diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4328cea..4148a57 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -124,7 +124,10 @@ jobs: cache-suffix: unit-${{ matrix.shard.id }} # Install genomics extra so pyfaidx / pysam are present for the # error-path tests in tests/sources/test_{fasta,bam}.py. - linux-editable-target: ".[dev,test,genomics]" + # chem carries rdkit, which the drug-discovery, molnet and molecular-splitter + # tests exercise. It is an extra so that installing the package does not pull a + # chemistry toolkit, but the tests that cover it must still have it. + linux-editable-target: ".[dev,test,genomics,chem]" - name: Run unit tests shell: bash @@ -286,7 +289,9 @@ jobs: with: python-version: "3.11" cache-suffix: perf - linux-editable-target: ".[dev,test,benchmark]" + # chem carries rdkit, needed by tests/benchmarks/test_bench_dti.py and + # test_bench_molnet.py. + linux-editable-target: ".[dev,test,benchmark,chem]" - name: Run performance tests shell: bash @@ -335,7 +340,10 @@ jobs: with: python-version: "3.11" cache-suffix: coverage - linux-editable-target: ".[dev,test,genomics]" + # chem carries rdkit, which the drug-discovery, molnet and molecular-splitter + # tests exercise. It is an extra so that installing the package does not pull a + # chemistry toolkit, but the tests that cover it must still have it. + linux-editable-target: ".[dev,test,genomics,chem]" - name: Download all coverage data artifacts uses: actions/download-artifact@v4