Merge branch 'main' of https://github.com/monarch-initiative/mondolib …

…into main

.cruft.json

@@ -0,0 +1,24 @@
+{
+  "template": "https://github.com/monarch-initiative/monarch-project-template",
+  "commit": "e386290d6a462687e324034af29e879f18ee7364",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "mondolib",
+      "github_org_name": "monarch-initiative",
+      "__project_slug": "mondolib",
+      "project_description": "Python library for mondo.",
+      "min_python_version": "3.9",
+      "file_name": "main",
+      "greeting_recipient": "World",
+      "full_name": "Harshad Hegde",
+      "email": "[email protected]",
+      "__author": "Harshad Hegde <[email protected]>",
+      "license": "MIT",
+      "github_token_for_doc_deployment": "GH_TOKEN",
+      "github_token_for_pypi_deployment": "PYPI_TOKEN",
+      "_template": "https://github.com/monarch-initiative/monarch-project-template"
+    }
+  },
+  "directory": null
+}

.github/workflows/deploy-docs.yml

@@ -0,0 +1,43 @@
+name: Auto-deployment of Documentation
+on:
+  push:
+    branches: [ main ]
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/[email protected]
+      with:
+        fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+
+    - name: Set up Python 3.
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.9
+
+    - name: Install Poetry.
+      uses: snok/[email protected]
+
+    - name: Install dependencies.
+      run: |
+        poetry install --with docs
+        
+    - name: Build documentation.
+      run: |
+        echo ${{ secrets.GH_TOKEN }} >> src/mondolib/token.txt
+        mkdir gh-pages
+        touch gh-pages/.nojekyll
+        cd docs/
+        poetry run sphinx-apidoc -o . ../src/mondolib/ --ext-autodoc -f
+        poetry run sphinx-build -b html . _build
+        cp -r _build/* ../gh-pages/
+    
+    - name: Deploy documentation.
+      if: ${{ github.event_name == 'push' }}
+      uses: JamesIves/[email protected]
+      with:
+        branch: gh-pages
+        force: true
+        folder: gh-pages
+        token: ${{ secrets.GH_TOKEN }}

.github/workflows/pypi-publish.yml

@@ -0,0 +1,36 @@
+name: Publish Python Package
+
+on:
+  workflow_dispatch:
+  release:
+    types: [created]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/[email protected]
+
+      - name: Set up Python
+        uses: actions/[email protected]
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry
+        run: pip install poetry poetry-dynamic-versioning
+
+      - name: Install dependencies
+        run: poetry install --no-interaction
+
+      - name: Build source and wheel archives
+        run: poetry build
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}
+
+

.github/workflows/qc.yml

@@ -0,0 +1,36 @@
+name: mondolib QC
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ "3.8", "3.9", "3.10" ]
+
+    steps:
+      - uses: actions/[email protected]
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        uses: snok/[email protected]
+      - name: Install dependencies
+        run: poetry install --no-interaction
+
+      - name: Check common spelling errors
+        run: poetry run tox -e codespell
+
+      - name: Check code quality with flake8
+        run: poetry run tox -e lint
+
+      - name: Test with pytest and generate coverage file
+        run: poetry run tox -e py

.gitignore

@@ -1,3 +1,134 @@
+# 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/
+
+# User-defined
 .idea/
 .template.db
 tests/input/example-relation-graph.tsv.gz

.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+default_language_version:
+  python: python3
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-toml
+  - id: trailing-whitespace
+- repo: https://github.com/psf/black
+  rev: 23.7.0
+  hooks:
+  - id: black
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.0.278
+  hooks:
+  - id: ruff
+    args: [--fix, --exit-non-zero-on-fix]
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.4
+  hooks:
+  - id: codespell
+    additional_dependencies:
+      - tomli

CONTRIBUTING.md

@@ -0,0 +1,32 @@
+# Contribution Guidelines
+
+When contributing to this repository, please first discuss the changes you wish to make via an issue, email, or any other method, with the owners of this repository before issuing a pull request.
+
+## How to contribute
+
+### Reporting bugs or making feature requests
+
+To report a bug or suggest a new feature, please go to the [monarch-initiative/mondolib issue tracker](https://github.com/monarch-initiative/mondolib/issues), as we are
+consolidating issues there.
+
+Please supply enough details to the developers to enable them to verify and troubleshoot your issue:
+
+* Provide a clear and descriptive title as well as a concise summary of the issue to identify the problem.
+* Describe the exact steps which reproduce the problem in as many details as possible.
+* Describe the behavior you observed after following the steps and point out what exactly is the problem with that behavior.
+* Explain which behavior you expected to see instead and why.
+* Provide screenshots of the expected or actual behaviour where applicable.
+
+
+### The development lifecycle
+
+1. Create a bug fix or feature development branch, based off the `main` branch of the upstream repo, and not your fork. Name the branch appropriately, briefly summarizing the bug fix or feature request. If none come to mind, you can include the issue number in the branch name. Some examples of branch names are, `bugfix/breaking-pipfile-error` or `feature/add-click-cli-layer`, or `bugfix/issue-414`
+2. Make sure your development branch has all the latest commits from the `main` branch.
+3. After completing work and testing locally, push the code to the appropriate branch on your fork.
+4. Create a pull request from the bug/feature branch of your fork to the `main` branch of the upstream repository.
+
+Note: All the development must be done on a branch on your fork.
+
+ALSO NOTE: github.com lets you create a pull request from the main branch, automating the steps above.
+
+> A code review (which happens with both the contributor and the reviewer present) is required for contributing.

LICENSE

@@ -0,0 +1,22 @@
+
+The MIT License (MIT)
+
+Copyright (c) 2023 Chris Mungall
+
+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.