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Update pyprophet to 2.2.9 #51284

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clean up recipe
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mencian committed Oct 10, 2024
commit 6b08fd2488325b24f51c8885a1700559ac1d5896
21 changes: 13 additions & 8 deletions recipes/pyprophet/meta.yaml
Original file line number Diff line number Diff line change
@@ -17,33 +17,35 @@ build:
- {{ 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


requirements:
build:
- {{ compiler('c') }}
host:
- python
- pip
- cython <1
- numpy >=1.9
- pypdf2
- cython
- numpy
- pypdf
Comment on lines +28 to +30
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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

run:
- python
- {{ pin_compatible("numpy") }}
- scipy
- python-duckdb
- pandas >=0.17
- numexpr >=2.1
- scikit-learn >=0.17
- matplotlib-base
- seaborn
- seaborn-base
- tabulate
- pyarrow
- xgboost
- hyperopt
- statsmodels >=0.8.0
- click
- dataclasses
- pypdf2
- pypdf
- typing-extensions

test:
@@ -54,9 +56,12 @@ test:

about:
home: https://github.com/PyProphet/pyprophet
license: BSD License
license: "BSD-3-Clause"
license_family: BSD
summary: Python reimplementation of mProphet peak scoring
license_file: LICENSE
summary: "PyProphet: Semi-supervised learning and scoring of OpenSWATH results.."
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dev_url: https://github.com/PyProphet/pyprophet

extra:
additional-platforms:
- linux-aarch64
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