,
mygene 3.2.2, nano 7.1, nanomax-analysis-utils 0.4.4, ncbi-vdb 3.0.2, NetLogo 6.2.2 + 6.3.0, nettle 3.8.1,
networkx 3.0, Nextflow 22.10.6, nlohmann_json 3.11.2, numba 0.56.4, NVHPC 22.9 + 22.11 + 23.1, NVSHMEM 2.8.0,
OpenMPI 4.1.5, Optuna 3.1.0, ORCA 5.0.4, PAML 4.10.5, panaroo 1.3.2, ParallelIO 2.5.10, parasail 2.6, Pillow 9.4.0,
PIPITS 3.0, PLINK 2.00a3.7, plotly.py 5.12.0 + 5.13.1, PLUMED 2.8.1, poetry 1.2.2, polymake 4.8, preseq 3.2.0,
presto 1.0.0-20230113, PROJ 9.1.1, protobuf 3.21.9, psycopg2 2.9.5, pybind11 2.10.3, PyCharm 2022.3.2,
py-cpuinfo 9.0.0, pyFAI 0.21.3, pyfaidx 0.7.1, pyGenomeTracks 3.8, pygraphviz 1.10, pymca 5.7.6, Pysam 0.20.0,
PySCF 2.1.1, PyTables 3.8.0, Python 3.11.2, python-parasail 1.3.3, PyZMQ 24.0.1, QCG-PilotJob 0.13.1,
QIIME2 2022.11, QtPy 2.3.0, QUAST 5.2.0, R 4.2.2, Ray-project 2.2.0, RDKit 2022.09.4, Redis 7.0.8, redis-py 4.5.1,
ReFrame 4.0.5, RepeatMasker 4.1.4, RepeatModeler 2.0.4, rjags 4-13, RMBlast 2.13.0, ROOT 6.22.08, Salmon 1.9.0,
SAMtools 1.17, Scalasca 2.6.1, scikit-learn 1.2.1, SciPy-bundle 2023.02, SDL2 2.26.3, SeqKit 2.3.1, silx 1.0.0,
snakemake 7.22.0, SNAP-HMM 20221022, SpaceRanger 2.0.1, SPAdes 3.15.5, spaln 2.4.13f, Spark 3.3.1,
SRA-Toolkit 3.0.3, SSW 1.2.4, STAR 2.7.10b, STAR-CCM+ 18.02.008, SVG 2.87, TensorFlow-Datasets 4.8.3,
Tkinter 3.10.8, tqdm 4.64.1, Trilinos 13.4.1, Trim_Galore 0.6.10, Trinity 2.15.1, TWL-NINJA 0.98-cluster_only,
Unidecode 1.3.6, vsc-mympirun 5.3.0, VSEARCH 2.22.1, wget 1.21.3, wxWidgets 3.2.2.1, x264 20230226,
Xerces-C++ 3.2.4, XlsxWriter 3.0.8, xtb 6.5.1, Xvfb 21.1.6
- minor enhancements, including:
- add additional extensions to R 4.2.1 (#17043, #17125, #17224, #17493, #17523)
- add additional extensions to Bioconductor 3.15 (#17126, #17315, #17494)
- add sanity check command to OpenMolcas v22.10 (#17128)
- add Set::Object and Heap::Fibonacci extensions to Perl 5.32.1 (#17151)
- add additional extensions to Python 3.10.8 (required for scipy test suite) (#17159)
- enhance OpenFold 1.0.1 for standalone usage (#17206)
- add SDL2 dependency for FFmpeg 5.0.1 to build ffplay (#17213)
- set $JULIA_DEPOT_PATH and $JULIA_HISTORY in Julia easyconfigs (#17216)
- add Devel::Size + Math::Utils extension to recent Perl easyconfigs (#17246, #17466)
- combine errors of extension patch check into a single failure (#17286)
- add case-insensitive name clash test (#17303)
- add ffnvcodec build dependency to all recent FFmpeg easyconfigs (#17316)
- use 'import deap.base' in sanity check for deap extension in SciPy-bundle 2022.05 (#17429)
- add source URL to cuDNN 8.8 easyconfig (#17439)
- add missing zstd dep to Boost (#17482)
- various bug fixes, including:
- fix postinstallcmds and clarify download instructions for netMHC + netMHCpan 4.0a (#9739, #9740)
- fix OpenBLAS 0.3.15 patch to correctly set the CPU core type for Tiger Lake (#15845)
- add alternative checksum for UCX 1.13.1 after source tarball was changed in-place (without actual code changes) (#17077)
- fix build of TensorFlow 2.5+ on aarch64 (#17101)
- explictely download qe-gipaw source tarball from qe-gipaw GitHub repository in QuantumESPRESSO 7.1 easyconfigs (#17129)
- add patch for GCCcore 11.1.0 + 11.2.0 to fix AVX2 bug (#17135)
- add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2 (#17140)
- fix source URL for p7zip v17.x (#17144)
- add patches for Qt5 5.15.5 to fix compilation failures in abseil and breakpad with glibc 2.34 (#17165)
- remove dependency on Pillow from scikit-bio v0.5.7 (#17178)
- correctly specify path to libfabric installation prefix in PMIx 4.1.0 easyconfig (#17204)
- use GCC as toolchain for serial variants of HDF5, since it has a FORTRAN API (#17221)
- fix CMake print summary for long hostnames for NECI (#17230)
- add missing pmix patch to OpenMPI 4.1.1 easyconfig used in iomkl/2021a and iomkl/2021b (#17240)
