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Update pyprophet to 2.2.9 #51284

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Update pyprophet to 2.2.9 #51284

wants to merge 8 commits into from

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@BiocondaBot BiocondaBot commented Oct 9, 2024

Update pyprophet: 2.2.52.2.9

install with bioconda Conda

Info Link or Description
Recipe recipes/pyprophet (click to view/edit other files)
Summary PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
Home https://github.com/PyProphet/pyprophet
Releases https://pypi.org/pypi/pyprophet/json

This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Oct 9, 2024
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coderabbitai bot commented Oct 9, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request introduces comprehensive modifications to the meta.yaml file for the pyprophet package. The version number is updated from 2.2.5 to 2.2.8, and the SHA256 hash value is changed to a new checksum. The build number is reset from 3 to 0. The source URL is modified to reflect the new version in its path. In the requirements section, version constraints for cython and numpy are removed, pypdf2 is renamed to pypdf, and python-duckdb, pyarrow, libgomp, and llvm-openmp are added as new dependencies. Additionally, seaborn is replaced with matplotlib-base, and the dataclasses requirement has been removed. The license is specified as "BSD-3-Clause" with a new license_file entry added. The summary is updated for clarity, and a new dev_url is included. The overall structure of the file remains consistent, with no changes to the build or test commands.

Possibly related PRs

  • Update meta.yaml for spec2vec #49857: The changes in the meta.yaml file for spec2vec include updates to the version and requirements, similar to the modifications made in the meta.yaml for pyprophet.
  • Update pysradb to 2.2.2 #51132: The update to the meta.yaml file for pysradb includes a version increment and a SHA256 checksum update, paralleling the version and checksum changes in the pyprophet PR.
  • Update bactopia-py to 1.2.0 #51154: The bactopia-py update involves a version change and SHA256 checksum update in its meta.yaml, similar to the changes made in the pyprophet PR.
  • Update peaks2utr to 1.3.3 #51170: The peaks2utr update reflects a version increment and SHA256 checksum update, akin to the changes in the pyprophet PR.
  • Update qtlseq to 2.2.5 #51172: The qtlseq update includes a version increment and SHA256 checksum update, which is consistent with the changes made in the pyprophet PR.
  • Update qtlseq to 2.2.6 #51191: The update to qtlseq also involves a version increment and SHA256 checksum update, similar to the modifications in the pyprophet PR.
  • Update vclean to 0.2.1 #51223: The vclean update includes a version increment and SHA256 checksum update, paralleling the changes in the pyprophet PR.
  • Update bactopia-py to 1.2.1 #51226: The bactopia-py update involves a version change and SHA256 checksum update, similar to the modifications made in the pyprophet PR.
  • Update civicpy to 3.1.2 #51252: The civicpy update reflects a version increment and SHA256 checksum update, akin to the changes in the pyprophet PR.
  • Update pybiolib to 1.2.188 #51299: The pybiolib update includes a version increment and SHA256 checksum update, consistent with the changes made in the pyprophet PR.

Suggested reviewers

  • mencian

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Actionable comments posted: 2

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between a19d85e and 6b08fd2.

📒 Files selected for processing (1)
  • recipes/pyprophet/meta.yaml (3 hunks)
🧰 Additional context used
🔇 Additional comments (5)
recipes/pyprophet/meta.yaml (5)

2-2: Version and hash updates look good.

The version has been correctly updated to 2.2.7, and the corresponding SHA256 hash has been updated. This is consistent with the PR objective of updating pyprophet to version 2.2.7.

Also applies to: 4-4


15-15: Build number reset is correct.

The build number has been appropriately reset to 0 for the new version. This is the expected practice when updating to a new package version.


59-59: License updates are appropriate.

The license has been updated to the more specific "BSD-3-Clause" and a license_file entry has been added. These changes improve the clarity of the licensing information and ensure that the license file is included in the package.

Also applies to: 61-61


62-63: Summary and dev_url updates are beneficial.

The summary has been updated to provide a more detailed description of the package's purpose. Additionally, a dev_url has been added, which is helpful for users who want to access the development repository. These changes improve the metadata and usability of the package.


35-35: Verify run requirements changes.

The following changes have been made to the run requirements:

  1. Added python-duckdb and pyarrow as new dependencies.
  2. Replaced seaborn with seaborn-base.
  3. Updated pypdf2 to pypdf.

