diff --git a/RELEASE_NOTES b/RELEASE_NOTES index f3ce7640d11..a72de567996 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,107 @@ 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 17,511 easyconfig files, for 3,161 different software packages, -incl. 39 different (compiler) toolchains. +The latest version of easybuild-easyconfig provides 18,021 easyconfig files, for 3,224 different software packages, +incl. 40 different (compiler) toolchains. + + +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) +- 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 `$__EGL_VENDOR_LIBRARY_DIRS` in recent Mesa easyconfigs, since Mesa easyblock now appends to it (#18630) + - set `$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) diff --git a/setup.py b/setup.py index a8bebcc31f8..9b812bdf2ec 100644 --- a/setup.py +++ b/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 = '4.8.1.dev0' +VERSION = '4.8.1' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2])