Easybuild

EasyBuild v4.8.1 is primarily a bugfix and update release, but it also includes various enhancements.

The executive summary for this release:

- Support for various additional hooks that can be used to customize EasyBuild, including pre_run_shell_cmd_hook which allows tweaking shell commands right before they are run by EasyBuild;

- 2 new custom easyblocks, for sympy and tensorflow-compression;

- Easyconfigs for various recent software versions, including Clang 16.0.6, CP2K 2023.1, FFmpeg 6.0, GCC 13.2.0, OpenFOAM 11, Pillow 10.0.0, TensorFlow 2.13.0, ...;

- Support for installing 83 new software applications and libraries;


Highlights for this release are listed below.
More details are available in the [release notes](https://docs.easybuild.io/release-notes/#release_notes_eb481) which includes links to the respective pull requests for more detailed information.

Highlighted enhancements & updates

(enhancements or updates that (may) warrant updating existing installations are marked with `(***)`)

- support for additional hooks: `pre_build_and_install_loop_hook` + `post_build_and_install_loop_hook`, `cancel_hook`, `fail_hook`, `pre_postiter_hook` + `post_postiter_hook`, and `pre_run_shell_cmd_hook` + `post_run_shell_cmd_hook`; see https://docs.easybuild.io/hooks for more information;

- add `--silence-hook-trigger` configuration option to suppress printing of a debug message every time a hook is triggered;

- add support for using fine grained Github tokens;

- add support for submodule filtering and specifying extra Git configuration in `git_config`;

- new custom easyblocks for `sympy` and `tensorflow-compression`;

- add options to `MesonNinja` generic easyblock to customize `build_cmd`, `install_cmd`, `build_dir`;

- add support to `PerlModule` generic easyblock to customize prefix option used in installation command;

- updates and enhancements to custom easyblocks for Clang, CP2K, CUDA, FreeSurfer, LLVM, Mesa, MXNet, OpenCV, OpenFOAM, PETSc, PyTorch, scipy, Score-P, TensorFlow;

- `(***)` add extensions to recent versions of R (`tabletools`, `flextables`) and R-bundle-Bioconductor (`UCell`, `decoupleR`, `RnBeads`), use "[`eb --skip --rebuild`](https://docs.easybuild.io/partial-installations/#partial_installation_skip)" to install the missing extensions;


Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with `(***)`)

- improve error reporting w.r.t. missing checksums;

- `(***)` only add extensions in module file if there are extensions;

- enhance `PythonPackage` easyblock to deal with `posix_local` installation scheme used by Python in recent Debian/Ubuntu versions;

- `(***)` improve depot management in `JuliaPackage` easyblock;

- `(***)` set `$JULIA_DEPOT_PATH` in Julia easyconfigs with default value;

- bug fixes for various custom easyblocks, incl. imkl-FFTW, Java, `(***)` MATLAB, Mesa, OpenMPI, STAR-CCM+, TensorFlow;

- `(***)` fix regression in GCC 12.1 + 12.2 with wrong warnings;

- fix installation of Python bindings for recent Arrow easyconfigs;

- `(***)` various additional patches for recent PyTorch versions to fix bugs and/or failing tests;

- `(***)` additional bug fixes in easyconfigs for Abseil, at-spi2-core, Automake, FreeSurfer, jupyter-server, JupyterHub, LIBSVM, MPFR, RapidJSON, ScaLAPACK, tRNAscan-SE;

- `(***)` update `Java/11` wrapper to `Java/11.0.20`;

- `(***)` use `GCC/12.2.0` toolchain for GSL 2.7, remove easyconfig for GSL 2.7 with `GCCcore/12.2.0`;

- `(***)` add patch for PMIx 4.x to use lchown so links are not followed;

- `(***)` add hpctestlib to the `$PYTHONPATH` in ReFrame 4.2.0 easyconfig;

- add alternative checksum for Extrae v4.0.4;

- `(***)` disable wx support in gnuplot 5.4.6;

- 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`;



Supported software

Support for installing 83 new software packages has been added, including (but not limited to):

- Ax
- Boost.Python-NumPy
- CatBoost
- ChIPseeker
- cryptography
- GAPPadde
- GenerativeModels
- hatchling
- IsoQuant
- Jupyter-bundle
- JupyterNoteboo
- maturin
- Mikado
- NanoCaller
- Omnipose
- Optax
- pv
- Python-bundle-PyPI
- Sabre
- scib-metrics
- scikit-plot
- setuptools-rust
- tensorflow-compression
- torchvf
- TXR
- virtualenv

This brings the total number of supported software packages to 3,244 (excluding extensions)!
An up-to-date list of supported software is available [here](https://docs.easybuild.io/version-specific/supported-software).

