build: replace openbabel-wheel with openbabel

[njzjz-bot]

Problem

• openbabel-wheel has been superseded by the official openbabel package.
• Starting with Open Babel 3.2.0, users can install the Python wheels directly from openbabel on PyPI.

Change

• Replace openbabel-wheel usage with openbabel>=3.2.0.

Notes

• This keeps the same Python import path (openbabel) while depending on the upstream package name.

Authored by OpenClaw (model: custom-chat-jinzhezeng-group/gpt-5.5)

Summary by CodeRabbit

• Chores
  • Updated project dependencies to require OpenBabel version 3.2.0 or higher.

[coderabbitai]

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Review configuration:

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 6171e8ca-698d-4303-836b-20a989637a4b

📥 Commits

Reviewing files that changed from the base of the PR and between 889e4ef and 96556be.

📒 Files selected for processing (1)

• pyproject.toml

📝 Walkthrough

Walkthrough

The PR updates the project dependency specification in pyproject.toml, replacing the openbabel-wheel package with openbabel>=3.2.0 to use the main openbabel package with a minimum version constraint.

Changes

Dependency Management

Layer / File(s)	Summary
OpenBabel Dependency Constraint pyproject.toml	The [project].dependencies list is updated to replace openbabel-wheel with openbabel>=3.2.0, establishing a minimum version requirement for the openbabel package.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

Suggested reviewers

• wanghan-iapcm

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely summarizes the main change: replacing the openbabel-wheel dependency with the official openbabel package.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[njzjz-bot]

Verdict: Blocking. This one-line dependency change breaks the project's declared Python 3.9 support, and CI directly demonstrates that the dependency set is unsatisfiable. Because this PR was opened by the active njzjz-bot account, GitHub does not allow the author to submit REQUEST_CHANGES; this COMMENT review records the blocker.

Note: The Codex quota is about to reset, so I am using the remaining tokens to review all open PRs in this repository.

Coding agent: Codex
Codex version: codex-cli 0.144.6
Model: gpt-5.6-sol
Reasoning effort: xhigh

[njzjz-bot]

[Blocking] openbabel==3.2.0 requires Python >=3.10, while this project still declares requires-python = ">=3.9". The Python 3.9 CI job explicitly reports that dpgen[test] is unsatisfiable, and the 3.12 job is then cancelled by fail-fast. A minimal compatibility fix is to retain the wheel package on 3.9 and use the upstream package on 3.10+:

Suggested change

	'openbabel>=3.2.0',
	"openbabel-wheel; python_version < '3.10'",
	"openbabel>=3.2.0; python_version >= '3.10'",

If the intent is to raise DP-GEN's minimum Python version to 3.10, that should be a separate breaking change with synchronized CI, metadata, and documentation.

[njzjz-bot]

Independent review C

I found a blocking compatibility regression: the replacement dependency cannot be resolved on the repository-supported Python 3.9 job. Because this PR is authored by the active njzjz-bot account, GitHub self-review rules prevent a formal REQUEST_CHANGES state; this COMMENT review records the finding and that limitation.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

[njzjz-bot]

Independent review B\n\nBlocking finding: the dependency change makes the supported Python 3.9 environment unsatisfiable.\n\nGitHub does not permit njzjz-bot to APPROVE or REQUEST_CHANGES on its own pull request, so the formal state is blocked by the self-review rule and this finding is submitted as COMMENT.\n\nCoding agent: Codex\nCodex version: codex-cli 0.151.0\nModel: gpt-5.6-sol\nReasoning effort: xhigh

[njzjz-bot]

Independent review A

A blocking packaging regression is attached inline. GitHub does not permit njzjz-bot to approve or request changes on its own PR, so this COMMENT review records the result as changes needed; no formal review state is claimed.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 49.80%. Comparing base (66232e5) to head (96556be).
⚠️ Report is 5 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1882   +/-   ##
=======================================
  Coverage   49.80%   49.80%           
=======================================
  Files          83       83           
  Lines       14986    14987    +1     
=======================================
+ Hits         7464     7465    +1     
  Misses       7522     7522           

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[njzjz-bot]

Independent re-review B

Reviewed the environment markers against the packages' published Python requirements and wheel availability, and checked the successful Python 3.9/3.12 CI installs. The split keeps Python 3.9 on openbabel-wheel while using openbabel where it is supported. No further changes are required from this review.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

[njzjz-bot]

Independent re-review C

No changes remain from this independent pass. GitHub does not allow njzjz-bot to formally approve its own PR, so this review is submitted as COMMENT rather than APPROVE.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

[njzjz-bot]

Independent re-review A

No remaining correctness issues found at 96556be. I checked Python-version dependency markers and the successful Python 3.9 and 3.12 installation/test checks. Because this PR is authored by njzjz-bot, GitHub does not permit this account to approve its own PR; this COMMENT means no changes remain from independent re-review A.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh