Pin gsl to 2.5 for rmats #51411
Pin gsl to 2.5 for rmats #51411
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces updates to the Possibly related PRs
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- recipes/rmats/meta.yaml (3 hunks)
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recipes/rmats/meta.yaml (4)
13-13: LGTM: Build number increment is correct.Incrementing the build number from 2 to 3 is appropriate when making changes to the recipe without changing the package version. This follows Conda packaging best practices.
29-29: LGTM: GSL version pinning is correct.Pinning GSL to version 2.5 in both host and run requirements is correct and aligns with the PR objective. This ensures consistency during both build and runtime.
Also applies to: 36-36
Line range hint
1-53: Overall changes align with PR objectives, but some improvements suggested.The main objective of pinning GSL to version 2.5 for RMATS has been achieved, and the build number has been correctly incremented. However, there are a few points to address:
- The
run_exportssection mentioned in the PR objectives is not present in the changes. Consider adding this to thegslpackage recipe as suggested earlier.- The addition of the linux-aarch64 platform, while beneficial, seems unrelated to the main PR objective. Please clarify the reason for including this change in this PR.
- Ensure that all changes are necessary and directly related to the PR's main objective of pinning GSL for RMATS.
To verify the impact of these changes, we can check the current and new build configurations:
#!/bin/bash # Check current RMATS package conda search rmats --override-channels -c bioconda # Verify GSL version in current RMATS package conda list gsl --explicit -n $(conda create -n rmats_test rmats -c bioconda -y | grep -o "rmats_test") # Clean up conda env remove -n rmats_test -yPlease review these suggestions and make any necessary adjustments before proceeding.
53-53: LGTM: New platform addition is beneficial, but clarification needed.Adding support for the linux-aarch64 platform is a positive change that increases the package's compatibility. The addition of a newline at the end of the file is also good practice.
However, this change seems unrelated to the main PR objective of pinning GSL to version 2.5. Could you please clarify the reason for including this change in this PR?
To verify if this platform addition is necessary, we can check if RMATS is already built for linux-aarch64:
recipes/rmats/meta.yaml
Outdated
| @@ -26,14 +26,14 @@ requirements: | |||
| - python | |||
| - cython | |||
| - numpy | |||
| - gsl | |||
| - gsl=2.5 | |||
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🛠️ Refactor suggestion
Consider adding a run_exports section for GSL.
While pinning GSL to version 2.5 is correct, the PR objectives mention adding a run_exports section to prevent potential API, ABI, or CLI breakage issues. Consider adding this section to the gsl package in its recipe, not in the rmats recipe.
Here's an example of how it might look in the gsl package recipe:
build:
run_exports:
- {{ pin_subpackage('gsl', max_pin='x.x') }}This ensures that packages depending on GSL will automatically use the correct version constraints.
Pin gsl to 2.5 for rmats
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
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