diff --git a/.github/workflows/test_pipelines.yml b/.github/workflows/test_pipelines.yml index ccf3803d..2ec48234 100755 --- a/.github/workflows/test_pipelines.yml +++ b/.github/workflows/test_pipelines.yml @@ -3,8 +3,6 @@ name: Python package on: [push] jobs: - Test: - if: github.event_name == 'pull_request' || github.event_name == 'push' Test: if: github.event_name == 'pull_request' || github.event_name == 'push' runs-on: ubuntu-latest @@ -12,8 +10,6 @@ jobs: matrix: test: ["config", "design", "pipeline"] assay: ["atac", "chip-rx", "chip", "rna-rx", "rna", "snp"] - test: ["config", "design", "pipeline"] - assay: ["atac", "chip-rx", "chip", "rna-rx", "rna", "snp"] steps: - uses: actions/checkout@v3 @@ -28,7 +24,6 @@ jobs: key: ${{ runner.os }}-env-${{ hashFiles('**/testing.yml') }} restore-keys: | ${{ runner.os }}-env- - - name: Setup conda uses: conda-incubator/setup-miniconda@v3 with: @@ -41,7 +36,6 @@ jobs: shell: pwsh run: | pip install . - - name: Cache singularity if: matrix.test == 'pipeline' id: cache-singularity @@ -51,7 +45,6 @@ jobs: key: ${{ runner.os }}-singularity-${{ hashFiles('tmp/*') }} restore-keys: | ${{ runner.os }}-singularity- - - uses: eWaterCycle/setup-apptainer@v2 if: matrix.test == 'pipeline' with: @@ -63,7 +56,6 @@ jobs: run: | apptainer remote add --no-login SylabsCloud cloud.sylabs.io apptainer remote use SylabsCloud - - name: Pull singularity images if: matrix.test == 'pipeline' && steps.cache-singularity.outputs.cache-hit != 'true' shell: bash @@ -77,10 +69,9 @@ jobs: elif [[ "${{ matrix.assay }}" == "rna-rx" ]]; then apptainer pull --force library://asmith151/seqnado/seqnado_report:latest fi - - name: Test ${{ matrix.test }} ${{ matrix.assay }} shell: pwsh env: TMPDIR: /tmp run: | - pytest tests/test_pipelines.py::test_${{ matrix.test }}[${{ matrix.assay }}] -vv -s --cores 4 \ No newline at end of file + pytest tests/test_pipelines.py::test_${{ matrix.test }}[${{ matrix.assay }}] -vv -s --cores 4