Skip to content

Install the chem extra in the jobs that exercise RDKit #9

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
mahdi-shafiei merged 1 commit into from
Aug 28, 2026
Merged

Install the chem extra in the jobs that exercise RDKit #9

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 11 additions & 3 deletions .github/workflows/ci.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
Loading