Demonstrate using PyStow for API configuration

[cthoyt]

• Replace builtin code for configuration access and writing
• Write documentation on how this works

[cthoyt]

@cmungall @pkalita-lbl can you please set the BIOPORTAL_API_KEY environment variable for GHA to make this test pass?

[pkalita-lbl]

Sorry I don't have permission to do that either

[pkalita-lbl]

can you please set the BIOPORTAL_API_KEY environment variable for GHA

I think I have permission to do this now. I can add my BioPortal API key as a repo secret named BIOPORTAL_API_KEY. That's what you're after right?

[cthoyt]

@pkalita-lbl yes that's it

[pkalita-lbl]

Done!

[pkalita-lbl]

I attempted to start fresh by clearing out my old stored keys (in ~/Library/Application\ Support/ontology-access-kit/, for what it's worth) and test out these changes but I ran into a bit of trouble. See comments below.

Also when I tried running the BioPortal tests without an API key set, like so:

python -m unittest -v tests/test_implementations/test_bioportal.py

The test setup errored out instead of skipping the test cases:

Traceback (most recent call last):
  File "/Users/PAKalita/Work/ontology-access-kit/tests/test_implementations/test_bioportal.py", line 25, in setUp
    impl = cls()
  File "<string>", line 8, in __init__
  File "/Users/PAKalita/Work/ontology-access-kit/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py", line 53, in __post_init__
    self.client = self.ontoportal_client_class()
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/lib/python3.9/site-packages/ontoportal_client/api.py", line 113, in __init__
    api_key = pystow.get_config(self.name, value_key, raise_on_missing=True)
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/lib/python3.9/site-packages/pystow/config_api.py", line 102, in get_config
    raise ValueError(f"Could not look up {module}/{key} and no default given")
ValueError: Could not look up bioportal/api_key and no default given

[pkalita-lbl]

I'm a little confused by this because it seems like just BIOPORTAL_API_KEY is the required when using an environment variable. I.e. this works:

BIOPORTAL_API_KEY=[redacted] runoak -i bioportal: search swim

As opposed to:

OAKLIB_BIOPORTAL_API_KEY=[redacted] runoak -i bioportal: search swim

[pkalita-lbl]

When I tried running this:

runoak set-apikey -e bioportal [redacted]

(also, note the -e is required) I got this error:

Traceback (most recent call last):
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/bin/runoak", line 5, in <module>
    main()
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/lib/python3.9/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/lib/python3.9/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/Users/PAKalita/Work/ontology-access-kit/src/oaklib/cli.py", line 2220, in set_apikey
    set_apikey_value(endpoint, keyval)
  File "/Users/PAKalita/Work/ontology-access-kit/src/oaklib/utilities/apikey_manager.py", line 42, in set_apikey_value
    pystow.write_config(APP_NAME, key, value)
  File "/Users/PAKalita/Work/ontology-access-kit/.venv/lib/python3.9/site-packages/pystow/config_api.py", line 135, in write_config
    cfp.set(module, key, value)
  File "/Users/PAKalita/.pyenv/versions/3.9.11/lib/python3.9/configparser.py", line 1204, in set
    super().set(section, option, value)
  File "/Users/PAKalita/.pyenv/versions/3.9.11/lib/python3.9/configparser.py", line 902, in set
    raise NoSectionError(section) from None
configparser.NoSectionError: No section: 'oaklib'