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Update pbtk to version 3.4.0 #51779

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merged 1 commit into from
Oct 29, 2024
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Update pbtk to version 3.4.0

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  run_exports:
    - ...

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Case run_exports statement
semantic versioning {{ pin_subpackage("myrecipe", max_pin="x") }}
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@jmattick jmattick mentioned this pull request Oct 29, 2024
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coderabbitai bot commented Oct 29, 2024

📝 Walkthrough

Walkthrough

The pull request introduces updates to the meta.yaml file for the pbtk package, specifically changing the version from 3.1.1 to 3.4.0. Along with the version increment, the SHA256 checksum has been updated from 4dbe08d880a4b54d7c84ecdf9849feead71ac5330277a66f57a2915447169814 to 31ff50c9a182b25f1d7e717e3ad764ec106a2ca81dc307a7c76242230e884b92. Additionally, a new line has been added in the build section to specify binary_relocation: False, indicating a change in the handling of binaries during the build process. No other modifications were made to the structure or content of the file, and the overall format remains consistent with the previous version.

Possibly related PRs

Suggested labels

autobump, new version

Suggested reviewers

  • mencian

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 6434446 and 322c6ed.

📒 Files selected for processing (1)
  • recipes/pbtk/meta.yaml (2 hunks)
🔇 Additional comments (3)
recipes/pbtk/meta.yaml (3)

29-29: LGTM: Appropriate build setting for binary package

The addition of binary_relocation: False is correct for this package as it's a repackaged binary (as noted in skip-lints). This prevents conda from attempting to modify binary paths, which is appropriate for pre-built binaries.


Line range hint 1-44: Consider adding explicit requirements section

While the package configuration is generally good, consider adding an explicit requirements section to document any runtime dependencies. This helps users understand the package's dependencies and ensures reproducible environments.

Example addition:

requirements:
  run:
    # Add runtime dependencies if any

Additionally, verify if the package has any specific version requirements for its dependencies.


2-3: Verify breaking changes in version 3.4.0

This is a significant version bump from 3.1.1 to 3.4.0. While the run_exports section is properly configured with max_pin='x.x', it's important to verify there are no breaking changes that could affect downstream dependencies.

✅ Verification successful

Version update appears safe for downstream dependencies

Based on the analysis of the meta.yaml file and package structure:

  1. The package is properly configured with run_exports using pin_subpackage with max_pin='x.x', ensuring compatibility constraints for downstream dependencies
  2. This is a binary package (as indicated by binary_relocation: False and the skip-lint comment) primarily providing command-line tools
  3. The test commands show that the package mainly exposes CLI tools rather than a Python API, reducing the risk of breaking changes affecting downstream code
  4. No direct package imports were found in other recipes, suggesting limited direct code dependencies
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for potential breaking changes by examining release notes and issues
# between versions 3.1.1 and 3.4.0

# Search for release notes or changelog
rg -i -A 5 "changelog|release.*notes|breaking.*changes" 

# Search for version-specific discussions or issues
gh issue list -R PacificBiosciences/pbtk --search "3.4.0 in:title,body"

Length of output: 7218


Script:

#!/bin/bash
# Let's try to find more information about potential breaking changes by:
# 1. Looking for test files that might indicate API usage
# 2. Checking package dependencies and requirements
# 3. Looking for documentation or README files

# Check meta.yaml for dependencies and requirements
cat recipes/pbtk/meta.yaml

# Look for test files and documentation
fd -t f "test|README|CHANGES|HISTORY|NEWS" recipes/pbtk/

# Search for any imports or API usage patterns
rg -l "from pbtk|import pbtk" recipes/

Length of output: 1034


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@jmattick
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@bioconda-bot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 pbtk-3.4.0-h9ee0642_0.tar.bz2 linux-64.zip GitHub Actions
showYou may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>

@jmattick
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@pb-dseifert @armintoepfer

@@ -26,6 +26,7 @@ extra:
build:
number: 0
skip: True # [osx]
binary_relocation: False
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Can you explain why this is needed for your packages?

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We have had to add this previously to our packages to resolve build issues:
#44388

@armintoepfer armintoepfer merged commit f598e3f into bioconda:master Oct 29, 2024
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4 participants