Please ensure that:

  1. The new dependencies (python-duckdb and pyarrow) are necessary for the updated version.
  2. The switch to seaborn-base doesn't remove any required functionality.
  3. The update from pypdf2 to pypdf is consistent with the package's needs.

Run the following script to check if these changes are consistent with other recipes and if they might affect other packages:

Also applies to: 40-40, 42-42, 48-48

✅ Verification successful

Run requirements changes are consistent and well-isolated.

  • python-duckdb is only added to recipes/pyprophet/meta.yaml, ensuring no unintended impact on other recipes.
  • pyarrow and seaborn-base updates are consistently applied across multiple recipes, maintaining stability.
  • The update from pypdf2 to pypdf in pyprophet does not affect other recipes.
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check usage of new and updated dependencies in other recipes
echo "Checking python-duckdb usage:"
rg --type yaml 'python-duckdb' recipes/
echo "Checking pyarrow usage:"
rg --type yaml 'pyarrow' recipes/
echo "Checking seaborn-base usage:"
rg --type yaml 'seaborn-base' recipes/
echo "Checking pypdf usage:"
rg --type yaml 'pypdf' recipes/

Length of output: 5344

run_exports:
- {{ pin_subpackage(name, max_pin="x") }}
entry_points:
- pyprophet=pyprophet.main:cli
script: python -m pip install --no-deps --ignore-installed .
script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
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💡 Codebase verification

Inconsistent usage of --no-build-isolation flag across recipes.

The --no-build-isolation flag is only used in recipes/pyprophet/meta.yaml. Other recipes do not utilize this flag, which might lead to inconsistent build behaviors and dependency resolutions.

  • recipes/pyprophet/meta.yaml uses --no-build-isolation
🔗 Analysis chain

Verify the impact of --no-build-isolation flag.

The build script now includes the --no-build-isolation flag. This allows the build to access packages in the build environment, which might affect how the package is built and its dependencies are resolved.

Please confirm that this change is intentional and doesn't introduce any unexpected behavior. You can run the following script to check if this flag is used consistently across other recipes:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check if --no-build-isolation is used consistently
rg --type yaml 'script:.*--no-build-isolation' recipes/

Length of output: 5344

Comment on lines +28 to +30
- cython
- numpy
- pypdf
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💡 Codebase verification

Potential Compatibility Issues Detected.

The changes to the host requirements may affect other recipes:

  1. Dependency Naming:

    • pypdf2 is still used in multiple recipes (tobias, tetrimmer, jcvi).
    • Renaming it to pypdf in pyprophet may lead to inconsistencies or dependency conflicts.
  2. Version Constraints:

    • Removing version constraints for cython and numpy could introduce compatibility issues with other recipes that specify particular versions.
    • Multiple recipes have specific version requirements for pyarrow, indicating that changes to its dependencies should be managed carefully.

Please review and address these potential issues to ensure build compatibility across all recipes.

🔗 Analysis chain

Verify host requirements changes.

The following changes have been made to the host requirements:

  1. Version constraints for cython and numpy have been removed.
  2. pypdf2 has been renamed to pypdf.

These changes might affect the build process and compatibility. Please ensure that:

  1. The package builds successfully with the latest versions of cython and numpy.
  2. The rename from pypdf2 to pypdf is correct and doesn't break any functionality.

Run the following script to check if these changes are consistent with other recipes using these packages:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check usage of cython, numpy, and pypdf in other recipes
echo "Checking cython usage:"
rg --type yaml 'cython' recipes/
echo "Checking numpy usage:"
rg --type yaml 'numpy' recipes/
echo "Checking pypdf usage:"
rg --type yaml 'pypdf' recipes/

Length of output: 5344

@BiocondaBot BiocondaBot changed the title Update pyprophet to 2.2.7 Update pyprophet to 2.2.8 Oct 12, 2024
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Actionable comments posted: 1

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between f7a98ca and 96f28d1.

📒 Files selected for processing (1)
  • recipes/pyprophet/meta.yaml (3 hunks)
🧰 Additional context used
🔇 Additional comments (6)
recipes/pyprophet/meta.yaml (6)

2-2: Version and hash update look good.

