Updated irma to 1.2.0

[aaronKol]

Updated irma recipe (1.1.4 -> 1.2.0)

[coderabbitai]

📝 Walkthrough

Walkthrough

This pull request includes changes across three files related to the IRMA package. The first modification in irma-check-dir-writable.patch alters the error handling for the output directory's writability. Instead of aborting the script when the directory is not writable, it now issues a warning message and allows the script to continue execution. The second change in label-fix-bin-cmds.patch simplifies the variable assignments for executable paths in the LABEL file by directly referencing the executable names, enhancing readability. Lastly, the meta.yaml file is updated to reflect a new version number (from 1.1.4 to 1.2.0), a new source URL for the package, and an updated SHA256 checksum. The patches section remains unchanged, retaining references to the previously mentioned patches.

Possibly related PRs

• Update irma recipe to version 1.1.4 #51522: This PR directly modifies the same error handling logic in the irma-check-dir-writable.patch file, changing the control flow from aborting to issuing a warning, which is the same change made in the main PR.

Suggested labels

please review & merge

Suggested reviewers

• wm75

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between e17dd11 and 2597369.

📒 Files selected for processing (3)

• recipes/irma/irma-check-dir-writable.patch (1 hunks)
• recipes/irma/label-fix-bin-cmds.patch (1 hunks)
• recipes/irma/meta.yaml (1 hunks)

🧰 Additional context used

🔇 Additional comments (7)

recipes/irma/irma-check-dir-writable.patch (1)

Line range hint 1-11: Clarify the rationale for changing directory writability check from error to warning

The modification changes the behavior of the script when the output directory is not writable. Instead of aborting the script, it now issues a warning and continues execution. While this change might allow the script to proceed in some edge cases, it could lead to potential issues:

1. The script might encounter runtime errors or data loss if it attempts to write to a non-writable directory later in its execution.
2. This change could introduce a security vulnerability if the script continues with insufficient permissions.
3. Users might miss the warning message and face unexpected behavior during script execution.

Could you please clarify the reasoning behind this change? Are there specific scenarios where continuing execution despite a potentially non-writable output directory is beneficial?

To further investigate the impact of this change, let's examine how the destination_directory is used throughout the script:

This will help us understand the potential risks associated with continuing execution when the directory might not be writable.

✅ Verification successful

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The change from aborting to issuing a warning when the output directory is not writable is localized to the recipes/irma/irma-check-dir-writable.patch file and does not affect other parts of the codebase.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Search for uses of $destination_directory after the writability check
rg -A 5 '\$destination_directory' IRMA

Length of output: 85

---

Script:

#!/bin/bash
# Search for the IRMA script or directory within the repository
fd -e sh -e bash -e zsh -t f -g 'IRMA*' .

Length of output: 43

---

Script:

#!/bin/bash
# Search for all occurrences of $destination_directory in the repository
rg '\$destination_directory' .

Length of output: 365

recipes/irma/label-fix-bin-cmds.patch (2)

15-16: Approve formatting improvement in conditional statement.

The addition of a space before the then keyword in the if statement improves readability and adheres to common shell scripting conventions. This change is beneficial for code maintainability.

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3-9: Verify the intentionality and impact of simplified executable path assignments.

The changes to muscle, FastTreeMP, and PARALLEL variable assignments simplify the code by directly using the executable names instead of constructing paths with $bin and $OS variables. While this improves readability and flexibility, it also removes explicit path control and OS-specific naming.

Please confirm:

1. Is this change intentional and aligned with the project's conventions?
2. Are there any potential issues with relying on PATH for these executables across different environments?
3. Was the OS-specific naming (_$OS suffix) necessary, and if so, how will its removal be handled?

To check for any unintended consequences, you can run:

This script will help verify the executables' locations and versions, ensuring the changes don't lead to using unintended versions.

recipes/irma/meta.yaml (4)

2-2: Version update looks good.

The version has been correctly updated from 1.1.4 to 1.2.0, which aligns with the PR objectives.

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9-9: Source URL update looks correct, but needs verification.

The source URL has been updated to reflect the new version, changing from 202402.zip to 202408.zip. This aligns with the version update.

Please confirm that this is the correct and latest URL for IRMA version 1.2.0. You can verify this by checking the official IRMA download page or contacting the package maintainers.

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Line range hint 12-51: Verify if unchanged sections need updates.

The patches, build instructions, requirements, test, and about sections remain unchanged. While this suggests compatibility with the existing setup, it's important to verify if the new version (1.2.0) requires any updates to these sections.

Please confirm that:

1. The existing patches are still applicable and necessary for version 1.2.0.
2. The build instructions and requirements are still correct for the new version.
3. The test files (test1.fa and test2.fastq) are still valid and sufficient for testing version 1.2.0.
4. The about section, including the license information, is still accurate.

If any changes are needed, please update the relevant sections accordingly.

🧰 Tools

🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

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10-10: SHA256 checksum update needs verification.

The SHA256 checksum has been updated to match the new source file.

Please verify that the provided SHA256 checksum is correct for the new zip file. You can do this by downloading the zip file and running:

Ensure that the output matches the checksum in the meta.yaml file.

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