protpen 1.0.0__tar.gz

protpen-1.0.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          # hatch-vcs needs the full history and tags to derive the
+          # version from the pushed tag.
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install build tool
+        run: python -m pip install --upgrade pip build
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - name: Upload build artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Download build artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

protpen-1.0.0/.github/workflows/tests.yml

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+name: Tests
+
+on:
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[test]"
+
+      - name: Check code style (black)
+        run: black --check protpen/ tests/
+
+      - name: Run tests
+        # test_eggnog.py and test_foldseek.py are excluded because they
+        # require EggNOG-mapper and Foldseek to be installed, which this
+        # environment doesn't provide.
+        run: pytest tests/ --ignore=tests/test_eggnog.py --ignore=tests/test_foldseek.py

protpen-1.0.0/.gitignore

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+# Byte-compiled / cache
+__pycache__/
+*.py[cod]
+.pytest_cache/
+
+# Packaging / build artifacts
+*.egg-info/
+*.egg
+build/
+dist/
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# Logs
+logs/
+*.log
+
+# OS cruft
+.DS_Store
+Thumbs.db

protpen-1.0.0/CONTRIBUTING.md

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+# Contributing to ProtPen
+
+Thanks for your interest in ProtPen! This project is a community effort, and contributions of any size — bug fixes, documentation tweaks, new tools, or entirely new pipeline modules — are very welcome, whether you're a first-time contributor or a regular.
+
+## Ways to Contribute
+
+- **Report bugs or request features**: please use the [Issues](../../issues) tab. Include enough detail (input data, command run, error message, environment) for others to reproduce the problem.
+- **Improve documentation**: fixes to the README, this file, or inline code comments are always appreciated.
+- **Add a new tool or module**: ProtPen is designed as a [modular pipeline](README.md#modular-design-and-extensibility), and we'd love to see it grow. New annotation tools, structure search methods, or enrichment steps are a great fit. For more information, see [Adding a New Module](#adding-a-new-module) below.
+- **Fix bugs or improve existing code**: pull requests for open issues are very welcome.
+
+No contribution is too small — even a typo fix is appreciated.
+
+## Adding a New Module
+
+Because each pipeline step communicates only through file-based inputs/outputs (mainly TSV and FASTA), adding a new tool doesn't require touching the rest of the codebase. A new module should generally:
+
+- Live in its own file under `protpen/` (e.g. `my_tool.py`), with a corresponding `cli_my_tool.py` wrapper exposing a command-line interface.
+- Accept and produce standardized file formats consistent with the rest of the pipeline.
+- Include unit tests under `tests/`.
+- Be documented in the README's [Scripts](README.md#scripts) table and [Pipeline Workflow](README.md#pipeline-workflow) section.
+
+If you're not sure whether an idea fits, feel free to open an issue to discuss it first.
+
+## Tests and Coding Style
+
+Install the test/dev dependencies first:
+
+```bash
+pip install -e ".[test]"
+```
+
+**Tests** are written with `pytest` and live under `tests/`. Run the suite with:
+
+```bash
+pytest tests/ --ignore=tests/test_eggnog.py --ignore=tests/test_foldseek.py
+```
+
+`test_eggnog.py` and `test_foldseek.py` are excluded because they require EggNOG-mapper and Foldseek to be installed locally; CI runs the same exclusion (see [`.github/workflows/tests.yml`](.github/workflows/tests.yml)). If your change touches `eggnog.py` or `foldseek.py`, please also run those two files' tests locally if you have the tools installed.
+
+**Coding style** is enforced with [`black`](https://black.readthedocs.io/). Format your changes before opening a PR:
+
+```bash
+black protpen/ tests/
+```
+
+CI checks formatting with `black --check protpen/ tests/` and will fail if any file isn't formatted — make sure to run `black` locally first.
+
+## Pull Request Guidelines
+
+- Keep pull requests focused on a single change where possible to make review easier.
+- Add or update tests for any behavior you change, and make sure tests pass and code is formatted (see [Tests and Coding Style](#tests-and-coding-style) above) — CI checks both on every PR.
+- Update relevant documentation (README, docstrings, SLURM script comments) alongside code changes.
+- Be ready to discuss and iterate on feedback. Code review is a normal and friendly part of the process.
+
+## Code of Conduct
+
+Be respectful and constructive. We want ProtPen to be a welcoming project for contributors of all backgrounds and experience levels.
+
+## Contributors
+
+- Diya Mathai
+- Stefan Schulze
+
+Want to see your name here? Open a pull request!