Merged easyblocks PRs for EasyBuild 5.0 (20250108)

# Merged easyblocks PRs for EasyBuild 5.0 (20250108) *(220 PRs)* ``` gh pr list --repo easybuilders/easybuild-easyblocks --state merged --json number,title,url --template '{{range .}}{{tablerow .number .title .url}}{{end}}' --limit 1000 --base 5.0.x | sed 's/^/- /g' ``` ### Done #### more - 3525 Rename `post_install_step` to `post_processing_step` https://github.com/easybuilders/easybuild-easyblocks/pull/3525 - https://github.com/easybuilders/easybuild-docs/pull/297 - 3343 update easyblock to let EasyBuild framework take care of prepend to `$PYTHONPATH` or `$EBPYTHONPREFIXES` + make `PythonBundle` and `PythonPackage` aware of `--prefer-... https://github.com/easybuilders/easybuild-easyblocks/pull/3343 - https://github.com/easybuilders/easybuild-docs/pull/297 - 3227 set CMake installation `LIBDIR` to `lib` by default in `CMakeMake` easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3227 - https://github.com/easybuilders/easybuild-docs/pull/297 - 3064 rename `run` method to `install_extension`, and likewise for `prerun` to `pre_install_extension`, `postrun` to `post_install_extension`, and `run_async` to `install_e... https://github.com/easybuilders/easybuild-easyblocks/pull/3064 - https://github.com/easybuilders/easybuild-docs/pull/297 - 3025 enhance `ConfigureMake` easyblock to error out on unknown configure options https://github.com/easybuilders/easybuild-easyblocks/pull/3025 - https://github.com/easybuilders/easybuild-docs/pull/297 - 3022 enable `download_dep_fail`, `use_pip`, `sanity_pip_check` by default in `PythonPackage` easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3022 - https://github.com/easybuilders/easybuild-docs/pull/297 #### `module_load_environment` / `--module-search-path-headers` There changes will be covered by general docs on `module_load_environment` and `--module-search-path-headers` - 3631 adopt `module_load_environment` in ROOT easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3631 - 3630 adopt `module_load_environment` in RepeatModeler and RepeatMasker easyblocks https://github.com/easybuilders/easybuild-easyblocks/pull/3630 - 3629 enhance handling of `PETSC_ARCH` and adopt `module_load_environment` in SLEPc easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3629 - 3628 adopt `module_load_environment` in NVHPC easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3628 - 3627 set minimum supported version of PETSc to v3.9 and adopt `module_load_environment` https://github.com/easybuilders/easybuild-easyblocks/pull/3627 - 3626 adopt `module_load_environment` in custom easyblock for R https://github.com/easybuilders/easybuild-easyblocks/pull/3626 - 3625 adopt `module_load_environment` in custom easyblock for TINKER https://github.com/easybuilders/easybuild-easyblocks/pull/3625 - 3622 adopt `module_load_environment` in custom easyblock for PyTorch https://github.com/easybuilders/easybuild-easyblocks/pull/3622 - 3620 adopt `module_load_environment` in custom easyblock for optiSLang https://github.com/easybuilders/easybuild-easyblocks/pull/3620 - 3619 adopt `module_load_environment` in custom easyblock for OCaml https://github.com/easybuilders/easybuild-easyblocks/pull/3619 - 3618 revamp NEURON easyblock, incl. adopt `module_load_environment` https://github.com/easybuilders/easybuild-easyblocks/pull/3618 - 3616 adopt `module_load_environment` in MRtrix easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3616 - 3615 fix Molpro easyblock in module-only mode + adopt `module_load_environment` https://github.com/easybuilders/easybuild-easyblocks/pull/3615 - 3613 adopt `module_load_environment` in Mathematica easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3613 - 3612 adopt `module_load_environment` in imkl-FFTW easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3612 - 3611 adopt `module_load_environment` in Libint easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3611 - 3610 adopt `module_load_environment` in Java easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3610 - 3609 adopt `module_load_environment` in itac easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3609 - 3608 remove `make_module_req_guess` with default settings from HDF5 easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3608 - 3607 adopt `module_load_environment` in GROMACS easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3607 - 3606 adopt `module_load_environment` in FSL easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3606 - 3604 adopt `module_load_environment` in freetype easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3604 - 3603 adopt `module_load_environment` in Trinity easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3603 - 3602 adopt `module_load_environment` in VEP easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3602 - 3601 adopt `module_load_environment` in FreeSurfer easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3601 - 3600 adopt `module_load_environment` in FLUENT easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3600 - 3598 