Replace `run_cmd` and `run_cmd_qa` with `run_shell_cmd`

[branfosj]

The todo list for replacing run_cmd and run_cmd_qa with run_shell_cmd for EB5.

Please make sure this issue is updated with links to the PRs for the changes. PRs can contain multiple easyblock updates, but please consider the required testing so that there is not too many tests to be done for any one PR. Also, remember that some easyblocks are also used via easyblock = 'EB_name' or inherited.

run_cmd only

• adf.py: replace run_cmd with run_shell_cmd in custom easyblock for ADF (adf.py) #3091
• amber.py: replace run_cmd with run_shell_cmd in custom easyblock for Amber (amber.py) #3094
• anaconda.py: replace run_cmd with run_shell_cmd in custom easyblock for Anaconda (anaconda.py) #3090
• ansys.py: replace run_cmd with run_shell_cmd in custom easyblock for ANSYS (ansys.py) #3099
• ant.py: replace run_cmd with run_shell_cmd in custom easyblock for ant (ant.py) #3098
• arb.py: remove unused custom easyblock for ARB (arb.py) #3096 replace run_cmd with run_shell_cmd in arb.py #3095
• atlas.py: remove unused custom easyblock for ATLAS (atlas.py) #3103 replace run_cmd with run_shell_cmd in custom easyblock for ATLAS (atlas.py) #3097
• bazel.py: replace run_cmd with run_shell_cmd in custom easyblock for Bazel (bazel.py) #3102
• binutils.py: replace run_cmd with run_shell_cmd in custom easyblock for binutils (binutils.py) #3105
• blacs.py: remove unused custom easyblock for BLACS (blacs.py) #3104
• boost.py: replace run_cmd with run_shell_cmd in custom easyblock for Boost (boost.py) #3100
• bzip2.py: replace run_cmd with run_shell_cmd in custom easyblock for bzip2 (bzip2.py) #3101
• cfdemcoupling.py: remove unused custom easyblock for CFDEMcoupling (cfdemcoupling.py) #3151
• charmm.py: remove unused custom easyblock for CHARMM (charmm.py) #3108
• chimera.py: replace run_cmd with run_shell_cmd in custom easyblock for Chimera (chimera.py) #3109
• clang.py: replace run_cmd with run_shell_cmd in custom easyblock for Clang (clang.py) #3139
• comsol.py: replace run_cmd with run_shell_cmd in custom easyblock for COMSOL (comsol.py) #3110
• cp2k.py: replace run_cmd with run_shell_cmd in custom easyblock for CP2K (cp2k.py) #3113
• cppcheck.py: remove unused custom easyblock for cppcheck (cppcheck.py) #3111
• cryptography.py: replace run_cmd with run_shell_cmd in custom easyblock for cryptography (cryptography.py) #3107
• cudacompat.py: replace run_cmd with run_shell_cmd in custom easyblock for CUDAcompat (cudacompat.py) #3112
• dl_poly_classic.py: remove unused custom easyblock for DL_POLY_Classic (dl_poly_classic.py) #3152
• dm_reverb.py: replace run_cmd with run_shell_cmd in custom easyblock for dm-reverb (dm_reverb.py) #3153
• dolfin.py: remove unused custom easyblock for DOLFIN (dolfin.py) #3154
• doxygen.py: remove unneeded custom easyblock for Doxygen (doxygen.py) #3114
• dualsphysics.py: use run_shell_cmd in custom easyblock for DualSPHysics #3293
• esmf.py: replace run_cmd with run_shell_cmd in custom easyblock for ESMF (esmf.py) #3115
• espresso.py: remove unused custom easyblock for ESPResSo (espresso.py) #3117 replace run_cmd with run_shell_cmd in custom easyblock for ESPResSo (espresso.py) #3116
• faststructure.py: remove unused custom easyblock for fastStructure (faststructure.py) #3155
• fdtd_solutions.py: replace run_cmd with run_shell_cmd in custom easyblock for FDTD_Solutions (fdtd_solutions.py) #3156
• flexiblas.py: replace run_cmd with run_shell_cmd in custom easyblock for FlexiBLAS (flexiblas.py) #3136
• fluent.py: replace run_cmd with run_shell_cmd in custom easyblock for FLUENT (fluent.py) #3135
• freefem.py: remove unused custom easyblock for FreeFEM (freefem.py) #3157
• fsl.py: replace run_cmd with run_shell_cmd in custom easyblock for FSL (fsl.py) #3134
