Enhancement: Make check_resource_dir a general data folder routine

[RHammond2]

Enhancement: Make check_resource_dir a general data folder routine

This PR is in service of #777 to enable the usage of the functionality in h2integrate/resource/utilities/file_tools.py::check_resource_dir more broadly applicable to other data types (e.g. feedstocks). By creating the general check_data_dir with a thin wrapper for check_resource_dir that populates the data_type arg with "resource" much of the same usage is maintained through the resource data classes. Similarly the existing tests are able to be used with comparable test coverage and minimal changed code.

Section 1: Type of Contribution

• Feature Enhancement
  • Framework
  • New Model
  • Updated Model
  • Tools/Utilities
  • Other (please describe):
• Bug Fix
• Documentation Update
• CI Changes
• Other (please describe):

Section 3: General PR Checklist

• PR description thoroughly describes the new feature, bug fix, etc.
• Added tests for new functionality or bug fixes
• Tests pass (If not, and this is expected, please elaborate in the Section 6: Test Results)
• Documentation
  • Docstrings are up-to-date
  • Related docs/ files are up-to-date, or added when necessary
  • Documentation has been rebuilt successfully
  • Examples have been updated (if applicable)
• CHANGELOG.md
  • At least one complete sentence has been provided to describe the changes made in this PR
  • After the above, a hyperlink has been provided to the PR using the following format:
    "A complete thought. [PR XYZ]((https://github.com/NatLabRockies/H2Integrate/pull/XYZ)", where
    XYZ should be replaced with the actual number.

Section 4: Related Issues

N/A

Section 5: Impacted Areas of the Software

Section 5.1: New Files

N/A

Section 5.2: Modified Files

• h2integrate/resource/utilities/file_tools.py: removed in favor of moving check_resource_dir to the below modified file.
• h2integrate/core/utilities/file_utils.py:
  • check_data_dir: General data_type checking data directory checking with default handling, exactly as prescribed from the previous check_resource_dir, except with the flexibility of working with multiple data_type, e.g. "resource", "feedstock", or whatever types of data might be used later.
  • check_resource_dir: partial function of check_data_dir with data_type="resource" pre-populated.
  • check_feedstock_dir: Same as above, but for "feedstock".
• h2integrate/core/test/test_utilities.py
  • temp_resource_dir_env: New fixture to ensure the environment variable is set and unset regardless of a test failure.
  • test_check_resource_dir_environment_var : uses a fixture to modify the RESOURCE_DIR environment variable.
• test/conftest.py:
  • pytest_sessionstart: Stores the original RESOURCE_DIR value in a temporary variable.
  • pytest_sessionfinish: Restores the original `RESOURCE_DIR value from the temporary variable.

Section 6: Additional Supporting Information

This PR stems from a tangential issue in #777 where there is a need to reuse existing functionality, but is hard-coded for a specific use case making this work worthy of its own PR.

Section 7: Test Results, if applicable

[elenya-grant]

Thanks for working on generalizing this method, Rob! I think it's a pretty slick solution you've come up with. I have some small comments and questions on the PR but they should be pretty simple.

I don't believe I've seen any new tests for the check_data_dir or check_feedstock_dir. I think it could be good to add some basic tests on check_data_dir to ensure that new errors are thrown when expected. It may also be good to have one test with check_feedstock_dir just to check that it works before that directory exists in H2I.

Thanks for working on this! If it came in as-is I wouldn't have any concerns. All my comments are pretty small and non-blocking.

Update: can you update the doc page docs/getting_started/environment_variables.md for setting the FEEDSTOCK_DIR as an environment variable (this could also happen in your other PR)

[elenya-grant]

are these lines supposed to be here?

[elenya-grant]

what do they do? I've never seen partial or update_wrapper used. Could you add some in-line comments?

[RHammond2]

partial functions create wrapper functions with the args/kwargs partially passed. It's a convenient way to pre-fill function calls with common parameterizations. For instance, check_resource_dir is now just a wrapper equal to check_data_dir(data_type="resource"), enabling the resource classes to use basically the same folder checking function calls as before this PR.

update_wrapper simply applies the docstring from one function to another, and is primarily for partial functions so that they can also have documentation.

[elenya-grant]

that is very slick! Thanks for explaining that!

[elenya-grant]

This looks great Rob! Thanks for working through the annoying debugging process and making this method generalizable! I think this looks awesome!

[johnjasa]

Thanks for this, @RHammond2 and @elenya-grant, and I'm sorry it was such a bear to debug! Really glad you got it working so well.