Apply the LINCC Frameworks python project template

.copier-answers.yml

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+# Changes here will be overwritten by Copier
+_commit: v1.4.3
+_src_path: gh:lincc-frameworks/python-project-template
+author_email: [email protected]
+author_name: Grant Merz
+create_example_module: true
+custom_install: true
+include_benchmarks: false
+include_docs: true
+include_notebooks: true
+mypy_type_checking: none
+package_name: deepdisc
+preferred_linter: pylint
+project_license: MIT
+project_name: deepdisc
+use_gitlfs: none
+use_isort: true

.github/workflows/build-documentation.yml

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+# This workflow will install Python dependencies, build the package and then build the documentation.
+
+name: Build documentation
+
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
+        pip install .
+    - name: Install notebook requirements
+      run: |
+        sudo apt-get install pandoc
+    - name: Build docs
+      run: |
+        sphinx-build -T -E -b html -d docs/build/doctrees ./docs docs/build/html

.github/workflows/linting.yml

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+# This workflow will install Python dependencies, then perform static linting analysis.
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Lint
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .
+        pip install .[dev]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Analyze code with linter
+
+      run: |
+        pylint -rn -sn --recursive=y ./src --rcfile=./src/.pylintrc

.github/workflows/pre-commit-ci.yml

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+# This workflow runs pre-commit hooks on pull requests to enforce coding style.
+# To ensure correct configuration, please refer to:
+#   https://lincc-ppt.readthedocs.io/en/latest/practices/ci_precommit.html
+
+name: Run pre-commit hooks
+
+on:
+  pull_request:
+
+jobs:
+  pre-commit-ci:
+    runs-on: ubuntu-latest
+    env: 
+      SKIP: "check-lincc-frameworks-template-version,pytest-check,no-commit-to-branch,validate-pyproject,check-added-large-files,sphinx-build"
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0 
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .
+        pip install .[dev]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - uses: pre-commit/[email protected]
+      with:
+        extra_args: --from-ref ${{ github.event.pull_request.base.sha }} --to-ref ${{ github.event.pull_request.head.sha }}
+    - uses: pre-commit-ci/[email protected]
+      if: always()

.github/workflows/publish-to-pypi.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/smoke-test.yml

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+# This workflow will run daily at 06:45.
+# It will install Python dependencies and run tests with a variety of Python versions.
+# See documentation for help debugging smoke test issues:
+#    https://lincc-ppt.readthedocs.io/en/latest/practices/ci_testing.html#version-culprit
+
+name: Unit test smoke test
+
+on:
+
+  # Runs this workflow automatically
+  schedule:
+    - cron: 45 6 * * *
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10']
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .
+        pip install .[dev]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: List dependencies
+      run: |
+        pip list
+    - name: Run unit tests with pytest
+      run: |
+        python -m pytest tests

.github/workflows/testing-and-coverage.yml

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+# This workflow will install Python dependencies, run tests and report code coverage with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Unit test and code coverage
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10']
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .
+        pip install .[dev]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Run unit tests with pytest
+      run: |
+        python -m pytest tests --cov=deepdisc --cov-report=xml
+    - name: Upload coverage report to codecov
+      uses: codecov/codecov-action@v3

.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
+_version.py
+
+# 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/
+_readthedocs/
+
+# 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/
+
+# vscode
+.vscode/
+
+# dask
+dask-worker-space/
+
+# tmp directory
+tmp/
+
+# Mac OS
+.DS_Store
+
+# Airspeed Velocity performance results
+_results/
+_html/