Various software updates have been added, including (but not limited to):

- ABINIT 9.10.3
- Arcade-Learning-Envionment 0.8.1
- archspec 0.2.1
- Bazel 6.3.1
- BCFtools 1.18
- BEDTools 2.31.0
- Boost 1.82.0
- CDO 2.2.2
- Clang 16.0.6
- CP2K 2023.1
- CUDA 12.2.2
- ecBuild 3.8.0
- FFmpeg 6.0
- FreeSurfer 7.4.1
- GCC 13.2.0
- GHC 9.2.2
- gnuplot 5.4.8
- GTK4 4.11.3
- h5py 3.9.0
- Horovod 0.28.1
- Hypre 2.29.0
- ImageMagick 7.1.1-15
- magma 2.7.1
- medaka 1.8.1 + 1.9.1
- Mesa 23.1.4
- MXNet 1.9.1
- OpenAI-Gym 0.26.2
- OpenCV 4.8.0
- OpenFOAM 11
- Pillow 10.0.0
- PLUMED 2.9.0
- pocl 4.0
- QIIME2 2023.5.1
- Qt5 5.15.10
- QuantumESPRESSO 7.2
- SAMtools 1.18
- SciPy-bundle 2023.07
- Score-P 8.1
- sympy 1.12
- SUNDIALS 6.6.0
- TensorFlow 2.13.0
- Valgrind 3.21.0
- wxPython 4.2.1
- zarr 2.16.0

These changes result from various contributions, made by 33 different contributors:

* 25 merged pull requests for EasyBuild framework
* 40 merged pull requests for easyblocks
* 339 merged pull requests for easyconfigs


Thanks to everyone who contributed to this release in one way or another!

To upgrade to EasyBuild v4.8.1, there are [several options](https://docs.easybuild.io/installation/#updating).
Two particularly easy options include:

* `eb --install-latest-eb-release`

* `eb --from-pr 18761` use easyconfig from [PR 18761](https://github.com/easybuilders/easybuild-easyconfigs/pull/18761)

EasyBuild v4.8.0 is primarily a feature release, but it also includes various minor bug fixes, enhancements, and updates.

The executive summary for this release:

- Easyconfigs for the 2023a update of the foss + intel common toolchains;

- 2 new easyblocks: a generic PerlBundle easyblock, and a custom easyblock for Rust;

- Easyconfigs for various recent software versions, including elastix 5.0.0, GROMACS 2023.1, PyTorch 1.13.1, VTK 9.2.6, ...;

- Support for installing 76 new software applications and libraries;

Highlights for this release are listed below. More details are available in the release notes [2] which includes links to the respective pull requests for more detailed information.

Highlighted enhancements & updates

(enhancements or updates that (may) warrant updating existing installations are marked with `(***)`)

- add `PerlBundle` generic easyblock for installing a bundle of Perl modules;

- add custom easyblock for Rust, which makes sure that all shared libraries use RPATH rather than RUNPATH if `--rpath` is used;

- add support for `install_cmds` in `Binary` easyblock;

- update OpenBLAS easyblock since make shared is necessary and sufficient with OpenBLAS 0.3.23 + recent parallel build fixes;

- `(***)` add extra packages to recent R easyconfigs;

- `(***)` add extra packages to recent R-bundle-Bioconductor easyconfigs;

- `(***)` enable building static libs and check for `libexslt.*` in libxslt;


Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with `(***)`)

- fix regex for extracting glibc version from output of '`ldd --version`' in Gentoo Linux;

- stop running tests with Python 2.7 since it is no longer supported in GitHub Actions;

- patch CMake's `UnixPaths.cmake` script if `--sysroot` is set;

- use upstream patch for symbol compatibility in XZ 5.2.5;

- `(***)` change base compiler for `intel/2023.03` to `GCCcore/12.3.0` (required to use it as `intel/2023a`);

- `(***)` use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2;

- `(***)` stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2;

- `(***)` fix exec permissions for all binaries & scripts of L_RNA_scaffolder 20190530;

