Easybuild

Support for installing 25 new software packages has been added, including (but not limited to):

- AMAPVox
- buildingspy
- CDBtools
- f90wrap
- Miller
- NVSHMEM
- paladin
- PyMOL
- python-irodsclient
- ruffus
- TELEMAC-MASCARET
- x13as

This brings the total number of supported software packages to 2,798 (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):

- ASE 3.22.1
- biogeme 3.2.10
- Delly 1.1.5
- ESMF 8.3.0
- FDS 6.7.9
- Go 1.18.3
- GPAW 22.8.0
- IPython 8.5.0
- Julia 1.8.2
- LIBSVM 3.30
- netcdf4-python 1.6.1
- Nipype 1.8.5,
- OpenCV 4.6.0
- OpenMM 7.7.0
- Perl 5.36.0
- PyTorch 1.12.0
- PyTorch-Lightning 1.7.7
- RDFlib 6.2.0
- SAMtools 1.16.1
- scikit-learn 1.1.2
- Score-P 7.1
- SuiteSparse 5.13.0
- SUNDIALS 6.3.0
- sympy 1.11.1
- torchvision 0.13.1
- TRIQS 3.1.1
- UCX 1.13.1
- VEP 107
- Wayland 1.21.0
- wxWidgets 3.2.1

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

* 17 merged pull requests for EasyBuild framework
* 20 merged pull requests for easyblocks
* 159 merged pull requests for easyconfigs


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


To upgrade to EasyBuild v4.6.2, 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 16465` use easyconfig from [PR 16465](https://github.com/easybuilders/easybuild-easyconfigs/pull/16465)

EasyBuild v4.9.2 is primarily a bugfix & update release, but it also includes various enhancements.


The executive summary for this release:

- Easyconfigs for the `foss/2024a` and `intel/2024a` common toolchains;
- Support for installing 107 (!) new software applications, tools, and libraries, including HERRO, MAGIC, pyMBE, Sagemath, Single-cell-python-bundle, Visit;
- Easyconfigs for various recent software versions, including AlphaPulldown 2.0.0b4, Clang + LLVM 18.1.8, CUDA 12.5.0 + 12.6.0, FFmpeg 7.0.2, GCC 14.2.0, jax 0.4.25, ORCA 6.0.0, OpenFOAM 12 + v2406, R 4.4.1, SciPy-bundle 2024.05, WRF 4.5.1, and many more;
- Bug fixes/enhanchements/changes to easyblocks/easyconfigs that require reinstallation (more info below, marked with `(***)`);

Highlights for this release are listed below. More details are available in the [release notes](https://docs.easybuild.io/release-notes/#release_notes_eb493) 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 support for `--extra-source-urls` to fetch sources from additional URLs;

- use Intel's oneAPI Fortran compiler by default for version 2024.0.0 and newer;

- enhancements to generic easyblocks: `Cargo`, `JuliaPackage`, `PythonBundle`, `PythonPackage`, `RPackage`, `RubyGem`;

- `(***)` enhance custom easyblock for GCC to use with-arch option for nvptx with 13.1+;

- additional updates & enhancements to custom easyblocks for Bazel, binutils, Boost, ESMF, Extrae, Geant4, MCR, impi, LAMMPS, OpenFOAM, ORCA, psmpi, PETSc, PyTorch, QuantumESPRESSO, Tensorflow, Tkinter;

- `(***)` add additional extensions to `R-bundle-CRAN` easyconfigs;

- `(***)` add Qt support to VTK 9.3.0;

- `(***)` also build & install the plugins with OpenFOAM v2406;


Prominent bug fixes & changes

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

- `(***)` patch `ctypes` for Python installations when filtering `LD_LIBRARY_PATH` + fix path to `ldconfig` when using alternate sysroot ;

- merge of the `ConfigureMake` and `CMakeMake` versions of the easyblock for QuantumESPRESSO;

- bug fixes in generic easyblocks: `Cargo`, `CargoPythonPackage`, `PythonBundle`, `PythonPackage`;

- bug fixes in custom easyblocks for ANSYS, EasyBuild, Extrae, impi, OCaml, OpenFOAM, OpenMPI, OpenSSL_wrapper, PALM, Python, WPS;

- `(***)` add patch to fix implicit function declaration in OpenMPI 4.1.4;

