snakemake-logger-plugin-snkmt 0.1.0__tar.gz

snakemake_logger_plugin_snkmt-0.1.0/.github/workflows/release-please.yml

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+on:
+  push:
+    branches:
+      - main
+
+name: release-please
+
+jobs:
+  release-please:
+    permissions:
+      contents: write
+      pull-requests: write
+      issues: write
+    runs-on: ubuntu-latest
+    outputs:
+      release_created: ${{ steps.release.outputs.release_created }}
+    steps:
+      - uses: googleapis/release-please-action@v4
+        id: release
+        with:
+          release-type: python
+
+  publish-pypi:
+    runs-on: ubuntu-latest
+    needs: release-please
+    if: ${{ needs.release-please.outputs.release_created }}
+    environment:
+      name: release
+    permissions:
+      id-token: write
+      
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Pixi
+        uses: prefix-dev/setup-pixi@v0.8.3
+        with:
+          environments: publish
+          pixi-version: v0.42.1
+
+      - name: Build source and wheel distribution + check build
+        # this will build the source and wheel into the dist/ directory
+        run: |
+          pixi run --environment publish check-build
+
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

snakemake_logger_plugin_snkmt-0.1.0/.github/workflows/test.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches-ignore: []
+
+permissions:
+  contents: read
+  checks: write
+  issues: write
+  pull-requests: write
+
+jobs:
+  quality-control:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the code
+        uses: actions/checkout@v4
+
+      - name: Install Pixi
+        uses: prefix-dev/setup-pixi@v0.8.3
+        with:
+          environments: dev
+          pixi-version: v0.42.1
+
+      - name: Ruff Format
+        if: always()
+        run: |
+          pixi run --environment dev format --check
+
+      - name: Ruff lint
+        if: always()
+        run: |
+          pixi run --environment dev lint --diff
+      - name: Mypy
+        if: always()
+        run: |
+          pixi run --environment dev type-check
+
+      - name: Collect QC
+        run: echo "All quality control checks passed"
+
+  testing:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Pixi
+        uses: prefix-dev/setup-pixi@v0.8.3
+        with:
+          environments: dev
+          pixi-version: v0.42.1
+
+      - name: Run tests
+        run: pixi run --environment dev test --show-capture=all -s -vv
+
+      - name: Upload lockfile as artifact
+        uses: actions/upload-artifact@v4
+        if: always()
+        id: upload-artifact
+        with:
+          name: pixi.lock.testing-${{ github.run_number }}
+          path: pixi.lock
+          retention-days: 1
+          overwrite: true

snakemake_logger_plugin_snkmt-0.1.0/.gitignore

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+### Generated by gibo (https://github.com/simonwhitaker/gibo)
+### https://raw.github.com/github/gitignore/4488915eec0b3a45b5c63ead28f286819c0917de/Python.gitignore
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+pixi.lock
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+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/
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

snakemake_logger_plugin_snkmt-0.1.0/CHANGELOG.md

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+# Changelog
+
+## 0.1.0 (2025-06-02)
+
+
+### Bug Fixes
+
+* properly set workflow status ([9b79c42](https://github.com/cademirch/snakemake-logger-plugin-snkmt/commit/9b79c42f89699cad8cd69ed49bf690766fa5d80a))
+* update database creation to handle migrations ([27829b1](https://github.com/cademirch/snakemake-logger-plugin-snkmt/commit/27829b11fb4ee603e2b4d7432f279e3c2a725934))
+
+
+### Dependencies
+
+* fix dev dep ([c4a68bf](https://github.com/cademirch/snakemake-logger-plugin-snkmt/commit/c4a68bf501860f577e3ca37d4d3a510ba47a8c36))
+
+
+### Documentation
+
+* update readme ([41a6aed](https://github.com/cademirch/snakemake-logger-plugin-snkmt/commit/41a6aed19b4a06acf55edf5de667c2fe28fd231e))
+
+## Changelog

snakemake_logger_plugin_snkmt-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Cade Mirchandani
+
+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.