- include required stereo_chemical_props.txt for OpenFold 1.0.1 (#17242)
- add patch for PAPI 7.0.0 to fix compilation error (#17244)
- also update $PERL5LIB for RepeatMasker v4.1.4 (#17245)
- add alternative source_url for MariaDB > 10.4 (#17250)
- remove use of rysnc in building Kent_tools (#17252)
- add missing pkgconf build dependency in recent libxslt easyconfigs (#17254)
- add psycopg2, PyYAML, and Cartopy dependencies to QGIS 3.28.1 (#17257)
- fix postinstallcmds in shovill easyconfigs (#17279)
- allow multiple easyconfigs with same name if they differ by CUDA version included in versionsuffix (#17289)
- remove duplicate SlamDunk easyconfig using lowercase name (#17301)
- use https in homepage + source URL for GenomeThreader 1.7.3 (#17338)
- consistently use Check capitailisation (#17351)
- add alternative checksum for spatial 7.3-14 extension in R 4.1.x easyconfigs (#17356)
- fix homepage + source URL for ELPA (due to switch to new domain) (#17357)
- fix homepage in ELPA easyconfigs (due to switch to new domain) (#17358)
- rename libpsml for consistency with libPSML (#17359)
- replace obsolete pycrypto with pycryptodome in Python 3.10.x easyconfigs (#17412)
- update deap to version 1.3.3 in SciPy-bundle 2022.05 easyconfigs (since deap 1.3.1 is broken) (#17413)
- add patch for Qt5 5.12.2 with GCCcore/11.2.0 to fix template bug (#17464)
- replace src include path with installation dir for HDF5 (#17469, #17488)
- disable Python support for OTF2 v2.2, since we're not including Python 2.x as dependency (#17499)
- update homepage and source urls of DFT-D3 (#17528)
- use Binary easyblock for ANIcalculator to prevent RPATH sanity check failures (#17536)
- other changes:
- fix invalid escape sequences in easyconfigs by using raw strings (r"...") (#11149)
- add exception for ncbi-vdb 3.0.0 dependency variant (#17131)
- use proper source tarball instead of cloning GitHub repository for wxWidgets v3.2.1 (#17167)
- enable -fPIC in GEOS 3.11.1 (required by GDAL) (#17196)
- fix website/docs links in README (#17232)
- remove commented out line and delete unused patch for TALON (#17298)
- re-enable disabled tests (#17304)
- rename MAGMA to MAGMA-gene-analysis to avoid name collision (#17345)
- Archive ARB and blasr patch files (#17346)
- Archive BAMM, BamM, and GroopM to avoid BAMM/BamM name collision (#17348)
- consistently use NanoFilt capitalisation (#17349)
- rename ncl to NEXUS-CL to avoid case-insensitive name clash (#17350)
- rename python graphviz to graphviz-python to avoid case-insensitive name clash (#17352)
- archive charmm and CHARMM easyconfigs to avoid case-insensitive name clash (#17364)
4.7.0 (Janurary 9th 2023)
-------------------------
feature release
- added easyconfigs for foss/2022b, intel/2022b common toolchains (#16961 and #16962)
- see also https://docs.easybuild.io/en/latest/Common-toolchains.html
- added easyconfigs for NVHPC-based toolchains nvompi/2022.07 and nvofbf/2022.07 (#16724)
- added example easyconfig files for 107 new software packages:
- Alfred (#16780), attrdict3 (#16856), bamFilters (#16735), bcl-convert (#16351), Beagle (#346), Boost.MPI (#15757),
captum (#16477), CAT-BAT (#16577, #16634), cdo-bindings (#16669), Chemaxon-Marvin (#13954), CliMetLab (#16842),
CloudCompare (#16944), cmocean (#16659), COBRApy (#16616), CodAn (#16902), CoSymLib (#17049), CPPE (#16749),
cryoCARE (#16534), CTPL (#16498), CUDA-Samples (#16914), cwltool (#16503), Cytoscape (#16682), DeepLabCut (#16391),
DeepMod2 (#17008), Dice (#16752), dlb (#16845), DRAGMAP (#16532), ecBuild (#16842), EGTtools (#16704),
ESM-2 (#16528), flair-NLP (#15588), FMS (#16965), Godon (#16574), gsw (#16643), HighFive (#16737), humann (#16853),
HyperQueue (#16753), IJulia (#16494, #16665), infercnvpy (#16712), InParanoid (#16572), jupyter-server (#14844),
