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feat: Bump meryl version #3266

Merged
merged 1 commit into from
Sep 20, 2024
Merged

feat: Bump meryl version #3266

merged 1 commit into from
Sep 20, 2024

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fgvieira
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@fgvieira fgvieira commented Sep 20, 2024 •
edited by coderabbitai bot
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QC

While the contributions guidelines are more extensive, please particularly ensure that:

  • test.py was updated to call any added or updated example rules in a Snakefile
  • input: and output: file paths in the rules can be chosen arbitrarily
  • wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:)
  • temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to
  • the meta.yaml contains a link to the documentation of the respective tool or command under url:
  • conda environments use a minimal amount of channels and packages, in recommended ordering

Summary by CodeRabbit

  • New Features
    • Updated the meryl package to version 1.4.1, enhancing functionality and performance.
  • Bug Fixes
    • Various library dependencies have been updated to newer versions, which may resolve existing issues and improve stability.
  • Chores
    • Updated package URLs in the environment files to reflect the latest versions of dependencies.

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coderabbitai bot commented Sep 20, 2024 •
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Walkthrough

The changes involve updates to package dependencies across multiple environment files related to the meryl project. Specifically, several packages have been upgraded to newer versions, including meryl, libgomp, libgcc, libgcc-ng, libstdcxx, and others. The updates reflect modifications in both the environment.linux-64.pin.txt and environment.yaml files, ensuring that the project utilizes the latest available versions of its dependencies.

Changes

File(s) Change Summary
bio/meryl/count/environment.linux-64.pin.txt, bio/meryl/sets/environment.linux-64.pin.txt, bio/meryl/stats/environment.linux-64.pin.txt Updated multiple package versions, including meryl from 2013-0 to 1.4.1 and several libraries from 13.2.0 to 14.1.0.
bio/meryl/count/environment.yaml, bio/meryl/sets/environment.yaml, bio/meryl/stats/environment.yaml Updated meryl dependency version from 2013 to 1.4.1.

Possibly related PRs

  • perf: autobump bio/igv-reports #3120: Updates to the environment.linux-64.pin.txt file include similar package updates, particularly for libgomp, libgcc-ng, and ca-certificates.
  • perf: autobump bio/bbtools #3127: Similar updates to environment.linux-64.pin.txt for libgomp, libgcc-ng, and ca-certificates suggest a common goal of maintaining up-to-date package versions across different projects.
  • perf: autobump bio/rseqc/bam_stat #3154: Changes in environment.linux-64.pin.txt include updates to libgcc, libstdcxx, and python, which align with the updates made in the main PR.
  • perf: autobump bio/ucsc/gtfToGenePred #3159: The updates to environment.linux-64.pin.txt for libgcc, libgcc-ng, and openssl reflect a similar maintenance effort to ensure compatibility and security.
Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 6e42aef and 36fafee.

Files selected for processing (6)
  • bio/meryl/count/environment.linux-64.pin.txt (1 hunks)
  • bio/meryl/count/environment.yaml (1 hunks)
  • bio/meryl/sets/environment.linux-64.pin.txt (1 hunks)
  • bio/meryl/sets/environment.yaml (1 hunks)
  • bio/meryl/stats/environment.linux-64.pin.txt (1 hunks)
  • bio/meryl/stats/environment.yaml (1 hunks)
Additional comments not posted (27)
bio/meryl/sets/environment.yaml (1)

6-6: Clarify the reason for updating meryl to version 1.4.1 and verify compatibility.

Updating the meryl package from version 2013 to 1.4.1 is a significant change, as the new version follows semantic versioning. While this improves clarity and reproducibility, such a major version jump might introduce breaking changes.

Please provide more context on the rationale behind choosing this specific version. Have you verified that version 1.4.1 is compatible with existing workflows and scripts that rely on meryl?

To help users adapt to any breaking changes, consider providing a changelog or migration guide highlighting the key differences between the old and new versions.

bio/meryl/count/environment.yaml (1)

6-6: Dependency version update looks good!

The meryl dependency has been updated from version 2013 to 1.4.1, which aligns with the PR objective. Using semantic versioning provides better clarity on the version being used.

bio/meryl/sets/environment.linux-64.pin.txt (6)

6-6: LGTM!

Updating libgomp to version 14.1.0 is a good idea to leverage the latest bug fixes and improvements.

8-8: LGTM!

