Development

.github/workflows/clean.yml

@@ -0,0 +1,33 @@
+name: cleanup caches by a branch
+on:
+  pull_request:
+    types:
+      - closed
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v3
+
+      - name: Cleanup
+        run: |
+          gh extension install actions/gh-actions-cache
+
+          REPO=${{ github.repository }}
+          BRANCH="refs/pull/${{ github.event.pull_request.number }}/merge"
+
+          echo "Fetching list of cache key"
+          cacheKeysForPR=$(gh actions-cache list -R $REPO -B $BRANCH | cut -f 1 )
+
+          ## Setting this to not fail the workflow while deleting cache keys. 
+          set +e
+          echo "Deleting caches..."
+          for cacheKey in $cacheKeysForPR
+          do
+              gh actions-cache delete $cacheKey -R $REPO -B $BRANCH --confirm
+          done
+          echo "Done"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/python-app.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a single version of Python
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
-name: Python application
+name: master
 
 on:
   push:
@@ -13,27 +13,68 @@ permissions:
   contents: read
 
 jobs:
-  build:
-
+  dependency-install:
     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"
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pre-commit
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
 
+  test:
+    needs: dependency-install
+    runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python 3.10
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: "3.10"
+        cache: 'pip'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest
+        pip install pytest pytest-mock
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
         python -m pytest
+
+  devops:
+    needs: test
+    environment: development
+    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"
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pre-commit
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with pylint
+      run: |
+        pip install pylint
+        pylint --fail-under=9.8 --rcfile=.pylintrc utilities
+    - name: code coverage
+      run: |
+        mkdir -p ./coverage
+        pip install pytest-cov pytest-mock
+        python -m pytest --cov --cov-report=xml:./coverage/coverage.xml
+
+    - name: Upload coverage
+      uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
+        files: ./coverage/coverage.xml # optional

.github/workflows/static.yml

@@ -0,0 +1,79 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy Documentation on Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main"]
+
+  # 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 only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install -U sphinx
+        pip install furo
+
+    - name: Build documentation
+      run: |
+        cd docs
+
+
+        sphinx-apidoc -e -M --force -o . ..
+        make html
+    - name: Upload build data
+      uses: actions/upload-artifact@v3
+      with:
+        name: documentation
+        path: ./docs/_build/html
+
+  deploy:
+    needs: build
+    environment:
+      name: documentation
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+      - name: Download built directory
+        uses: actions/download-artifact@v3
+        with:
+          name: documentation
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          # Upload entire repository
+          path: '.'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1
+        with:
+          folder: build

.gitignore

@@ -0,0 +1,145 @@
+# 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/
+/archive/
+/archive_resized/
+/checkpoints/
+/exported_models/
+archive.lnk
+
+colab_notebook.ipynb
+/.vscode/
+
+/cut_ims/
+/ims/
+
+/cut_masks/
+/masks/
+
+

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+
+repos:
+
+
+# - repo: https://github.com/jendrikseipp/vulture
+#   rev: v2.3
+#   hooks:
+#     # dead code detector
+#   - id: vulture
+
+- repo: https://github.com/jorisroovers/gitlint
+  rev: v0.17.0
+  hooks:
+    # git commit message linter
+  - id: gitlint