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try to use mamba instead of pure python
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aryarm authored Oct 31, 2023
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17 changes: 9 additions & 8 deletions .github/workflows/tests.yml
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Expand Up @@ -12,18 +12,19 @@ jobs:

steps:
- uses: actions/checkout@v4
- name: Setup Python # Set Python version
uses: actions/setup-python@v4
- name: Set up mamba
uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: test
auto-activate-base: false
python-version: ${{ matrix.python-version }}
- name: Install test dependencies
run: |
# $CONDA is an environment variable pointing to the root of the miniconda directory
$CONDA/bin/conda install -y -n base -c conda-forge -c bioconda bcftools
# Install pip and pytest
miniforge-version: latest
miniforge-variant: Mambaforge
use-mamba: true
- name: Install conda dependencies
run: conda install -c conda-forge -c bioconda bcftools pip
- name: Install pytest and trtools
run: |
python -m pip install --upgrade pip
pip install pytest pytest-cov trtools
- name: Test with pytest
run: |
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