zarr

[laraPPr]

• link to support ticket: #2023071360000183
• website: https://zarr.readthedocs.io/en/stable/index.html
• installation docs: https://zarr.readthedocs.io/en/stable/installation.html
• toolchain: foss/2022b
• easyblock to use:
• required dependencies:
  • python, 3.10.8
  • SciPy-bundle, 2023.02
• optional dependencies:
• notes:
  • Started on updating zarr-2.13.3-foss-2022a.eb to new toolchain but installation is failing with new version of the extention numcodecs. easyconfig in wip.
• effort: (TBD)
• other install methods
  • conda: yes (link?) / no
  • container image: yes (link?) / no
  • pre-built binaries (RHEL8 Linux x86_64): yes (link?) / no
  • easyconfig outside EasyBuild: yes / no

[laraPPr]

There is config file in wip but is failing to install zarr

this is the error:

== 2023-08-04 14:25:17,400 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:126 in __init__): cmd " /apps/gent/RHEL8/zen2-ib/software/Python/3.10.8-GCCcore-12.2.0/bin/python -m pip install --prefix=/data/gent/461/vsc46128/easybuild/RHEL8/zen2-ib/software/zarr/2.16.0-foss-2022b  --no-deps  --ignore-installed  --no-index  --no-build-isolation  ." exited with exit code 1 and output:
Processing /tmp/vsc46128/zarr/2.16.0/foss-2022b/numcodecs/numcodecs-0.11.0
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'error'
  error: subprocess-exited-with-error
  
   Preparing metadata (pyproject.toml) did not run successfully.
   exit code: 1
  > [13 lines of output]
      Traceback (most recent call last):
        File "/apps/gent/RHEL8/zen2-ib/software/Python/3.10.8-GCCcore-12.2.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
          main()
        File "/apps/gent/RHEL8/zen2-ib/software/Python/3.10.8-GCCcore-12.2.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/apps/gent/RHEL8/zen2-ib/software/Python/3.10.8-GCCcore-12.2.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 152, in prepare_metadata_for_build_wheel
          return hook(metadata_directory, config_settings)
        File "/apps/gent/RHEL8/zen2-ib/software/Python/3.10.8-GCCcore-12.2.0/lib/python3.10/site-packages/setuptools/build_meta.py", line 188, in prepare_metadata_for_build_wheel
          self.run_setup()
        File "/apps/gent/RHEL8/zen2-ib/software/Python/3.10.8-GCCcore-12.2.0/lib/python3.10/site-packages/setuptools/build_meta.py", line 174, in run_setup
          exec(code, locals())
        File "<string>", line 5, in <module>
      ModuleNotFoundError: No module named 'cpuinfo'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

 Encountered error while generating package metadata.
> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

[boegel]

This indicates there's a missing dependency on https://pypi.org/project/py-cpuinfo?

[laraPPr]

Should I than add py-cpuinfo to the extentions to see if this resolves the error? Or as a dependency?

[boegel]

We already have separate easyconfigs for py-cpuinfo, so a dependency makes more sense.

It's possible that zarr (or one of its dependencies) has started requiring py-cpuinfo, where that wasn't the case yet with zarr-2.13.3-foss-2022a.eb

[laraPPr]

That did the trick, Thanks for the help. I'll open a pr.