bioversions 0.5.560__tar.gz → 0.5.561.dev0__tar.gz

bioversions-0.5.561.dev0/.cruft.json

@@ -0,0 +1,26 @@
+{
+  "template": "https://github.com/cthoyt/cookiecutter-snekpack",
+  "commit": "1884310d930f56787c96d4eba45bcb4a5225f7cb",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "package_name": "bioversions",
+      "package_name_stylized": "Bioversions",
+      "short_description": "Get the current version for biological databases",
+      "author_name": "Charles Tapley Hoyt",
+      "author_email": "cthoyt@gmail.com",
+      "github_organization_name": "biopragmatics",
+      "github_repository_name": "bioversions",
+      "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/bioversions",
+      "_template": "https://github.com/cthoyt/cookiecutter-snekpack"
+    }
+  },
+  "directory": null
+}

bioversions-0.5.561.dev0/.github/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+cthoyt@gmail.com.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

bioversions-0.5.561.dev0/.github/CONTRIBUTING.md

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+# 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/bioversions`](https://github.com/biopragmatics/bioversions)
+   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>/bioversions.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/bioversions.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.

bioversions-0.5.561.dev0/.github/codecov.yml

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+# see https://docs.codecov.com/v4.6/docs/codecov-yaml
+ignore:
+  - "src/bioversions/__main__.py"
+  - "src/bioversions/cli.py"

bioversions-0.5.561.dev0/.github/workflows/cruft.yml

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+# 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 "you@example.com"
+          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.

bioversions-0.5.561.dev0/.github/workflows/tests.yml

@@ -0,0 +1,91 @@
+# This file configures the continuous integration (CI) system on GitHub.
+# Introductory materials can be found here: https://docs.github.com/en/actions/learn-github-actions/understanding-github-actions.
+# Documentation for editing this file can be found here: https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions
+
+name: Tests
+
+# by default, give the GITHUB_TOKEN no permissions
+# See https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/controlling-permissions-for-github_token
+permissions: {}
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  lint:
+    name: Code Quality
+    permissions:
+      # give only read-only access to the contents of the repository
+      # this is the only permission this job requires, so keep it to the least privilege
+      # i.e., not to issues, discussions, actions, etc.
+      contents: read
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ "3.12", "3.10" ]
+        tox-command: ["manifest", "lint", "pyroma", "mypy"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: "Install uv"
+        uses: "astral-sh/setup-uv@v3"
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+      - name: "Run command"
+        run: |
+          uvx -p ${{ matrix.python-version }} --with tox-uv tox -e ${{ matrix.tox-command }}
+
+  docs:
+    name: Documentation
+    permissions:
+      contents: read
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # We only test documentation on the latest version
+        # sphinx 8.0 / sphinx-rtd-theme 3.0 discontinued Python 3.9 support
+        # a year early, which prompted re-thinking about this.
+        python-version: [ "3.12" ]
+    steps:
+      - uses: actions/checkout@v4
+      - name: "Install uv"
+        uses: "astral-sh/setup-uv@v3"
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+      - name: Install dependencies
+        run: |
+          sudo apt-get install graphviz
+      - name: Check RST conformity with doc8
+        run: uvx -p ${{ matrix.python-version }} --with tox-uv tox -e doc8
+      - name: Check docstring coverage
+        run: uvx -p ${{ matrix.python-version }} --with tox-uv tox -e docstr-coverage
+      - name: Check documentation build with Sphinx
+        run: uvx -p ${{ matrix.python-version }} --with tox-uv tox -e docs-test
+  tests:
+    name: Tests
+    permissions:
+      contents: read
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-latest ]
+        python-version: [ "3.12", "3.10" ]
+    steps:
+      - uses: actions/checkout@v4
+      - name: "Install uv"
+        uses: "astral-sh/setup-uv@v3"
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+      - name: Test with pytest and generate coverage file
+        run:
+          uvx -p ${{ matrix.python-version }} --with tox-uv tox -e py
+      - name: Upload coverage report to codecov
+        uses: codecov/codecov-action@v4
+        if: success()
+        with:
+          file: coverage.xml

bioversions-0.5.561.dev0/.github/workflows/update.yml

@@ -0,0 +1,44 @@
+name: Update Database
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 0 * * *"
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+        with:
+          persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
+          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          pip install tox tox-uv
+      - name: Create local changes
+        run: |
+          tox -e update
+      - name: Commit files
+        run: |
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git commit -m "🪝 Automatically update" -a
+      - name: bump2version release
+        run: |
+          tox -e bumpversion-release
+      - name: Release to PyPI
+        run: |
+          tox -e release-headless
+        env:
+          UV_PUBLISH_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          UV_PUBLISH_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      - name: bump2version patch
+        run: |
+          tox -e bumpversion -- patch
+      - name: Push changes
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.ref }}