Easybuild

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

EasyBuild v4.6.1 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-v4-6-1-september-12th-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 `(***)`)

- run `python` in the same process as `eb` wrapper script by using exec (which improves startup performance of `eb` command);

- reduce the number of command line options for `cmake` command in `CMakeMake` generic easyblock;

- enhance `PythonPackage` easyblock to make sure all test command output makes it to the EasyBuild log, also when `return_output_ec=True` is used;

- updates and enhancements for various software-specific easyblocks: GROMACS, LAMMPS, libQGLViewer, NVHPC, PyTorch;

- `(***)` add extra symlinks and sanity checks for libtinfo in ncurses;

- speed up OpenMPI 4.1.4 configure by not running `autogen.pl --force`, but only running required Autotools commands;


Prominent bug fixes & changes

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

- use `det_cmake_version` function to determine CMake version in `CMakeMake` generic easyblock (rather than assuming that CMake is loaded as a build dependency);

- don’t enable building of ld.gold when installing binutils on a RISC-V system + don’t configure GCC to use gold as default linker on a RISC-V system;

- make Amber easyblock aware of FlexiBLAS;

- tweak Amber(Tools) easyblock to run tests from top-level directory, and enable running of tests for AmberTools v20 + v21;

- work around miscompilation of OpenBLAS on POWER by compiling with `-fstack-protector-strong`;

- various fixes for installing PyTorch on POWER systems;

- `(***)` 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;

- `(***)` use versioned symbols in ncurses built with system toolchain (by adding `--with-versioned-syms` configure option);

- `(***)` add CVE patch for XZ 5.2.5 + attempt to fix symbol patch for all OSs;

- `(***)` add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9;

- simplify AlphaFold `foss/2021a` easyconfigs by using a fleshed out patched OpenMM dependency;

- `(***)` add patch to fix missing sync in LINCS and SETTLE CUDA kernels for GROMACS 2020 and 2021;

- `(***)` fix checksum for Stacks v2.62 (due to silent re-release without version bump);

- `(***)` consistently add maeparser + CoordgenLibs dependencies to OpenBabel 3.1.1 easyconfigs;

- `(***)` update `Java/11` to 11.0.16 and `Java/17` to 17.0.4;



Supported software

Support for installing 37 new software packages has been added, including (but not limited to):

* BigDFT
* colossalai
* Dakota
* FastFold
* how_are_we_stranded_here
* libmad
* MetaMorpheus
* muMerge
* olaFlow
* OpenFAST
* OpenFold
* pyGenomeTracks
* RheoTool
* Satsuma2
* UCC-CUDA
* VESTA

This brings the total number of supported software packages to 2,773 (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):

* AmberTools 22.3
* BCFtools 1.15.1
* binutils 2.39
* BLAST+ 2.13.0
* CDO 2.0.5
* CoordgenLibs 3.0.1,
* Elk 8.5.2,
* FFmpeg 4.4.2 + 5.0.1
* FreeSurfer 7.3.2
* GATE 9.2
* GCC(core) 12.2.0
* GDB 12.1
* gnuplot 5.4.4
* Graphviz 5.0.0
* HDF5 1.12.2
* HTSlib 1.15.1
* Hypre 2.25.0,
* jax 0.3.14,
* LAMMPS 23Jun2022
* Libint 2.7.2
* maeparser 1.3.0
* matplotlib 3.5.2
* MATSim 14.0
* medaka 1.6.0
* Megalodon 2.5.0
* MetaEuk 6,
* MUMPS 5.5.1
* netCDF-Fortran 4.6.0
* ont-remora 1.0.0
* OpenFOAM v2206
* ParaView 5.10.1
* Perl 5.36.0
* Pyomo 6.4.2
* PyStan 3.5.0
* PyYAML 6.0
* scikit-bio 0.5.7
* scikit-learn 1.1.2
* SCOTCH 7.0.1
* spglib-python 2.0.0
* SUMO 1.14.1
* Valgrind 3.19.0
* ViennaRNA 2.5.1
* wxPython 4.1.1
* zfp 1.0.0


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

* 16 merged pull requests for EasyBuild framework
* 20 merged pull requests for easyblocks
* 266 merged pull requests for easyconfigs


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


To upgrade to EasyBuild v4.6.1, 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 16240` use easyconfig from [PR 16240](https://github.com/easybuilders/easybuild-easyconfigs/pull/16240)

EasyBuild v4.6.0 is primarily a feature release, but it also includes various minor bug fixes, enhancements, and updates.

