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Packages using nonstandard python search paths #21456

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Micket opened this issue Sep 20, 2024 · 0 comments
Open
38 tasks

Packages using nonstandard python search paths #21456

Micket opened this issue Sep 20, 2024 · 0 comments

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@Micket
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Micket commented Sep 20, 2024

After going through and dropping the standard PYTHONPATH environment variables for my EBPYTHONPREFIXES change, I've found:

  • OpenMM-7.7.0-foss-2022a.eb
  • OpenMM-7.7.0-foss-2022a-CUDA-11.7.0.eb
  • OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb
  • OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb
  • OpenMM-8.0.0-foss-2023a.eb
  • OpenMM-8.0.0-foss-2022a.eb

uses the nonstandard path

'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg'

which is just strange

  • FSL-6.0.5.1-foss-2021a.eb uses 'PYTHONPATH': ['fsl/lib/python%(pyshortver)s/site-packages'] (seems like an easy fix?)
  • CIRIquant-1.1.2-20221201-foss-2021b-Python-2.7.18.eb uses 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/CIRIquant' (is the module file even correct by specifying the subdir here?)
  • CRISPResso2-2.1.2-foss-2020b*.eb uses 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2'] (and here?)

There is also

  • Graphviz
  • Spark
  • SRA-Toolkit
  • Stata
  • PLUMED
  • PySCF
  • vcflib
  • pyMBE
  • pypmt
  • pycubescd
  • PYTHIA
  • gmsh
  • GIMIC
  • Claire
  • FLANN
  • FIGARO
  • NanoCaller
  • ADIOS
  • ASAP
  • ESIpy
  • KMC
  • SUPPA
  • SISSO++
  • IsoQuant
  • TELEMAC-MASCARET
  • HOOMD-blue
  • MEME
  • manta
  • MBX

which are use something silly like lib or bin or lib/python as their paths. Sigh. So many. Some of these matter more than others.

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