adopt `module_load_environment` in CUDAcompat easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3598 - 3597 replace `'HEADERS'` magic string with global MODULE_LOAD_ENV_HEADERS https://github.com/easybuilders/easybuild-easyblocks/pull/3597 - 3596 adopt `module_load_environment` in WRF + WPS easyblocks https://github.com/easybuilders/easybuild-easyblocks/pull/3596 - 3594 adopt `module_load_environment` in AOCC easyblock + fix compatibility with `--module-only` https://github.com/easybuilders/easybuild-easyblocks/pull/3594 - 3593 adopt `module_load_environment` in XALT easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3593 - 3592 adopt `module_load_environment` in Xmipp easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3592 - 3587 adopt `module_load_environment` in CUDA easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3587 - 3586 adopt `module_load_environment` in Clang easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3586 - 3585 fix module load environment in Anaconda and Conda easyblocks https://github.com/easybuilders/easybuild-easyblocks/pull/3585 - 3584 honor `--module-search-path-headers` in easyblocks that hardcode CPATH https://github.com/easybuilders/easybuild-easyblocks/pull/3584 - 3579 adopt `module_load_environment`: ANSYS https://github.com/easybuilders/easybuild-easyblocks/pull/3579 - 3578 adopt `module_load_environment`: ABAQUS https://github.com/easybuilders/easybuild-easyblocks/pull/3578 - 3577 adopt `module_load_environment`: Anaconda https://github.com/easybuilders/easybuild-easyblocks/pull/3577 - 3562 adopt `module_load_environment`: Conda https://github.com/easybuilders/easybuild-easyblocks/pull/3562 - 3561 adopt `module_load_environment` in generic `Rpm` easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3561 - 3560 adopt module_load_environment in `SystemMPI` generic easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3560 - 3559 split `SystemCompilerGCC` out of `SystemCompiler` and adopt `module_load_environment` https://github.com/easybuilders/easybuild-easyblocks/pull/3559 - 3556 adopt `module_load_environment`: GCC https://github.com/easybuilders/easybuild-easyblocks/pull/3556 - 3555 adopt `module_load_environment`: imkl https://github.com/easybuilders/easybuild-easyblocks/pull/3555 - 3553 adopt `module_load_environment`: impi https://github.com/easybuilders/easybuild-easyblocks/pull/3553 - 3552 adopt `module_load_environment`: intel-compilers https://github.com/easybuilders/easybuild-easyblocks/pull/3552 - 3551 adopt `module_load_environment`: IntelBase, Advisor, Inspector, VTune https://github.com/easybuilders/easybuild-easyblocks/pull/3551 - 3550 adopt `module_load_environment`: icc, ifort, iccifort https://github.com/easybuilders/easybuild-easyblocks/pull/3550 #### removed blocks TODO added in https://github.com/easybuilders/easybuild-docs/pull/297 - 3621 remove unused Primer3 easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3621 - 3617 remove custom easyblock for MTL4, because it has no active easyconfigs https://github.com/easybuilders/easybuild-easyblocks/pull/3617 - 3424 remove unused custom easyblock for BamTools https://github.com/easybuilders/easybuild-easyblocks/pull/3424 - 3423 remove (20) unused software-specific easyblocks https://github.com/easybuilders/easybuild-easyblocks/pull/3423 - 3265 remove unused easyblock for `ncurses` (`ncurses.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3265 - 3292 remove unused custom easyblock for Modeller (modeller.py) https://github.com/easybuilders/easybuild-easyblocks/pull/3292 - 3285 remove unused custom easyblock for HEALPix (healpix.py) https://github.com/easybuilders/easybuild-easyblocks/pull/3285 - 3271 remove custom easyblock for WRF-Fire https://github.com/easybuilders/easybuild-easyblocks/pull/3271 - 3216 remove unused custom easyblock for libsmm (`libsmm.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3216 - 3211 remove unused custom easyblock for Mono (`mono.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3211 - 3208 remove unused custom easyblock for MSM (`msm.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3208 - 3205 remove unused custom easyblock for MyMediaLite (`mymedialite.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3205 - 3202 remove unused custom easyblock for NEMO (`nemo.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3202 - 3194 remove unneeded custom easyblock for OpenIFS (`openifs.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3194 - 3191 remove unused custom easyblock for TotalView (`totalview.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3191 - 3185 remove unused custom easyblock for pplacer (`pplacer.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3185 - 3182 remove unused custom easyblock for python_meep (`python_meep.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3182 - 3181 remove unused custom easyblock for PGI (`pgi.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3181 - 3178 remove unused custom easyblock for SNPhylo (`snphylo.