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EasyBuild v4.7.2
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@boegel boegel released this 27 May 23:00
· 18 commits to develop since this release
easybuild-v4.7.2
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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 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.

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.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 17986 # use easyconfig from PR #17986

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