KaHIP (#16861), KITE (#16550), lagrangian-filtering (#16654), LHAPDF (#17028), librttopo (#16856), libwpe (#16088),
Magics (#16842), matlab-proxy (#14270), mcu (#16566), MEMOTE (#16772), memtester (#16763), meson-python (#16911),
minizip (#16856), MITgcmutils (#16623), MONAI (#16519), MOOSE (#13824), mstore (#16892, #17029),
MultilevelEstimators (#15630, #16665), n2v (#16535), NanoLyse (#16575), napari (#16468), NECI (#16751),
nf-core-mag (#16613), oceanspy (#16640), olego (#16909), OmegaFold (#16698), OVITO (#16811), Panedr (#16564),
Parcels (#16838), polars (#16989), PsiCLASS (#16906), pyccel (#16823), PyCheMPS2 (#16710), PyDamage (#16576),
PyImageJ (#16757), pysteps (#16783), python-libsbml (#16610), python-telegram-bot (#16442), pyWannier90 (#16447),
resolos (#16649), RLCard (#16695), SAP (#5200), scikit-misc (#16457), scvi-tools (#16457), SELFIES (#17032),
SeuratDisk (#16951), sfftk (#16466), simint (#16886), SISSO++ (#15759), slamdunk (#15197), spaCy (#17027),
Sphinx-RTD-Theme (#16736), SPOOLES (#16756), Squidpy (#16880), svist4get (#16505), task-spooler (#17048),
TBA (#16497), TensorFlow-Datasets (#16421), TFEA (#16476), TinyXML (#16992), tokenizers (#15587),
torchsampler (#16464), trimesh (#16858), UCX-ROCm (#17033), wpebackend-fdo (#16093), xmitgcm (#16637)
- added additional easyconfigs for various supported software packages, including:
- Albumentations 1.3.0, ANSYS 2022R2, AOCC 4.0.0, archspec 0.1.4, ArviZ 0.12.1, ASAP 2.1, astropy 5.1.1,
basemap 1.3.6, BBMap 39.01, BEDOPS 2.4.41, Blender 3.3.1, Blosc 1.21.3, Blosc2 2.4.3, bokeh 2.4.3, Bonnie++ 2.00a,
boto3 1.26.37, BRAKER 2.1.6, CDO 2.1.1, cdsapi 0.5.1, CharLS 2.4.1, CheMPS2 1.8.12, CMake 3.24.3, CubeGUI 4.8,
CubeLib 4.8, CubeWriter 4.8, CUDA 11.8.0 + 12.0.0, cuDNN 8.6.0.163 + 8.7.0.84, cURL 7.86.0, cutadapt 4.2,
cuTENSOR 1.6.1.5, dask 2022.10.0, DAS_Tool 1.1.3, DBus 1.15.2, dcm2niix 1.0.20220720, DCMTK 3.6.7, deepdiff 5.8.1,
dm-reverb 0.7.0, double-conversion 3.2.1, Doxygen 1.9.5, ecCodes 2.27.0, exiv2 0.27.5, Fiji 2.9.0, Filtlong 0.2.1,
FLANN 1.9.1, FlexiBLAS 3.2.1, fontconfig 2.14.1, FreeXL 1.0.6, g2clib 1.7.0, GATK 4.3.0.0, GD 2.75, GDCM 3.0.20,
Gdk-Pixbuf 2.42.10, GeneMark-ET 4.71, gensim 4.2.0, geopandas 0.12.2, gettext 0.21.1, gh 2.20.2, Ghostscript 10.0.0,
git 2.38.1, GLib 2.75.0, GlobalArrays 5.8.2, GnuTLS 3.7.8, GObject-Introspection 1.74.0, GRASS 8.2.0, GTK3 3.24.35,
HarfBuzz 5.3.1, HTSeq 2.0.2, hwloc 2.8.0, Hyperopt 0.2.7, ICU 72.1, imagecodecs 2022.9.26, imageio 2.22.2,
ImageMagick 7.1.0-53, imbalanced-learn 0.9.0, JasPer 4.0.0, jax 0.3.23, JupyterLab 3.5.0, Leptonica 1.83.0,
libavif 0.11.1, libdap 3.20.11, libdeflate 1.15, libdrm 2.4.114, libfabric 1.16.1, libffi 3.4.4, libglvnd 1.6.0,
libgpg-error 1.46, libidn 1.41, libjpeg-turbo 2.1.4, LibLZF 3.6, libpciaccess 0.17, libpng 1.6.38, librsvg 2.55.1,
LibSoup 3.0.8, libspatialindex 1.9.3, libspatialite 5.0.1, libtasn1 4.19.0, LibTIFF 4.4.0, libxml2 2.10.3,
libxml2-python 2.9.13, line_profiler 4.0.0, LittleCMS 2.14, LLVM 15.0.5, lz4 1.9.4, makedepend 1.0.7, Mako 1.2.4,
MATLAB-Engine 2021b, Mesa 22.2.4, Meson 0.64.0, MIGRATE-N 5.0.4, Miniconda3 4.12.0, mold 1.7.1, Molden 7.1,
MotionCor2 1.5.0, MoviePy 1.0.3, MRChem 1.1.1, MRCPP 1.4.1, nano 7.0, NanoFilt 2.8.0, nanoget 1.18.1,
nanomath 1.2.1, ncbi-vdb 3.0.0, NCCL 2.16.2, NCCL-tests 2.13.6, NCO 5.1.3, nglview 3.0.3, NiBabel 4.0.2,
Ninja 1.11.1, nodejs 18.12.1, NSPR 4.35, NSS 3.85, NVHPC 22.7, NVSHMEM 2.7.0, Octave 7.1.0, OPARI2 2.0.7,
OpenFOAM 10, OpenFold 1.0.1, OpenImageIO 2.3.17.0, OpenMolcas 22.10, openpyxl 3.0.10, openslide-python 1.2.0,
OpenStackClient 6.0.0, OSU-Micro-Benchmarks 6.2, OTF2 3.0.2, Pango 1.50.12, PAPI 7.0.0, pauvre 0.2.3, PETSc 3.17.4,
phonopy 2.16.3, pigz 2.7, Pillow 9.2.0, Pint 0.19.2, pixman 0.42.2, PMIx 4.2.2, poppler 22.12.0, psutil 5.9.3,