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3178 - 3177 remove unused custom easyblock for SAS (`sas.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3177 - 3176 remove unused custom easyblock for Samcef (`samcef.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3176 - 3175 remove unused custom easyblock for Doris (`doris.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3175 - 3174 remove unused custom easyblock for BiSearch (`bisearch.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3174 - 3173 remove unused custom easyblock for ALADIN (`aladin.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3173 - 3172 remove unused custom easyblock for ACML (`acml.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3172 - 3157 remove unused custom easyblock for FreeFEM (`freefem.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3157 - 3155 remove unused custom easyblock for fastStructure (`faststructure.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3155 - 3154 remove unused custom easyblock for DOLFIN (`dolfin.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3154 - 3152 remove unused custom easyblock for DL_POLY_Classic (`dl_poly_classic.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3152 - 3151 remove unused custom easyblock for CFDEMcoupling (`cfdemcoupling.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3151 - 3138 remove unused custom easyblock for VSC-tools (`vsc_tools.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3138 - 3126 remove unused custom easyblock for IMOD (`imod.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3126 - 3125 remove unused custom easyblock for IronPython (`ironpython.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3125 - 3117 remove unused custom easyblock for ESPResSo (`espresso.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3117 - 3114 remove unneeded custom easyblock for Doxygen (`doxygen.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3114 - 3111 remove unused custom easyblock for cppcheck (`cppcheck.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3111 - 3108 remove unused custom easyblock for CHARMM (`charmm.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3108 - 3104 remove unused custom easyblock for BLACS (`blacs.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3104 - 3103 remove unused custom easyblock for ATLAS (`atlas.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3103 - 3096 remove unused custom easyblock for ARB (`arb.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3096 - 3066 remove custom easyblock for EggLib (no longer used) https://github.com/easybuilders/easybuild-easyblocks/pull/3066 #### `run_shell_cmd` These changes are covered by general docs on `run_shell_cmd` - 3342 use `run_shell_cmd` (and use f-strings) in custom easyblock for GAMESS-US https://github.com/easybuilders/easybuild-easyblocks/pull/3342 - 3327 use `work_dir` option for `run_shell_cmd` instead of global `chdir` in custom easyblock for Go https://github.com/easybuilders/easybuild-easyblocks/pull/3327 - 3415 Replace `run_cmd` with `run_shell_cmd` in custom easyblock for MetalWalls https://github.com/easybuilders/easybuild-easyblocks/pull/3415 - 3414 use `run_shell_cmd` in custom easyblock for ABAQUS https://github.com/easybuilders/easybuild-easyblocks/pull/3414 - 3413 use `run_shell_cmd` in custom easyblock for WIEN2k https://github.com/easybuilders/easybuild-easyblocks/pull/3413 - 3411 Replace `run_cmd` with `run_shell_cmd` in custom easyblock for QuantumESPRESSO https://github.com/easybuilders/easybuild-easyblocks/pull/3411 - 3308 use `run_shell_cmd` in testsuite https://github.com/easybuilders/easybuild-easyblocks/pull/3308 - 3299 use `run_shell_cmd` in custom easyblock for OpenFOAM https://github.com/easybuilders/easybuild-easyblocks/pull/3299 - 3298 use `run_shell_cmd` in custom easyblock for Mathematica https://github.com/easybuilders/easybuild-easyblocks/pull/3298 - 3297 use `run_shell_cmd` in custom easyblock for WPS https://github.com/easybuilders/easybuild-easyblocks/pull/3297 - 3295 use `run_shell_cmd` in custom easyblock for CPLEX https://github.com/easybuilders/easybuild-easyblocks/pull/3295 - 3293 use `run_shell_cmd` in custom easyblock for DualSPHysics https://github.com/easybuilders/easybuild-easyblocks/pull/3293 - 3291 use `run_shell_cmd` in custom easyblock for Qt https://github.com/easybuilders/easybuild-easyblocks/pull/3291 - 3290 use `run_shell_cmd` in custom easyblock for RepeatMasker https://github.com/easybuilders/easybuild-easyblocks/pull/3290 - 3289 use `run_shell_cmd` in custom easyblock for RepeatModeler https://github.com/easybuilders/easybuild-easyblocks/pull/3289 - 3288 use `run_shell_cmd` in custom easyblock for Stata https://github.com/easybuilders/easybuild-easyblocks/pull/3288 - 3286 use `run_shell_cmd` in custom easyblock for Maple https://github.com/easybuilders/easybuild-easyblocks/pull/3286 - 3274 use `run_shell_cmd` in custom easyblock for CUDA https://github.com/easybuilders/easybuild-easyblocks/pull/3274 - 3270 use `run_shell_cmd` in custom easyblock for WRF https://github.com/easybuilders/easybuild-easyblocks/pull/3270 - 3244 replace `run_cmd` with `run_shell_cmd` in custom easyblock for LAMMPS (`lammps.