- `(***)` update SUNDIALS dependency for Cantera v2.6.0 to v6.5.1 + add missing dependencies;

- `(***)` fix incorrect version for GMAP-GSNAP 2021-12-17 (was 2021-21-17);

- `(***)` fix toolchain for networkx-3.0 (`foss/2022b` -> `gfbf/2022b`);

- `(***)` bump OpenSSL 1.1 wrapper fallback to 1.1.1u;



Supported software

Support for installing 76 new software packages has been added, including (but not limited to):

- alleleIntegrator
- BayesPrism
- Circuitscape
- DALI
- DaliLite
- ecFlow
- FragPipe
- GLIMPSE
- KerasTuner
- mannkendall
- MONAI-Label
- NanoStat
- pastml
- Perl-bundle-CPAN
- PyBioLib
- PyWBGT
- Sniffles
- Tapenade
- timm
- wrapt
- xclip

This brings the total number of supported software packages to 3,161 (excluding extensions)!
An up-to-date list of supported software is available [here](https://docs.easybuild.io/version-specific/supported-software).

Various software updates have been added, including (but not limited to):

- alleleCount 4.2.1
- BayesTraits 3.0.2
- Bowtie2 2.5.1
- Cellpose 2.2.2
- CUDA 12.1.1 + 12.2.0
- CVXOPT 1.3.1
- deepTools 3.5.2
- DMTCP 3.0.0
- dorado 0.3.0 + 0.3.1
- duplex-tools 0.3.3
- fastp 0.23.4
- FreeSurfer 7.4.0
- GATK 4.4.0.0
- GCC 11.4.0
- Geant4 11.1.2
- GROMACS 2023.1
- Horovod 0.25.0
- Julia 1.9.0
- LibLZF 3.6
- MAGeCK 0.5.9.5
- MaxQuant 2.4.2.0
- MMseqs2 14-7e284
- MuJoCo 2.2.2
- ncbi-vdb 3.0.5
- ont-fast5-api 4.1.1
- openpyxl 3.1.2
- ParaView 5.11.1
- Perl 5.36.1
- PSI4 1.7
- Pysam 0.21.0
- Python 3.11.3
- PyTorch 1.13.1
- Rust 1.70.0
- seqtk 1.4
- SUNDIALS 6.5.1
- TransDecoder 5.5.0
- Transformers 4.29.2 + 4.30.2
- VTK 9.2.6
- xarray 2023.4.2
- zlib-ng 2.0.7

These changes result from various contributions, made by 25 different contributors:

* 9 merged pull requests for EasyBuild framework
* 13 merged pull requests for easyblocks
* 301 merged pull requests for easyconfigs


Thanks to everyone who contributed to this release in one way or another!

To upgrade to EasyBuild v4.8.0, there are [several options](https://docs.easybuild.io/installation/#updating).
Two particularly easy options include:

* `eb --install-latest-eb-release`

* `eb --from-pr 18282` use easyconfig from [PR 18282](https://github.com/easybuilders/easybuild-easyconfigs/pull/18282)

EasyBuild v4.7.2 is primarily a bugfix and update release, but it also includes various minor enhancements.

The executive summary for this release:

- Various small enhancements and bug fixes to EasyBuild framework, easyblocks, and easyconfigs;

- Easyconfigs for various recent software versions, including AlphaFold 2.3.4, CP2K 2022.1, GCC 12.3.0 + 13.1.0, R-bundle-Bioconductor 3.16, ...;

- Support for installing 89 new software applications and libraries;

Highlights for this release are listed below. More details are available in the [release notes](https://docs.easybuild.io/release-notes/#release_notes_eb472) which includes links to the respective pull requests for more detailed information.

Highlighted enhancements & updates

(enhancements or updates that (may) warrant updating existing installations are marked with `(***)`)

- extend (experimental) support for generating container images with Apptainer;

- 2 new generic easyblocks for installing Rust crates with cargo: Cargo and CargoPythonPackage;

- `(***)` enhance PyTorch easyblock to use FlexiBLAS for PyTorch >= 1.11.0;

- `(***)` add additional extensions to recent R and R-bundle-Bioconductor easyconfigs;

- `(***)` switch bamtofastq + Longshot to `Cargo` easyblock;

- `(***)` add egg file to OpenCV 4.6.0 python package for pip + pkgconfig file;

