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Bump requests from 2.27.1 to 2.31.0 in /docs #269

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Bump requests from 2.27.1 to 2.31.0 in /docs

Bump requests from 2.27.1 to 2.31.0 in /docs #269

Workflow file for this run

.github/workflows/python-ci.yml at 807729e
# This GitHub Action workflow will
# - Format code using Black
# - Build project with all dependencies
# - Check code with flake8 linter
# - Run tests with pytest
# ubuntu-latest has 7GB RAM and 14GB SSD. macos-latest has 14GB RAM and 14GB SSD. Using macos assuming more RAM -> faster tests -> less timeouts
# Nonetheless, our tests seem to need >10 GB RAM and >16,7 GB SSD Space. Test refactoring needed.
# https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
name: Build and test
on:
push:
branches: [ main ]
pull_request:
branches: [ main ]
jobs:
formatting:
outputs:
new_sha: ${{ steps.sha.outputs.SHA }}
runs-on: macos-latest
steps:
- name: Checkout code
uses: actions/checkout@v3
with:
ref: ${{ github.event.pull_request.head.ref }} # ${{ github.event.pull_request.head.sha }}
- name: Setup Python 3.8
uses: actions/setup-python@v2
with:
python-version: "3.8"
cache: 'pip'
- name: Setup isort and Black
run: |
python -m pip install --upgrade pip
pip install isort black
- name: Run isort
run: |
isort --profile black .
- name: Run Black formatter
run: |
black .
- name: Commit changes
uses: EndBug/add-and-commit@v8
with:
message: 'Fix styling'
add: '*.py'
- name: Get commit hash
id: sha
run: |
sha_new=$(git rev-parse HEAD)
echo $sha_new
echo "::set-output name=SHA::$sha_new"
build:
if: always()
needs: formatting
runs-on: macos-latest
steps:
- name: Checkout to latest changes
uses: actions/checkout@v3
with:
ref: ${{ needs.formatting.outputs.new_sha }}
fetch-depth: 0
- name: Set up Python 3.8
uses: actions/setup-python@v2
with:
python-version: "3.8"
cache: 'pip'
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install flake8 pytest pytest-cov pytest-github-actions-annotate-failures
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
pip install -e .
- name: Install model dependencies
run: |
python src/medigan/execute_model/install_model_dependencies.py
lint:
needs: build
runs-on: macos-latest
steps:
- name: Checkout to latest changes
uses: actions/checkout@v3
with:
ref: ${{ needs.formatting.outputs.new_sha }}
fetch-depth: 0
- name: Set up Python 3.8
uses: actions/setup-python@v2
with:
python-version: "3.8"
cache: 'pip'
- name: Install cached dependencies
run: |
python -m pip install --upgrade pip
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
pip install flake8
pip install -e .
- 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 --max-line-length=88 --extend-ignore=E203,E501
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=88 --extend-ignore=E203,E501 --statistics
test:
needs: build
runs-on: macos-latest #windows-latest
steps:
- name: Checkout to latest changes
uses: actions/checkout@v3
with:
ref: ${{ needs.formatting.outputs.new_sha }}
fetch-depth: 0
- name: Set up Python 3.8
uses: actions/setup-python@v2
with:
python-version: "3.8"
cache: 'pip'
- name: Install cached dependencies
run: |
python -m pip install --upgrade pip
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
pip install pytest pytest-cov pytest-github-actions-annotate-failures
pip install -e .
python src/medigan/execute_model/install_model_dependencies.py
# for windows: pip install -r requirements.txt
# for mac/linux: if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- name: Test with pytest
run: |
pytest tests -W ignore::DeprecationWarning --verbose --failed-first --log-cli-level=INFO #--cov=. --cov-report html #--capture=tee-sys