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3244 - 3243 replace `run_cmd` with `run_shell_cmd` in custom easyblock for OCaml (`ocaml.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3243 - 3219 replace `run_cmd` with `run_shell_cmd` in custom easyblock for LAPACK (`lapack.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3219 - 3218 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Libint (`libint.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3218 - 3217 replace `run_cmd` with `run_shell_cmd` in custom easyblock for libQGLViewer (`libqglviewer.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3217 - 3215 replace `run_cmd` with `run_shell_cmd` in custom easyblock for MATLAB (`matlab.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3215 - 3214 replace `run_cmd` with `run_shell_cmd` in custom easyblock for PSI/PSI4 (`psi.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3214 - 3213 replace `run_cmd` with `run_shell_cmd` in custom easyblock for MCR (`mcr.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3213 - 3212 replace `run_cmd` with `run_shell_cmd` in custom easyblock for METIS (`metis.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3212 - 3210 replace `run_cmd` with `run_shell_cmd` in custom easyblock for MrBayes (`mrbayes.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3210 - 3209 replace `run_cmd` with `run_shell_cmd` in custom easyblock for MRtrix (`mrtrix`) https://github.com/easybuilders/easybuild-easyblocks/pull/3209 - 3207 replace `run_cmd` with `run_shell_cmd` in custom easyblock for MUMmer (`mummer`) https://github.com/easybuilders/easybuild-easyblocks/pull/3207 - 3206 replace `run_cmd` with `run_shell_cmd` in custom easyblock for MXNet (`mxnet.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3206 - 3204 replace `run_cmd` with `run_shell_cmd` in custom easyblock for NAMD (`namd.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3204 - 3203 replace `run_cmd` with `run_shell_cmd` in custom easyblock for NCL (`ncl.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3203 - 3201 replace `run_cmd` with `run_shell_cmd` in custom easyblock for NEURON (`neuron.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3201 - 3200 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Nim (`nim.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3200 - 3199 replace `run_cmd` with `run_shell_cmd` in custom easyblock for numpy (`numpy.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3199 - 3198 replace `run_cmd` with `run_shell_cmd` in custom easyblock for NVHPC (`nvhpc.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3198 - 3197 replace `run_cmd` with `run_shell_cmd` in custom easyblock for NWChem (`nwchem.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3197 - 3195 replace `run_cmd` with `run_shell_cmd` in custom easyblock for OpenBLAS (`openblas.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3195 - 3193 replace `run_cmd` with `run_shell_cmd` in custom easyblock for OpenSSL / OpenSSL_wrapper (`openssl.py` and `openssl_wrapper.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3193 - 3192 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Siesta (`siesta.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3192 - 3190 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Trinity (`trinity.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3190 - 3189 replace `run_cmd` with `run_shell_cmd` in custom easyblock for UCX Plugins (`ucx_plugins.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3189 - 3188 replace `run_cmd` with `run_shell_cmd` in custom easyblock for VEP (`vep.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3188 - 3187 replace `run_cmd` with `run_shell_cmd` in custom easyblock for VMD (`vmd.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3187 - 3180 replace `run_cmd` with `run_shell_cmd` in custom easyblock for TINKER (`tinker.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3180 - 3179 replace `run_cmd` with `run_shell_cmd` in custom easyblock for TensorRT (`tensorrt.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3179 - 3171 replace `run_cmd` with `run_shell_cmd` in custom easyblock for pybind11 (`pybind11.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3171 - 3169 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Python (`python.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3169 - 3168 replace `run_cmd` with `run_shell_cmd` in custom easyblock for PETSc (`petsc.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3168 - 3167 replace `run_cmd` with `run_shell_cmd` in custom easyblock for ParMETIS (`parmetis.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3167 - 3166 replace `run_cmd` with `run_shell_cmd` in custom easyblock for PALM (`palm.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3166 - 3165 replace `run_cmd` with `run_shell_cmd` in custom easyblock for TensorFlow (`tensorflow.