Revert "CI: pin numpy to <2.3 & rdkit to <2025.3.3"

[njzjz]

Reverts #837

Both issues have been fixed

Summary by CodeRabbit

• Chores
  • Removed version constraints on chemistry and numeric dependencies in CI workflows (e.g., rdkit and numpy), switching to more permissive installs so the latest compatible package releases are used during automated tests.

[codspeed-hq]

Merging this PR will improve performance by 11.76%

⚠️ Unknown Walltime execution environment detected

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For the most accurate results, we recommend using CodSpeed Macro Runners: bare-metal machines fine-tuned for performance measurement consistency.

⚡ 1 improved benchmark
✅ 1 untouched benchmark
⏩ 2 skipped benchmarks¹

Performance Changes

	Mode	Benchmark	BASE	HEAD	Efficiency
⚡	WallTime	test_import	11.1 ms	10 ms	+11.76%

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_{Comparing revert-837-fix-parmed-import (4460213) with devel (4ae8b2c)}

Footnotes

1. 2 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩

[Copilot]

Pull request overview

This PR reverts a previous change (PR #837) that added temporary version constraints for numpy (<2.3) and rdkit (<2025.3.3) in CI workflows. According to the PR description, the underlying compatibility issues that necessitated these pins have now been resolved.

Changes:

• Remove numpy and rdkit version constraints from the test workflow
• Remove rdkit version constraint from the pyright workflow

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
.github/workflows/test.yml	Removes 'numpy<2.3' and 'rdkit<2025.3.3' version pins from CI dependencies
.github/workflows/pyright.yml	Removes 'rdkit<2025.3.3' version pin from type checking workflow dependencies

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[njzjz]

parmed released v4.3.1 but didn't upload it to pypi.

[coderabbitai]

📝 Walkthrough

Walkthrough

Removes version constraints from rdkit in .github/workflows/pyright.yml and rdkit plus numpy in .github/workflows/test.yml, changing pip install lines to use unconstrained package names.

Changes

Cohort / File(s)	Summary
GitHub Actions — pyright workflow \.github/workflows/pyright\.yml	Replaced rdkit<2025.3.3 (quoted) with an unconstrained rdkit in the pip install extras list.
GitHub Actions — test workflow \.github/workflows/test\.yml	Removed version pins rdkit<2025.3.3 and numpy<2.3 from the pip install command and switched to unconstrained rdkit and openbabel-wheel installs.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• CI: pin numpy to <2.3 & rdkit to <2025.3.3 #837: Modifies CI install commands for rdkit/numpy; directly related as it also changes version pinning for the same packages.

Suggested reviewers

• wanghan-iapcm

🚥 Pre-merge checks | ✅ 4

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately describes the main change: reverting version constraints on numpy and rdkit in CI configuration files.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Merge Conflict Detection	✅ Passed	✅ No merge conflicts detected when merging into devel

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✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch revert-837-fix-parmed-import

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[coderabbitai]

Actionable comments posted: 1

🤖 Fix all issues with AI agents

In @.github/workflows/pyright.yml:
- Line 16: The rdkit package was unpinned in the workflow command (the run step
installing packages), but RDKit 2025.03.3 is incompatible with NumPy 2.x;
restore a version constraint (e.g., rdkit<2025.3.3) in the install command used
in the run step to prevent installing the problematic release, keep the rest of
the packages unchanged, and add a brief inline comment referencing RDKit issue
#7477 so the pin is not removed until NumPy 2.0 compatibility is confirmed.

📜 Review details

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 2fa782d and 307eb67.

📒 Files selected for processing (2)

• .github/workflows/pyright.yml
• .github/workflows/test.yml

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• GitHub Check: Upload results

🔇 Additional comments (1)

.github/workflows/test.yml (1)

29-29: LGTM - version constraints for rdkit and numpy removed.

The change removes both rdkit<2025.3.3 and numpy<2.3 pins as intended by this revert. Since the matrix tests against both Python 3.8 and 3.12, ensure that the upstream compatibility fixes work across both Python versions.

Verify the CI passes after this change, as the PR relies on upstream fixes being in place for both rdkit and numpy.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.27%. Comparing base (4ae8b2c) to head (4460213).

Additional details and impacted files

@@           Coverage Diff           @@
##            devel     #921   +/-   ##
=======================================
  Coverage   86.27%   86.27%           
=======================================
  Files          86       86           
  Lines        8032     8032           
=======================================
  Hits         6930     6930           
  Misses       1102     1102           

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