- `(***)` add missing FastTreeMP binary for FastTree;

- `(***)` bump versions in Java wrappers to latest builds that include `ppc64le`;


Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with (***)`)

- fix `--check-github` as gist url now includes username;

- `(***)` force building torchvision with CUDA support if CUDA is included as dependency by setting `$FORCE_CUDA`;

- `(***)` use CUDA variant of OpenMM 7.5.1 as dependency for AlphaFold 2.3.0;

- `(***)` add missing OpenJPEG dependency for recent GDAL versions;

- `(***)` upgrade traitlets, ipywidgets, and widgetsnbextension + downgrade jupyterlab_widgets extensions in IPython v8.5.0 to fix known issues;

- `(***)` add missing dependencies and add patch for fix incorrect ids for BRAKER v2.1.6;

- `(***)` FLINT needs BLAS so move it up from GCC level;

- add patch for scipy 1.10.1 extension in SciPy-bundle 2023.02 to fix broken test;

- exclude flaky test_optim + add patch to fix test_quantization for PyTorch 1.12.1 + make excluded tests for PyTorch 1.12.1 consistent;

- add make 4.3 as build dependency for recent OpenBLAS versions;

- add alternative checksum for MONAI 1.0.1;

- add historical repo paths to install command for old versions of texlive;



Supported software

Support for installing 89 new software packages has been added, including (but not limited to):

- AGeNT
- Annocript
- BoltzTraP2
- Casanovo
- CellOracle
- ColabFold
- DiCE-ML
- ESPResSo
- FunGAP
- GLI
- HTSplotter
- IsoSeq
- LoRDEC
- OptaDOS
- PGPLOT
- pod5-file-format
- pytesseract
- Python-bundle
- PyTorch-bundle
- Raven
- Scalene
- SoPlex
- sysbench
- TOPAS
- turbinesFoam

This brings the total number of supported software packages to 3,085 (excluding extensions)!
An up-to-date list of supported software is available [here](https://docs.easybuild.io/version-specific/supported-software).


Various software updates have been added, including (but not limited to):

- AlphaFold 2.3.4
- Arrow 11.0.0
- Clang 15.0.5
- CP2K 9.1 + 2022.1
- GCC 12.3.0 + 13.1.0
- `intel/2023.03` (incl. intel-compilers 22023.1.0, impi 2021.9.0, imkl 2023.1.0)
- OpenMM 8.0.0
- picard 3.0.0
- R-bundle-Bioconductor 3.16
- ReFrame 4.2.0
- UCC-CUDA 1.1.0

These changes result from various contributions, made by 27 different contributors:

* 14 merged pull requests for EasyBuild framework
* 15 merged pull requests for easyblocks
* 316 merged pull requests for easyconfigs

Thanks to everyone who contributed to this release in one way or another!

To upgrade to EasyBuild v4.7.2, there are [several options](https://docs.easybuild.io/installation/#updating).
Two particularly easy options include:

* `eb --install-latest-eb-release`

* `eb --from-pr 17986` use easyconfig from [PR 17986](https://github.com/easybuilders/easybuild-easyconfigs/pull/17986)

EasyBuild v4.7.1 is primarily a bugfix and update release, but it also includes various minor enhancements.

The executive summary for this release:

- Various small enhancements and bug fixes to EasyBuild framework, easyblocks, and easyconfigs;

- Easyconfigs for various recent software versions: AlphaFold 2.3.0, HDF5 1.14.0, networkx 3.0, TensorFlow v2.11.0, Trilinos 13.4.1, ...;

- Additional easyconfigs using the latest 2022b toolchains, incl. SciPy-bundle 2023.02 with `gfbf/2022b` (subtoolchain of `foss/2022b`);

- Support for installing 99 new software applications and libraries;

Highlights for this release are listed below. More details are available in the [release notes](https://docs.easybuild.io/release-notes/#release_notes_eb471) which includes links to the respective pull requests for more detailed information.