- `(***)` disable auto-vectorizer (`-ftree-vectorize`) for OpenFOAM v10 + v11 when using toolchain that with GCC >= 11;

- `(***)` add patch for HDF5 v1.14.3 to suppress fp exceptions;

- `(***)` fix easyconfigs for recent versions of QuantumESPRESSO;

- `(***)` add patch to fix Qt6 issues with ParaView v5.12.0, e.g. representation selection;

- fix download URLs for old Intel software (2018-2023) by using `IRC_NAS` instead of `irc_nas`;


Supported software

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

- absl-py
- BayesOpt
- CORSIKA
- dictys
- EGA-QuickView
- fish
- Flax
- GPflow
- HERRO
- LRBinner
- MAGIC
- MBX
- nifty
- OpenForceField-Toolkit
- PEcAn
- pyMBE
- Sagemath
- SharedMeatAxe
- Single-cell-python-bundle
- torch-em
- Visit
- Zoltan

This brings the total number of supported software packages to 3,656 (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):

- AlphaPulldown 2.0.0b4
- AmberTools 26.3
- Arrow 16.1.0
- Biopython 1.84
- CUDA 12.5.0 + 12.6.0
- CellOracle 0.18.0
- Clang 18.1.8
- cutadapt 4.9
- dorado 0.7.3
- Extrae 4.2.0
- FFmpeg 7.0.2
- GCC 14.2.0
- GDAL 3.9.0
- GLM 1.0.1
- GPAW 24.6.0
- genomepy 0.16.1
- Highway 1.2.0
- IQ-TREE 2.3.5
- jax 0.4.25
- LLVM 18.1.8
- MPICH 4.2.1
- MariaDB 11.6.0
- Mesa 24.1.3
- matplotlib 3.9.2
- NanoCaller 3.6.0
- ORCA 6.0.0
- OpenFOAM 12 + v2406
- Optax 0.2.2
- Perl-bundle-CPAN 5.38.2
- Pillow-SIMD 10.4.0
- PostgreSQL 16.4
- PyAEDT 0.9.9
- PyWavelets 1.7.0
- Pygments 2.18.0
- Python-bundle-PyPI 2024.06
- pyGenomeTracks 3.9
- QuantumESPRESSO 7.3.1
- R-bundle-CRAN 2024.06
- R 4.4.1
- RDKit 2024.03.3,
- ReFrame 4.6.2
- Rust 1.79.0
- SciPy-bundle 2024.05
- SeqKit 2.8.2
- SingleM 0.16.0
- SuiteSparse 7.7.0
- TELEMAC-MASCARET 8p5r0
- UCX-CUDA 1.16.0
- WRF 4.5.1
- X11 20240607
- XGBoost 2.1.1
- xarray 2024.5.0


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

* 31 merged pull requests for EasyBuild framework;
* 52 merged pull requests for easyblocks;
* 367 merged pull requests for easyconfigs;


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


To upgrade to EasyBuild v4.9.3, there are [several options](https://docs.easybuild.io/installation/#updating).

Two particularly easy options include:

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

* `eb --from-pr 21412` use easyconfig from [PR 21412](https://github.com/easybuilders/easybuild-easyconfigs/pull/21412)

EasyBuild v4.9.2 is primarily a bugfix & update release, but it also includes various enhancements.

The executive summary for this release:

- EasyBuild API version checks to avoid mixing major versions across the EasyBuild components;

- Bug fix for `--from-commit`, so easyconfigs for dependencies are found if they're available in the commit;

- 4 new sofware-specific easyblocks: AEDT, MetalWalls, optiSLang, QuantumESPRESSO with CMake;

- Support for installing 82 new software applications, tools, and libraries;

- Easyconfigs for various recent software versions, including BLIS 1.0, Clang 17.0.6, GCC 13.3.0 + 14.1.0, IOR 4.0.0, OCaml 5.1.1, OpenMPI 5.0.3, PyTorch-bundle 2.1.2, Python 3.12.3, TensorFlow 2.15.1, and many more;

- Bug fixes/changes to easyblocks/easyconfigs that require reinstallation (more info below, marked with `(***)`);


Highlights for this release are listed below. More details are available in the [release notes](https://docs.easybuild.io/release-notes/#release_notes_eb492) 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 `(***)`)

