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Update el_gato version to 1.20.1 #51484

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merged 4 commits into from
Oct 18, 2024

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Alan-Collins
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Update el_gato to 1.20.0

Replaces #51051. Hopefully fixed the build issues experienced in that PR.

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coderabbitai bot commented Oct 18, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

This pull request involves significant updates to the el_gato package, specifically modifying two key files: build.sh and meta.yaml. The build.sh file has been deleted; it previously facilitated the installation of the package by executing a pip command and managing directory structures for database files. The meta.yaml file has been updated to reflect a new version number, changing from "1.19.0" to "1.20.1", and includes a new hash value. Notably, the package name is now dynamically set, and the build section has been modified to specify noarch: python and includes a new script that creates a directory and copies database files into it, followed by a command to install the package using pip. Additional changes include the introduction of a new build requirement for Python, the removal of the setuptools dependency, and the addition of new runtime dependencies. Minor formatting adjustments were made in the about section, adding fields for license family, development URL, and documentation URL, alongside a stylistic update to the summary line.

Possibly related PRs

  • add pantax #50983: The changes in build.sh for the pantax package involve installation scripts similar to those in the main PR, which also includes a shell script for package installation.
  • add recipe for sizemeup #51033: The build.sh script for sizemeup includes directory creation and installation commands, paralleling the main PR's focus on installation scripts.
  • Add FMSI #51277: The build.sh script in the fmsi package also enhances the build process, similar to the changes made in the main PR's build.sh.
  • add gfainject #51287: The gfainject package introduces a build.sh script that automates the build process, akin to the main PR's focus on installation scripts.
  • Adding the devider recipe  #51365: The devider package's build.sh script facilitates building a binary, which relates to the main PR's changes in installation scripts.

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autobump, new version

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  • mencian

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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (2)
recipes/el_gato/meta.yaml (2)

17-20: Build script changes look good, with a minor suggestion.

The new build script effectively replaces the deleted build.sh file. It correctly sets up the database files and installs the package using pip with appropriate flags.

Consider using $PREFIX/share instead of $PREFIX/bin for storing the database files, as it's more appropriate for non-executable data:

- - mkdir -p $PREFIX/bin/db
- - cp -rf el_gato/db/* $PREFIX/bin/db/
+ - mkdir -p $PREFIX/share/el_gato/db
+ - cp -rf el_gato/db/* $PREFIX/share/el_gato/db/

Don't forget to update any references to this path in the package code if you make this change.


26-26: Requirements changes look good, with a minor suggestion.

The addition of Python as a build requirement is appropriate. The new run requirements for colorama (Linux only) and importlib-metadata (Python <= 3.8) address platform-specific needs.

Consider specifying a minimum version for colorama and importlib-metadata to ensure compatibility:

- - colorama  # [linux]
- - importlib-metadata  # [py <= 38]
+ - colorama >=0.4.0  # [linux]
+ - importlib-metadata >=4.0.0  # [py <= 38]

Please verify these minimum versions against the package's requirements.

Also applies to: 39-40

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between c8e118e and 3e4f22f.

📒 Files selected for processing (2)
  • recipes/el_gato/build.sh (0 hunks)
  • recipes/el_gato/meta.yaml (3 hunks)
💤 Files with no reviewable changes (1)
  • recipes/el_gato/build.sh
🧰 Additional context used
🔇 Additional comments (4)
recipes/el_gato/meta.yaml (4)

2-3: Version and hash update looks good.

The version has been correctly updated to 1.20.0 as per the PR objective, and the hash has been updated accordingly.


49-53: About section updates look good.

The additions to the about section (license family, dev URL, and doc URL) provide more comprehensive metadata for the package. The minor stylistic change to the summary (adding quotes) is also fine.


Line range hint 1-53: Overall changes align well with PR objectives.

The updates to the meta.yaml file successfully accomplish the PR objective of updating el_gato to version 1.20.0. The changes include:

  1. Version and hash update
  2. New build script replacing the deleted build.sh file
  3. Adjusted run_exports pinning
  4. Updated requirements
  5. Enhanced about section metadata

These changes comprehensively address the version update and should resolve the build issues mentioned in the PR objectives.

To ensure all changes are consistent, please run the following script to check for any remaining references to the old version:

#!/bin/bash
# Description: Check for any remaining references to the old version

# Test: Search for the old version number
rg '1\.19\.0' --type yaml --type python

22-22: Run exports pinning change looks good, but verify impact.

The change from max_pin='x.x' to max_pin='x' allows for more flexible version compatibility. This means the package will be compatible with any future versions that share the same major version number.

Please verify that this change aligns with the package's versioning strategy and doesn't introduce any compatibility issues. Run the following script to check for any explicit version pins in the package code:

@Alan-Collins Alan-Collins changed the title Update el_gato version to 1.20.0 Update el_gato version to 1.20.1 Oct 18, 2024
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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (2)
recipes/el_gato/meta.yaml (2)

17-20: LGTM! Consider adding a comment for clarity.

The new build script effectively replaces the deleted build.sh file. It ensures that the database files are properly installed with the package.

Consider adding a brief comment explaining the purpose of the --no-deps --no-build-isolation --no-cache-dir flags in the pip install command for better maintainability.


51-51: LGTM! Consider updating the doc_url.

The changes in the 'about' section improve consistency and provide more comprehensive metadata. The use of template variables in dev_url and doc_url is good for maintainability.

Consider updating the doc_url to use the {{ user }} variable for consistency:

doc_url: "https://github.com/{{ user }}/{{ name }}/blob/{{ version }}/README.md"

Also applies to: 53-53, 55-57

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 6ab050e and 85eb6c4.

📒 Files selected for processing (1)
  • recipes/el_gato/meta.yaml (3 hunks)
🧰 Additional context used
🔇 Additional comments (4)
recipes/el_gato/meta.yaml (4)

2-3: Verify the correct version number.

The version has been updated to "1.20.1", which is different from the version mentioned in the PR title (1.20.0). Please confirm if this is the intended version.

The hash update is consistent with the version change.


22-22: LGTM! Improved version compatibility.

The update to max_pin='x' allows for more flexible version compatibility, which is consistent with the package update and may help with dependency management.


26-26: LGTM! Verify new dependencies if needed.

The addition of Python as a build requirement and the new run requirements (colorama for Linux and importlib-metadata for Python <= 3.8) appear appropriate for the updated package version.

Please verify that these new dependencies are indeed necessary for the 1.20.1 version of el_gato.

Also applies to: 39-40


42-44: LGTM! Good documentation of lint skip reason.

The addition of the 'extra' section with the skip-lints entry clearly explains why noarch: python is not used. This improves the maintainability of the package by documenting the reason for a potential lint warning.

@bgruening bgruening merged commit 6a8bc71 into bioconda:master Oct 18, 2024
7 checks passed
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2 participants