snakesee 0.1.0__tar.gz

snakesee-0.1.0/.github/CODEOWNERS

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+*  @nh13

snakesee-0.1.0/.github/pull_request_template.md

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+## Description
+
+<!-- Briefly describe the changes in this PR -->
+
+## Type of Change
+
+- [ ] Bug fix
+- [ ] New feature
+- [ ] Documentation update
+- [ ] CI/CD change
+- [ ] Other (please describe):
+
+## Checklist
+
+- [ ] I have read the [CONTRIBUTING](../CONTRIBUTING.md) guidelines
+- [ ] My code follows the project's style guidelines
+- [ ] I have added tests that prove my fix/feature works
+- [ ] New and existing tests pass locally
+- [ ] I have updated documentation as needed
+
+## Testing
+
+<!-- Describe how you tested these changes -->
+
+## Related Issues
+
+<!-- Link to related issues if applicable -->
+Closes #
+
+## Additional Notes
+
+<!-- Any additional information that reviewers should know -->

snakesee-0.1.0/.github/workflows/publish.yml

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+name: publish
+
+on:
+  push:
+    tags:
+      - '[0-9]+.[0-9]+.[0-9]+'
+
+env:
+  UV_VERSION: 0.8.22
+
+jobs:
+  on-main-branch-check:
+    runs-on: ubuntu-latest
+    outputs:
+      on_main: ${{ steps.contains_tag.outputs.retval }}
+    steps:
+      - name: git config --global remote.origin.followRemoteHEAD never
+        run: git config --global remote.origin.followRemoteHEAD never
+
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: rickstaa/action-contains-tag@v1
+        id: contains_tag
+        with:
+          reference: "main"
+          tag: "${{ github.ref_name }}"
+
+  tests:
+    name: tests
+    needs: on-main-branch-check
+    if: ${{ needs.on-main-branch-check.outputs.on_main == 'true' }}
+    uses: "./.github/workflows/tests.yml"
+
+  build-sdist:
+    name: build source distribution
+    needs: tests
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "${{ env.UV_VERSION }}"
+          python-version: "3.12"
+
+      - name: Build package
+        run: uv build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: snakesee-sdist
+          path: dist/*.tar.gz
+
+  publish-to-pypi:
+    runs-on: ubuntu-latest
+    needs: build-sdist
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: packages
+          pattern: 'snakesee-*'
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: packages/
+          skip-existing: true
+          verbose: true
+
+  make-changelog:
+    runs-on: ubuntu-latest
+    needs: publish-to-pypi
+    outputs:
+      release_body: ${{ steps.git-cliff.outputs.content }}
+    steps:
+      - name: Checkout the Repository at the Tagged Commit
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: ${{ github.ref_name }}
+
+      - name: Generate a Changelog
+        uses: orhun/git-cliff-action@v4
+        id: git-cliff
+        with:
+          config: pyproject.toml
+          args: --latest --verbose
+        env:
+          GITHUB_REPO: ${{ github.repository }}
+
+  make-github-release:
+    runs-on: ubuntu-latest
+    environment: github
+    permissions:
+      contents: write
+      pull-requests: read
+    needs: make-changelog
+    steps:
+      - name: Download the sdist
+        uses: actions/download-artifact@v4
+
+      - name: Create GitHub Release
+        id: create_release
+        uses: softprops/action-gh-release@v2
+        with:
+          name: ${{ github.ref_name }}
+          body: ${{ needs.make-changelog.outputs.release_body }}
+          draft: false
+          prerelease: false

snakesee-0.1.0/.github/workflows/tests.yml

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+name: Static Analysis, Unit Tests, and Documentation
+
+on:
+  push:
+    branches:
+      - "**"
+    tags:
+      - "!**"
+  workflow_call:
+
+env:
+  UV_VERSION: 0.8.22
+
+permissions:
+  contents: read
+  pull-requests: write
+
+jobs:
+  Tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        PYTHON_VERSION: ["3.11", "3.12", "3.13"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "${{ env.UV_VERSION }}"
+          python-version: "${{ matrix.PYTHON_VERSION }}"
+          enable-cache: 'true'
+          cache-suffix: "${{ matrix.PYTHON_VERSION }}"
+
+      - name: Install dependencies
+        run: |
+          uv sync --group dev --group docs
+
+      - name: Test the library
+        run: |
+          uv run poe check-all
+
+      - name: Run docs
+        run: |
+          set -euo pipefail
+          uv run poe build-docs
+
+      - name: Upload code coverage
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