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-v4-6-0-july-8th-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 `(***)`)

- add support for OneAPI compilers using toolchain option '`oneapi`';

- add support for setting environment variables via '`pushenv`' with modextravars;

- fall back to sequential extension install if parallel install is not implemented;

- one new software-specific custom easyblock for STAR-CCM+;

- updates and enhancements for various software-specific easyblocks: FFTW, Libint, OpenSSL, Siesta, TensorFlow, WPS;

- add support for allowing some PyTorch tests to fail + print warning if one or more tests fail;

- easyconfigs for `foss/2022a` and `intel/2022a` common toolchains (see also [here](https://docs.easybuild.io/en/latest/Common-toolchains.html#overview-of-common-toolchains));

- `(***)` additional extensions for R v4.2.0 (see [`--skip`](https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip));

- `(***)` add patch for GCCcore 11.3.0 to support using `-fuse-ld=mold`;


Prominent bug fixes & changes

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

- tweak '`eb`' wrapper script to correctly handle errors when python command being considered fails to run;

- tweak `is_patch_for` function to make it more robust;

- tweak `apply_patch` function to not create `.orig` files (by default) when applying patch files;

- make sure that `CMakeMakeCp` generic easyblock uses correct build dir;

- make VEP easyblock compatible with `--sanity-check-only`;

- only load temporary module file during sanity check for pybind11 for stand-alone installations, so it can be installed as extension;

- switch to Rust 1.60.0 build dependency for bamtofastq, since build fails with Rust 1.52.1;

- `(***)` avoid that pygmo v2.18.0 installs stuff in Python installation directory + add custom sanity check paths to pygmo easyconfigs;

- `(***)` correct `configopts` in deal.II v9.1.1 easyconfig;


Supported software

Support for installing 24 new software packages has been added, including (but not limited to):

- fio
- G-PhoCS
- Gibbs2
- Minipolish
- NetPyNE
- SISSO
- sklearn-pandas
- SWIPE
- topaz
- uncertainty-calibration

This brings the total number of supported software packages to 2,736 (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):

- AlphaFold 2.2.2
- Arrow 8.0.0
- CellRanger 7.0.0
- deal.II 9.3.3
- FSL 6.0.5.1
- GDAL 3.5.0
- geopandas 0.11.0
- GEOS 3.10.3
- h5py 3.7.0
- HDF5 1.13.1
- ImageMagick 7.1.0-37
- jemalloc 5.3.0
- Leptonica 1.82.0
- libRmath 4.2.0
- libxc 5.2.3
- MaSuRCA 4.0.9
- mold 1.3.0
- netCDF 4.9.0
- NEURON 7.8.2
- NLopt 2.7.1
- nvtop 2.0.2
- PLUMED 2.8.0,
- PRISMS-PF 2.2
- PROJ 9.0.0
- PyTorch 1.11.0
- Qt5 5.15.5
- QuantumESPRESSO 7.1
- R 4.2.1
- Ray-project 1.13.0
- ReFrame 3.11.2
- SpectrA 1.0.1
- TensorFlow 2.7.1
- UCX-CUDA 1.12.1
- WPS 3.9.1


These changes result from various contributions, made by 24 different contributors:

- 17 merged pull requests for EasyBuild framework
- 17 merged pull requests for easyblocks
- 149 merged pull requests for easyconfigs


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


To upgrade to EasyBuild v4.6.0, 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 15832` use easyconfig from [PR 15832](https://github.com/easybuilders/easybuild-easyconfigs/pull/15832)

EasyBuild v4.5.5 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-v4-5-5-june-8th-2022) which includes links to the respective pull requests for more detailed information.

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant re-installing easyconfigs are marked with `(***)`)

- set `$FFT(W)_LIB_DIR` to imkl-FFTW’s lib path in build environment if `usempi` toolchain option is enabled;

- fix '`eb --show-system-info`' on Apple M1 system;

- remove system-compiled binutils dirs from `$LDFLAGS` in binutils easyblock;

- `(***)` add patch for OpenMPI 4.1.1 to support building using `--with-cuda=internal`;

- `(***)` disable use of `-ftree-vectorize` for OpenFOAM v2112 with foss/2021b;

- `(***)` also symlink `cert.pem` in from-source OpenSSL installation (if it exists), to ensure that system certificates are found;

- use `x.py` to bootstrap Rust so that build options are properly passed through;

- `(***)` add hwloc dependency to tbb v2021.4.0;