pybedtools 0.9.0, PyBerny 0.6.3, pydantic 1.10.2, pydicom 2.3.0, pyproj 3.4.0, PyQt5 5.15.5, pytest 7.1.3,
Python 3.10.8, python-isal 1.1.0, PyTorch 1.12.1, PyTorch-Geometric 2.1.0, PyTorch-Lightning 1.8.4, QCA 2.3.5,
QGIS 3.28.1, QIIME2 2022.8, QScintilla 2.11.6, Qt5 5.15.7, Qtconsole 5.3.2, QtKeychain 0.13.2, QtPy 2.2.1,
rasterio 1.3.4, re2c 3.0, ReFrame 3.12.0, RStudio-Server 2022.07.2+576, Ruby 3.0.5, Rust 1.65.0, SAP 1.1.3,
scanpy 1.9.1, scikit-image 0.19.3, SCons 4.4.0, Score-P 8.0, Seaborn 0.12.1, SentencePiece 0.1.97, Seurat 4.3.0,
SignalP 6.0g, SimPEG 0.18.1, SLEPc 3.17.2, SNAP 2.0.1, SpaceRanger 2.0.0, SQLite 3.39.4, STAR-CCM+ 17.06.007,
SuperLU_DIST 8.1.0, tensorboardX 2.5.1, TensorFlow 2.8.4, tensorflow-probability 0.16.0, tesseract 5.3.0,
texinfo 6.8, TM-align 20190822, tmux 3.3a, TOBIAS 0.14.0, TOML-Fortran 0.3.1, Transformers 4.24.0,
typing-extensions 4.4.0, UCC 1.1.0, UCX-CUDA 1.13.1, util-linux 2.38.1, Valgrind 3.20.0, Vim 9.0.0950, VTK 9.2.2,
wandb 0.13.6, WebKitGTK+ 2.37.1, WPS 4.4, WRF 4.4, wxPython 4.2.0, wxWidgets 3.2.0, X11 20221110, xarray 2022.9.0,
XCFun 2.1.1, XGBoost 1.7.2, Xmipp 3.22.07, XZ 5.2.7, yaml-cpp 0.7.0, zarr 2.13.3, zlib-ng 2.0.6
- minor enhancements, including:
- enable building of dev tools in recent PyQt5 easyconfigs (#16469)
- add extensions to R v4.2.1: LMERConvenienceFunctions (#16512), HGNChelper 4.2.1 (#16744)
- add extensions to R-bundle-Bioconductor 3.15: SPOTlight (#16569), HiCcompare (#16581), ROntoTools (#16636),
scDblFinder (#16686), numbat (#16777), HiCBricks (#16913), zellkonverter (#16952)
- add libmad dependency to SoX v14.4.2 (#16758)
- also install subtree support in recent git easyconfigs (#16784, #16785)
- add extensions to ESM-2 to enhance it for esmfold (#16841)
- add libwebp dependency to Pillow-SIMD 9.2.0 to add webp support (#16844)
- add KaHIP dependency to OpenFOAM v2206 (#16974)
- enable dataset support for recent versions of Arrow (#16956)
- various bug fixes, including:
- define $JUPYTER_PATH via modextrapaths rather than modextravars for IRkernel 1.x (#15776)
- add patches to fix PyTorch 1.10.0 build on POWER (#15904)
- fix installation of Python 2.7.18 with GCCcore/11.2.0 (was broken due to 0.0.0 version for some extensions) (#16485)
- add patch for M4 1.4.18 to fix glibc v2.34 SIGSTKSZ compatibility (#16486)
- add patch for pybind11 2.6.0 to fix failing test due to extra whitespace (#16487)
- work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml (#16490)
- fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x (#16502)
- add OpenBLAS patches to disable FMA in [cz]cal and fix crash in zdot (#16510)
- add missing Perl build dependency GStreamer + add patch to skip trying to make files suid (#16516)
- build nodejs with OpenSSL and ICU provided as proper dependencies (#16529)
- also define $JUPYTER_CONFIG_PATH in IPython and JupyterLab easyconfigs (#16556)
- define $GTKDOCIZE as 'echo' before generating configure script for recent HarfBuzz versions (#16570)
- disable use of -Werror in recent NSS easyconfigs (#16571)
- use 'cpan.metacpan.org' rather than 'www.cpan.org' in extension source_urls for recent Perl easyconfigs (#16611)
- avoid that zlib + htslib are downloaded and built during installation of MetaBAT (#16624)
- add patch to fix installation of MetaBAT 2.15 on non-x86_64 systems (#16633)
- add missing pyWannier90 dependency for mcu + enhance sanity check (#16667)
- fix source_urls for colossalai 0.1.8 (no longer available via PyPI, only via GitHub repo) (#16693)
- add patches to fix or skip PyTorch 1.12.1 tests (#16793)
- fix checksum for cell2location 0.05-alpha and add missing build dependency on flex (#16819)
- upgrade dependency on libdeflate to common v1.8 in fastp and vt easyconfigs using GCC(core)/10.3.0 (#16839)