- implement EasyBuild API version checks to avoid mixing major versions across the EasyBuild components;

- 4 software-specific easyblock for AEDT, MetalWalls, optiSLang, QuantumESPRESSO with CMake;

- enhancement to PythonPackage generic easyblock;

- add a sanity check for OpenFOAM's `wmake` to make sure it finds the compiler commands;

- refactor GAMESS-US easyblock to directly write install.info;

- additional updates & enhancements to custom easyblocks for ABAQUS, Clang, CUDA, FFTW, Java, Mesa, OpenMPI, OpenSSL, torchvision, UCX-Plugins;

- `(***)` additional extensions for R-bundle-CRAN v2023.12;


Prominent bug fixes & changes

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

- symlink downloaded repo at specified commit when using `--from-commit` so easyconfigs for dependencies are found;

- bug fixes for `CargoPythonBundle` generic easyblock;

- bug fixes in custom easyblocks for intel-compilers and Python;

- `(***)` add patch to fix CVE-2024-27322 in R v3.6.x, v4.0.x, v4.1.x, v4.2.x, v4.3.x;

- `(***)` fix detection of CC/CXX compilers for `wmake` in OpenFOAM v2306 + v2312;

- `(***)` change arrow-R dependency of R-bundle-Bioconductor v3.18 to v14.0.1;

- `(***)` add dependencies required for GUI in Cellpose 2.2.2 easyconfigs;

- `(***)` add missing dependencies for funannotate;

- `(***)` make sure mummerplot can use gnuplot if available for recent MUMmer;

- remove easyconfigs for CellBender v0.3.1, since this version has been redacted due to a serious bug (see [here](https://github.com/broadinstitute/CellBender/issues/306));


Supported software

Support for installing 82 new software packages has been added, including (but not limited to):

- AEDT
- AMGX
- Cassiopeia
- CheckM2
- Compass
- CVX
- EasyMocap
- FDMNES
- HiGHS
- HOMER
- LangChain
- libabigail
- LIBSVM-MATLAB
- Lightning
- MetalWalls
- ml-collections
- MOFA2
- orthAgogue
- planarity
- PRRTE
- PSM2
- PyHMMER
- PyVista
- SCReadCounts
- TF-COMB
- TorchIO
- VAMPIRE-ASM
- WGDgc

This brings the total number of supported software packages to 3,552 (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):

- AFNI 24.0.02
- alevin-fry 0.9.0
- BCFtools 1.19
- BLIS 1.0
- BWA 0.7.18
- Boost 1.85.0
- CGAL 5.6.1
- CellRank 2.0.2
- Clang 17.0.6
- dask 2024.5.1
- deal.II 9.5.2
- dorado 0.5.3
- ESPResSo 4.2.2
- FMM3D 1.0.4
- GAMESS-US 20220930-R2 + 20230930-R2
- GCC 13.3.0 + 14.1.0
- GOATOOLS 1.4.5
- GTDB-Tk 2.4.0
- gemmi 0.6.5
- gmsh 4.12.2,
- HDDM 0.9.9
- HTSlib 1.19.1
- HyPhy 2.5.60
- h5py 3.11.0
- IOR 4.0.0
- Jupyter-bundle 20240522 (incl. JupyterHub 4.1.5, JupyterLab 4.2.0, JupyterNotebook 7.2.0, ...)
- Kalign 3.4.0
- kallisto 0.50.1
- MATSim 15.0
- MetaMorpheus 1.0.5
- MuJoCo 3.1.4
- mold 2.31.0
- NanoPlot 1.42.0
- nglview 3.1.2
- nvtop 3.1.0
- OCaml 5.1.1
- OpenMPI 5.0.3
- PhyML 3.3.20220408
- PyTorch-bundle 2.1.2
- Python 3.12.3
- petsc4py 3.20.3
- polars 0.20.2
- py3Dmol 2.1.0
- pyiron 0.5.1
- ROOT 6.30.06
- Rust 1.78.0
- SAMtools 1.19.2
- SentencePiece 0.2.0
- Seurat 5.1.0
- SimNIBS 4.0.1
- Spack 0.21.2
- Squidpy 1.4.1
- SymEngine 0.11.2
- scikit-learn 1.4.2
- TensorFlow 2.15.1
- Transformers 4.39.3
- tokenizers 0.15.2
- UCX 1.16.0
- Valgrind 3.23.0
- VisPy 0.14.1
- zlib-ng 2.1.6

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

* 16 merged pull requests for EasyBuild framework
* 27 merged pull requests for easyblocks
* 326 merged pull requests for easyconfigs


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


To upgrade to EasyBuild v4.9.2, there are [several options](https://docs.easybuild.io/installation/#updating).

