Clean up Python code and GitHub Actions

[pkalita-lbl]

Fixes #2

These changes are just general tidying up of the initial commit of the repo. They do not represent any significant changes to the gocam Python module or CLI functionality.

Python code

• Remove unused or empty files and directories; remove unused variables and functions; remove commented out code.
• Rename a number of variables and functions, mainly in src/gocam/translation/minerva_wrapper.py, to make things more readable and/or accurately reflect their purpose.
• Add more docstrings to src/gocam/translation/minerva_wrapper.py.
• De-duplicate code in src/gocam/translation/minerva_wrapper.py.
• Update typing annotations to accurately reflect actual usage.
• Fix how the __version__ variable is set and add a CLI option to show the version.

Testing

• Standardize testing around pytest; previously tests were a mix of unittest and pytest-style tests, while the Makefile was invoking tests via the unittest module.
• Add additional assertions to MinervaWrapper test; remove unnecessary printing and file writing.
• Add new test for the gocam.cli module.

Infrastructure

• Declare directly used dependencies in pyproject.toml; previously it was relying on transitive dependencies brought in by linkml.
• Update GitHub Actions workflows to use built-in Poetry virtual environment caching via actions/setup-python@v5.
• Setup PyPI publishing workflow for Trusted Publishing

cc: @cmungall

[github-actions]

PR Preview Action v1.4.7
🚀 Deployed preview to https://geneontology.github.io/gocam-py/pr-preview/pr-4/
on branch gh-pages at 2024-07-11 19:06 UTC

[kltm]

Eyeballing the changes: increasing specificity and detail from the template.