tidy up test names #992
Workflow file for this run
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name: Python package | |
on: [push] | |
jobs: | |
Test: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
test: ["config", "design", "pipeline"] | |
assay: ["atac", "chip-rx", "chip", "rna-rx", "rna", "snp"] | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: eWaterCycle/setup-apptainer@v2 | |
with: | |
apptainer-version: 1.1.2 | |
- name: Add singularity hub remote | |
run: | | |
apptainer remote add --no-login SylabsCloud cloud.sylabs.io | |
apptainer remote use SylabsCloud | |
- name: Cache conda | |
id: cache-conda | |
uses: actions/cache@v3 | |
with: | |
path: | | |
~/mambaforge/envs/test | |
key: ${{ runner.os }}-conda-${{ hashFiles('**/testing.yml') }} | |
restore-keys: | | |
${{ runner.os }}-conda- | |
- name: Cache pip | |
id: cache-pip | |
uses: actions/cache@v3 | |
with: | |
path: ~/.cache/pip | |
key: ${{ runner.os }}-pip-${{ hashFiles('**/testing.yml') }} | |
restore-keys: | | |
${{ runner.os }}-pip- | |
- name: Set up conda using miniforge | |
uses: conda-incubator/setup-miniconda@v3 | |
with: | |
environment-file: testing.yml | |
miniforge-variant: Mambaforge | |
miniforge-version: latest | |
use-mamba: true | |
- name: Install the package | |
shell: pwsh | |
run: | | |
pip install . | |
- name: Test ${{ matrix.test }} ${{ matrix.assay }} | |
shell: pwsh | |
run: | | |
pytest tests/test_pipelines.py::test_${{ matrix.test }}[${{ matrix.assay }}] -vv -s --cores 4 |