• gamess_us.py: use run_shell_cmd (and use f-strings) in custom easyblock for GAMESS-US #3342 (having first done refactor GAMESS-US easyblock to directly write install.info #3047 to eliminate use of run_cmd_qa)
• gate.py: replace run_cmd with run_shell_cmd in custom easyblock for GATE (gate.py) #3133
• gcc.py: replace run_cmd with run_shell_cmd in custom easyblock for GCC (gcc.py) #3137
• go.py: replace run_cmd with run_shell_cmd in custom easyblock for Go (go.py) #3132
• gromacs.py: replace run_cmd with run_shell_cmd in custom easyblock for GROMACS (gromacs.py) #3131
• gurobi.py: replace run_cmd with run_shell_cmd in custom easyblock for Gurobi (gurobi.py) #3130
• hadoop.py: replace run_cmd with run_shell_cmd in custom easyblock for Hadoop (hadoop.py) #3129
• hpl.py: replace run_cmd with run_shell_cmd in custom easyblock for HPL (hpl.py) #3128
• hpcg.py: replace run_cmd with run_shell_cmd in custom easyblock for HPCG (hpcg.py) #3158
• icc.py: replace run_cmd with run_shell_cmd in custom easyblock for icc (icc.py) #3159
• imkl.py: replace run_cmd with run_shell_cmd in custom easyblock for imkl (imkl.py) #3122
• imod.py: remove unused custom easyblock for IMOD (imod.py) #3126
• impi.py: replace run_cmd with run_shell_cmd in custom easyblock for impi (impi.py) #3124
• intel_compilers.py: replace run_cmd with run_shell_cmd in custom easyblock for intel_compilers (intel_compilers.py) #3127
• ironpython.py: remove unused custom easyblock for IronPython (ironpython.py) #3125
• itac.py: replace run_cmd with run_shell_cmd in custom easyblock for itac (itac.py) #3123
• java.py: replace run_cmd with run_shell_cmd in custom easyblock for Java (java.py) #3120
• lammps.py: replace run_cmd with run_shell_cmd in custom easyblock for LAMMPS (lammps.py) #3244
• lapack.py: replace run_cmd with run_shell_cmd in custom easyblock for LAPACK (lapack.py) #3219
• libint.py: replace run_cmd with run_shell_cmd in custom easyblock for Libint (libint.py) #3218
• libqglviewer.py: replace run_cmd with run_shell_cmd in custom easyblock for libQGLViewer (libqglviewer.py) #3217
• libsmm.py: remove unused custom easyblock for libsmm (libsmm.py) #3216
• matlab.py: replace run_cmd with run_shell_cmd in custom easyblock for MATLAB (matlab.py) #3215
• mcr.py: replace run_cmd with run_shell_cmd in custom easyblock for MCR (mcr.py) #3213
• metis.py: replace run_cmd with run_shell_cmd in custom easyblock for METIS (metis.py) #3212
• mono.py: remove unused custom easyblock for Mono (mono.py) #3211
• mrbayes.py: replace run_cmd with run_shell_cmd in custom easyblock for MrBayes (mrbayes.py) #3210
• mrtrix.py: replace run_cmd with run_shell_cmd in custom easyblock for MRtrix (mrtrix) #3209
• msm.py: remove unused custom easyblock for MSM (msm.py) #3208
• mummer.py: replace run_cmd with run_shell_cmd in custom easyblock for MUMmer (mummer) #3207
• mxnet.py: replace run_cmd with run_shell_cmd in custom easyblock for MXNet (mxnet.py) #3206
• mymedialite.py: remove unused custom easyblock for MyMediaLite (mymedialite.py) #3205
• namd.py: replace run_cmd with run_shell_cmd in custom easyblock for NAMD (namd.py) #3204
• ncl.py: replace run_cmd with run_shell_cmd in custom easyblock for NCL (ncl.py) #3203
• nemo.py: remove unused custom easyblock for NEMO (nemo.py) #3202
• neuron.py: replace run_cmd with run_shell_cmd in custom easyblock for NEURON (neuron.py) #3201
• nim.py: replace run_cmd with run_shell_cmd in custom easyblock for Nim (nim.py) #3200
• numpy.py: replace run_cmd with run_shell_cmd in custom easyblock for numpy (numpy.py) #3199
• nvhpc.py: replace run_cmd with run_shell_cmd in custom easyblock for NVHPC (nvhpc.py) #3198
• nwchem.py: replace run_cmd with run_shell_cmd in custom easyblock for NWChem (nwchem.py) #3197
• ocaml.py: replace run_cmd with run_shell_cmd in custom easyblock for OCaml (ocaml.py) #3243 remove unneeded custom easyblock for OCaml (ocaml.py) #3196
• openifs.py: remove unneeded custom easyblock for OpenIFS (openifs.py) #3194