Updating libgcc to version 14.1.0 is a good idea to leverage the latest bug fixes and improvements.

9-9: LGTM!

Updating libgcc-ng to version 14.1.0 is a good idea to leverage the latest bug fixes and improvements.

10-10: LGTM!

Updating libstdcxx to version 14.1.0 is a good idea to leverage the latest bug fixes and improvements.

11-11: LGTM!

Updating libstdcxx-ng to version 14.1.0 is a good idea to leverage the latest bug fixes and improvements.

12-12: LGTM!

Updating meryl to version 1.4.1 is a good idea to leverage the latest bug fixes and improvements. This change is consistent with the PR objective of bumping the meryl version.

bio/meryl/stats/environment.linux-64.pin.txt (6)

6-6: LGTM!

The libgomp package has been updated to the latest major version 14.1.0. The URL has been updated accordingly.

8-8: LGTM!

The libgcc package has been updated to the latest major version 14.1.0. The URL has been updated accordingly.

9-9: LGTM!

The libgcc-ng package has been updated to the latest major version 14.1.0. The URL has been updated accordingly.

10-10: LGTM!

The libstdcxx package has been added with version 14.1.0, which is consistent with the other updated packages.

11-11: LGTM!

The libstdcxx-ng package has been added with version 14.1.0, which is consistent with the other updated packages.

12-12: Verify the meryl package version change.

The meryl package version has been updated from 2013-0 to 1.4.1, which appears to be a significant change. Please ensure that this version change is intentional and does not introduce any compatibility issues or unintended consequences for the project.

bio/meryl/count/environment.linux-64.pin.txt (13)

6-6: LGTM!

The ca-certificates package has been updated to a newer version 2024.8.30. The URL format is valid.

7-7: LGTM!

The ld_impl_linux-64 package build number has been updated to hf3520f5_7. The URL format is valid.

8-8: LGTM!

The tzdata package has been updated to a newer version 2024a. The URL format is valid.

9-9: LGTM!

The libgomp package has been updated to a newer version 14.1.0. The URL format is valid.

11-11: LGTM!

The libgcc package has been updated to a newer version 14.1.0. The URL format is valid.

12-12: LGTM!

The libexpat package has been updated to a newer version 2.6.3. The URL format is valid.

13-13: LGTM!

The libgcc-ng package has been updated to a newer version 14.1.0. The URL format is valid.

14-14: LGTM!

The libstdcxx package has been updated to a newer version 14.1.0. The URL format is valid.

15-15: LGTM!

The openssl package has been updated to a newer version 3.3.2. The URL format is valid.

16-16: LGTM!

The bzip2 package build number has been updated to h4bc722e_7. The URL format is valid.

25-25: LGTM!

The libsqlite package has been updated to a newer version 3.46.1. The URL format is valid.

26-26: LGTM!

The meryl package has been updated to a newer version 1.4.1. The URL format is valid.

29-29: LGTM!

The python package has been updated to a newer version 3.12.5. The URL format is valid.

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@johanneskoester johanneskoester merged commit 448a1cb into snakemake:master Sep 20, 2024
8 checks passed
@fgvieira fgvieira deleted the meryl branch September 20, 2024 09:17
johanneskoester pushed a commit that referenced this pull request Sep 20, 2024
@github-actions
chore: release 4.5.0 (#3252)
d18524d 
🤖 I have created a release \*beep\* \*boop\*
---
##
[4.5.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.4.0...v4.5.0)
(2024-09-20)


### Features

* Add wrappers for ROOT rootcp CLI tool
([#3251](https://www.github.com/snakemake/snakemake-wrappers/issues/3251))
([0be5d56](https://www.github.com/snakemake/snakemake-wrappers/commit/0be5d566f4767b7cd2ea9ba78b0d83a6f79a4803))
* Bump meryl version
([#3266](https://www.github.com/snakemake/snakemake-wrappers/issues/3266))
([448a1cb](https://www.github.com/snakemake/snakemake-wrappers/commit/448a1cb793d04f7bd280c36bc4dd37d2d06aa104))
* Enhance phys/root/filter functionality
([#3250](https://www.github.com/snakemake/snakemake-wrappers/issues/3250))
([4797d76](https://www.github.com/snakemake/snakemake-wrappers/commit/4797d76630b0cc6ea05778a49727f7917b7874dc))
* Parse threads
([#3249](https://www.github.com/snakemake/snakemake-wrappers/issues/3249))
([9e63554](https://www.github.com/snakemake/snakemake-wrappers/commit/9e63554b0cf19b2a22513566a576105c39f47e3b))