Highlighted enhancements

(enhancements that (may) warrant updating existing installations are marked with `(***)`)

- add support for `%(start_dir)s` easyconfig template;

- add pre/post extension hook that is triggered before/after individual extension installations;

- enforce absolute paths as start dir of extensions;

- updates and enhancements for various generic easyblocks: `GoPackage`, `MesonNinja`, `PythonPackage`;

- updates and enhancements for various software-specific easyblocks: EasyBuildMeta, ELPA, Maple, Mathematica, NAMD, pybind11, Python, QScintilla, scipy, TensorFlow, Trilinos;

- `(***)` add additional extensions to Python 3.10.8 (required for scipy test suite) (see [`--skip`](https://docs.easybuild.io/partial-installations/#partial_installation_skip));

- `(***)` add extensions to Perl 5.32.1 (see [`--skip`](https://docs.easybuild.io/partial-installations/#partial_installation_skip));

- `(***)` add additional extensions to R 4.2.1 (see [`--skip`](https://docs.easybuild.io/partial-installations/#partial_installation_skip));

- `(***)` add additional extensions to Bioconductor 3.15 (see [`--skip`](https://docs.easybuild.io/partial-installations/#partial_installation_skip));

- `(***)` enhance OpenFold 1.0.1 for standalone usage;

- `(***)` add SDL2 dependency for FFmpeg 5.0.1 to build ffplay;

- `(***)` add ffnvcodec build dependency to all recent FFmpeg easyconfigs;

- `(***)` set `$JULIA_DEPOT_PATH` and `$JULIA_HISTORY` in Julia easyconfigs;

- `(***)` add missing zstd dep to Boost;


Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with `(***)`)

- restore initial environment before processing each easystack item ([support for easystack files is still experimental](https://docs.easybuild.io/easystack-files));

- various fixes and improvements for the EasyBuild framework test suite;

- `(***)` fix `$JULIA_DEPOT_PATH` in installation of multiple `JuliaPackage` extensions;

- `(***)` fix checking of CUDA/ROCR-Runtime dependencies for Clang to determine default build targets;

- `(***)` fix linking numexpr with Intel MKL's VML library for imkl >= 2021.x;

- bug fixes for various generic easyblocks: `CMakeMake`, `CMakePythonPackage`, `PythonPackage`, `PythonBundle`;

- bug fixes for various software-specific easyblocks: FlexiBLAS, netCDF, NVHPC, PyTorch;

- `(***)` add patch for GCCcore 11.1.0 + 11.2.0 to fix AVX2 bug;

- `(***)` add missing pmix patch to OpenMPI 4.1.1 easyconfig used in `iomkl/2021a` and `iomkl/2021b`;

- `(***)` replace obsolete `pycrypto` with `pycryptodome` in Python 3.10.x easyconfigs;

- `(***)` update deap to version 1.3.3 in SciPy-bundle 2022.05 easyconfigs (since deap 1.3.1 is broken) (see [`--skip`](https://docs.easybuild.io/partial-installations/#partial_installation_skip));

- `(***)` replace `src` include path with installation dir for HDF5;

- `(***)` use GCC as toolchain for serial variants of HDF5, since it has a FORTRAN API;

- `(***)` add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2;

- `(***)` fix `postinstallcmds` in shovill easyconfigs;

- `(***)` add psycopg2, PyYAML, and Cartopy dependencies to QGIS 3.28.1

- `(***)` add alternative checksum for spatial 7.3-14 extension in R 4.1.x easyconfigs;

- `(***)` enable `-fPIC` in GEOS 3.11.1 (required by GDAL);

- add alternative checksum for UCX 1.13.1 after source tarball was changed in-place (without actual code changes);

- rename some software names in existing easyconfigs, or archive these easyconfigs, to avoid case-insensitive name clashes;



Supported software

Support for installing 99 (!) new software packages has been added, including (but not limited to):

- CatLearn
- Cellpose
- chemprop
- cuSPARSELt
- DensPart
- dorado
- fastjet
- finder
- genomepy
- grid
- Health-GPS
- HiCMatrix
- Inferelator
- kineto
- LASSO-Python
- netMHCII
- PfamScan
- plot1cell
- PyTorch-Ignite
- rapidNJ
- scArches
- scib
- smfishHmrf
- Strainberry
- VirSorter2
- YODA

This brings the total number of supported software packages to 2,995 (excluding extensions)!
An up-to-date list of supported software is available [here](https://docs.easybuild.io/version-specific/supported-software).