• openblas.py: replace run_cmd with run_shell_cmd in custom easyblock for OpenBLAS (openblas.py) #3195
• openssl_wrapper.py: replace run_cmd with run_shell_cmd in custom easyblock for OpenSSL / OpenSSL_wrapper (openssl.py and openssl_wrapper.py) #3193
• openssl.py: replace run_cmd with run_shell_cmd in custom easyblock for OpenSSL / OpenSSL_wrapper (openssl.py and openssl_wrapper.py) #3193
• palm.py: replace run_cmd with run_shell_cmd in custom easyblock for PALM (palm.py) #3166
• parmetis.py: replace run_cmd with run_shell_cmd in custom easyblock for ParMETIS (parmetis.py) #3167
• perl.py: replace run_cmd with run_shell_cmd in custom easyblock for Perl (perl.py) #3162
• petsc.py: replace run_cmd with run_shell_cmd in custom easyblock for PETSc (petsc.py) #3168
• pgi.py: remove unused custom easyblock for PGI (pgi.py) #3181
• pplacer.py: remove unused custom easyblock for pplacer (pplacer.py) #3185 replace run_cmd with run_shell_cmd in custom easyblock for pplacer (pplacer.py) #3183
• psi.py: needed for replace run_cmd with run_shell_cmd in custom easyblock for PSI/PSI4 (psi.py) #3214
• pybind11.py: replace run_cmd with run_shell_cmd in custom easyblock for pybind11 (pybind11.py) #3171
• python.py: replace run_cmd with run_shell_cmd in custom easyblock for Python (python.py) #3169
• python_meep.py: remove unused custom easyblock for python_meep (python_meep.py) #3182
• qscintilla.py: replace run_cmd with run_shell_cmd in custom easyblock for QScintilla (qscintilla.py) #3150
• root.py: replace run_cmd with run_shell_cmd in custom easyblock for ROOT (root.py) #3149
• rosetta.py: replace run_cmd with run_shell_cmd in custom easyblock for Rosetta (rosetta.py) #3147 remove unused custom easyblock for Rosetta (rosetta.py) #3148
• rust.py: replace run_cmd with run_shell_cmd in custom easyblock for Rust (rust.py) #3146
• scalapack.py: drop support for versions < 2.0 and replace run_cmd with run_shell_cmd in custom easyblock for ScaLAPACK (scalapack.py) #3106
• scipion.py: replace run_cmd with run_shell_cmd in custom easyblock for Scipion (scipion.py) #3140
• scotch.py: replace run_cmd with run_shell_cmd in custom easyblock for SCOTCH (scotch.py) #3141
• sepp.py: replace run_cmd with run_shell_cmd in custom easyblock for SEPP (sepp.py) #3142
• slepc.py: replace run_cmd with run_shell_cmd in custom easyblock for SLEPc (slepc.py) #3143
• siesta.py: replace run_cmd with run_shell_cmd in custom easyblock for Siesta (siesta.py) #3192
• star_ccm.py: replace run_cmd with run_shell_cmd in custom easyblock for STAR-CCM+ (star_ccm.py) #3144
• tbb.py: replace run_cmd with run_shell_cmd in custom easyblock for tbb (tbb.py) #3145
• tensorflow_compression.py: replace run_cmd with run_shell_cmd in custom easyblock for tensorflow_compression (tensorflow_compression.py) #3164
• tensorflow.py: replace run_cmd with run_shell_cmd in custom easyblock for TensorFlow (tensorflow.py) #3165
• tensorrt.py: replace run_cmd with run_shell_cmd in custom easyblock for TensorRT (tensorrt.py) #3179
• tinker.py: replace run_cmd with run_shell_cmd in custom easyblock for TINKER (tinker.py) #3180
• totalview.py: remove unused custom easyblock for TotalView (totalview.py) #3191
• trinity.py: replace run_cmd with run_shell_cmd in custom easyblock for Trinity (trinity.py) #3190
• ucx_plugins.py: replace run_cmd with run_shell_cmd in custom easyblock for UCX Plugins (ucx_plugins.py) #3189
• vep.py: replace run_cmd with run_shell_cmd in custom easyblock for VEP (vep.py) #3188
• vmd.py: replace run_cmd with run_shell_cmd in custom easyblock for VMD (vmd.py) #3187
• vsc_tools.py: remove unused custom easyblock for VSC-tools (vsc_tools.py) #3138
• wxpython.py: replace run_cmd with run_shell_cmd in custom easyblock for wxPython (wxpython.py) #3093
• xmipp.py: replace run_cmd with run_shell_cmd in custom easyblock for Xmipp (xmipp.py) #3092