snakemake_logger_plugin_snkmt-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: snakemake-logger-plugin-snkmt
+Version: 0.1.0
+Summary: Snakemake logger plugin that writes logs to SQLite database.
+Author-email: Cade Mirchandani <cmirchan@ucsc.edu>
+License-File: LICENSE
+Requires-Python: <4.0,>=3.11
+Requires-Dist: snakemake-interface-logger-plugins>=1.2.0
+Requires-Dist: sqlalchemy>=2.0.38
+Provides-Extra: dev
+Requires-Dist: loguru>=0.7.3; extra == 'dev'
+Requires-Dist: pytest>=8.3.5; extra == 'dev'
+Requires-Dist: ruff>=0.9.10; extra == 'dev'
+Requires-Dist: snakemake>=9.0.1; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# Snakemake Logger Plugin: snkmt
+
+**This plugin is still under development and thus may not be fully stable or feature-complete. Use it at your own discretion and report any issues or suggestions to the repository's issue tracker.**
+
+## Introduction
+
+The **Snakemake Logger Plugin: snkmt** is a logger plugin for Snakemake that writes workflow execution logs to a SQLite database. This plugin enables detailed tracking of workflows, rules, jobs, and associated files, providing a structured and queryable format for analyzing workflow execution. This enables visual monitoring of workflows using [snkmt](https://github.com/cademirch/snkmt). 
+
+## Usage
+1. Install via pip: `pip install snakemake-logger-plugin-snkmt`
+2. Run Snakemake with the `--logger snkmt` option to enable the snkmt logger. 
+
+## Options
+TODO
+
+## Design
+1. **Log Handler**:
+   - The `sqliteLogHandler` class processes log records and delegates them to event handlers.
+   - Manages database sessions and ensures transactional consistency.
+
+2. **Event Handlers**:
+   - Specialized handlers process specific log events (e.g., workflow start, job info, errors).
+   - Handlers parse log records and update the database models accordingly.
+
+3. **Database Models**:
+   - SQLAlchemy models represent key entities such as workflows, rules, jobs, files, and errors.
+   - Models capture attributes and relationships for comprehensive logging. Model definitions are maintained in the[snkmt repo](https://github.com/cademirch/snkmt).
+
+## Development
+
+TODO
+
+## Contributing
+
+Contributions are welcome! Please follow these steps:
+
+1. Fork the repository and create a new branch.
+2. Make your changes and ensure all tests pass.
+3. Submit a pull request with a detailed description of your changes.
+
+## License
+
+This project is licensed under the MIT License. See the `LICENSE` file for details.

snakemake_logger_plugin_snkmt-0.1.0/README.md

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+# Snakemake Logger Plugin: snkmt
+
+**This plugin is still under development and thus may not be fully stable or feature-complete. Use it at your own discretion and report any issues or suggestions to the repository's issue tracker.**
+
+## Introduction
+
+The **Snakemake Logger Plugin: snkmt** is a logger plugin for Snakemake that writes workflow execution logs to a SQLite database. This plugin enables detailed tracking of workflows, rules, jobs, and associated files, providing a structured and queryable format for analyzing workflow execution. This enables visual monitoring of workflows using [snkmt](https://github.com/cademirch/snkmt). 
+
+## Usage
+1. Install via pip: `pip install snakemake-logger-plugin-snkmt`
+2. Run Snakemake with the `--logger snkmt` option to enable the snkmt logger. 
+
+## Options
+TODO
+
+## Design
+1. **Log Handler**:
+   - The `sqliteLogHandler` class processes log records and delegates them to event handlers.
+   - Manages database sessions and ensures transactional consistency.
+
+2. **Event Handlers**:
+   - Specialized handlers process specific log events (e.g., workflow start, job info, errors).
+   - Handlers parse log records and update the database models accordingly.
+
+3. **Database Models**:
+   - SQLAlchemy models represent key entities such as workflows, rules, jobs, files, and errors.
+   - Models capture attributes and relationships for comprehensive logging. Model definitions are maintained in the[snkmt repo](https://github.com/cademirch/snkmt).
+
+## Development
+
+TODO
+
+## Contributing
+
+Contributions are welcome! Please follow these steps:
+
+1. Fork the repository and create a new branch.
+2. Make your changes and ensure all tests pass.
+3. Submit a pull request with a detailed description of your changes.
+
+## License
+
+This project is licensed under the MIT License. See the `LICENSE` file for details.

