Applying latest changes on aieng-template (#6)

Applying latest changes from aieng-template, which includes Ruff for python checks, pip-audit and documentation.

.github/workflows/docs_build.yml

@@ -0,0 +1,45 @@
+name: docs (build)
+
+on:
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/docs_build.yml
+      - '**.py'
+      - '**.ipynb'
+      - poetry.lock
+      - pyproject.toml
+      - '**.rst'
+      - '**.md'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+      - name: Install dependencies, build docs and coverage report
+        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.9'
+          cache: 'poetry'
+      - run: |
+          python3 -m pip install --upgrade pip && python3 -m pip install poetry
+          poetry env use '3.9'
+          source $(poetry env info --path)/bin/activate
+          poetry install --with docs,test
+          cd docs && rm -rf source/reference/api/_autosummary && make html
+          cd .. && coverage run -m pytest -m "not integration_test" && coverage xml && coverage report -m
+#      - name: Upload coverage to Codecov
+#        uses: Wandalen/[email protected]
+#        with:
+#          action: codecov/[email protected]
+#          with: |
+#            token: ${{ secrets.CODECOV_TOKEN }}
+#            file: ./coverage.xml
+#            name: codecov-umbrella
+#            fail_ci_if_error: true
+#          attempt_limit: 5
+#          attempt_delay: 30000

.github/workflows/docs_deploy.yml

@@ -0,0 +1,55 @@
+name: docs
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/static_code_checks.yml
+      - .github/workflows/docs_build.yml
+      - .github/workflows/docs_deploy.yml
+      - .github/workflows/tests.yml
+      - '**.py'
+      - '**.ipynb'
+      - poetry.lock
+      - pyproject.toml
+      - '**.rst'
+      - '**.md'
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+        with:
+          submodules: 'true'
+      - name: Install dependencies, build docs and coverage report
+        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.9'
+          cache: 'poetry'
+      - run: |
+          python3 -m pip install --upgrade pip && python3 -m pip install poetry
+          poetry env use '3.9'
+          source $(poetry env info --path)/bin/activate
+          poetry install --with docs,test
+          cd docs && rm -rf source/reference/api/_autosummary && make html
+          cd .. && coverage run -m pytest -m "not integration_test" && coverage xml && coverage report -m
+#      - name: Upload coverage to Codecov
+#        uses: Wandalen/[email protected]
+#        with:
+#          action: codecov/[email protected]
+#          with: |
+#            token: ${{ secrets.CODECOV_TOKEN }}
+#            file: ./coverage.xml
+#            name: codecov-umbrella
+#            fail_ci_if_error: true
+#          attempt_limit: 5
+#          attempt_delay: 30000
+      - name: Deploy to Github pages
+        uses: JamesIves/[email protected]
+        with:
+          branch: github_pages
+          folder: docs/build/html

.github/workflows/integration_tests.yaml

@@ -0,0 +1,61 @@
+name: tests
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/static_code_checks.yml
+      - .github/workflows/docs_build.yml
+      - .github/workflows/docs_deploy.yml
+      - .github/workflows/tests.yml
+      - '**.py'
+      - '**.ipynb'
+      - poetry.lock
+      - pyproject.toml
+      - '**.rst'
+      - '**.md'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/static_code_checks.yml
+      - .github/workflows/docs_build.yml
+      - .github/workflows/docs_deploy.yml
+      - .github/workflows/tests.yml
+      - '**.py'
+      - '**.ipynb'
+      - poetry.lock
+      - pyproject.toml
+      - '**.rst'
+      - '**.md'
+
+jobs:
+  python-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+      - name: Install poetry
+        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.9'
+      - name: Install dependencies and check code
+        run: |
+          poetry env use '3.9'
+          source $(poetry env info --path)/bin/activate
+          poetry install --with docs,test
+          coverage run -m pytest florist/tests/integration && coverage xml && coverage report -m
+#      - name: Upload coverage to Codecov
+#        uses: Wandalen/[email protected]
+#        with:
+#          action: codecov/[email protected]
+#          with: |
+#            token: ${{ secrets.CODECOV_TOKEN }}
+#            file: ./coverage.xml
+#            name: codecov-umbrella
+#            fail_ci_if_error: true
+#          attempt_limit: 5
+#          attempt_delay: 30000