- `(***)` define `$HHLIB` as path to HH-suite installation directory, required by Perl scripts;

- `(***)` add missing parallel and tbl2asn dependencies for prokka 1.14.5;

- `(***)` also build shared library + fix `$PYTHONPATH` for gmsh 4.9.0;

- add missing dependencies + switch to non-static build for Arriba v2.1.0;

- `(***)` add R dependency to vcflib 1.0.3, and move from `GCC/11.2.0` to `foss/2021b` toochain;

- `(***)` update fallback version for OpenSSL 1.1 wrapper to v1.1.1o;

- `(***)` install `sklearn` meta-package with scikit-learn v1.0.1;


Highlighted enhancements & changes

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

- change '`eb`' command to import `easybuild.framework` to check if EasyBuild framework is available;

- add toolchain definitions for `nvompi` (NVHPC + OpenMPI),
`nvpsmpi` (NVHPC + ParaStationMPI), and `gfbf` (GCC, FlexiBLAS, FFTW);

- add support for FFTW.MPI toolchain component;

- add support for customizing EasyBuild command used in jobs via --job-eb-cmd;

- add support to ConfigureMake for tweaking (first part of) test command via 'test_cmd';

- 1 new software-specific easyblock for FFTW.MPI;

- updates and enhancements for various software-specific easyblocks: ABAQUS, Clang, cuDNN, FFTW, LLVM, Mesa, MrBayes, NEURON, OpenMPI, OpenSSL wrapper, R, SuperLU, TensorFlow;

- don't use `gold` linker by default for GCC >= 11.3;

- add candidates for 2022a common toolchains: `foss/2022.05`, `intel/2022.05`;

- `(***)` also build BLIS backend for FlexiBLAS v3.0.4 with GCC/10.3.0;

- `(***)` additional extensions for R-bundle-Bioconductor 3.14 + R v4.1.2 (see [--skip](https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip));

- `(***)` update Arrow to use EasyBuild-provided versions of some dependencies and enable all compression codecs;

- `(***)` add `csh` -> `tcsh` symlink in recent tcsh easyconfigs;

Supported software

Support for installing 35 new software packages has been added, including (but not limited to):

* Albumentations
* arosics
* CellTypist
* detectron2
* EigenExa
* FFTW.MPI
* FreeBarcodes
* GTK4
* i7z
* ModelTest-NG
* OGDF
* panito
* parameterized
* ruamel.yaml
* SCGid
* scPred
* smooth-topk
* SPOTPY
* UCC
* Wayland
* XGrafix
* XPLOR-NIH

This brings the total number of supported software packages to 2,711 (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):

* ABAQUS 2022
* ARGoS 3.0.0
* astropy 5.0.4
* Bazel 4.2.2 + 5.1.1
* binutils 2.38
* BLIS 0.9.0
* Boost 1.79.0
* cryoDRGN 1.0.0
* CUDA 11.7.0
* FlexiBLAS 3.2.0
* GCC 9.5.0 + 11.3.0 + GCC 12.1.0
* Go 1.18.1
* GTDB-Tk 2.0.0
* GTK3 3.24.33
* gzip 1.12,
* Hypre 2.24.0
* IMB 2021.3
* IQ-TREE 2.2.1
* jax 0.3.9
* libfabric 1.15.1
* LLVM 14.0.3
* magma 2.6.2
* Mathematica 13.0.0
* Mesa 22.0.3
* mold 1.2.1
* MUMPS 5.5.0
* Nim 1.6.6
* OpenMPI 4.1.4
* OSU-Micro-Benchmarks 5.9
* Perl 5.34.1
* PMIx 4.1.2
* Python 3.10.4
* R 4.2.0
* R-bundle-Bioconductor 3.15
* ReFrame 3.11.0
* Rust 1.60.0
* SAMtools 1.15.1
* SciPy-bundle 2022.05
* SeqKit 2.2.0
* Spack 0.17.2
* Spark 3.2.1
* SuperLU 5.3.0
* ToFu 1.5.0
* UCX 1.12.1
* X11 2022050
* zlib 1.2.12


These changes result from various contributions, made by 21 different contributors:

* 17 merged pull requests for EasyBuild framework
* 25 merged pull requests for easyblocks
* 272 merged pull requests for easyconfigs


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

To upgrade to EasyBuild v4.5.5, 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 15635` use easyconfig from [PR 15635](https://github.com/easybuilders/easybuild-easyconfigs/pull/15635)