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3165 - 3164 replace `run_cmd` with `run_shell_cmd` in custom easyblock for tensorflow_compression (`tensorflow_compression.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3164 - 3163 update `run_async` methods in `RPackage`, `Rmpi`, and `Rserve` easyblocks to use submit `run_shell_cmd` call into thread pool https://github.com/easybuilders/easybuild-easyblocks/pull/3163 - 3162 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Perl (`perl.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3162 - 3159 replace `run_cmd` with `run_shell_cmd` in custom easyblock for icc (`icc.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3159 - 3158 replace `run_cmd` with `run_shell_cmd` in custom easyblock for HPCG (`hpcg.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3158 - 3156 replace `run_cmd` with `run_shell_cmd` in custom easyblock for FDTD_Solutions (`fdtd_solutions.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3156 - 3153 replace `run_cmd` with `run_shell_cmd` in custom easyblock for dm-reverb (`dm_reverb.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3153 - 3150 replace `run_cmd` with `run_shell_cmd` in custom easyblock for QScintilla (`qscintilla.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3150 - 3149 replace `run_cmd` with `run_shell_cmd` in custom easyblock for ROOT (`root.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3149 - 3147 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Rosetta (`rosetta.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3147 - 3146 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Rust (`rust.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3146 - 3145 replace `run_cmd` with `run_shell_cmd` in custom easyblock for tbb (`tbb.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3145 - 3144 replace `run_cmd` with `run_shell_cmd` in custom easyblock for STAR-CCM+ (`star_ccm.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3144 - 3143 replace `run_cmd` with `run_shell_cmd` in custom easyblock for SLEPc (`slepc.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3143 - 3142 replace `run_cmd` with `run_shell_cmd` in custom easyblock for SEPP (`sepp.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3142 - 3141 replace `run_cmd` with `run_shell_cmd` in custom easyblock for SCOTCH (`scotch.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3141 - 3140 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Scipion (`scipion.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3140 - 3139 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Clang (`clang.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3139 - 3137 replace `run_cmd` with `run_shell_cmd` in custom easyblock for GCC (`gcc.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3137 - 3136 replace `run_cmd` with `run_shell_cmd` in custom easyblock for FlexiBLAS (`flexiblas.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3136 - 3135 replace `run_cmd` with `run_shell_cmd` in custom easyblock for FLUENT (`fluent.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3135 - 3134 replace `run_cmd` with `run_shell_cmd` in custom easyblock for FSL (`fsl.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3134 - 3133 replace `run_cmd` with `run_shell_cmd` in custom easyblock for GATE (`gate.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3133 - 3132 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Go (`go.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3132 - 3131 replace `run_cmd` with `run_shell_cmd` in custom easyblock for GROMACS (`gromacs.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3131 - 3130 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Gurobi (`gurobi.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3130 - 3129 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Hadoop (`hadoop.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3129 - 3128 replace `run_cmd` with `run_shell_cmd` in custom easyblock for HPL (`hpl.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3128 - 3127 replace `run_cmd` with `run_shell_cmd` in custom easyblock for intel_compilers (`intel_compilers.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3127 - 3124 replace `run_cmd` with `run_shell_cmd` in custom easyblock for impi (`impi.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3124 - 3123 replace `run_cmd` with `run_shell_cmd` in custom easyblock for itac (`itac.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3123 - 3122 replace `run_cmd` with `run_shell_cmd` in custom easyblock for imkl (`imkl.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3122 - 3120 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Java (`java.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3120 - 3115 replace `run_cmd` with `run_shell_cmd` in custom easyblock for ESMF (`esmf.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3115 - 3113 replace `run_cmd` with `run_shell_cmd` in custom easyblock for CP2K (`cp2k.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3113 - 3112 replace `run_cmd` with `run_shell_cmd` in custom easyblock for CUDAcompat (`cudacompat.