Two particularly easy options include:

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

* `eb --from-pr 20801` use easyconfig from [PR 20801](https://github.com/easybuilders/easybuild-easyconfigs/pull/20801)

EasyBuild v4.9.1 is primarily a bugfix & update release, but it also includes various enhancements.

Executive summary

- Support for `--from-commit` and `--include-easyblocks-from-commit`;

- 1 new sofware-specific easyblocks for DualSPHysics;

- Support for installing 101 (!) new software applications, tools, and libraries;

- Easyconfigs for various recent software versions, including CuPy 13.0.0, Gurobi 11.0.0, OCaml 4.14.0, OpenFOAM v2312, ParaView-5.12.0, R 4.3.3, R-bundle-Bioconductor 3.18, WIEN2k 23.2, and many more;

- Fixes/changes to easyblocks/easyconfigs that require reinstallation, including for GCC, OpenMPI, and Python (more info below);


Highlights for this release are listed below. More details are available in the [release notes](https://docs.easybuild.io/release-notes/#release_notes_eb491) 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 `(***)`)

- new software-specific easyblock for DualSPHysics;

- enhancement to generic easyblocks: Conda, GoPackage, PerlModule, PythonPackage;

- updated & enhancements to custom easyblocks for Clang-AOMP, GCC, Gurobi, LAMMPS, MCR, OCaml, OpenSSL wrapper, PyTorch, VEP, WIEN2k;

- `(***)` significant improvements to QuantumESPRESSO easyblock, incl. running the test suite;

- enhancements to GCC easyblock and additional patch for recent GCC versions to support installation on RISC-V systems;

- `(***)` add extensions to R-bundle-CRAN v2023.12 (use [`--rebuild --skip`](https://docs.easybuild.io/partial-installations/#partial_installation_skip));

- `(***)` add support for Vulkan software rendering in Mesa v23.1.9 by adding Wayland dependency;

- `(***)` add MODIStsp extension (+ required dependencies) to R 4.2.2 (use [`--rebuild --skip`](https://docs.easybuild.io/partial-installations/#partial_installation_skip));


Prominent bug fixes & changes

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

- bug fixes for generic easyblocks: Cargo, CMakeMake,

- bug fixes in custom easyblocks for BerkeleyGW, Clang, LAMMPS, LibInt, NVHPC, OpenFOAM, OpenMPI, PETSc, Python, PyTorch, QuantumESPRESSO, R, SLEPc, torchvision;

- `(***)` fix link order in PETSc easyblock for SCOTCH >= 7.x;

- `(***)` do not rename GCC's include-fixed directory by default + add script to regenerate it;
**Re-installing GCC 13.2.0 is required to ensure compatibility with CUDA 12.4.0**, [see easyblocks PR 3254 for more info](https://github.com/easybuilders/easybuild-easyblocks/pull/3254).

- `(***)` add patch for adding a write memory barrier to all OpenMPI 4.1.x easyconfigs, to bug in smcuda component;
**We recommend re-installing OpenMPI 4.1.x to pick up this fix.**

- `(***)` add patch to fix tree-optimization bug in GCC 12.3.0 + 13.1.0 + 13.2.0 for ARM architectures with SVE support;

- `(***)` add patch for GCCcore 13.2.0 to fix unguarded use of is_convertible builtin;

- add patch to fix multiarch support for RISC-V to all GCCcore 12.x and 13.x easyconfigs;

- `(***)` move setuptools_scm extension from hatchling to Python easyconfig;
**We strongly recommend to install the missing extensions for Python/3.11.3-GCCcore-12.3.0 and Python/3.11.5-GCCcore-13.2.0 using [`eb --rebuid --skip`](https://docs.easybuild.io/partial-installations/#partial_installation_skip)** (or the reinstall these modules).

