Reformat and name steps for the Conda CI job
Follow the same conventions as for the other CI jobs.
@@ -106,34 +106,38 @@ jobs:
conda:
timeout-minutes: 20
- runs-on: ubuntu-latest
+ runs-on: ${{ matrix.os }}-latest
strategy:
matrix:
+ os: [ubuntu]
python-version: [3.7]
defaults:
run:
shell: bash -l {0} # needed for conda activation
env:
HTSLIB_CONFIGURE_OPTIONS: "--disable-libcurl"
+
steps:
- - uses: actions/checkout@v2
+ - name: Checkout pysam
+ uses: actions/checkout@v2
+
- uses: conda-incubator/setup-miniconda@v2
with:
channel-priority: strict
activate-environment: testenv
auto-activate-base: false
use-only-tar-bz2: true
- - run: conda config --add channels bioconda --add channels conda-forge
- - run: conda install python=${{ matrix.python-version }} cython
- - name: Create sdist
- run: python setup.py sdist
- - name: Ensure sdist does not contain config.h
- run: "! tar -tf dist/pysam-*.tar.gz | grep '/config.h$'"
- - name: Install
- run: python setup.py install
- - name: Prepare test data
+
+ - name: Set up Conda and Python ${{ matrix.python-version }}
run: |
- conda install "samtools>=1.11" "bcftools>=1.11" "htslib>=1.11" pytest
- make -C tests/pysam_data
- make -C tests/cbcf_data
- - run: pytest
+ conda config --add channels bioconda --add channels conda-forge
+ conda install python=${{ matrix.python-version }} cython
+
+ - name: Build (directly from checkout)
+ run: python setup.py install
+
+ - name: Install test prerequisites via Conda
+ run: conda install "samtools>=1.11" "bcftools>=1.11" "htslib>=1.11" pytest
+
+ - name: Run tests
+ run: REF_PATH=':' pytest
