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Update gfainject to 0.1.1 #52099

Merged
merged 11 commits into from
Nov 18, 2024
Merged

Update gfainject to 0.1.1 #52099

merged 11 commits into from
Nov 18, 2024

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Update gfainject: 0.1.00.1.1

install with bioconda Conda

Info Link or Description
Recipe recipes/gfainject (click to view/edit other files)
Summary Inject alignment into pangenome graphs
Home https://github.com/AndreaGuarracino/gfainject
Releases https://github.com/AndreaGuarracino/gfainject/tags
Recipe Maintainer(s) @AndreaGuarracino
Author @AndreaGuarracino

This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Nov 13, 2024
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coderabbitai bot commented Nov 13, 2024

📝 Walkthrough
📝 Walkthrough
📝 Walkthrough
📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request involves updates to the meta.yaml file for the gfainject package. The primary changes include an increment in the version number from 0.1.0 to 0.1.1 and a modification of the SHA256 checksum for the source tarball, changing it from a4388e524d5942f53d2fa94a93b2e82c926506c27cfdf04c04fbe8669a7ecebf to a11f41ee94614d8c089454fdb3d0fb96e2f305db46895e2f64d974fa1707e739. Additionally, several new build requirements have been introduced in the build section of the file, including cmake, make, pkg-config, and the C and C++ compilers. These changes reflect updates necessary for the proper building and functioning of the gfainject package, but no other structural or content modifications were made to the meta.yaml file.

Possibly related PRs

  • add gfainject #51287: This PR adds the gfainject package and includes a meta.yaml file where the initial version is set to 0.1.0, which is directly related to the changes made in the main PR that updates the version to 0.1.1.

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Actionable comments posted: 1

🧹 Outside diff range and nitpick comments (2)
recipes/gfainject/patches/fix-sort-bam-args.patch (1)

9-12: LGTM! Consider enhancing the comment.

The patch correctly adds the missing Option<u64> argument. However, the comment could be more descriptive about the purpose of this parameter.

-        None  // Add the missing Option<u64> argument
+        None  // Max memory limit for sorting (None means unlimited)
recipes/gfainject/meta.yaml (1)

Line range hint 1-48: Overall: Changes blocked by missing patch file

The version update and build requirement changes look good, but this PR is blocked by the missing patch file patches/fix-sort-bam-args.patch. This needs to be addressed before the PR can be merged.

Please:

  1. Create and add the patch file
  2. Update this PR with the patch file
  3. Consider documenting the reason for the patch in the recipe (e.g., link to upstream issue/PR)
🧰 Tools
🪛 yamllint

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

(syntax)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between d384638 and 7ffc3dc.

📒 Files selected for processing (2)
  • recipes/gfainject/meta.yaml (2 hunks)
  • recipes/gfainject/patches/fix-sort-bam-args.patch (1 hunks)
🔇 Additional comments (4)
recipes/gfainject/patches/fix-sort-bam-args.patch (1)

5-12: Verify the function signature in the codebase.

Let's confirm that this matches the expected function signature.

recipes/gfainject/meta.yaml (3)

1-2: LGTM: Version update matches PR objectives

🧰 Tools
🪛 yamllint

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

(syntax)


23-27: Verify necessity of all new build requirements

The added build requirements look appropriate, particularly for zlib-ng compilation. However, let's verify if all are necessary.

#!/bin/bash
# Description: Check build system and dependency requirements in the source code

echo "Checking for CMake build system..."
fd -e CMakeLists.txt

echo "Checking for pkg-config dependencies..."
fd -e pc

echo "Checking for C/C++ source files..."
fd -e c -e cpp -e cc -e h -e hpp

9-11: Verify SHA256 checksum for the new version

Let's verify that the SHA256 checksum matches the source tarball.

Comment on lines 12 to 14
patches:
- patches/fix-sort-bam-args.patch # We'll create this patch

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⚠️ Potential issue

Critical: Missing patch file referenced in meta.yaml

The recipe references a patch file patches/fix-sort-bam-args.patch that hasn't been created yet. This will cause the build to fail.

Please ensure that:

  1. The patch file is created and added to the repository
  2. The patch correctly fixes the convert_bam_to_gbam function by adding the missing Option<u64> argument

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I've uploaded the patches/fix-sort-bam-args.patch file. Why do you say it has not been created yet?

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@AndreaGuarracino, I apologize for the confusion earlier. I can now confirm that patches/fix-sort-bam-args.patch exists in the repository. Thank you for adding it. The build should proceed correctly now.

🔗 Analysis chain
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Search for the patch file 'fix-sort-bam-args.patch' in the repository
fd 'fix-sort-bam-args.patch'

Length of output: 78

@AndreaGuarracino AndreaGuarracino merged commit 949c149 into master Nov 18, 2024
6 checks passed
@AndreaGuarracino AndreaGuarracino deleted the bump/gfainject branch November 18, 2024 17:56
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4 participants