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njzjz merged 1 commit into from
May 27, 2026
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build: replace openbabel-wheel with openbabel #974

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2 changes: 1 addition & 1 deletion .github/workflows/benchmark.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ jobs:
**/requirements*.txt
**/pyproject.toml
- name: Install dependencies
run: uv pip install --system .[test,amber,ase,pymatgen,benchmark] rdkit openbabel-wheel
run: uv pip install --system .[test,amber,ase,pymatgen,benchmark] rdkit 'openbabel>=3.2.0'
- name: Run benchmarks
uses: CodSpeedHQ/action@v4
with:
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2 changes: 1 addition & 1 deletion .github/workflows/pyright.yml
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Expand Up @@ -13,7 +13,7 @@ jobs:
with:
python-version: '3.12'
- run: pip install uv
- run: uv pip install --system -e .[amber,ase,pymatgen] rdkit openbabel-wheel
- run: uv pip install --system -e .[amber,ase,pymatgen] rdkit 'openbabel>=3.2.0'
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@coderabbitai coderabbitai Bot May 27, 2026

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⚠️ Potential issue | 🔴 Critical | 🏗️ Heavy lift

Critical: Package version openbabel>=3.2.0 does not exist on PyPI.

This is the same issue as in benchmark.yml. The latest available openbabel version on PyPI is 3.1.1.1, which does not satisfy the >=3.2.0 constraint. The Pyright type-checking workflow will fail at dependency installation.

🤖 Prompt for AI Agents 
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In @.github/workflows/pyright.yml at line 16, The workflow's dependency install
line uses a non-existent PyPI spec `openbabel>=3.2.0`; update the run step
string (the `run: uv pip install --system -e .[amber,ase,pymatgen] rdkit
'openbabel>=3.2.0'` command) to use a valid package spec such as
`openbabel==3.1.1.1` (or `openbabel>=3.1.1.1,<3.2`) so the installer can
succeed, and apply the same change to the identical install line in
benchmark.yml if present.

- uses: jakebailey/pyright-action@v3
with:
version: 1.1.363
2 changes: 1 addition & 1 deletion .github/workflows/test.yml
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Expand Up @@ -26,7 +26,7 @@ jobs:
**/pyproject.toml
cache-suffix: "py${{ matrix.python-version }}"
- name: Install dependencies
run: uv pip install --system .[test,amber,ase,pymatgen] coverage ./tests/plugin rdkit openbabel-wheel
run: uv pip install --system .[test,amber,ase,pymatgen] coverage ./tests/plugin rdkit 'openbabel>=3.2.0'
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@coderabbitai coderabbitai Bot May 27, 2026

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⚠️ Potential issue | 🔴 Critical | 🏗️ Heavy lift

Critical: Package version openbabel>=3.2.0 does not exist on PyPI.

This is the same blocking issue affecting all three workflows. The openbabel package latest version is 3.1.1.1, not 3.2.0 or higher. Both Python 3.10 and 3.13 test jobs will fail during dependency installation.

🤖 Prompt for AI Agents 
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In @.github/workflows/test.yml at line 29, The workflow run step installs a
non-existent package version "openbabel>=3.2.0" causing CI installs to fail;
update the pip install invocation in the run step (the install command string)
to a valid constraint such as "openbabel>=3.1.1.1" or pin to
"openbabel==3.1.1.1" (or remove the openbabel spec if not required), then re-run
the Python 3.10 and 3.13 test jobs to confirm dependency installation succeeds.

- name: Test
run: cd tests && coverage run --source=../dpdata -m unittest && cd .. && coverage combine tests/.coverage && coverage report
- name: Run codecov
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