- add patches for PyTorch v2.1.2 to fix test failures;

- add patch to fix PyTorch 1.12.x and 1.13.x for Linux 6+;

- (***) add missing zlib + OpenSSL deps to Ruby easyconfigs + promote binutils to runtime dependency;


Supported software

Support for installing 101 (!) new software packages has been added, including (but not limited to):

- AMICA
- Circlator
- Clarabel.rs
- DeepLoc
- devbio-napari
- EpiSCORE
- ExtremeLy
- GenomeComb
- GRASP-suite
- IDG
- IonQuant
- libspectre
- MLflow
- MSFragger
- noise
- PAGAN2
- phyluce
- python-casacore
- QuPath
- RHEIA
- SemiBin
- Sentence-Transformers
- SQLAlchemy
- Vamb
- zUMIs

This brings the total number of supported software packages to 3,470 (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):

- anvio 8
- arrow-R 14.0.0.2
- BerkeleyGW 3.1.0 + 4.0
- Cartopy 0.22.0
- Clang-Python-bindings 16.0.6
- CUDA 12.3.2 + 12.4.0
- CuPy 13.0.0
- CVXPY 1.4.2
- DeepLabCut 2.3.6
- EggLib 3.3.0
- ESMF 8.4.2
- FDS 6.8.0
- Flask 3.0.0
- FLINT 3.1.1
- GATK 4.5.0.0
- GLFW 3.4
- GROMACS 2024.1
- Gurobi 11.0.0
- HeFFTe 2.4.0
- LAMMPS 2Aug2023_update2
- likwid 5.3.0
- matplotlib 3.8.2
- medaka 1.11.3
- MOABB 1.0.0
- MONAI 1.3.0
- NCCL 2.20.5
- NGSpeciesID 0.3.0
- NLTK 3.8.1
- NVHPC 24.1
- OCaml 4.14.0
- ONNX 1.15.0
- OpenFOAM v2306 + v2312
- OpenSSL/3 (wrapper)
- PAPI 7.1.0
- ParaView 5.12.0
- PETSc 3.20.3
- plotly.py 5.18.0
- PyQt5 5.15.10
- PyTables 3.9.2
- pytest-rerunfailures 14.0
- python-irodsclient 2.0.0,
- PyTorch-Lightning 2.2.1
- Qt5 5.15.13
- Qt6 6.6.3
- QuantumESPRESSO 7.3
- R 4.3.3
- R-bundle-Bioconductor 3.18
- rMATS-turbo 4.2.0
- Ruby 3.3.0
- Rust 1.76.0
- scikit-learn 1.4.0
- Score-P 8.4,
- SLEPc 3.20.1
- timm 0.9.7
- VEP 111
- WIEN2k 23.2
- wrf-python 1.3.4.1
- YODA 1.9.9


These changes result from various contributions, made by 34 different contributors:

* 28 merged pull requests for EasyBuild framework
* 43 merged pull requests for easyblocks
* 575 (!) merged pull requests for easyconfigs


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


To upgrade to EasyBuild v4.9.1, there are [several options](https://docs.easybuild.io/installation/#updating).
Two particularly easy options include:

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

* `eb --from-pr 20299` use easyconfig from [PR 20299](https://github.com/easybuilders/easybuild-easyconfigs/pull/20299)

EasyBuild v4.9.0 is primarily a feature release, mainly because it includes the 2023b version of the common toolchains (foss + intel), but it also includes various bug fixes, and much more.

The executive summary for this release:

- improved support for using recent version of Environment Modules as modules tool;

- new generic CargoPythonBundle easyblock;

- 3 new custom easyblocks: for flook, HPCC, and PALM;

- easyconfigs for `foss/2023b` and `intel/2023b`;

- Easyconfigs for various recent software versions, including GROMACS 2023.3, NWChem 7.2.2, Python-bundle-PyPI 2023.10, PyTorch 2.1.2, R 4.3.2, SciPy-bundle 2023.11, Spark 3.5.0, VTK 9.3.0, ...;

- Support for installing 77 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_eb490) 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 generic `CargoPythonBundle` easyblock;

- 3 new software-specific easyblocks for flook, HPCC, PALM;

- update easyblocks for intel-compilers, impi, imkl to support latest versions;