snakesee-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Random things
+.DS_Store
+.idea/
+
+# pixi
+.pixi/
+pixi.lock

snakesee-0.1.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.4
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format

snakesee-0.1.0/.readthedocs.yml

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+version: 2
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+  jobs:
+    post_install:
+      - pip install uv==0.6.10
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install --group docs .
+mkdocs:
+  configuration: mkdocs.yml

snakesee-0.1.0/CONTRIBUTING.md

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+# Contributing to snakesee
+
+Thank you for your interest in contributing to snakesee!
+
+## Development Setup
+
+### Prerequisites
+
+- Python 3.11 or later
+- [pixi](https://pixi.sh/) (recommended) or uv
+
+### Setup with pixi
+
+```bash
+# Clone the repository
+git clone https://github.com/nh13/snakesee.git
+cd snakesee
+
+# Install development environment
+pixi run install-dev
+
+# Run all checks (lint, type check, tests)
+pixi run check
+
+# Run tests only
+pixi run test
+
+# Auto-fix linting issues
+pixi run fix
+
+# Build documentation
+pixi run docs
+```
+
+### Setup with uv
+
+```bash
+# Clone the repository
+git clone https://github.com/nh13/snakesee.git
+cd snakesee
+
+# Create virtual environment and install
+uv sync --group dev --group docs
+uv pip install -e '.[logo]'
+
+# Run checks
+uv run poe check-all
+```
+
+## Code Style
+
+This project uses:
+
+- **ruff** for linting and formatting
+- **mypy** for type checking
+- **pytest** for testing
+
+All code should:
+
+- Pass `ruff format` (formatting)
+- Pass `ruff check` (linting)
+- Pass `mypy` (type checking)
+- Have tests with >65% coverage
+
+## Running Checks
+
+```bash
+# Run all checks
+pixi run check
+# or
+uv run poe check-all
+
+# Auto-fix linting issues
+pixi run fix
+# or
+uv run poe fix-all
+
+# Run just tests
+pixi run test
+# or
+uv run pytest
+```
+
+## Pull Request Process
+
+1. Fork the repository and create a feature branch
+2. Make your changes
+3. Ensure all checks pass: `pixi run check`
+4. Update documentation if needed
+5. Submit a pull request
+
+## Release Process
+
+Releases are automated via GitHub Actions when a SemVer tag is pushed:
+
+```bash
+# Ensure everything is committed and pushed
+git push origin main
+
+# Create and push a tag
+git tag 0.2.0
+git push origin 0.2.0
+```
+
+The CI will automatically:
+1. Run all tests
+2. Build the source distribution
+3. Publish to PyPI
+4. Generate changelog with git-cliff
+5. Create a GitHub release
+
+## Commit Messages
+
+We use [Conventional Commits](https://www.conventionalcommits.org/) for generating changelogs:
+
+- `feat:` New features
+- `fix:` Bug fixes
+- `docs:` Documentation changes
+- `test:` Test changes
+- `refactor:` Code refactoring
+- `style:` Code style changes
+- `chore:` Maintenance tasks
+
+Examples:
+```
+feat: add support for filtering by rule name
+fix: handle missing log files gracefully
+docs: update keyboard shortcuts table
+```
+
+## Logger Plugin Development
+
+The repository includes an optional Snakemake logger plugin in `snakemake-logger-plugin-snakesee/`.
+
+### Plugin Setup
+
+```bash
+# Install the plugin in development mode
+cd snakemake-logger-plugin-snakesee
+pip install -e .
+
+# Run plugin tests
+pytest tests/
+```
+
+### Plugin Structure
+
+- `src/snakemake_logger_plugin_snakesee/handler.py` - Main LogHandler implementation
+- `src/snakemake_logger_plugin_snakesee/events.py` - Event types and serialization
+- `src/snakemake_logger_plugin_snakesee/writer.py` - JSONL event file writer
+
+The plugin writes events to `.snakesee_events.jsonl` which snakesee reads via `snakesee/events.py`.
+
+## Questions?
+
+Open an issue at https://github.com/nh13/snakesee/issues

snakesee-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 Fulcrum Genomics LLC
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.