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fixed dependencies

fixed dependencies #48

Workflow file for this run

name: Test
on:
push:
branches: [master]
pull_request:
branches: [master, devel]
jobs:
test:
runs-on: ${{ matrix.os }}
defaults:
run:
shell: bash -e {0} # -e to fail on error
strategy:
fail-fast: false
matrix:
python: ["3.8", "3.10"]
os: [ubuntu-latest]
env:
OS: ${{ matrix.os }}
PYTHON: ${{ matrix.python }}
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@v2
- name: Set up Python ${{ matrix.python }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python }}
- name: Get pip cache dir
id: pip-cache-dir
run: |
echo "::set-output name=dir::$(pip cache dir)"
- name: Restore pip cache
uses: actions/cache@v2
with:
path: ${{ steps.pip-cache-dir.outputs.dir }}
key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}
restore-keys: |
pip-${{ runner.os }}-${{ env.pythonLocation }}-
- name: Install test dependencies
run: |
python -m pip install --upgrade pip wheel
pip install codecov
- name: Install dependencies
run: |
pip install ".[dev,test]"
- name: Install R package dependencies
run: |
Rscript --vanilla -e "install.packages(c('BiocManager', 'statmod'), repos='http://cran.us.r-project.org'); library('BiocManager'); BiocManager::install('edgeR')"
- name: Test
env:
MPLBACKEND: agg
PLATFORM: ${{ matrix.os }}
DISPLAY: :42
run: |
pytest -v --cov --color=yes
- name: Upload coverage
env:
CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
# run: |
# codecov --required --flags=unittests
uses: codecov/codecov-action@v3
with:
token: ${{secrets.CODECOV_TOKEN}}