run_cmd_qa

• abaqus.py: use run_shell_cmd in custom easyblock for ABAQUS #3414
• acml.py: remove unused custom easyblock for ACML (acml.py) #3172
• aladin.py: remove unused custom easyblock for ALADIN (aladin.py) #3173
• bisearch.py: remove unused custom easyblock for BiSearch (bisearch.py) #3174
• cplex.py: use run_shell_cmd in custom easyblock for CPLEX #3295
• cuda.py: use run_shell_cmd in custom easyblock for CUDA #3274
• doris.py: remove unused custom easyblock for Doris (doris.py) #3175
• geant4.py: drop support for versions < 9.5 in custom easyblock for Geant4 #3296 and fix --module-only + cleanup for custom easyblock for Geant4 #3302
• healpix.py: remove unused custom easyblock for HEALPix (healpix.py) #3285
• maple.py: use run_shell_cmd in custom easyblock for Maple #3286
• mathematica.py: use run_shell_cmd in custom easyblock for Mathematica #3298
• modeller.py: remove unused custom easyblock for Modeller (modeller.py) #3292
• molpro.py: remove unused custom easyblock for Molpro (molpro.py) #3294
• openfoam.py: use run_shell_cmd in custom easyblock for OpenFOAM #3299
• qt.py: use run_shell_cmd in custom easyblock for Qt #3291
• repeatmasker.py: use run_shell_cmd in custom easyblock for RepeatMasker #3290
• repeatmodeler.py: use run_shell_cmd in custom easyblock for RepeatModeler #3289
• samcef.py: remove unused custom easyblock for Samcef (samcef.py) #3176
• sas.py: remove unused custom easyblock for SAS (sas.py) #3177
• snphylo.py: remove unused custom easyblock for SNPhylo (snphylo.py) #3178
• stata.py: use run_shell_cmd in custom easyblock for Stata #3288
• wien2k.py: use run_shell_cmd in custom easyblock for WIEN2k #3413
• wps.py: use run_shell_cmd in custom easyblock for WPS #3297
• wrf.py: use run_shell_cmd in custom easyblock for WRF #3270
• wrf_fire.py: remove custom easyblock for WRF-Fire #3271

Nothing to do

• a nothing to do: aocc.py, aomp.py, allinea.py, advisor.py, armadillo.py
• b nothing to do: bwa.py, bwise.py, bowtie2.py, bioconductor.py, berkeleygw.py, blat.py, blender.py, bowtie.py, bamtools.py
• c nothing to do: cblas.py, cgal.py, clang_aomp.py, code_server.py, cudnn.py, chapel.py, cufflinks.py, crispr_dav.py, cmake.py
• d nothing to do: db.py
• e nothing to do: extrae.py, eigen.py, epd.py, elsi.py, easybuildmeta.py, egglib.py, elpa.py
• f nothing to do: flex.py, ferret.py, fftw.py, freesurfer.py, foldx.py, fftwmpi.py, freetype.py
• g nothing to do: g2lib.py, gctf.py, ghc.py, g2clib.py
• h nothing to do: hypre.py, hdf5.py, hpcc.py
• i nothing to do: imkl_fftw.py, ifort.py, inspector.py, ipp.py, iccifort.py
• j nothing to do: jaxlib.py
• k no easyblocks
• l nothing to do: lua.py, libxml2.py, llvm.py, libdrm.py
• m nothing to do: mvapich2.py, mothur.py, motioncor2.py, metagenome_atlas.py, mutil.py, mamba.py, mesa.py, metavelvet.py, mpich.py, mumps.py, mtl4.py
• n nothing to do: numexpr.py, nose.py, nccl.py, netcdf_fortran.py, netcdf.py, netcdf4_python.py, ncurses.py
• o nothing to do: opencv.py, orca.py, octave.py, openbabel.py, openmpi.py
• p nothing to do: psmpi.py, pytorch.py, pyzmq.py, primer3.py, pasha.py, paraver.py, pbdmpi.py, pdt.py, pyquante.py, picard.py, pbdslap.py
• q nothing to do: quantumespresso.py
• r nothing to do: reticulate.py, r.py, ruby.py, rserve.py, rmpi.py
• s nothing to do: superlu.py, suitesparse.py, sympy.py, scalasca1.py, shrimp.py, swig.py, scipy.py, score_p.py, samtools.py, soapdenovo.py
• t nothing to do: torchvision.py, tkinter.py, tornado.py, tau.py, trilinos.py
• u nothing to do: ufc.py
• v nothing to do: velvet.py, vtune.py
• x nothing to do: xcrysden.py, xml.py, xalt.py
• y no easyblocks
• z no easyblocks

[boegel]

Last hurdle here is the ABAQUS easyblock, which is being dealt with in:

• use run_shell_cmd in custom easyblock for ABAQUS #3414

(and adding a CI check to make sure that no easyblocks rely on run_cmd or run_cmd_qa...)