BUG: numpy.distutils.core in GA setup environment

[jklenzing]

Describe the bug OMMBV is a requirement for multiple downstream packages, but is having trouble being installed in github actions.

To Reproduce Full test log: https://github.com/pysat/pysatMissions/runs/2355919399?check_suite_focus=true Relevant lines:

Collecting OMMBV
  Downloading OMMBV-0.5.4.tar.gz (63 kB)
    ERROR: Command errored out with exit status 1:
     command: /opt/hostedtoolcache/Python/3.8.9/x64/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gxwybpdy/ommbv_73b9476528ad4c2eb8bef97b755571c7/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gxwybpdy/ommbv_73b9476528ad4c2eb8bef97b755571c7/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-o_jptcji
         cwd: /tmp/pip-install-gxwybpdy/ommbv_73b9476528ad4c2eb8bef97b755571c7/
    Complete output (5 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gxwybpdy/ommbv_73b9476528ad4c2eb8bef97b755571c7/setup.py", line 2, in <module>
        import numpy.distutils.core
    ModuleNotFoundError: No module named 'numpy'

Additional context apexpy uses a similar setup file and installs successfully. Not sure if this is syntax issue that needs to be updated.

[jklenzing]

Update: this can be installed by using

pip install --no-binary :OMMBV: OMMBV

but this requires dropping it from the requirements file

[rstoneback]

Thanks for the reminder @jklenzing. I'll put this on my to-do list.

[rstoneback]

Working on this now.

[rstoneback]

An update was posted in #51 and is now on pypi.

[rstoneback]

Update: this can be installed by using

pip install --no-binary :OMMBV: OMMBV

but this requires dropping it from the requirements file

I don't understand why the --no-binary option here matters. According to https://pip.pypa.io/en/stable/cli/pip_install/#cmdoption-no-binary that options disables using binary packages, and OMMBV doesn't have one.

[rstoneback]

I've removed the version file over in #53

[jklenzing]

Update: this can be installed by using

pip install --no-binary :OMMBV: OMMBV

but this requires dropping it from the requirements file

I don't understand why the --no-binary option here matters. According to https://pip.pypa.io/en/stable/cli/pip_install/#cmdoption-no-binary that options disables using binary packages, and OMMBV doesn't have one.

It's extra confusing as github actions is configured to ignore binary files by default already. It's possible that this flag will grab a different version of numpy, which seems to be the source of the issue.

[rstoneback]

Thats for the update. Speaking of GitHub Actions, I have OMMBV compiling fortran on windows, and python setup.py develop reports ok, but actually importing the fortran modules fails. You wouldn't happen to have the secret sauce to windows fortran?

[jklenzing]

nope

[jklenzing]

Just ran another test at pysatMissions. If I try to automate OMMBV with everything else, it tries to download 0.5.5, tries to load, then says

    File "/tmp/pip-install-y4ex95_0/ommbv_e1c4ef8b4e524631bca2bd7c098bdd6d/setup.py", line 17, in <module>
      from numpy.distutils.core import setup, Extension
  ModuleNotFoundError: No module named 'numpy'

It then tries 0.5.4, gets the same message, and gives up.

Running a separate manual install without the --no-binary option works just fine, so maybe something is not importing right?

[rstoneback]

apexpy has the same line in their setup, from numpy.distutils.core import setup, Extension

[jklenzing]

Looking through the logs, it's failing during the metadata check:

  Downloading OMMBV-0.5.5.tar.gz (63 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'error'
  ERROR: Command errored out with exit status 1:

My working theory is that the requirements are not being passed through. This is handled differently in apexpy. I've put together a branch at my fork using setup.cfg to manage metadata, which may fix the issue. I'll add a PR once I'm sure it passes the tests. https://github.com/jklenzing/OMMBV/tree/sty/meta

[jklenzing]

While I'm playing with this code, are you interested in a github actions version of this to replace travis?

[rstoneback]

I've got one, https://github.com/rstoneback/OMMBV/pull/53

Thanks. I would appreciate any improvements!

I think I have things up to spec, overall. There is the windows build issue. Looks like windows compiles fortran fine but can't actually import fortran modules.

[rstoneback]

Looking through the logs, it's failing during the metadata check:

  Downloading OMMBV-0.5.5.tar.gz (63 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'error'
  ERROR: Command errored out with exit status 1:

My working theory is that the requirements are not being passed through. This is handled differently in apexpy. I've put together a branch at my fork using setup.cfg to manage metadata, which may fix the issue. I'll add a PR once I'm sure it passes the tests. https://github.com/jklenzing/OMMBV/tree/sty/meta

Also have started a setup.cfg over in #53

[jklenzing]

apexpy uses a pyproject.toml file. Looks like https://www.python.org/dev/peps/pep-0518/ documents the rationale for usage, which seems to apply to this problem.

[rstoneback]

Another attempt is up and out!

[jklenzing]

Confirmed that this is working on Github Actions. Now I have to update some syntax for the core code. Thanks!