Document

[enryH]

• add description of design choices and explain the Python package setup
• update repository to latest common changes

[albsantosdel]

Can we change RasmussenLab by your_GitHub_user_name or something like that?

[enryH]

I actually run the template itself, to make sure everything works. so this would need a organization your_GitHub_user_name.

[albsantosdel]

Careful with having a default LICENSE. Not all packages will have a MIT license.
Also, copyright is set as Copyright (c) 2023: Jakob Nybo Nissen.

[enryH]

which would be a good default LICENSE?

[Copilot]

Pull Request Overview

This PR introduces comprehensive documentation of design decisions and updates project metadata and tooling configurations to align with the latest standards.

• Add a root-level developing.md detailing design choices and include it in Sphinx.
• Update linting, formatting, and build configurations in pyproject.toml and setup.cfg.
• Refresh repository metadata (authors, license, README, Sphinx conf, CI workflow).

Reviewed Changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
setup.cfg	Added Flake8 configuration (exclude, max-line-length, aggressive)
pyproject.toml	Updated authors, dev dependencies, Ruff and Black settings
docs/index.md	Added developing entry to documentation index
docs/developing.md	New Sphinx include for the root developing.md
docs/conf.py	Updated author metadata and documented Sphinx extensions
docs/.gitignore	Ignore build artifacts (_build, reference, jupyter_execute)
developing.md	Added detailed design and packaging guide
README.md	Updated usage instructions, template notes, and ReadTheDocs link
LICENSE	Updated copyright year and author
.readthedocs.yaml	Added placeholder for apt_packages in ReadTheDocs config
.github/workflows/cicd.yml	Changed lint target to src, removed PyPI credentials lines

Comments suppressed due to low confidence (5)

docs/index.md:33

• [nitpick] The entry developing is lowercase and may be inconsistent with other titles; consider capitalizing it (e.g., Developing).

developing

developing.md:37

• The link text references [project.toml] but the actual file is pyproject.toml; update the label to match the filename.

[`project.toml`](pyproject.toml) file is the main configuration file for the Python package

README.md:14

• [nitpick] This bullet appears to be nested under the previous item due to extra indentation; align it with the other top-level list items.

    - also the folder `src/python_package` 

.github/workflows/cicd.yml:122

• The PyPI publish step no longer has credentials configured; re-add the required pypi_token: ${{ secrets.PYPI_API_TOKEN }} (or appropriate inputs) so the action can authenticate.

      # register PyPI integration:

.github/workflows/cicd.yml:37

• [nitpick] Limiting lint to src skips code in tests (and other directories); consider using ruff check . or including additional directories to ensure all code is linted.

          ruff check src

[angelphanth]

Thank you for this template and the documentation 😃 🎉

I used the template to publish to pypi: hugging-mapper. It was my first time building on Read The Docs -- I'm pumped!!! I learned A LOT, thank you.

Some things I encountered during:

1. (pyproject.toml) I couldn't use a requirements.txt and had to list the dependencies under [project] for pypi
2. (.github/workflows/cicd.yml) maybe its overkill but i added an additional job to test the build before publishing. Link (git repo file) to the added job code
3. (.github/workflows/cicd.yml) when running the tests I used -v flag for troubleshooting: python -m pytest -vvv

[enryH]

Thanks Angel for trying it directly and the hints. I will test and update accordingly. I hope you enjoyed also the excitement when your Python Package was automatically published to PyPI:)

[enryH]

I will add a hint in the document specifying that it's possible to add testing of installation of the package from the build distribution. This can be handy in case non code files are shipped with the package and you want to make sure that loading these works as expected. Angel tested the installation and ran pytest again using the manifest. maybe you do not even want to checkout your repo in that job so you make sure not to rely on any local package files:

  test_sdist:
    name: Test built source distribution
    needs: build_source_dist
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4 
      
      - uses: actions/download-artifact@v4
        with:
          name: artifact
          path: ./dist

      - uses: actions/setup-python@v5
        with:
          python-version: "3.11"

      - name: Install test dependencies
        run: |
          python -m pip install --upgrade pip
          pip install pytest

      - name: Install built sdist
        run: |
          pip install ./dist/*.tar.gz

      - name: Run tests
        run: python -m pytest -vvv

[sayalaruano]

Regarding choosing a license, this tool guide helps to make this decision, depending on the specificities of the project.