- fix checksum for dlllogger extension in OpenFold v1.0.0 (#16694)
- make sure that Python dependency is actually used for VTK 9.0.1 (#16741)
- fix homepage for pocl v1.8 (#16857)
- fix source_urls in MUMPS easyconfigs (#16931, #16932)
- fix installation of Bowtie2 v2.4.4+ on non-x86_64 systems (#16946)
- add missing OpenSSL dependency to DCMTK 3.6.7 (#16979)
- fix source URL for PCRE2 (#16987)
- add pkgconf dependency for ICU and add patch to avoid trouble with long path names for nodejs-16.15.1/GCCcore-11.3.0 (#16990)
- add patch for libwpe 1.13.3 to avoid build issues on CentOS 7 (#17001)
- add missing zlib and zstd to GnuTLS (#17013)
- add missing pkgconf build dependency to Transformers v4.24.0 (#17020)
- fix checksums for xxx-rocm-4.5.0.tar.gz source tarballs for Clang-AOMP 4.5.0 (#17042)
- replace useless test step for simint 0.7 with (lightweight) sanity check command (#17044)
- other changes:
- only give read permissions in GitHub Actions workflows (#16263)
- remove ExomeDepth from recent R-bundle-Bioconductor easyconfigs (#16492)
- include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0 (#16578)
- use new EasyBuild logo in README (#16641)
- rename hyperopt to Hyperopt, to be consistent with existing Hyperopt easyconfigs (#16697)
- automatically cancel Github Action workflow runs for outdated commits (#16754)
- use geo moduleclass for SimPEG 0.14.1 (#16847)
4.6.2 (October 21st 2022)
-------------------------
update/bugfix release
- add easyconfig for intel/2022.09 toolchain (#16435)
- added example easyconfig files for 25 new software packages:
- AGAT (#16261), AMAPVox (#16438), Avogadro2 (#16257), buildingspy (#16308), CDBtools (#16436),
Compress-Raw-Zlib (#16307), CUDAcompat (#15892), CWIPI (#16342), enchant-2 (#16082, #16319), f90wrap (#16346),
Imath (#16276), Mamba (#16432), Miller (#16221), nghttp2 (#16096), ngtcp2 (#16098), NVSHMEM (#16254),
pairsnp (#16331), paladin (#16320), PyMOL (#16394), python-irodsclient (#16328), ruffus (#16428),
TELEMAC-MASCARET (#16274), torchdata (#16344), Waylandpp (#16092), x13as (#16163)
- added additional easyconfigs for various supported software packages, including:
- Amber 22.0, AMS 2022.102, ASE 3.22.1, atools 1.5.1, Beast 2.6.7, biogeme 3.2.10, Boost.Python 1.79.0, ccache 4.6.3,
dbus-glib 0.112, Delly 1.1.5, ESMF 8.3.0, expat 2.4.9, FDS 6.7.9, file 5.43, FLTK 1.3.8, FTGL 2.4.0, gc 8.2.2,
GitPython 3.1.27, Go 1.18.3, GPAW 22.8.0, Guile 3.0.8, htop 3.2.1, hunspell 1.7.1, IPython 8.5.0, jq 1.6,
Julia 1.8.2, LDC 1.30.0, libcint 5.1.6, libconfig 1.7.3, libreadline 8.2, LibSoup 3.0.7, LIBSVM 3.30,
libwebp 1.2.4, likwid 5.2.2, MariaDB 10.9.3, matplotlib 3.5.2, ncdu 1.17, netcdf4-python 1.6.1, Nextflow 22.10.0,
NFFT 3.5.3, Nipype 1.8.5, numactl 2.0.16, onedrive 2.4.21, OpenCV 4.6.0, OpenEXR 3.1.5, OpenJPEG 2.5.0,
OpenMM 7.7.0, OpenPGM 5.2.122, OpenSSL 1.1.1q, Perl 5.36.0, Pillow-SIMD 9.2.0, pkgconf 1.9.3, PostgreSQL 14.4,
PyCharm 2022.2.2, PyTorch 1.12.0, PyTorch 1.12.0, PyTorch-Lightning 1.7.7, RDFlib 6.2.0, SAMtools 1.16.1,
scikit-learn 1.1.2, Score-P 7.1, SDL2 2.0.22, spaln 2.4.12, spglib-python 2.0.0, SuiteSparse 5.13.0, SUNDIALS 6.3.0,
sympy 1.11.1, tensorboard 2.10.0, torchvision 0.13.1, TRIQS 3.1.1, TRIQS-cthyb 3.1.0, TRIQS-dft_tools 3.1.0,
TRIQS-tprf 3.1.1, TRUST4 1.0.7, TurboVNC 3.0.1, typing-extensions 4.3.0, UCX 1.13.1, umap-learn 0.5.3, VEP 107,
VMD 1.9.4a57, Wayland 1.21.0, wxWidgets 3.2.1, xprop 1.2.5
- minor enhancements, including:
- configure recent pocl versions with -DLLC_HOST_CPU=native to avoid CPU auto-detection (#16246)
- add multi-dep exception to easyconfigs test suite for ncbi-vdb-3.0.0 which requires HDF5 1.10.x (#16316)
- enable running of LAPACK tests for recent OpenBLAS easyconfigs + add patch to fix failing LAPACK tests due to use of -ftree-vectorize (#16406)
