Final fix for yesterdays changes #265
Workflow file for this run
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# This is a basic workflow to help you get started with Actions | |
name: Testing | |
# Controls when the workflow will run | |
on: | |
# Triggers the workflow on push or pull request events but only for the main branch | |
push: | |
branches: | |
- main | |
- dev | |
- dev_1.0 | |
pull_request: | |
branches: | |
- main | |
- dev | |
- dev_1.0 | |
workflow_dispatch: # make is manually start-able | |
# A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
jobs: | |
# This workflow contains a single job called "test" | |
test: | |
runs-on: 'ubuntu-latest' | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Setup Mamba | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
python-version: '3.10' | |
miniforge-variant: Mambaforge | |
miniforge-version: latest | |
activate-environment: MPP | |
use-mamba: true | |
- name: Install environment | |
shell: bash -l {0} | |
run: | | |
mamba install -c conda-forge -c bioconda -y numpy pandas networkx matplotlib pytest setuptools pyscipopt"<4.0.0" foldseek mmseqs2 cd-hit mash tmalign diamond cvxpy pytest-cov rdkit">=2022.09.1" pytest-cases scikit-learn">=1.2,<1.6" pyyaml h5py | |
pip install grakel | |
- name: Run tests | |
shell: bash -l {0} | |
run: | | |
cd tests | |
pytest -m "not todo and not issue" --cov=../datasail/ --cov-report=xml | |
- name: Upload coverage to Codecov | |
uses: codecov/codecov-action@v3 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
fail_ci_if_error: false | |
files: coverage.xml |