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Update dnmtools to 1.4.4 #51510

Merged
merged 3 commits into from
Oct 21, 2024
Merged

Update dnmtools to 1.4.4 #51510

merged 3 commits into from
Oct 21, 2024

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@BiocondaBot BiocondaBot commented Oct 21, 2024

Update dnmtools: 1.4.31.4.4

install with bioconda Conda

Info Link or Description
Recipe recipes/dnmtools (click to view/edit other files)
Summary dnmtools is a set of tools for analyzing DNA methylation data from bisulfite sequencing.

Home | https://github.com/smithlabcode/dnmtools
Releases |
Recipe Maintainer(s) | @andrewdavidsmith, @guilhermesena1
Author | @smithlabcode


This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Oct 21, 2024
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coderabbitai bot commented Oct 21, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

This pull request introduces updates to the meta.yaml file for the dnmtools package, incrementing the version number from "1.4.3" to "1.4.4". The source section is modified to include a new SHA256 checksum, changing from 2ec96953d088cfde895d2b5afc77197850d50d7046bb6febce52a86db805ef17 to 56fc62ef1d41cdafa30c98d6cfbcb3707a125921618a1808075eaafb29d22edf, alongside an updated URL for the source tarball. The requirements section sees the addition of libtool in the build requirements, while llvm-openmp and libgomp are included in both the host and run requirements for macOS and Linux platforms. The about section has been updated to include a license_family field and a new dev_url field, with a slight rephrasing of the summary text. The extra section now includes additional-platforms for linux-aarch64 and osx-arm64. The test section has been added to specify commands for testing. Additionally, the build.sh script has been modified to export an environment variable for M4, add a command to regenerate configuration files, and update the make command to include compiler flags and parallel job specifications.

Possibly related PRs

  • Update d4tools to 0.3.11 #51110: The changes in the main PR regarding the meta.yaml file updates, including version and SHA256 checksum modifications, are similar to the updates made in this PR for the d4tools package, which also involves version and checksum changes in its meta.yaml.
  • Update r-grain to 1.4.4 #51313: This PR updates the r-grain package's version and SHA256 checksum in its meta.yaml, paralleling the version and checksum updates in the main PR for the dnmtools package.
  • Update r-grain to 1.4.5 #51467: Similar to the main PR, this PR updates the r-grain package's version and SHA256 checksum in its meta.yaml, reflecting the same type of changes made in the main PR.

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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (4)
recipes/dnmtools/build.sh (2)

4-4: LGTM: autoreconf added for configuration regeneration

Running autoreconf -if is a good practice to ensure all configuration scripts are up-to-date. This is especially important when updating package versions.

Consider adding a comment explaining why this step is necessary, e.g.:

# Regenerate configuration files
autoreconf -if

7-7: LGTM: Improved make command with parallel build support

The updated make command now includes:

  1. ${CXXFLAGS}, which allows for flags set by the build system.
  2. -j"${CPU_COUNT}" for parallel compilation, which can significantly speed up the build process.

These are excellent improvements that enhance build flexibility and performance.

Consider breaking the long line for better readability:

make CXXFLAGS="${CXXFLAGS} -O3 -DNDEBUG -D_LIBCPP_DISABLE_AVAILABILITY" \
     -j"${CPU_COUNT}"
recipes/dnmtools/meta.yaml (2)

36-38: Test section addition is good, but could be expanded.

The addition of a test section with a basic command to run 'dnmtools' is appropriate. However, consider expanding the tests to cover more functionality if possible.

Would you like assistance in generating more comprehensive test commands?

🧰 Tools
🪛 yamllint

[error] 37-37: trailing spaces

(trailing-spaces)


33-33: Minor: Remove trailing spaces.

There are trailing spaces on lines 33 and 37. While these don't affect functionality, removing them improves code cleanliness.

Also applies to: 37-37

🧰 Tools
🪛 yamllint

[error] 33-33: trailing spaces

(trailing-spaces)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between c529722 and 7f214c8.

📒 Files selected for processing (2)
  • recipes/dnmtools/build.sh (1 hunks)
  • recipes/dnmtools/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/dnmtools/meta.yaml

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

(syntax)


[error] 33-33: trailing spaces

(trailing-spaces)


[error] 37-37: trailing spaces

(trailing-spaces)

🔇 Additional comments (9)
recipes/dnmtools/build.sh (3)

3-3: LGTM: Explicit M4 path set

Setting the M4 environment variable ensures the correct version of m4 is used during the build process. This is a good practice, especially in cross-compilation environments.


5-5: LGTM: Improved robustness in configure command

Adding quotes around "${PREFIX}" in the configure command is a good practice. It ensures correct handling of paths that may contain spaces.


1-8: Overall: Excellent improvements to the build process

The changes in this file collectively enhance the build process for dnmtools:

  1. Explicit setting of the M4 path ensures the correct tool is used.
  2. Addition of autoreconf ensures up-to-date configuration files.
  3. Quoting of ${PREFIX} improves robustness against paths with spaces.
  4. Updated make command allows for system-specific flags and parallel compilation.

These changes should result in a more reliable and potentially faster build process, which is particularly beneficial for cross-platform compatibility and CI/CD pipelines.

recipes/dnmtools/meta.yaml (6)

1-1: Version update looks good.

The package version has been correctly updated to "1.4.4" as per the PR objective.

🧰 Tools
🪛 yamllint

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

(syntax)


8-9: Source section update is correct.

The URL and SHA256 checksum have been properly updated to match the new version 1.4.4.


23-23: Build requirement addition is appropriate.

The addition of 'libtool' to the build requirements is consistent with the changes in the build process mentioned in the AI summary.


28-29: Host and run requirements update looks good.

The addition of 'llvm-openmp' for macOS and 'libgomp' for Linux in both host and run requirements suggests improved OpenMP support across platforms.

Also applies to: 33-34


42-43: About section updates are appropriate and informative.

The additions of license family information and dev_url, along with the minor update to the summary text, provide more comprehensive metadata for the package.

Also applies to: 46-46, 48-48


54-56: Extra section update expands platform support.

The addition of linux-aarch64 and osx-arm64 as additional platforms is a positive change, expanding support to ARM-based systems.

@mencian mencian merged commit e115088 into master Oct 21, 2024
7 checks passed
@mencian mencian deleted the bump/dnmtools branch October 21, 2024 07:35
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