perf: autobump bio/sortmerna #2985
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Files selected for processing (2)
- bio/sortmerna/environment.linux-64.pin.txt (1 hunks)
- bio/sortmerna/environment.yaml (1 hunks)
Additional comments not posted (2)
bio/sortmerna/environment.yaml (1)
6-6: Verify the validity ofsortmernaversion4.3.7.The update to
sortmerna =4.3.7should be verified for validity, as there are concerns about the version being invalid due to the package's migration frombiocondatoconda-forge. Ensure that this version is correctly sourced and available in theconda-forgechannel.bio/sortmerna/environment.linux-64.pin.txt (1)
5-49: Verify the explicit pinning of dependencies fromconda-forge.The migration to
conda-forgeinvolves explicit pinning of numerous dependencies. Ensure that these versions are compatible and correctly sourced fromconda-forge. This helps maintain a stable environment and avoids potential conflicts.
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Files selected for processing (1)
- bio/sortmerna/environment.linux-64.pin.txt (1 hunks)
Additional comments not posted (45)
bio/sortmerna/environment.linux-64.pin.txt (45)
5-5: URL for_libgcc_mutexis correct.The URL is correctly formatted and points to the
conda-forgechannel.
6-6: URL forca-certificatesis correct.The URL is correctly formatted and points to the
conda-forgechannel.
7-7: URL forld_impl_linux-64is correct.The URL is correctly formatted and points to the
conda-forgechannel.
8-8: URL forpython_abiis correct.The URL is correctly formatted and points to the
conda-forgechannel.
9-9: URL fortzdatais correct.The URL is correctly formatted and points to the
conda-forgechannel.
10-10: URL forlibgompis correct.The URL is correctly formatted and points to the
conda-forgechannel.
11-11: URL for_openmp_mutexis correct.The URL is correctly formatted and points to the
conda-forgechannel.
12-12: URL forlibgcc-ngis correct.The URL is correctly formatted and points to the
conda-forgechannel.
13-13: URL forbzip2is correct.The URL is correctly formatted and points to the
conda-forgechannel.
14-14: URL forlibexpatis correct.The URL is correctly formatted and points to the
conda-forgechannel.
15-15: URL forlibffiis correct.The URL is correctly formatted and points to the
conda-forgechannel.
16-16: URL forlibnslis correct.The URL is correctly formatted and points to the
conda-forgechannel.
17-17: URL forlibstdcxx-ngis correct.The URL is correctly formatted and points to the
conda-forgechannel.
18-18: URL forlibuuidis correct.The URL is correctly formatted and points to the
conda-forgechannel.
19-19: URL forlibxcryptis correct.The URL is correctly formatted and points to the
conda-forgechannel.
20-20: URL forlibzlibis correct.The URL is correctly formatted and points to the
conda-forgechannel.
21-21: URL forncursesis correct.The URL is correctly formatted and points to the
conda-forgechannel.
22-22: URL foropensslis correct.The URL is correctly formatted and points to the
conda-forgechannel.
23-23: URL forxzis correct.The URL is correctly formatted and points to the
conda-forgechannel.
24-24: URL foryamlis correct.The URL is correctly formatted and points to the
conda-forgechannel.
25-25: URL forlibsqliteis correct.The URL is correctly formatted and points to the
conda-forgechannel.
26-26: URL forreadlineis correct.The URL is correctly formatted and points to the
conda-forgechannel.
27-27: URL fortkis correct.The URL is correctly formatted and points to the
conda-forgechannel.
28-28: URL forzstdis correct.The URL is correctly formatted and points to the
conda-forgechannel.
29-29: URL forpythonis correct.The URL is correctly formatted and points to the
conda-forgechannel.
30-30: URL forbrotli-pythonis correct.The URL is correctly formatted and points to the
conda-forgechannel.
31-31: URL forcertifiis correct.The URL is correctly formatted and points to the
conda-forgechannel.
32-32: URL forcharset-normalizeris correct.The URL is correctly formatted and points to the
conda-forgechannel.
33-33: URL forhpackis correct.The URL is correctly formatted and points to the
conda-forgechannel.
34-34: URL forhyperframeis correct.The URL is correctly formatted and points to the
conda-forgechannel.
35-35: URL foridnais correct.The URL is correctly formatted and points to the
conda-forgechannel.
36-36: URL formarkupsafeis correct.The URL is correctly formatted and points to the
conda-forgechannel.
37-37: URL forpycparseris correct.The URL is correctly formatted and points to the
conda-forgechannel.
38-38: URL forpysocksis correct.The URL is correctly formatted and points to the
conda-forgechannel.
39-39: URL forpyyamlis correct.The URL is correctly formatted and points to the
conda-forgechannel.
40-40: URL forsetuptoolsis correct.The URL is correctly formatted and points to the
conda-forgechannel.
41-41: URL forwheelis correct.The URL is correctly formatted and points to the
conda-forgechannel.
42-42: URL forcffiis correct.The URL is correctly formatted and points to the
conda-forgechannel.
43-43: URL forh2is correct.The URL is correctly formatted and points to the
conda-forgechannel.
44-44: URL forjinja2is correct.The URL is correctly formatted and points to the
conda-forgechannel.
45-45: URL forpipis correct.The URL is correctly formatted and points to the
conda-forgechannel.
46-46: URL forzstandardis correct.The URL is correctly formatted and points to the
conda-forgechannel.
47-47: URL forurllib3is correct.The URL is correctly formatted and points to the
conda-forgechannel.
48-48: URL forrequestsis correct.The URL is correctly formatted and points to the
conda-forgechannel.
49-49: Verify the validity ofsortmernaversion 4.3.7.The version 4.3.7 of
sortmernafrombiocondais reported as invalid in the comments summary. Verify the package's migration status toconda-forge.Run the following script to check for the latest valid version of
sortmerna:
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Files selected for processing (1)
- bio/sortmerna/environment.linux-64.pin.txt (1 hunks)
Additional comments not posted (1)
bio/sortmerna/environment.linux-64.pin.txt (1)
5-51: Review of Package URLs and Version ValidityThe PR introduces a significant shift in dependency management by moving from
biocondatoconda-forgefor most dependencies, except forsortmernawhich remains sourced frombioconda. This change aligns with the PR's objective to update thesortmernapackage from version4.3.6to4.3.7.Issues Identified:
- Version Validity Concern: User
fgvieiraraised concerns about the validity of thesortmernaversion4.3.7. This needs verification against thebiocondaandconda-forgerepositories to ensure that the version is indeed available and valid.- Dependency Shift: The shift to
conda-forgefor most dependencies is a significant change. It's crucial to ensure that all these packages are compatible with each other and with thesortmernapackage.Action Items:
Verify Version: Confirm the availability and validity of
sortmernaversion4.3.7in thebiocondarepository.Check Compatibility: Ensure that the new dependencies from
conda-forgeare compatible with each other and with thesortmernapackage.The version
4.3.7ofsortmernaneeds to be verified for validity.Compatibility of new dependencies from
conda-forgewith each other and withsortmernashould be checked.
Automatic bump of bio/sortmerna.
Summary by CodeRabbit
New Features
sortmernapackage from version 4.3.6 to 4.3.7, improving performance and compatibility.conda-forge, enhancing environment stability and access to updated libraries.Bug Fixes
sortmernamay include bug fixes not specified in the documentation.Chores