Various software updates have been added, including (but not limited to):

- AlphaFold 2.3.0
- AUGUSTUS 3.5.0
- BCFtools 1.17
- Biopython 1.81
- Boost 1.81.0
- CFITSIO 4.2.0
- CUDA 12.1.0
- DIAMOND 2.1.0,
- epiScanpy 0.4.0
- FFmpeg 5.1.2
- GDAL 3.6.2
- GPyTorch 1.9.1
- h5py 3.8.0
- HTSlib 1.17
- Hypre 2.27.0
- `intel/2022.12` (incl. intel-compilers 2023.0.0, impi 2021.8.0, imkl 2023.0.0)
- jax 0.4.4
- MaSuRCA 4.1.0
- MATLAB 2022b
- MDAnalysis 2.4.2
- mpi4py 3.1.4
- NetLogo 6.3.0
- networkx 3.0
- numba 0.56.4
- NVHPC 23.1
- OpenMPI 4.1.5
- PLUMED 2.8.1
- pyGenomeTracks 3.8
- PySCF 2.1.1
- Python 3.11.2
- R 4.2.2
- ReFrame 4.0.5
- ROOT 6.22.08
- SAMtools 1.17,
- scikit-learn 1.2.1
- SciPy-bundle 2023.02,
- SPAdes 3.15.5
- TensorFlow 2.11.0
- Trilinos 13.4.1
- Xerces-C++ 3.2.4


These changes result from various contributions, made by 30 different contributors:

- 36 merged pull requests for EasyBuild framework
- 34 merged pull requests for easyblocks
- 386 merged pull requests for easyconfigs


Thanks to everyone who contributed to this release in one way or another!

To upgrade to EasyBuild v4.7.1, there are [several options](https://docs.easybuild.io/installation/#updating).
Two particularly easy options include:

- `eb --install-latest-eb-release`

- `eb --from-pr 17568` use easyconfig from [PR 17568](https://github.com/easybuilders/easybuild-easyconfigs/pull/17568)

EasyBuild v4.7.0 is primarily a feature release, but it also includes various minor bug fixes and enhancements.

Highlights for this release are listed below. More details are available in the [release notes](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-7-0-january-9th-2023) which includes links to the respective pull requests for more detailed information.


Highlighted enhancements

(enhancements that (may) warrant updating existing installations are marked with `(***)`)

- also run unit tests with Python 3.11;

- add support for checksums specified in external checksums.json file;

- take into account custom configuration options specified in easystack files - see also [docs](https://docs.easybuild.io/en/latest/Easystack-files.html);

- add support for using `--output-format=md` (MarkDown);

- add support for `postinstallmsgs`;

- add `gfbf` as subtoolchain of `foss`;

- make `iimkl` toolchain aware of `intel-compilers`;

- add generic easyblocks for installing (bundle of) Julia packages: `JuliaPackage` + `JuliaBundle`;

- updates and enhancements for various generic easyblocks, incl. `ConfigureMake`, `PythonPackage`;

- `(***)` updates and enhancements for various software-specific easyblocks: BerkeleyGW, Clang, Clang-AOMP, ESMF, libxml2, LLVM, OpenCV, OpenMPI, PETSc, QScintill, TensorFlow, Xmipp;


Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with `(***)`)

- print deprecation warning with running EasyBuild with Python 2;

- various tweaks to docstrings and help messages to fix problems with auto-generated documentation in MarkDown format;

- vendor `distutils.version.LooseVersion` as `easybuild.tools.LooseVersion`
(since `distutils` is deprecated in Python 3.10, to be removed in Python 3.12);

- auto-enable use of oneAPI C/C++ compilers for `intel-compilers` >= 2022.2.0;

- use `-march=x86-64 -mtune=generic` instead of `-xSSE2` when using Intel oneAPI compilers;

- drop support for easystack files using '`software`' top-level key;

- make PythonPackage easyblock compatible with `--sanity-check-only` by loading module early during sanity check step;

- `(***)` update HDF5 easyblock to use `--enable-threadsafe` configure option to make C API thread safe;

- `(***)` bug fixes for various software-specific easyblocks: ANSYS, Clang, MRtrix, PyTorch;


Supported software


New version of common toolchains: `foss/2022b`, `intel/2022b`

Support for installing 107 new software packages has been added, including (but not limited to):

- Alfred
- bamFilters
- CAT-BAT
- CloudCompare
- COBRApy
- CUDA-Samples
- DeepLabCut
- DRAGMAP
- ESM-2
- HighFive
- IJulia
- KaHIP
- LHAPDF
- Magics
- MEMOTE
- MONAI
- MOOSE
- MultilevelEstimators
- napari
- nf-core-mag
- OmegaFold
- pyccel
- PyDamage
- pyWannier90
- scvi-tools
- SELFIES
- SISSO++
- spaCy
- Squidpy
- TBA
- trimesh
- UCX-ROCm

This brings the total number of supported software packages to 2,904 (excluding extensions)!
An up-to-date list of supported software is available [here](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).

