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In reads aggregation, do not warn for samples without demux artifacts if they are aborted #366

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In reads aggregation, do not warn for samples without demux artifacts if they are aborted

In reads aggregation, do not warn for samples without demux artifacts if they are aborted #366

Workflow file for this run

.github/workflows/lint-code.yml at 3ad9fb1
name: Lint code
on: [push, pull_request]
jobs:
# Use ruff to check for code style violations
ruff-check:
runs-on: ubuntu-latest
steps:
- name: Checkout repo
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.10"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install ruff
- name: ruff --> Check for style violations
# Configured in pyproject.toml
run: ruff check .
# Use ruff to check code formatting
ruff-format:
runs-on: ubuntu-latest
steps:
- name: Checkout repo
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.10"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install ruff
- name: ruff --> Check code formatting
run: ruff format --check .
# Use mypy for static type checking
mypy-check:
runs-on: ubuntu-latest
steps:
- name: Checkout repo
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.10"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install mypy
# Start by installing type stubs
- name: mypy --> Install stubs
run: echo -e "y" | mypy --install-types . || exit 0
- name: mypy --> Static type checking
# Configured in pyprojet.toml
run: mypy .
# Use pipreqs to check for missing dependencies
pipreqs-check:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.10"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -r requirements.txt
pip install -r requirements-dev.txt
- name: Run pipreqs
run: |
pipreqs --savepath pipreqs.txt 2>&1 | tee pipreqs_output.log
if grep -q 'WARNING: Package .* does not exist or network problems' pipreqs_output.log; then
missing_packages=$(grep 'WARNING: Package .* does not exist or network problems' pipreqs_output.log | sed -E 's/.*Package "(.*)" does not exist.*/\1/')
echo "ERROR: Add unresolved packages to requirements. Missing package(s): $missing_packages. Example: '<pkg> @ git+https://github.com/<author>/<repo>.git'"
exit 1
fi
- name: Compare requirements
run: |
# Extract and sort package names
awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' requirements.txt | tr '[:upper:]' '[:lower:]' | sort -u > requirements.compare
awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' pipreqs.txt | tr '[:upper:]' '[:lower:]' | sort -u > pipreqs.compare
# Compare package lists
if cmp -s requirements.compare pipreqs.compare
then
echo "Requirements are the same"
exit 0
else
echo "Requirements are different"
echo ""
echo "=== current requirements.txt ==="
echo ""
cat requirements.compare
echo ""
echo "=== pipreqs requirements ==="
echo ""
cat pipreqs.compare
exit 1
fi
# Use Prettier to check various file formats
prettier:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Setup node
uses: actions/setup-node@v4
with:
node-version: "20"
- name: Install Prettier
run: npm install -g prettier
- name: Run Prettier --check
run: prettier --check .
# Use editorconfig to check all remaining file formats
editorconfig:
runs-on: ubuntu-latest
steps:
- name: Checkout repo
uses: actions/checkout@v4
- name: Setup node
uses: actions/setup-node@v4
with:
node-version: "20"
- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
- name: editorconfig --> Lint files
run: editorconfig-checker $(git ls-files | grep -v '.py\|.md\|.json\|.yml\|.yaml\|.html')