### Bug Fixes

* name of bamqc
([#1464](https://www.github.com/snakemake/snakemake-wrappers/issues/1464))
([ee04ec2](https://www.github.com/snakemake/snakemake-wrappers/commit/ee04ec22b24c8d380ef98f5cee677f4ff4730ad3))


### Performance Improvements

* autobump bio/cnv_facets
([#3253](https://www.github.com/snakemake/snakemake-wrappers/issues/3253))
([c5c8ddd](https://www.github.com/snakemake/snakemake-wrappers/commit/c5c8ddded41ba96fd8bbc69790e1e17998551734))
* autobump bio/emu/abundance
([#3256](https://www.github.com/snakemake/snakemake-wrappers/issues/3256))
([6e42aef](https://www.github.com/snakemake/snakemake-wrappers/commit/6e42aef12570e7708dedd4ed24a7406a69356d81))
* autobump bio/emu/collapse-taxonomy
([#3255](https://www.github.com/snakemake/snakemake-wrappers/issues/3255))
([969067e](https://www.github.com/snakemake/snakemake-wrappers/commit/969067e8a94210d99bb67dfb3525c076f7731d02))
* autobump bio/emu/combine-outputs
([#3254](https://www.github.com/snakemake/snakemake-wrappers/issues/3254))
([de2a1be](https://www.github.com/snakemake/snakemake-wrappers/commit/de2a1bef7e9d330c4d6484bf0f1f250d7ad6c0c9))
* autobump bio/freebayes
([#3257](https://www.github.com/snakemake/snakemake-wrappers/issues/3257))
([80630dd](https://www.github.com/snakemake/snakemake-wrappers/commit/80630dd19aa113ea94dd55f89f596b83e81ebc34))
* autobump bio/galah
([#3258](https://www.github.com/snakemake/snakemake-wrappers/issues/3258))
([285d57a](https://www.github.com/snakemake/snakemake-wrappers/commit/285d57a8dd082fb515250fdc370cca11142fff44))
* autobump bio/gdc-api/bam-slicing
([#3259](https://www.github.com/snakemake/snakemake-wrappers/issues/3259))
([27b6958](https://www.github.com/snakemake/snakemake-wrappers/commit/27b695863bc123ba93fff53a130a0d7a06b4b2c1))
* autobump bio/igv-reports
([#3260](https://www.github.com/snakemake/snakemake-wrappers/issues/3260))
([a7d57ba](https://www.github.com/snakemake/snakemake-wrappers/commit/a7d57ba191bb59060dc82b9009a11c78dbaba86e))
* autobump bio/lofreq/call
([#3262](https://www.github.com/snakemake/snakemake-wrappers/issues/3262))
([13626f0](https://www.github.com/snakemake/snakemake-wrappers/commit/13626f0b9d3d25bafd04a3253f37b6bfd91414bc))
* autobump bio/lofreq/indelqual
([#3261](https://www.github.com/snakemake/snakemake-wrappers/issues/3261))
([76c854e](https://www.github.com/snakemake/snakemake-wrappers/commit/76c854e127cd792b5f74f8dc357f09fddb07998c))
* autobump bio/multiqc
([#3263](https://www.github.com/snakemake/snakemake-wrappers/issues/3263))
([d4d1475](https://www.github.com/snakemake/snakemake-wrappers/commit/d4d14750f10aa5f10fd5b20f560e13985a0f758f))
* autobump bio/tabix/index
([#3264](https://www.github.com/snakemake/snakemake-wrappers/issues/3264))
([e39e97e](https://www.github.com/snakemake/snakemake-wrappers/commit/e39e97e96fa26ab40e34a207ed62410453d28bae))
* autobump bio/vep/annotate
([#3265](https://www.github.com/snakemake/snakemake-wrappers/issues/3265))
([7f0b02a](https://www.github.com/snakemake/snakemake-wrappers/commit/7f0b02ac64b40a5aca8bd08c90f8b7df80ea4bed))
---


This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
@coderabbitai coderabbitai bot mentioned this pull request Sep 24, 2024
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@johanneskoester johanneskoester johanneskoester approved these changes

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@fgvieira @johanneskoester