.github/workflows/publish.yml

@@ -0,0 +1,27 @@
+name: publish package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install apt dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install libcurl4-openssl-dev libssl-dev
+      - uses: actions/[email protected]
+      - name: Install poetry
+        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.9'
+      - name: Build package
+        run: poetry build
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/static_code_checks.yaml

@@ -1,26 +1,58 @@
-# only has to pass for python 3.9
-name: Static code checks
+name: code checks
 
 on:
   push:
     branches:
-      main
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - '**.py'
+      - poetry.lock
+      - pyproject.toml
+      - '**.ipynb'
   pull_request:
     branches:
-      main
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - '**.py'
+      - poetry.lock
+      - pyproject.toml
+      - '**.ipynb'
 
 jobs:
   run-code-check:
     runs-on: ubuntu-latest
     steps:
-
-      - name: Checkout code
-        uses: actions/checkout@v3
-
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v3
+      - uses: actions/[email protected]
+      - name: Install and configure Poetry
+        uses: snok/install-poetry@v1
         with:
-          python-version: 3.9
-
-      - name: precommit checker
-        uses: pre-commit/[email protected]
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.9'
+          cache: 'poetry'
+      - name: Install dependencies and check code
+        run: |
+          poetry env use '3.9'
+          source .venv/bin/activate
+          poetry install --with test --all-extras
+          pre-commit run --all-files
+      - name: pip-audit (gh-action-pip-audit)
+        uses: pypa/[email protected]
+        with:
+          virtual-environment: .venv/
+          # Ignoring security vulnerabilities in Pillow because pycyclops cannot update it to the
+          # version that fixes them (>10.0.1).
+          # Remove those when the issue below is fixed and pycyclops changes its requirements:
+          # https://github.com/SeldonIO/alibi/issues/991
+          ignore-vulns: |
+            PYSEC-2023-175
+            PYSEC-2023-227
+            GHSA-j7hp-h8jx-5ppr
+            GHSA-56pw-mpj4-fxww
+            GHSA-3f63-hfp8-52jq

.github/workflows/unit_tests.yaml

@@ -0,0 +1,61 @@
+name: tests
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/static_code_checks.yml
+      - .github/workflows/docs_build.yml
+      - .github/workflows/docs_deploy.yml
+      - .github/workflows/tests.yml
+      - '**.py'
+      - '**.ipynb'
+      - poetry.lock
+      - pyproject.toml
+      - '**.rst'
+      - '**.md'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/static_code_checks.yml
+      - .github/workflows/docs_build.yml
+      - .github/workflows/docs_deploy.yml
+      - .github/workflows/tests.yml
+      - '**.py'
+      - '**.ipynb'
+      - poetry.lock
+      - pyproject.toml
+      - '**.rst'
+      - '**.md'
+
+jobs:
+  python-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+      - name: Install poetry
+        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.9'
+      - name: Install dependencies and check code
+        run: |
+          poetry env use '3.9'
+          source $(poetry env info --path)/bin/activate
+          poetry install --with docs,test
+          coverage run -m pytest florist/tests/unit && coverage xml && coverage report -m
+#      - name: Upload coverage to Codecov
+#        uses: Wandalen/[email protected]
+#        with:
+#          action: codecov/[email protected]
+#          with: |
+#            token: ${{ secrets.CODECOV_TOKEN }}
+#            file: ./coverage.xml
+#            name: codecov-umbrella
+#            fail_ci_if_error: true
+#          attempt_limit: 5
+#          attempt_delay: 30000

.gitignore

@@ -166,3 +166,5 @@ yarn-error.log*
 *.tsbuildinfo
 next-env.d.ts
 /florist/tsconfig.json
+
+/metrics/