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Update pyprophet to 2.2.9 #51284

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Update pyprophet to 2.2.9 #51284

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a19d85e
Update pyprophet to 2.2.7
BiocondaBot Oct 9, 2024
6b08fd2
clean up recipe
mencian Oct 10, 2024
c718978
update dependencies
mencian Oct 10, 2024
f7a98ca
delete extra period in summary
mencian Oct 10, 2024
96f28d1
Update pyprophet to 2.2.8
BiocondaBot Oct 12, 2024
eb059fb
try export command
mencian Oct 16, 2024
c0e0bfd
disable aarch64 for now
mencian Oct 16, 2024
3aa2172
Update pyprophet to 2.2.9
BiocondaBot Oct 31, 2024
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31 changes: 19 additions & 12 deletions recipes/pyprophet/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{% set name = "pyprophet" %}
{% set version = "2.2.5" %}
{% set version = "2.2.8" %}
{% set hash_type = "sha256" %}
{% set hash_value = "f1d42ba53ecc0c0cac21e6938ad830f1260acb65ac69b3012a697f56e4badab3" %}
{% set hash_value = "373bcec312fbb54e3d86514e26680168287630ea291f695d41cac8d834aa4970" %}

package:
name: '{{ name|lower }}'
Expand All @@ -12,38 +12,42 @@ source:
'{{ hash_type }}': '{{ hash_value }}'

build:
number: 3
number: 0
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


requirements:
build:
- {{ compiler('c') }}
host:
- python
- pip
- cython <1
- numpy >=1.9
- pypdf2
- 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

- libgomp # [linux]
- llvm-openmp # [osx]
Comment on lines +28 to +32
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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

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

test:
Expand All @@ -54,9 +58,12 @@ 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."
dev_url: https://github.com/PyProphet/pyprophet

extra:
additional-platforms:
- linux-aarch64
Expand Down