update pyopenms as it seems to be compatible with numpy2 #51992
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/pyopenms/meta.yaml (2)
Line range hint
13-14: Hard-coded version in URL should be templatedThe URL contains a hard-coded version
3.2.0. This should be templated using the version variable to avoid maintenance issues in future releases:- url: https://github.com/OpenMS/OpenMS/releases/download/release%2F3.2.0/OpenMS-3.2.tar.gz + url: https://github.com/OpenMS/OpenMS/releases/download/release%2F{{ version }}/OpenMS-{{ version.rsplit('.', 1)[0] }}.tar.gz
Line range hint
44-58: Document run_exports workaround more explicitlyThe comment about run_exports bugs should be more specific to help future maintainers. Consider documenting:
- Which specific run_exports bugs are being worked around
- Link to relevant issue tracker entries
- Conditions under which this workaround can be removed
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📒 Files selected for processing (2)
recipes/pyopenms/conda_build_config.yaml(1 hunks)recipes/pyopenms/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/pyopenms/conda_build_config.yaml
[error] 13-13: syntax error: expected chomping or indentation indicators, but found '='
(syntax)
🔇 Additional comments (4)
recipes/pyopenms/conda_build_config.yaml (1)
13-15: Verify numpy version compatibility matrix with Python versions
Please verify that the numpy version constraints are appropriate for each Python version in the matrix. Currently, Python 3.9-3.11 use >=1.23.0 while Python 3.12 uses >=1.26.0.
Let's check the numpy version requirements for different Python versions:
✅ Verification successful
Numpy version constraints are appropriate for Python versions
The numpy version constraints in the recipe are correctly configured:
- Python 3.9-3.11: numpy >=1.23.0 (appropriate as these Python versions are compatible with numpy 1.23+)
- Python 3.12: numpy >=1.26.0 (required as Python 3.12 support was added in numpy 1.26.0)
The configuration follows numpy's Python version compatibility matrix and ensures proper builds for each Python version.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify numpy version compatibility with Python versions
# Expected: Find any incompatibilities between numpy and Python versions
# Check if there are any other recipes using similar numpy/Python combinations
rg -l "numpy.*1\.2[36]" --type yaml $(fd -e yaml -e yml . recipes/)
# Look for potential numpy version constraints in build scripts
rg "numpy.*1\.2[36]" --type python $(fd -e py . recipes/)
Length of output: 365883
Script:
#!/bin/bash
# Let's check the numpy version compatibility with Python versions
# First, let's check if there are any specific Python version constraints in the recipe
cat recipes/pyopenms/conda_build_config.yaml
# Let's also check the meta.yaml for any additional context
cat recipes/pyopenms/meta.yaml
Length of output: 2526
🧰 Tools
🪛 yamllint
[error] 13-13: syntax error: expected chomping or indentation indicators, but found '='
(syntax)
recipes/pyopenms/meta.yaml (3)
20-23: Build configuration changes look good
The build number increment is appropriate for rebuilding with updated numpy compatibility. The run_exports section correctly pins the subpackage version for ABI compatibility.
Line range hint 59-62: Consider enhancing test coverage
The current test only verifies basic import functionality. The TODO comment about running the full test suite should be addressed:
- What prevents running the full test suite?
- What specific tests would be most valuable to include?
Would you like me to help create a more comprehensive test plan or open an issue to track this enhancement?
Line range hint 41-41: Verify numpy2 compatibility
Since this PR aims to update pyopenms for numpy2 compatibility:
- Ensure that the package has been tested with numpy2
- Consider documenting any known compatibility issues or limitations
Run the following to check for numpy version-specific code:
Also applies to: 53-53
| - >=1.23.0 | ||
| - >=1.23.0 | ||
| - >=1.26.0 |
There was a problem hiding this comment.
Critical: Avoid using >= constraints for numpy to prevent ABI compatibility issues
Using >= constraints for numpy versions is risky as it can lead to ABI compatibility issues. Numpy has strict ABI compatibility requirements, and it's recommended to pin to specific minor versions using the x.* syntax.
Apply this diff to maintain ABI compatibility:
numpy:
- 1.23.*
- - >=1.23.0
- - >=1.23.0
- - >=1.26.0
+ - 1.23.*
+ - 1.23.*
+ - 1.26.*Reference: Numpy's binary compatibility policy recommends pinning to specific minor versions to ensure ABI compatibility.
📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| - >=1.23.0 | |
| - >=1.23.0 | |
| - >=1.26.0 | |
| - 1.23.* | |
| - 1.23.* | |
| - 1.26.* |
🧰 Tools
🪛 yamllint
[error] 13-13: syntax error: expected chomping or indentation indicators, but found '='
(syntax)
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@timosachsenberg or @jpfeuffer can you confirm that numpy> 2 works fine with pyopenms? |
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In theory it is/always was (if a new enough numpy was used to build it) but it could be that the latest release still has an unnecessary hardcoded version limit in its setup.py. |
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https://github.com/OpenMS/OpenMS/blob/release/3.2.0/src/pyOpenMS/setup.py#L257 I assume this will fail here: |
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Oh, it did not. Ah yes, we use "ignore-installed" anyway, since there is no pip stuff. In that case, it should be fine. It barely has any numpy python code. Only a recent enough numpy C API was important for building. |
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@jpfeuffer thanks a lot for the explanation, that is nice! @bgruening can this then be merged? |
see here
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