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3112 - 3110 replace `run_cmd` with `run_shell_cmd` in custom easyblock for COMSOL (`comsol.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3110 - 3109 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Chimera (`chimera.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3109 - 3107 replace `run_cmd` with `run_shell_cmd` in custom easyblock for cryptography (`cryptography.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3107 - 3106 drop support for versions < 2.0 and replace `run_cmd` with `run_shell_cmd` in custom easyblock for ScaLAPACK (`scalapack.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3106 - 3105 replace `run_cmd` with `run_shell_cmd` in custom easyblock for binutils (`binutils.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3105 - 3102 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Bazel (`bazel.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3102 - 3101 replace `run_cmd` with `run_shell_cmd` in custom easyblock for bzip2 (`bzip2.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3101 - 3100 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Boost (`boost.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3100 - 3099 replace `run_cmd` with `run_shell_cmd` in custom easyblock for ANSYS (`ansys.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3099 - 3098 replace `run_cmd` with `run_shell_cmd` in custom easyblock for ant (`ant.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3098 - 3094 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Amber (`amber.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3094 - 3093 replace `run_cmd` with `run_shell_cmd` in custom easyblock for wxPython (`wxpython.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3093 - 3092 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Xmipp (`xmipp.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3092 - 3091 replace `run_cmd` with `run_shell_cmd` in custom easyblock for ADF (`adf.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3091 - 3090 replace `run_cmd` with `run_shell_cmd` in custom easyblock for Anaconda (`anaconda.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3090 - 3046 convert all generic easyblocks to `run_shell_cmd` https://github.com/easybuilders/easybuild-easyblocks/pull/3046 ### No action needed - 3543 imports without the single folder letter https://github.com/easybuilders/easybuild-easyblocks/pull/3543 - minor change - 3540 remove use of deprecated `extract_errors_from_log` in `configuremake` https://github.com/easybuilders/easybuild-easyblocks/pull/3540 - minor change - 3539 inject custom '`%(python)s`' template value before getting value of '`buildcmd`' custom easyconfig parameter in `PythonPackage` easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3539 - minor change - 3537 be more careful when getting value of particular easyconfig parameter in `PythonBundle` and `PythonPackage` easyblock, to avoid trouble with unresolved template values https://github.com/easybuilders/easybuild-easyblocks/pull/3537 - minor change - 3535 remove unused custom easyblock for TAU + clean up custom easyblock for Paraver, only support Paravar >= v4.7 https://github.com/easybuilders/easybuild-easyblocks/pull/3535 - minor change - 3533 Remove code supporting obsolete versions from `IntelBase` family of easyblocks + remove unused custom easyblock for IPP https://github.com/easybuilders/easybuild-easyblocks/pull/3533 - minor change - 3526 retain custom easyconfig parameters supported by `MesonNinja` easyblock in custom easyblock for `scipy` https://github.com/easybuilders/easybuild-easyblocks/pull/3526 - minor change - 3515 remove use of deprecated `parse_log_for_error` in `RPackage` easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3515 - minor change - 3514 update `Python` easyblock to move `sitecustomize.py` into `site-packages` https://github.com/easybuilders/easybuild-easyblocks/pull/3514 - minor change - 3499 let `PythonPackage` easyblock fix python shebangs by default https://github.com/easybuilders/easybuild-easyblocks/pull/3499 - minor change - 3490 use `*DESCRIPTION` rather than `*/DESCRIPTION` in `RPackage.requires_deps` https://github.com/easybuilders/easybuild-easyblocks/pull/3490 - minor change - 3475 refactor search for `python_cmd` https://github.com/easybuilders/easybuild-easyblocks/pull/3475 - minor change - 3474 add missing `return` for customised `install_extension_async` methods in Rserve and Rmpi easyblocks https://github.com/easybuilders/easybuild-easyblocks/pull/3474 - minor change - 3470 take into account that '`pic`' toolchain option may not be defined in `CMakeMake` easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3470 - minor change - 3454 Make `MesonNinja` respect the toolchainopts with buildtype as well as `--debug` and `--optimization` flags https://github.com/easybuilders/easybuild-easyblocks/pull/3454 - minor change - 3452 Make `CMakeMake` respect the toolchainopts when selecting build type https://github.com/easybuilders/easybuild-easyblocks/pull/3452 - minor change - 3426 add check to make sure that easyblocks do not use `run_cmd` or `run_cmd_qa` https://github.com/easybuilders/easybuild-easyblocks/pull/3426 - minor change - 3425 use non-system toolchain for testing `--module-only` for ELPA and FFTW easyblocks, since they rely on toolchain options like 'pic' being set https://github.com/easybuilders/easybuild-easyblocks/pull/3425 - minor change - 3410 use `PYPI_SOURCE` constant in generic `PythonPackage` easyblock + custom easyblock for Python https://github.com/easybuilders/easybuild-easyblocks/pull/3410 - minor change - 3399 enhance `CMakeMake` easyblock to check whether correct `Python` installation was picked up by `CMake` https://github.com/easybuilders/easybuild-easyblocks/pull/3399 - minor change - 3320 use ERROR global from tools.config in TensorFlow easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3320 - minor change - 3318 use ERROR global from tools.config in clang easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3318 - minor change - 3309 consider both easybuild-easyblocks*.tar.gz and easybuild_easyblocks*tar.gz in CI workflows https://github.com/easybuilders/easybuild-easyblocks/pull/3309 - minor change - 3302 fix `--module-only` + cleanup for custom easyblock for Geant4 https://github.com/easybuilders/easybuild-easyblocks/pull/3302 - minor change - 3296 drop support for versions < 9.5 in custom easyblock for Geant4 https://github.com/easybuilders/easybuild-easyblocks/pull/3296 - minor change - 3264 use `sysconfig.get_config_vars` from Python standard library in `PythonPackage` easyblock (instead of `distutils.sysconfig.get_config_vars`) https://github.com/easybuilders/easybuild-easyblocks/pull/3264 - minor change - 3263 add warning if `.Renviron` detected during install of RPackage https://github.com/easybuilders/easybuild-easyblocks/pull/3263 - minor change - 3245 replace `log.warn` with `log.warning` https://github.com/easybuilders/easybuild-easyblocks/pull/3245 - minor change - 3242 update RPackage to make sure that asynchronous installation command is run in correct working directory https://github.com/easybuilders/easybuild-easyblocks/pull/3242 - minor change - 3221 enable `use_pip` for extensions that are installed along with Python https://github.com/easybuilders/easybuild-easyblocks/pull/3221 - minor change - 3170 fail on non-zero exit code in command to run Perl test suite https://github.com/easybuilders/easybuild-easyblocks/pull/3170 - minor change - 3080 don't change `installopts` easyconfig parameter value in-place in `PythonPackage` easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3080 - minor change - 3079 disable `use_pip` by default for PyTorch, except for recent versions (>= 2.0) https://github.com/easybuilders/easybuild-easyblocks/pull/3079 - minor change - 3074 remove `hidden=True` from `run_shell_cmd` in `PythonPackage` easyblock for consistency https://github.com/easybuilders/easybuild-easyblocks/pull/3074 - minor change - 3067 disable check for .mod files in Clang, AOCC, AOMP, and CPLEX easyblocks https://github.com/easybuilders/easybuild-easyblocks/pull/3067 - minor change - 3635 fix comment in icc/ifort easyblocks that still refered to `make_module_req_guess` https://github.com/easybuilders/easybuild-easyblocks/pull/3635 - minor change - 3634 enhance `get_lib_subdirs` in GROMACS easyblock to avoid symlinked paths https://github.com/easybuilders/easybuild-easyblocks/pull/3634 - minor change - 3605 Fix bug in FlexiBLAS easyblock to allow AOCL-BLAS to be default https://github.com/easybuilders/easybuild-easyblocks/pull/3605 - minor change - 3599 remove hardcoded CPLUS_INCLUDE_PATH in favor of module-search-path-headers in custom easyblock for Eigen https://github.com/easybuilders/easybuild-easyblocks/pull/3599 - minor change - 3589 enhance FlexiBLAS easyblock to add support for AOCL-BLAS backend https://github.com/easybuilders/easybuild-easyblocks/pull/3589 - minor change - 3574 Fix building PyTorch when using `setup.py` as the build command https://github.com/easybuilders/easybuild-easyblocks/pull/3574 - minor change - 3568 Fix `$PYTHONPATH` for hermetic python in TensorFlow builds https://github.com/easybuilders/easybuild-easyblocks/pull/3568 - minor change - 3563 fix error reporting for unknown value of `unrecognized_configure_options` in `ConfigureMake` https://github.com/easybuilders/easybuild-easyblocks/pull/3563 - minor change - 3557 Update easyblocks to use `EasyConfig.parallel` property https://github.com/easybuilders/easybuild-easyblocks/pull/3557 - minor change - 3548 Enhance Score-P EasyBlock for future releases and better oneAPI support. https://github.com/easybuilders/easybuild-easyblocks/pull/3548 - minor change - 3547 Use context managers for templating changes in `Bundle` easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3547 - minor change - 3546 switch default to `install_pip=True` in `python.py` https://github.com/easybuilders/easybuild-easyblocks/pull/3546 - minor change - 3544 remove Python 2 fallback in `openssl_wrapper` https://github.com/easybuilders/easybuild-easyblocks/pull/3544 - python 2 cleanup - 3019 don't auto-enable use of `-DSCOTCH_PTHREAD` when using MPI library other than Intel MPI in SCOTCH easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3019 - minor change - 3018 Use `LooseVersion` from `easybuild.tools` in all easyblocks https://github.com/easybuilders/easybuild-easyblocks/pull/3018 - minor change - 3015 stop importing from `easybuild.tools.py2vs3` (+ minor cleanup in init easyblocks test) https://github.com/easybuilders/easybuild-easyblocks/pull/3015 - minor change - 3014 fix test suite: stop testing with Python 3.5 and Lmod 6.x, stop using `toolchain.DUMMY` https://github.com/easybuilders/easybuild-easyblocks/pull/3014 - minor change - 3013 update version of `config.guess` used by `ConfigureMake` https://github.com/easybuilders/easybuild-easyblocks/pull/3013 - minor change - 2916 stop importing from deprecated easybuild.tools.py2vs3 module + stop testing with Python 2.7 and 3.5 https://github.com/easybuilders/easybuild-easyblocks/pull/2916 - minor change - 3639 bump version to 5.0.0beta2 https://github.com/easybuilders/easybuild-easyblocks/pull/3639 - version bump - 3636 add lexming to list of contributors of NEURON, GROMACS, PETSc and SLEPc easyblock https://github.com/easybuilders/easybuild-easyblocks/pull/3636 - minor change - 3266 also run easyblocks test suite with Python 3.12 https://github.com/easybuilders/easybuild-easyblocks/pull/3266 - CI - 3083 stop running easyblocks test suite with Lmod 7.x https://github.com/easybuilders/easybuild-easyblocks/pull/3083 - CI - 2917 bump version to 5.0.0.dev0 https://github.com/easybuilders/easybuild-easyblocks/pull/2917 - version bump #### reverted changes - 3335 restore custom easyblock for Molpro https://github.com/easybuilders/easybuild-easyblocks/pull/3335 - reverts 3294 - 3294 remove unused custom easyblock for Molpro (molpro.py) https://github.com/easybuilders/easybuild-easyblocks/pull/3294 - reverted by 3335 - 3237 Revert "remove unneeded custom easyblock for OCaml (`ocaml.py`)" https://github.com/easybuilders/easybuild-easyblocks/pull/3237 - reverts 3196 - 3196 remove unneeded custom easyblock for OCaml (`ocaml.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3196 - reverted by 3237 - 3186 Revert "remove unused custom easyblock for PSI (`psi.py`)" https://github.com/easybuilders/easybuild-easyblocks/pull/3186 - reverts 3184 - 3184 remove unused custom easyblock for PSI (`psi.py`) https://github.com/easybuilders/easybuild-easyblocks/pull/3184 - reverted by 3186 #### sync from develop - 3637 sync with develop (20250224) https://github.com/easybuilders/easybuild-easyblocks/pull/3637 - 3564 sync with develop (20250120) https://github.com/easybuilders/easybuild-easyblocks/pull/3564 - 3542 sync with develop (20241226) https://github.com/easybuilders/easybuild-easyblocks/pull/3542 - 3534 sync with develop (20241218) + version bump to `5.0.0beta1` https://github.com/easybuilders/easybuild-easyblocks/pull/3534 - 3506 sync with develop (2024-11-13) https://github.com/easybuilders/easybuild-easyblocks/pull/3506 - 3502 sync with develop (2024-11-10) https://github.com/easybuilders/easybuild-easyblocks/pull/3502 - 3500 sync with develop (2024-11-06) https://github.com/easybuilders/easybuild-easyblocks/pull/3500 - 3489 sync with develop (20241016) https://github.com/easybuilders/easybuild-easyblocks/pull/3489 - 3459 sync with develop (20240923) https://github.com/easybuilders/easybuild-easyblocks/pull/3459 - 3447 sync with develop (20240915) https://github.com/easybuilders/easybuild-easyblocks/pull/3447 - 3401 sync with develop (20240802) https://github.com/easybuilders/easybuild-easyblocks/pull/3401 - 3367 sync with develop (20240619) https://github.com/easybuilders/easybuild-easyblocks/pull/3367 - 3349 sync with develop (20240605) https://github.com/easybuilders/easybuild-easyblocks/pull/3349 - 3333 sync with develop (20240522) https://github.com/easybuilders/easybuild-easyblocks/pull/3333 - 3319 sync with develop (20240506) https://github.com/easybuilders/easybuild-easyblocks/pull/3319 - 3287 sync with develop (20240406) https://github.com/easybuilders/easybuild-easyblocks/pull/3287 - 3261 sync with develop (20240328) https://github.com/easybuilders/easybuild-easyblocks/pull/3261 - 3251 sync with develop (20240311) https://github.com/easybuilders/easybuild-easyblocks/pull/3251 - 3238 sync with develop (20240227) https://github.com/easybuilders/easybuild-easyblocks/pull/3238

Syntax	Example	Reference
# Header	Header	基本排版
- Unordered List	Unordered List
1. Ordered List	Ordered List
- [ ] Todo List	Todo List
> Blockquote	Blockquote
Bold font	Bold font
Italics font	Italics font
~~Strikethrough~~	~~Strikethrough~~
19^th^	19^th
H~2~O	H₂O
++Inserted text++	Inserted text
==Marked text==	Marked text
[link text](https:// "title")	Link
![image alt](https:// "title")	Image
`Code`	`Code`	在筆記中貼入程式碼
```javascript var i = 0; ```	`var i = 0;`
:smile:		Emoji list
{%youtube youtube_id %}	Externals
$L^aT_eX$	L^aT_eX
:::info This is a alert area. :::	This is a alert area.