Various software updates have been added, including (but not limited to):

- AOCC 4.0.0
- CDO 2.1.1
- CubeGUI/CubeLib/CubeWriter 4.8
- CUDA 11.8.0 + 12.0.0
- deepdiff 5.8.1
- FLANN 1.9.1
- GATK 4.3.0.0
- GDCM 3.0.20
- Ghostscript 10.0.0
- GRASS 8.2.0
- JasPer 4.0.0
- libspatialite 5.0.1
- LLVM 15.0.5
- Mesa 22.2.4
- mold 1.7.1
- MRChem 1.1.1
- ncbi-vdb 3.0.0
- nglview 3.0.3
- nodejs 18.12.1
- Octave 7.1.0
- OpenFOAM 10
- OpenFold 1.0.1
- OpenMolcas 22.10
- OpenStackClient 6.0.0
- PAPI 7.0.0,
- PETSc 3.17.4
- pyproj 3.4.0
- Python 3.10.8
- PyTorch 1.12.1
- PyTorch-Geometric 2.1.0
- QGIS 3.28.1
- Qt5 5.15.7
- QtPy 2.2.1
- ReFrame 3.12.0
- scanpy 1.9.1
- Score-P 8.0
- SignalP 6.0g
- SLEPc 3.17.2
- SNAP 2.0.1
- SpaceRanger 2.0.0
- SuperLU_DIST 8.1.0
- tensorboardX 2.5.1
- TensorFlow 2.8.4
- tesseract 5.3.0
- Valgrind 3.20.0
- Vim 9.0.0950
- VTK 9.2.2
- wandb 0.13.6
- WebKitGTK+ 2.37.1
- WPS/WRF 4.4
- wxPython 4.2.0
- X11 20221110
- Xmipp 3.22.07


These changes result from various contributions, made by 29 different contributors:

* 42 merged pull requests for EasyBuild framework
* 36 merged pull requests for easyblocks
* 469 merged pull requests for easyconfigs

Thanks to everyone who contributed to this release in one way or another!

To upgrade to EasyBuild v4.7.0, there are [several options](https://docs.easybuild.io/en/latest/Installation.html#updating-an-existing-easybuild-installation).
Two particularly easy options include:

* `eb --install-latest-eb-release`

* `eb --from-pr 17065` use easyconfig from [PR 17065](https://github.com/easybuilders/easybuild-easyconfigs/pull/17065)

EasyBuild v4.6.2 is primarily a bugfix and update release, but it also includes various minor enhancements.

Highlights for this release are listed below. More details are available in the [release notes](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-6-2-october-21st-2022) which includes links to the respective pull requests for more detailed information.

Highlighted enhancements

(enhancements that (may) warrant updating existing installations are marked with `(***)`)

- enable running of LAPACK tests for recent OpenBLAS easyconfigs;

- 2 new software-specific easyblocks: CUDA compatibility libraries (CUDAcompat) + mamba;

- updates and enhancements for various software-specific easyblocks: OpenFOAM, ESMF, netCDF, numexpr;

- enhance EasyBuildMeta easyblock: auto-enable installing with `pip`;


Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with `(***)`)

- `(***)` add patch to GCC 11.x + 12.x to fix vectorizer bug;

- `(***)` add patch to fix failing LAPACK tests due to use of `-ftree-vectorize`;

- correctly count the number of failing tests (not failing test suites) in PyTorch builds;

- `(***)` add patches to fix incompatibilites between ASE and other packages in 2022a toolchain;

- `(***)` fix execution permissions for `bin/ngm*` for NextGenMap v0.5.5;

- `(***)` add bzip2 and libxml2 as dependencies for netCDF 4.9.0;

- `(***)` add patch to detect available cores and remove unneeded deps for Unicycler 0.5.0;

- make `--inject-checksums` inject dictionary value for checksums which maps filename to SHA256 checksum;

- fix trying to generate RPATH wrappers for Clang;

- update easyconfigs to use `SYSTEM` template constant instead of `True` in dependencies;


Supported software