Merge branch 'master' into curation-25092024

.cruft.json

@@ -0,0 +1,27 @@
+{
+  "template": "https://github.com/cthoyt/cookiecutter-snekpack",
+  "commit": "d6ac604ce8428ddaaae55d372beef2621caed513",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "package_name": "biomappings",
+      "package_name_stylized": "Biomappings",
+      "short_description": "Curated and predicted mappings between biomedical identifiers in different namespaces",
+      "author_name": "Charles Tapley Hoyt",
+      "author_github": "cthoyt",
+      "author_email": "[email protected]",
+      "github_organization_name": "biopragmatics",
+      "github_repository_name": "biomappings",
+      "command_line_interface": true,
+      "gitlab": false,
+      "runner": "tox",
+      "__runner": "tox -e",
+      "__runner_uv": "--with tox-uv tox -e",
+      "__runner_pip": "tox tox-uv",
+      "__runner_tests": "py",
+      "__gh_slug": "biopragmatics/biomappings",
+      "_template": "https://github.com/cthoyt/cookiecutter-snekpack"
+    }
+  },
+  "directory": null
+}

docs/CODE_OF_CONDUCT.md → .github/CODE_OF_CONDUCT.md

@@ -1,8 +1,4 @@
----
-layout: page
-title: Contributor Covenant Code of Conduct
-permalink: /coc
----
+# Contributor Covenant Code of Conduct
 
 ## Our Pledge
 

.github/CONTRIBUTING.md

@@ -0,0 +1,116 @@
+# Contributing
+
+Contributions to this repository are welcomed and encouraged.
+
+## Code Contribution
+
+This project uses the [GitHub Flow](https://guides.github.com/introduction/flow)
+model for code contributions. Follow these steps:
+
+1. [Create a fork](https://help.github.com/articles/fork-a-repo) of the upstream
+   repository
+   at [`biopragmatics/biomappings`](https://github.com/biopragmatics/biomappings)
+   on your GitHub account (or in one of your organizations)
+2. [Clone your fork](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository)
+   with `git clone https://github.com/<your namespace here>/biomappings.git`
+3. Make and commit changes to your fork with `git commit`
+4. Push changes to your fork with `git push`
+5. Repeat steps 3 and 4 as needed
+6. Submit a pull request back to the upstream repository
+
+### Merge Model
+
+This repository
+uses [squash merges](https://docs.github.com/en/github/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/about-pull-request-merges#squash-and-merge-your-pull-request-commits)
+to group all related commits in a given pull request into a single commit upon
+acceptance and merge into the main branch. This has several benefits:
+
+1. Keeps the commit history on the main branch focused on high-level narrative
+2. Enables people to make lots of small commits without worrying about muddying
+   up the commit history
+3. Commits correspond 1-to-1 with pull requests
+
+### Code Style
+
+This project uses `tox` for running code quality checks. Start by installing
+it with `pip install tox tox-uv`.
+
+This project encourages the use of optional static typing. It
+uses [`mypy`](http://mypy-lang.org/) as a type checker. You can check if
+your code passes `mypy` with `tox -e mypy`.
+
+This project uses [`ruff`](https://docs.astral.sh/ruff/) to automatically
+enforce a consistent code style. You can apply `ruff format` and other pre-configured
+formatters with `tox -e format`.
+
+This project uses [`ruff`](https://docs.astral.sh/ruff/) and several plugins for
+additional checks of documentation style, security issues, good variable
+nomenclature, and more (see `pyproject.toml` for a list of Ruff plugins). You can check if your
+code passes `ruff check` with `tox -e lint`.
+
+Each of these checks are run on each commit using GitHub Actions as a continuous
+integration service. Passing all of them is required for accepting a
+contribution. If you're unsure how to address the feedback from one of these
+tools, please say so either in the description of your pull request or in a
+comment, and we will help you.
+
+### Logging
+
+Python's builtin `print()` should not be used (except when writing to files),
+it's checked by the
+[`flake8-print` (T20)](https://docs.astral.sh/ruff/rules/#flake8-print-t20) plugin to `ruff`. If
+you're in a command line setting or `main()` function for a module, you can use
+`click.echo()`. Otherwise, you can use the builtin `logging` module by adding
+`logger = logging.getLogger(__name__)` below the imports at the top of your
+file.
+
+### Documentation
+
+All public functions (i.e., not starting with an underscore `_`) must be
+documented using
+the [sphinx documentation format](https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html#the-sphinx-docstring-format).
+The [`darglint2`](https://github.com/akaihola/darglint2) tool
+reports on functions that are not fully documented.
+
+This project uses [`sphinx`](https://www.sphinx-doc.org) to automatically build
+documentation into a narrative structure. You can check that the documentation
+builds properly in an isolated environment with `tox -e docs-test` and actually
+build it locally with `tox -e docs`.
+
+### Testing
+
+Functions in this repository should be unit tested. These can either be written
+using the `unittest` framework in the `tests/` directory or as embedded
+doctests. You can check that the unit tests pass with `tox -e py`
+and that the doctests pass with `tox -e doctests`. These tests are required to pass for
+accepting a contribution.
+
+### Syncing your fork
+
+If other code is updated before your contribution gets merged, you might need to
+resolve conflicts against the main branch. After cloning, you should add the
+upstream repository with
+
+```shell
+$ git remote add biopragmatics https://github.com/biopragmatics/biomappings.git
+```
+
+Then, you can merge upstream code into your branch. You can also use the GitHub
+UI to do this by
+following [this tutorial](https://docs.github.com/en/github/collaborating-with-pull-requests/working-with-forks/syncing-a-fork).
+
+### Python Version Compatibility
+
+This project aims to support all versions of Python that have not passed their
+end-of-life dates. After end-of-life, the version will be removed from the Trove
+qualifiers in the `pyproject.toml` and from the GitHub Actions testing
+configuration.
+
+See https://endoflife.date/python for a timeline of Python release and
+end-of-life dates.
+
+## Acknowledgements
+
+These code contribution guidelines are derived from
+the [cthoyt/cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack)
+Python package template. They're free to reuse and modify as long as they're properly acknowledged.

