initialize repository

.github/workflows/page.yml

@@ -0,0 +1,68 @@
+name: Deploy doc
+
+on:
+  # Runs on pushes targeting the main branch (uncomment to next 3 lines to enable)
+  #  push:
+  #    branches:
+  #      - main
+  #      - master
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+
+      - name: Install Poetry
+        run: make install-poetry
+
+      - name: Pypi authentication
+        run: |
+          poetry config repositories.owkin https://pypi.owkin.com/simple/
+          poetry config http-basic.owkin "${{ secrets.PYPI_USERNAME }}" "${{ secrets.PYPI_PASSWORD }}"
+
+          poetry config repositories.sowce https://github.com/owkin/sowce.git
+          poetry config http-basic.sowce "${{ secrets.GIT_USERNAME }}" "${{ secrets.GIT_TOKEN }}"
+
+      - name: Install dependencies
+        run: poetry install --all-extras --with=docs
+
+      - name: Build docs
+        run: poetry run make docs
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: docs/_build/html
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1

.github/workflows/publish.yml

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+name: Publish
+on:
+  release:
+    types: [published]
+jobs:
+  publish-on-pypi-servers:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo and submodule
+        uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install Poetry
+        run: make install-poetry
+
+      - name: Pypi authentication
+        run: |
+          poetry config repositories.owkin https://pypi.owkin.com/simple/
+          poetry config http-basic.owkin "${{ secrets.PYPI_USERNAME }}" "${{ secrets.PYPI_PASSWORD }}"
+
+          poetry config repositories.sowce https://github.com/owkin/sowce.git
+          poetry config http-basic.sowce "${{ secrets.GIT_USERNAME }}" "${{ secrets.GIT_TOKEN }}"
+
+      - name: Install dependencies
+        run: poetry install --all-extras
+
+      - name: Publish package
+        run: poetry publish -r owkin --build

.github/workflows/python-app.yml

@@ -0,0 +1,76 @@
+name: Python dev
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+      - master # Just in case the repo has the deprecated main branch name
+
+jobs:
+  testing:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: ["3.9", "3.10"]
+    name: Testing Python ${{ matrix.python }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install Poetry
+        run: make install-poetry
+
+      - name: Pypi authentication
+        run: |
+          python -m poetry config virtualenvs.in-project false
+          python -m poetry config repositories.owkin https://pypi.owkin.com/simple/
+          python -m poetry config http-basic.owkin "${{ secrets.PYPI_USERNAME }}" "${{ secrets.PYPI_PASSWORD }}"
+          python -m poetry config repositories.seaborn_owkin https://github.com/owkin/seaborn_owkin.git
+          python -m poetry config http-basic.seaborn_owkin "${{ secrets.GIT_USERNAME }}" "${{ secrets.GIT_TOKEN }}"
+
+      - name: Install dependencies
+        run: poetry install --all-extras --with=testing
+
+      - name: Testing
+        run: poetry run make test
+
+  linting:
+    runs-on: ubuntu-latest
+    name: Test Linting
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+
+      - name: Install Poetry
+        run: make install-poetry
+
+      - name: Pypi authentication
+        run: |
+          python -m poetry config virtualenvs.in-project false
+          python -m poetry config repositories.owkin https://pypi.owkin.com/simple/
+          python -m poetry config http-basic.owkin "${{ secrets.PYPI_USERNAME }}" "${{ secrets.PYPI_PASSWORD }}"
+          python -m poetry config repositories.seaborn_owkin https://github.com/owkin/seaborn_owkin.git
+          python -m poetry config http-basic.seaborn_owkin "${{ secrets.GIT_USERNAME }}" "${{ secrets.GIT_TOKEN }}"
+
+      - name: Install dependencies
+        run: poetry install --all-extras --with=linting,docs
+
+      - name: Test pre-commit checks
+        run: poetry run make pre-commit-checks
+
+      - name: Test linting
+        run: poetry run make lint
+
+      - name: Test typing
+        run: poetry run make typing
+
+      - name: Test docs
+        run: poetry run make test-docs

.gitignore

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+# IDE settings
+.vscode/
+.idea/
+
+# 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/
+docs/api/
+
+# 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/
+
+# OS
+.DS_Store
+
+# Others
+notebooks/figures/*
+notebooks/necrosis_enrichment/*

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/sirosen/check-jsonschema
+    rev: 0.27.0
+    hooks:
+      - id: check-github-actions
+      - id: check-github-workflows
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+        name: Trim trailing whitespace
+      - id: end-of-file-fixer
+        name: Fix end of files
+        exclude: \.ipynb$
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.0.3
+    hooks:
+      - id: prettier
+        name: Format yaml files using `prettier`
+        files: \.(yaml|yml)$
+  - repo: https://github.com/python-poetry/poetry
+    rev: 1.6.0
+    hooks:
+      - id: poetry-check
+        name: Run poetry check to validate configuration
+  - repo: local
+    hooks:
+      # Linter
+      - id: ruff-linter
+        name: Lint with `ruff`
+        language: system
+        types: [python]
+        require_serial: true
+        entry: poetry run ruff check
+        args: [--fix]
+        files: ^(gbmosaic|tests)/
+      # Formatter
+      - id: ruff-format
+        name: Format with `ruff`
+        language: system
+        types: [python]
+        require_serial: true
+        entry: poetry run ruff format
+        files: ^(gbmosaic|tests)/
+      # Type checker
+      - id: mypy
+        name: Test typing with `mypy`
+        language: system
+        types: [python]
+        require_serial: true
+        entry: poetry run mypy
+        files: ^gbmosaic/
+      # Jupyter notebook formatter
+      - id: jupyter-nb-clear-output
+        name: Clear Jupyter notebook outputs
+        files: \.ipynb$
+        language: system
+        entry: poetry run jupyter nbconvert
+        args: [--ClearOutputPreprocessor.enabled=True, --inplace]

.pydocstyle

@@ -0,0 +1,4 @@
+[pydocstyle]
+convention = numpy
+match = (?!_).*\.py
+add_ignore = D105