- add GITHUB_(LOWER_)RELEASE to known constants in setup.cfg (#16422)
- add AMAPVox extension to R v4.2.1 (#16439)
- add OpenEXR depenency to POV-Ray 3.7.0.10 (#16408)
- various bug fixes, including:
- add patch for OpenBLAS 0.3.7-0.3.12 to fix miscomputation on POWER (#16199)
- skip flaky test in PyTorch 1.9.0 (#16258)
- add --with-versioned-syms to ncurses 6.2 and 6.3 (#16270)
- add missing pkg-config build dependency to Guile (#16317)
- add patches to fix incompatibilites between ASE and other packages in 2022a toolchain (#16332)
- add patches to fix PyTorch 1.11 on POWER (#16339)
- add patches for Ambertools 21 to Amber 20.11 to work with updated Amber easyblock (#16343)
- use Intel MPI from EasyBuild toolchain in AMS (#16363)
- fix execution permissions for bin/ngm* for NextGenMap v0.5.5 (#16383)
- fix using provided Qhull and freetype dependencies for matplotlib 3.5.2 by creating mplsetup.cfg rather than setup.cfg (#16396)
- fix GitHub download link in for libpsl 0.21.1 (#16397)
- stick to http in source URL for stride.tar.gz in VMD 1.9.4a51 easyconfigs due to problems with SSL certificate (#16403)
- add patch to detect available cores and remove unneeded deps for Unicycler 0.5.0 (#16407)
- add missing ICU + libunistring dependencies for libpsl 0.21.1 w/ GCCcore/10.3.0 (#16410)
- add patch to GCC 11.x + 12.x to fix vectorizer bug (#16411)
- fix checksum for GULP 6.1 (#16423)
- add bzip2 and libxml2 as dependencies for netCDF 4.9.0 (#16450)
- other changes:
- drop Java dep from ABAQUS 2022 (#16314)
- deprecate use of True in favour of SYSTEM for system-toolchain dependencies in easyconfigs using a recent toolchain version (>2019b) (#16384)
- update easyconfigs to use `SYSTEM` template constant instead of `True` in dependencies (#16386, #16418)
- update libxml2 + libxslt easyconfigs to use gnome.org source URL (#16429)
v4.6.1 (September 12th 2022)
----------------------------
update/bugfix release
- added example easyconfig files for 37 new software packages:
- AptaSUITE (#8583), BigDFT (#15860), colossalai (#15971), CrystFEL (#8407), Dakota (#15883, #16210),
FastFold (#15972), fastparquet (#15020), FOX-Toolkit (#15986), GLM-AED (#15879), hiredis (#16071),
how_are_we_stranded_here (#16220, #16227), indicators (#16209), JavaFX (#8583), json-fortran (#15979),
jupyter-resource-usage (#15834), libev (#16086), libmad (#16067), libplinkio (#13040), LuaJIT2-OpenResty (#16047),
MetaMorpheus (#15825), mgltools (#16226), miniasm (#15858), muMerge (#16115), nano (#16198), nghttp3 (#16097),
olaFlow (#16021), OpenFAST (#15983, #15983), OpenFold (#15971), Phantompeakqualtools (#15871),
pyGenomeTracks (#16143), QuickPIC (#15978), RheoTool (#16077), Satsuma2 (#16068), SMC++ (#16017), stripy (#15866),
UCC-CUDA (#15956), VESTA (#16217)
- added additional easyconfigs for various supported software packages, including:
- alevin-fry 0.6.0, AmberTools 22.3, arrow-R 8.0.0, ASE 3.22.1, BBMap 38.98, BCFtools 1.15.1, binutils 2.39,
BLAST+ 2.13.0, Bowtie2 2.4.5, BUSCO 5.4.3, CapnProto 0.10.2, Cartopy 0.20.3, ccache 4.6.1, cclib 1.7.2, CDO 2.0.5,
CellRanger-ATAC 2.1.0, CoordgenLibs 3.0.1, cURL 7.84.0, cuTENSOR 1.6.0.3, einops 0.4.1, Elk 8.5.2, Emacs 28.1,
Embree 3.13.4, FFmpeg 4.4.2 + 5.0.1, fio 3.32, Flask 2.2.2, Flye 2.9.1, fmt 9.1.0, FORD 6.1.15, FreeSurfer 7.3.2,
GATE 9.2, GATK 4.2.6.1, GCC(core) 12.2.0, GDB 12.1, Geant4 11.0.2, GetOrganelle 1.7.6.1, gifsicle 1.93, GLFW 3.3.8,
glib-networking 2.72.1, Globus-CLI 3.6.0, gnuplot 5.4.4, gperftools 2.10, Graphviz 5.0.0, Gurobi 9.5.2, HDF5 1.12.2,
HTSlib 1.15.1, Hypre 2.25.0, Jansson 2.14, jax 0.3.14, Kalign 3.3.2, kim-api 2.3.0, LAMMPS 23Jun2022, libcerf 2.1,
libdwarf 0.4.1, Libint 2.7.2, libQGLViewer 2.8.0, LibSoup 2.74.0, libzip 1.9.2, Lua 5.4.4, lxml 4.9.1,
