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build.yml
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name: build
on: [ push ]
jobs:
build:
runs-on: ${{ matrix.os }}
strategy:
max-parallel: 4
matrix:
os: [ ubuntu-latest, windows-latest ]
python-version: [ 3.7 ]
steps:
- uses: actions/checkout@master
- name: Setup conda
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
# Installing dependencies
- name: Install dependencies
shell: bash -l {0}
run: |
conda install --yes -c conda-forge numpy pandas scipy networkx=2.3 \
jinja2 plotly pathos sortedcontainers wordcloud \
python-igraph py2cytoscape matplotlib=2.2.3 matplotlib-base=2.2.3 pycairo seaborn \
defusedxml openpyxl jupyter
mkdir -p ~/.config/matplotlib
echo "backend:Agg" > ~/.config/matplotlib/matplotlibrc
pip install bioservices==1.6 matplotlib_venn
pip install nose python-coveralls nose-exclude nose-timer codecov
- name: Install MAGINE
shell: bash -l {0}
run: |
python setup.py build --build-lib=build/lib
python magine/copy_sample_dbs.py
- name: Test MAGINE
shell: bash -l {0}
run: |
nosetests build/lib/magine/tests --with-coverage --cover-inclusive \
--cover-package=build/lib/magine --logging-level=INFO --with-timer \
--cover-xml
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v2
with:
fail_ci_if_error: true