snakemake_logger_plugin_snkmt-0.1.0/pyproject.toml

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+[project]
+name = "snakemake-logger-plugin-snkmt"
+version = "0.1.0"
+description = "Snakemake logger plugin that writes logs to SQLite database."
+readme = "README.md"
+authors = [{ name = "Cade Mirchandani", email = "cmirchan@ucsc.edu" }]
+requires-python = "<4.0,>=3.11"
+dependencies = [
+    "snakemake-interface-logger-plugins>=1.2.0",
+    "sqlalchemy>=2.0.38",
+]
+
+[project.optional-dependencies]
+dev = ["pytest>=8.3.5", "snakemake>=9.0.1", "ruff>=0.9.10", "loguru>=0.7.3"]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.pixi.project]
+channels = ["conda-forge"]
+platforms = ["osx-arm64", "linux-64"]
+
+[tool.pixi.pypi-dependencies]
+snakemake-logger-plugin-snkmt = { path = ".", editable = true }
+
+[tool.pixi.environments]
+dev = { features = ["dev"] }
+publish = { features = ["publish"] }
+
+[tool.pixi.feature.dev.dependencies]
+pytest = ">=8.3.5,<9"
+ruff = ">=0.10.0,<0.11"
+mypy = ">=1.15.0,<2"
+pytest-cov = ">=6.0.0,<7"
+
+[tool.pixi.feature.dev.pypi-dependencies]
+snakemake-interface-logger-plugins = { git = "https://github.com/snakemake/snakemake-interface-logger-plugins.git" }
+snkmt = {git = "https://github.com/cademirch/snkmt.git", editable=true}
+
+
+[tool.mypy]
+ignore_missing_imports = true # Temporary until https://github.com/snakemake/snakemake-interface-common/pull/55
+disallow_untyped_defs = true
+warn_no_return = true
+
+[tool.pixi.feature.dev.tasks]
+format = "ruff format src"
+lint = "ruff check"
+type-check = "mypy src/"
+qc = { depends-on = ["format", "lint", "type-check"] }
+
+[tool.pixi.feature.dev.tasks.test]
+cmd = [
+  "pytest",
+  "--cov=snakemake_logger_plugin_snkmt",
+  "--cov-report=xml:coverage-report/coverage.xml",
+  "--cov-report=term-missing",
+]
+
+
+# Publish
+[tool.pixi.feature.publish.dependencies]
+twine = ">=6.1.0,<7"
+python-build = ">=1.2.2,<2"
+
+[tool.pixi.feature.publish.tasks]
+build = { cmd = "python -m build", description = "Build the package into the dist/ directory" }
+check-build = { cmd = "python -m twine check dist/*", depends-on = [
+  "build",
+], description = "Check that the package can be uploaded" }

snakemake_logger_plugin_snkmt-0.1.0/src/snakemake_logger_plugin_snkmt/__init__.py

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+from snakemake_interface_logger_plugins.base import LogHandlerBase
+from snakemake_interface_logger_plugins.settings import LogHandlerSettingsBase
+from snakemake_logger_plugin_snkmt.log_handler import sqliteLogHandler
+from dataclasses import dataclass, field
+from typing import Optional
+from pathlib import Path
+
+
+@dataclass
+class LogHandlerSettings(LogHandlerSettingsBase):
+    db: Optional[Path] = field(
+        default=None,
+        metadata={
+            "help": "Set absolute path for database file. ",
+            "env_var": False,
+            "required": False,
+        },
+    )
+
+
+class LogHandler(LogHandlerBase, sqliteLogHandler):
+    def __post_init__(self) -> None:
+        sqliteLogHandler.__init__(
+            self,
+            self.common_settings,
+            db_path=self.settings.db,  # type: ignore
+        )
+
+    @property
+    def writes_to_stream(self) -> bool:
+        """
+        Whether this plugin writes to stderr/stdout
+        """
+        return False
+
+    @property
+    def writes_to_file(self) -> bool:
+        """
+        Whether this plugin writes to a file
+        """
+        return False
+
+    @property
+    def has_filter(self) -> bool:
+        """
+        Whether this plugin attaches its own filter
+        """
+        return True
+
+    @property
+    def has_formatter(self) -> bool:
+        """
+        Whether this plugin attaches its own formatter
+        """
+        return True
+
+    @property
+    def needs_rulegraph(self) -> bool:
+        """
+        Whether this plugin requires the DAG rulegraph.
+        """
+        return True