perf: autobump bio/sortmerna #2985
Conversation
![snakedeploy-bot[bot]](https://avatars.githubusercontent.com/u/1858646?s=60&v=4){kind=small}
|
It seems |
|
Important Review skippedBot user detected. To trigger a single review, invoke the You can disable this status message by setting the WalkthroughThe changes involve upgrading the Changes
🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (Invoked using PR comments)
Other keywords and placeholders
CodeRabbit Configuration File (
|
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 0
Review details
Configuration used: CodeRabbit UI
Review profile: ASSERTIVE
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.
There was a problem hiding this comment.
Actionable comments posted: 0
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
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:
There was a problem hiding this comment.
Actionable comments posted: 0
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
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