maeparser 1.3.0, matplotlib 3.5.2, MATSim 14.0, MDAnalysis 2.2.0, medaka 1.6.0, Megalodon 2.5.0, Mercurial 6.2,
MetaEuk 6, Mini-XML-3.3.1, MUMmer 4.0.0rc1, MUMPS 5.5.1, netCDF-Fortran 4.6.0, NGSpeciesID 0.1.2.1,
ont-remora 1.0.0, OpenFOAM v2206, OTF2 3.0, parallel 20220722, ParaView 5.10.1, patchelf 0.15.0, Perl 5.36.0,
pftoolsV3 3.2.12, PLINK 2.00a3.6, pretty-yaml 21.10.1, PRSice 2.3.5, pugixml 1.12.1, Pyomo 6.4.2,
PyOpenCL 2021.2.13, Pysam 0.19.1, PyStan 3.5.0, PyYAML 6.0, RDKit 2022.03.5, scikit-bio 0.5.7, scikit-build 0.15.0,
scikit-learn 1.1.2, scikit-optimize 0.9.0, SCOTCH 7.0.1, SIONlib 1.7.7, SISSO 3.1, spglib-python 2.0.0, Stacks 2.62,
Stata 17, SUMO 1.14.1, tbb 2021.5.0, tqdm 4.64.0, Transformers 4.21.1, Trycycler 0.5.3, Unicycler 0.5.0,
Valgrind 3.19.0, ViennaRNA 2.5.1, VTune 2022.3.0.eb, wxPython 4.1.1, x264 20220620, Z3 4.10.2, zfp 1.0.0
- minor enhancements, including:
- add alternate download URL for Voro++ (#15898)
- add extra symlinks and sanity checks for libtinfo in ncurses (#15903)
- include some easyconfig constants in flake8 configuration file (#16040)
- add pigz dependency for cutadapt v3.4 + v3.5 (#16056)
- add sanity check commands for recent gettext versions (>= 0.20.x) (#16091)
- various bug fixes, including:
- use correct Matlab Runtime Compiler (v8.4) for FreeSurfer v7.1.1 (#13375)
- fix set-alias statements for MaxQuant v2.0.3.0 (#15743)
- add Autotools build dependency to R 4.2.0 w/ foss 2021b (#15822)
- add patch for BLIS to fix auto-detection of POWER (#15826)
- downgrade SPAdes dependency to v3.13.1 for Unicycler 0.4.9 since v3.15.3 is too new (#15840)
- explicitly enable HDF5 from kallisto v0.46.2 onwards (#15843)
- add CVE patch for XZ 5.2.5 + attempt to fix symbol patch for all OSs (#15856)
- use build enviroment set by EasyBuild and add missing dependency on zlib to minimap2 (#15859)
- add missing dependencies and execute tests on Trycycler v0.5.2 (#15864)
- add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9 (#15874)
- exclude (flaky) fault_tolerance_test and fix non-x86 build for TensorFlow 2.7.1 (#15882)
- work around miscompilation of OpenBLAS on POWER by compiling with -fstack-protector-strong (#15885)
- fix tests on POWER9 for BLIS 0.9.0 + fix auto-detect for POWER10 for BLIS (AMD) v2.0 + v3.0 (#15889)
- add and fix patches for PyTorch 1.9.0 on POWER (#15919)
- exclude Binary, PackedBinary and JAR easyblocks from binutils build requirements (#15932)
- consistently add libffi + elfutils dependencies to recent Clang easyconfigs (#15935, #16225)
- add patch to fix broken test on POWER for numpy in SciPy-bundle 2022.05 (#15968)
- refactor checksum test for extensions to use collect_exts_file_info (#15973)
- fix dependency on FOX Toolkit in SUMO (#15986)
- add missing SciPy-bundle dependency for rMATS-turbo (#15988)
- explictely download wannier90 source tarball from wannier90 GitHub repository in QuantumESPRESSO 7.1 easyconfigs (#15993)
- restore ploteig in EIGENSOFT 7.2.1 (#15996)
- add alternative checksum for plot3Drgl extension in R v4.1.x + v4.2.0 easyconfigs (#16011)
- add patch to fix missing sync in LINCS and SETTLE CUDA kernels for GROMACS 2020 (#16027) and 2021 (#16026)
- exclude failing test in TensorFlow 2.4.1 (#16042)
- skip NASA performance and remote server tests in netCDF v4.9.0 (#16050, #16158)
- use versioned symbols in ncurses built with system toolchain (by adding --with-versioned-syms configure option) (#16064)
- add patch to fix pkgconfig file for Blitz++ v1.0.2 (#16102)
- add missing BCFtools dependency for recent medaka versions (#16107)
- add GTK2 v2.24.33 as a dependency for Ghostscript v9.56.1 (#16112)
- fix checksum for Stacks v2.62 (due to silent re-release without version bump) (#16134)
- fix libsanitzer for glibc 2.36 to build GCCcore 11.3.0 (#16145)
- fix top level Makefile for AmberTools 20 and enable tests (#16150)
