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Update decom: add kmtricks dependancy #51386

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@maxibor maxibor commented Oct 14, 2024

After talking to the original author of decOM (@CamilaDuitama), this PR adds kmtricks dependancy to decOM.


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📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request modifies the meta.yaml file for the decOM package. It includes an increment in the build number from 0 to 1. Adjustments have been made to the entry points for the package, which now correctly map to the main functions of various modules, including decOM, decOM-aOralOut, decOM-format, decOM-LOO, decOM-CV, and decOM-MST. Each entry point points to its respective __main__ function. Additionally, a new runtime requirement, kmtricks, has been added to the run section. The indentation for some entries in the requirements section has been standardized for consistency. The test commands remain unchanged, preserving the help commands for each entry point.

Possibly related PRs

  • Update meta.yaml for spec2vec #49857: The changes in the meta.yaml file for spec2vec include an increment in the build number, similar to the build number update in the main PR for decOM.
  • Update PhyloAcc recipe #51090: The meta.yaml file for PhyloAcc also shows an increment in the build number, paralleling the changes made in the main PR.
  • Update Hsdecipher #51093: The meta.yaml for Hsdecipher includes a build number increment, which aligns with the changes in the main PR.

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please review & merge


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📥 Commits

Files that changed from the base of the PR and between 5453264 and fb22ae2.

📒 Files selected for processing (1)
  • recipes/decom/meta.yaml (2 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
  • recipes/decom/meta.yaml

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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (3)
recipes/decom/meta.yaml (3)

Line range hint 18-24: New entry points look good, consider adding a comment for clarity.

The addition of new entry points for various decOM subcommands is well-structured and consistent. This change improves the package's usability by allowing direct access to different functionalities from the command line.

Consider adding a brief comment above the entry_points section to explain the purpose of these commands, for example:

  # Entry points for decOM main command and subcommands
  entry_points:
    - decOM = decOM.__main__:main
    # ... (rest of the entry points)

40-40: New kmtricks dependency added, consider specifying a version.

The addition of 'kmtricks' as a runtime requirement aligns with the PR objectives. However, to ensure long-term compatibility and reproducibility, it's recommended to specify a version or version range for this dependency.

Consider updating the requirement to include a version specification, for example:

    - kmtricks >=1.0.0,<2.0.0

Replace 1.0.0 with the minimum compatible version and adjust the upper bound as needed. This helps prevent potential issues with future incompatible versions.


Line range hint 1-67: Overall changes look good, consider updating package version in the future.

The modifications to the meta.yaml file, including the build number increment, addition of new entry points, and the new kmtricks dependency, are well-implemented and align with the PR objectives. These changes improve the package's functionality and usability.

If these changes significantly alter the package's functionality or API, consider updating the package version (currently 0.0.32) in a future PR. This would follow semantic versioning principles and clearly communicate the extent of changes to users.

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📥 Commits

Files that changed from the base of the PR and between b9f01ab and 5453264.

📒 Files selected for processing (1)
  • recipes/decom/meta.yaml (2 hunks)
🧰 Additional context used
🔇 Additional comments (1)
recipes/decom/meta.yaml (1)

15-15: Build number increment looks good.

The build number has been correctly incremented from 0 to 1. This is appropriate when making changes to a package without changing its version.

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