- update numpy easyblock for v1.26+;

- updates and enhancements to custom easyblocks for Ferret, SuiteSparse;

- add easyconfigs for `foss/2023b` and `intel/2023b` (see also [common toolchains overview](https://docs.easybuild.io/common-toolchains/#common_toolchains_overview));


Prominent bug fixes & changes

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

- fix support for Environment Modules as modules tool to pass unit tests with v4.2+;

- adapt module function check for Environment Modules v4+;

- disable LLVM build downloads from CI in Rust;

- update SuiteSparse easyblock to only install SuiteSparse libraries with make install;

- fix specifying path to SuiteSparse header files and libraries in numpy, Trilinos, PETSc easyblocks;

- add support for allowing version mismatch + consider versionsuffix when creating `.modulerc` in `ModuleRC` easyblock;

- fix `det_pylibdir` provided by `PythonPackage` easyblock for Python 3.12+;

- bug fixes for custom easyblocks for Clang, CUDA, numpy, NWChem, PETSc, PyTorch, Rust, SuiteSparse, TensorFlow, Trilinos

- add patch to fix regression in GCC 12.x on AVX512 systems `(***)`;

- add patch for GCC 12.x to fix miscompiling C++ code causing double-free in case of exceptions `(***)`;

- add patch to fix detection of newer Intel CPUs in OpenBLAS 0.3.20 through 0.3.23;

- fix OpenBLAS 0.3.20+ on newer Intel CPUs;

- add patch to fix [cz]asums in OpenBLAS 0.3.24 `(***)`;

- add patch to work around potential crash in PyTorch 1.13.1 caused by GCC 12 compiler bug `(***)`;

- change toolchain in json-fortran easyconfigs to GCC, since it includes Fortran modules `(***)`;

- use GCC toolchain in kim-api, since it includes Fortran modules `(***)`;

- allow ITK legacy code and Python wrappers in ITK v5.2.1 `(***)`;


Supported software

Support for installing 77 new software packages has been added, including (but not limited to):

* BRiAl
* CellBender
* DIA-NN
* EUKulele
* FACE
* GFF3-toolkit
* HPCC
* iperf
* LoopTools
* MitoHiFi
* PFFT
* PySINDy
* R-bundle-CRAN
* scikit-lego
* SEACells
* solo
* Triton
* waLBerla

This brings the total number of supported software packages to 3,369 (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):

* Arrow 14.0.1
* Boost 1.83.0
* CellRanger 7.2.0
* CUDA 12.3.0
* f90wrap 0.2.11
* FPM 1.15.1
* GPyTorch 1.10
* GROMACS 2023.3
* ITK 5.3.0,
* LinBox 1.7.0
* magma 2.7.2,
* Molden 7.3
* NWChem 7.2.2
* phonopy 2.20.0
* PostgreSQL 16.1,
* Python-bundle-PyPI 2023.10
* PyTorch 2.1.2
* R 4.3.2
* SciPy-bundle 2023.11
* Seurat 4.4.0
* Spark 3.5.0
* SuiteSparse 7.1.0
* UCX-CUDA 1.15.0
* VTK 9.3.0
* XGBoost 2.0.2

These changes result from various contributions, made by 34 different contributors:

* 21 merged pull requests for EasyBuild framework
* 26 merged pull requests for easyblocks
* 276 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.9.0, there are [several options](https://docs.easybuild.io/installation/#updating).
Two particularly easy options include:

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

* `eb --from-pr 19464` use easyconfig from [PR 19464](https://github.com/easybuilders/easybuild-easyconfigs/pull/19464)

EasyBuild v4.8.2 is primarily a bugfix and update release, but it also includes various enhancements.

