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Support Tumor_Sample_Barcode as column name in clinical file #263

Support Tumor_Sample_Barcode as column name in clinical file

Support Tumor_Sample_Barcode as column name in clinical file #263

Workflow file for this run

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
name: Run all python tests
on:
push:
branches: [ master, next-minor-release ]
pull_request:
branches: [ master, next-minor-release ]
jobs:
lint:
name: Linting using flake8
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
with:
python-version: "3.9"
- name: Run flake8
uses: julianwachholz/flake8-action@v2
with:
checkName: "Python Lint"
path: .
config: flake8.ini
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
pytest:
needs: lint
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ ubuntu-latest, macos-latest ]
python-version: [ '3.7','3.8','3.9','3.10','3.11' ]
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
env:
PYTHON_VERSION: ${{ matrix.python-version }}
run: |
python -m pip install --upgrade pip
pip install pytest
if [[ $PYTHON_VERSION =~ ^2\.[0-9]+$ ]]; then pip install -r requirements/common.txt -r requirements/pip2.7.txt; fi
if [[ $PYTHON_VERSION =~ ^3\.[0-9]+$ ]]; then pip install -r requirements/common.txt -r requirements/pip3.txt; fi
- name: Test with pytest
env:
ONCOKB_API_TOKEN: ${{ secrets.ONCOKB_BOT_API_TOKEN }}
run: |
pytest
build-in-windows:
needs: lint
runs-on: windows-latest
strategy:
matrix:
python-version: [ '3.7','3.8','3.9','3.10','3.11' ]
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
env:
PYTHON_VERSION: ${{ matrix.python-version }}
run: |
python -m pip install --upgrade pip
pip install pytest
if ( $env:PYTHON_VERSION -match '^2\.[0-9]+$' )
{
pip install -r requirements/common.txt -r requirements/pip2.7.txt
}
if ( $env:PYTHON_VERSION -match '^3\.[0-9]+$' )
{
pip install -r requirements/common.txt -r requirements/pip3.txt
}
- name: Test with pytest
env:
ONCOKB_API_TOKEN: ${{ secrets.ONCOKB_BOT_API_TOKEN }}
run: |
pytest