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/checkout@v4.1.1
+ - name: Install dependencies, build docs and coverage report
+ run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+ - uses: actions/setup-python@v5.0.0
+ 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/wretry.action@v1.4.4
+# with:
+# action: codecov/codecov-action@v4.0.1
+# 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/checkout@v4.1.1
+ 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/setup-python@v5.0.0
+ 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/wretry.action@v1.4.4
+# with:
+# action: codecov/codecov-action@v4.0.1
+# 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/github-pages-deploy-action@v4.5.0
+ 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/checkout@v4.1.1
+ - name: Install poetry
+ run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+ - uses: actions/setup-python@v5.0.0
+ 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/wretry.action@v1.4.4
+# with:
+# action: codecov/codecov-action@v4.0.1
+# 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/checkout@v4.1.1
+ - name: Install poetry
+ run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+ - uses: actions/setup-python@v5.0.0
+ 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/checkout@v4.1.1
+ - name: Install and configure Poetry
+ uses: snok/install-poetry@v1
  with:
- python-version: 3.9
-
- - name: precommit checker
- uses: pre-commit/action@v3.0.1
+ virtualenvs-create: true
+ virtualenvs-in-project: true
+ - uses: actions/setup-python@v5.0.0
+ 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/gh-action-pip-audit@v1.0.8
+ 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/checkout@v4.1.1
+ - name: Install poetry
+ run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+ - uses: actions/setup-python@v5.0.0
+ 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/wretry.action@v1.4.4
+# with:
+# action: codecov/codecov-action@v4.0.1
+# 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/