The executive summary for this release:

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

- Easyconfigs for various recent software versions, including Cantera 3.0.0, mold 2.3.1, Perl-bundle-CPAN 5.38.0, PyTorch 2.0.1, ...;

- Support for installing 48 new software applications and libraries, incl. PyTensor, Qt6, SNAP-ESA;

Highlights for this release are listed below.
More details are available in the [release notes](https://docs.easybuild.io/release-notes/#release_notes_eb482) 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 `dependency_names` method to `EasyConfig` class to get set of names of (direct) dependencies;

- use more test programs in sanity check step of OpenMPI easyblock;

- updates and enhancements to various generic easyblocks, including `CMake`, `Conda`, `ConfigureMake`;

- updates and enhancements to custom easyblocks for imkl, numpy, Perl, PyTorch, WRF, wxPython;

- add patches to build Qt5 5.15.10 with Python 3 instead of Python 2.7;

- `(***)` don't disable building of third and fourth derivates in libxc 6.1.0;

- `(***)` also build Python bindings for ITK 5.2.1 with foss/2022a;

- `(***)` add extensions to recent versions of R and R-bundle-Bioconductor, 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 re-installing easyconfigs are marked with `(***)`)

- reset `tempfile.tempdir` to `None` to avoid that tmpdir path gets progressively deeper with each easystack item;

- only use `-DCMAKE_SKIP_RPATH=ON` for CMake < 3.5.0;

- fix `--sanity-check-only` and `--module-only` for UCX plugins;

- enhance TensorFlow easyblock to avoid use of `-mcpu=native` for XNNPACK component when building on aarch64;

- fix the blas/lapack name passed to meson when building recent scipy versions (>= 1.9.0) on top of Intel MKL;

- `(***)` add patch to improve CUDA 11 compatibility of GCCcore/12.2.0 and GCCcore/12.3.0;

- `(***)` add missing required extensions + fix wrong version of extensions in recent Perl easyconfigs;

- rename ACT to Artemis;

- rename `CVS` to `ConcurrentVersionsSystem`, to avoid problems with recent setuptools versions;

- add patch for recent OpenBLAS versions (0.3.23, 0.3.24) to fix flaky and hanging tests;

- `(***)` add patch to fix Open MPI 4.1.5 with PMIx >= 4.2.3;

- `(***)` fix invalid pointer access in UCX 1.11-1.14;

- `(***)` statically link Boost 1.75 in Cufflinks v20190706 installed with `GCC/11.2.0`, so Boost can be changed to build dependency;

- add patch to fix issue with automatic detection of NeoverseV1 CPU architecture in OpenBLAS v0.3.20;

- `(***)` add missing dependencies for MONAI to support extras required by MONAI-Label;

- `(***)` disable threadedmpi in recent SCOTCH easyconfigs using gompi toolchain;



Supported software

Support for installing 48 new software packages has been added, including (but not limited to):

* ALL
* bases2fastq
* biobakery-workflows
* CLEAR
* EveryBeam
* imutils
* Jmol
* MACS3
* MUSCLE3
* ProBiS
* PyPy
* PyTensor
* Qt6
* ResistanceGA
* scCODA
* SNAP-ESA
* starparser
* XBeach

This brings the total number of supported software packages to 3,292 (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):

* Amber 22.4
* BLAST+ 2.14.1
* Cantera 3.0.0
* CapnProto 1.0.1
* CGAL 5.6
* CUDA-Samples 12.1.1
* CuPy 12.1.0
* FastANI 1.34
* GDAL 3.7.1
* GMP 6.3.0
* GPAW 23.9.1
* HMMER 3.4
* IsoSeq 4.0.0
* libpng 1.6.40
* libxc 6.2.2
* MEGAN 6.25.3
* Mesa 23.1.9
* mold 2.3.1
* OpenBLAS 0.3.24
* OpenCV 4.8.1
* OpenMPI 4.1.6
* OrthoFinder 2.5.5
* ParaView 5.11.2
* Perl-bundle-CPAN 5.38.0
* pyEGA3 5.0.2
* Python 3.11.5
* PyTorch 2.0.1
* PyTorch-bundle 1.13.1
* RagTag 2.1.0
* RAxML-NG 1.2.0,
* RDFlib 7.0.0
* ReFrame 4.3.3
* Rust 1.73.0
* scikit-learn 1.3.1
* TensorRT 8.6.1
* UCX 1.15.0
* X11 20231019
* xtb 6.6.0

These changes result from various contributions, made by 23 different contributors:

* 15 merged pull requests for EasyBuild framework
* 20 merged pull requests for easyblocks
* 267 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.8.2, there are [several options](https://docs.easybuild.io/installation/#updating).
Two particularly easy options include:

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

* `eb --from-pr 19105` use easyconfig from [PR 19105](https://github.com/easybuilders/easybuild-easyconfigs/pull/19105)