The version has been correctly updated to 2.2.8, and the SHA256 hash has been updated accordingly. This is consistent with the PR objective of updating pyprophet.

Also applies to: 4-4


15-15: Build number reset is correct.

The build number has been appropriately reset to 0 for the new version. This is the expected practice when updating to a new package version.


61-61: License update and file addition look good.

The license has been updated to the more specific "BSD-3-Clause" and a license file has been added. These changes improve the clarity of the licensing terms and compliance. Good job on making these improvements.

Also applies to: 63-63


64-65: Metadata improvements look good.

The package summary has been updated to provide a more descriptive explanation of PyProphet's functionality. Additionally, a development URL has been added, which is helpful for users who want to access the source code or contribute to the project. These changes enhance the package's metadata and improve its discoverability.


35-36: Review run requirements changes carefully.

Several changes have been made to the run requirements:

  1. Platform-specific runtime requirements (libgomp for Linux, llvm-openmp for macOS) have been added, which is good for cross-platform compatibility.

  2. New dependencies python-duckdb and pyarrow have been added. These might introduce new functionalities or optimizations.

  3. seaborn has been replaced with matplotlib-base. This might change the package's visualization capabilities.

  4. pypdf2 has been renamed to pypdf, consistent with the change in host requirements.

Please verify these changes:

  1. Confirm that the new dependencies (python-duckdb, pyarrow) are necessary and don't introduce conflicts with other packages.
  2. Check if replacing seaborn with matplotlib-base maintains all required functionality.
  3. Ensure the rename from pypdf2 to pypdf is consistent across the entire package and doesn't break any functionality.
#!/bin/bash
# Check usage of new dependencies in the package
echo "Checking duckdb usage:"
rg --type python 'duckdb' .
echo "Checking pyarrow usage:"
rg --type python 'pyarrow' .
echo "Checking matplotlib usage:"
rg --type python 'matplotlib' .

Also applies to: 39-39, 44-45, 50-50


20-20: Verify the intention behind using --no-build-isolation flag.

The build script now includes the --no-build-isolation flag. This allows the build to access packages in the build environment, which might affect how the package is built and its dependencies are resolved.

Please confirm that this change is intentional and doesn't introduce any unexpected behavior. Consider checking if this flag is used consistently across other recipes to maintain build consistency.

Comment on lines +28 to +32
- cython
- numpy
- pypdf
- libgomp # [linux]
- llvm-openmp # [osx]
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💡 Codebase verification

Potential compatibility issues due to removed version constraints and pypdf renaming.

  • Many recipes specify version constraints for cython and numpy. Removing these constraints in pyprophet/meta.yaml may lead to compatibility issues during builds or runtime.
  • The renaming from pypdf2 to pypdf could cause inconsistencies, as some recipes still reference pypdf2. This may result in import errors or broken functionality.
🔗 Analysis chain

Review host requirements changes carefully.

Several changes have been made to the host requirements:

  1. Version constraints for cython and numpy have been removed. This might lead to compatibility issues if the package is sensitive to specific versions of these dependencies.

  2. pypdf2 has been renamed to pypdf. Ensure this change is correct and consistent with the package's requirements. Check if other recipes still use pypdf2, as this might lead to inconsistencies.

  3. Platform-specific compiler requirements (libgomp for Linux, llvm-openmp for macOS) have been added, which is good for cross-platform compatibility.

Please verify these changes:

  1. Confirm that the package builds successfully with the latest versions of cython and numpy.
  2. Check if the rename from pypdf2 to pypdf is correct and doesn't break any functionality.
  3. Ensure the new compiler requirements are necessary and correctly specified.
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check usage of cython, numpy, and pypdf in other recipes
echo "Checking cython usage:"
rg --type yaml 'cython' recipes/
echo "Checking numpy usage:"
rg --type yaml 'numpy' recipes/
echo "Checking pypdf usage:"
rg --type yaml 'pypdf' recipes/

Length of output: 121240

@BiocondaBot BiocondaBot changed the title Update pyprophet to 2.2.8 Update pyprophet to 2.2.9 Oct 31, 2024
@BiocondaBot BiocondaBot closed this Jan 8, 2025
@BiocondaBot BiocondaBot deleted the bump/pyprophet branch January 8, 2025 15:18
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