.github/FUNDING.yml

@@ -0,0 +1,3 @@
+# https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/displaying-a-sponsor-button-in-your-repository
+github:
+  - cthoyt

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,17 @@
+<!--
+Thanks for contributing to `biomappings`.
+To help us out with reviewing, please consider the following:
+
+- Does this pull request include a summary of the change? (See below.)
+- Does this pull request include a descriptive title?
+- Does this pull request include references to any relevant issues?
+
+Caution: the maintainers often take an active role in pull requests,
+and may push to your branch. Therefore, you should always sync your
+local copy of the repository with the remote before continuing your
+work.
+-->
+
+## Summary
+
+<!-- What's the purpose of the change? What does it do, and why? -->

.github/codecov.yml

@@ -0,0 +1,4 @@
+# see https://docs.codecov.com/v4.6/docs/codecov-yaml
+ignore:
+  - "src/biomappings/__main__.py"
+  - "src/biomappings/cli.py"

.github/workflows/cruft.yml

@@ -0,0 +1,80 @@
+# from https://cruft.github.io/cruft/#automating-updates-with-github-actions
+
+name: Update repository with Cruft
+
+permissions: {}
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 2 * * 1" # Every Monday at 2am
+
+jobs:
+  update:
+    permissions:
+      contents: write
+      pull-requests: write
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        include:
+          - add-paths: .
+            body: Use this to merge the changes to this repository.
+            branch: cruft/update
+            commit-message: "chore: accept new Cruft update"
+            title: New updates detected with Cruft
+          - add-paths: .cruft.json
+            body: Use this to reject the changes in this repository.
+            branch: cruft/reject
+            commit-message: "chore: reject new Cruft update"
+            title: Reject new updates detected with Cruft
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install Cruft
+        run: pip3 install cruft
+
+      - name: Check if update is available
+        continue-on-error: false
+        id: check
+        run: |
+          CHANGES=0
+          if [ -f .cruft.json ]; then
+            if ! cruft check; then
+              CHANGES=1
+            fi
+          else
+            echo "No .cruft.json file"
+          fi
+
+          echo "has_changes=$CHANGES" >> "$GITHUB_OUTPUT"
+
+      - name: Run update if available
+        if: steps.check.outputs.has_changes == '1'
+        run: |
+          git config --global user.email "[email protected]"
+          git config --global user.name "GitHub"
+
+          cruft update --skip-apply-ask --refresh-private-variables
+          git restore --staged .
+
+      - name: Create pull request
+        if: steps.check.outputs.has_changes == '1'
+        uses: peter-evans/create-pull-request@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          add-paths: ${{ matrix.add-paths }}
+          commit-message: ${{ matrix.commit-message }}
+          branch: ${{ matrix.branch }}
+          delete-branch: true
+          branch-suffix: timestamp
+          title: ${{ matrix.title }}
+          body: |
+            This is an autogenerated PR. ${{ matrix.body }}
+
+            [Cruft](https://cruft.github.io/cruft/) has detected updates from the Cookiecutter repository.

.github/workflows/ndex.yml

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@master
       - uses: actions/setup-python@v2
         with:
-          python-version: "3.9"
+          python-version: "3.12"
       - name: Install dependencies
         run: |
           pip install tox