- add missing patches + enable running tests for AmberTools 21 with intel/2021a (#16151) and intel/2021b (#16152)
- replace HDF5 v1.13.1 with v1.12.1 as dependency, since we shouldn't use odd minor versions of HDF5 which are not stable releases (#16153)
- remove modextrapaths to add top-level install directory to $PATH for recent InterProScan easyconfigs (now done by default by Binary easyblock) (#16167)
- fix sources + source URL + homepage for Molekel v5.4.0 (#16219)
- consistently add maeparser + CoordgenLibs dependencies to OpenBabel 3.1.1 easyconfigs (#16231)
- fix checksum for CUDA 11.4.1 aarch64 installer (#16234)
- remove incorrect comment for Boost dependency in OpenBabel 3.1.1 easyconfigs (#16238)
- add direct Pango dependency in recent ImageMagick easyconfigs (#16237)
- other changes:
- remove superflous -DCMAKE_BUILD_TYPE=Release, use of 'build_type = Release', or enabling separate_build_dir from easyconfigs using CMakeMake easyblock (#13384)
- synchronize ncurses easyconfigs using system toolchain (#15903)
- stick to Java/11 as dependency for Bazel 5.1.1 (which is available for x86_64, aarch64, ppc64le) (#15906)
- speed up OpenMPI 4.1.4 configure by not running "autogen.pl --force", but only running required Autotools commands (#15957)
- replace sed commands by upstreamed patches for BLIS built with intel-compilers toolchain (#15958)
- simplify AlphaFold foss/2021a easyconfigs by using a fleshed out patched OpenMM dependency (#15981)
- update Java/11 to 11.0.16 and Java/17 to 17.0.4 (#16001)
- remove unecessary patch in recent JupyterLab (#16030)
- update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is deprecated) (#16070)
- make check for toolchain value in dependency spec in easyconfigs test suite aware that dumped easyconfig uses SYSTEM constant (#16126)
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)
------------------------
update/bugfix release
- added example easyconfig files for 29 new software packages:
- Abseil (#15102), AMS (#13155), ArchR (#15119), CMAverse (#14963), CmdStanR (#15198), CONN (#15052),
Devito (#14984, #15009), GraphMap (#10299), gRPC (#14728), Hydra (#15025), jupyter-server-proxy (#14844),
M1QN3 (#15002), MAGeCK (#15082), matplotlib-inline (#15084), MEGAN (#15064), MNE-Python (#15174),
ONNX (#15158), ONNX-Runtime (#15158), ont-remora (#15162), Optuna (#15021), patch (#15035),
porefoam (#15067), presto (#15119), PyFrag (#15184), skorch (#15175), SlamDunk (#15197), SPM (#15050),
STRique (#14980), XML-Compile (#15177)
- added additional easyconfigs for various supported software packages, including:
- ABAQUS 2021, AlphaFold 2.1.2, AmberTools 21, archspec 0.1.3, Bandage 0.9.0, BLIS 3.1, c-ares 1.18.1,
CCL 1.12.1, CharLS 2.3.4, Clang-Python-bindings 13.0.1, dcm2niix 1.0.20211006, DFTB+ 21.1, DIRAC 22.0,
ELPA 2021.11.001, FlexiBLAS 3.1.3, FLUENT 2021R2, GATK 4.2.5.0, GetOrganelle 1.7.5.3, IgBLAST 1.18.0,
IntelClusterChecker 2021.5.0, intervaltree-python 3.1.0, ITSx 1.1.3, Julia 1.7.2, kallisto 0.48.0,
KMC 3.2.1, libobjcryst 2021.1.2, libtree 3.0.3, loompy 3.0.7, matplotlib 3.5.1, MCR R2022a,
MDAnalysis 1.1.1+ 2.0.0, MDTraj 1.9.7, medaka 1.5.0, meshalyzer 20200308, MRtrix 3.0.3, NiBabel 3.2.2,
NLTK 3.7, numexpr 2.8.1, ont-fast5-api 4.0.2, OpenAI-Gym 0.21.0, OpenBLAS 0.3.20, ORCA 5.0.3,
parallel-fastq-dump 0.6.6, PIPITS 2.8, pocl 1.8, pycocotools 2.0.4, pyEGA3 4.0.0, pyobjcryst 2.2.1,
RE2 2022-02-01, SAMtools 1.15, SBCL 2.2.1, shovill 1.1.0, SKESA 2.4.0, SOCI 4.0.3, sympy 1.9, TensorFlow 2.5.3,
VirtualGL 3.0, vsc-mympirun 5.2.10, VSEARCH 2.21.1, VTK 9.1.0, VTune 2022.2.0, XGBoost 1.5.0
- minor enhancements, including:
- add Flask-Session to Flask v1.1.4 and Flask v2.0.2 (#15027)
- add check to verify that patch files touched in PRs have a description in place (#15061)