Merge pull request #19101 from SebastianAchilles/eb482

prepare release notes for EasyBuild v4.8.2 + bump version to 4.8.2

RELEASE_NOTES

@@ -3,10 +3,89 @@ 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 18,021 easyconfig files, for 3,224 different software packages,
+The latest version of easybuild-easyconfig provides 18,407 easyconfig files, for 3,292 different software packages,
 incl. 40 different (compiler) toolchains.
 
 
+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)
 --------------------------
 

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 = '4.8.2.dev0'
+VERSION = '4.8.2'
 
 MAJ_VER = VERSION.split('.')[0]
 MAJMIN_VER = '.'.join(VERSION.split('.')[0:2])