Update assembly_finder recipe #51449
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📝 WalkthroughWalkthroughThe pull request introduces updates to the Possibly related PRs
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/assembly_finder/meta.yaml (1)
23-25: Host requirements updates look good.The Python version requirement has been correctly updated to >=3.11, and setuptools has been added to the host requirements. These changes align with the PR objectives.
Consider adding a comment explaining the reason for updating the Python version requirement, e.g.:
# Updated to Python 3.11 due to new features or dependencies requiring this version - python >=3.11
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📒 Files selected for processing (2)
- recipes/assembly_finder/meta.yaml (2 hunks)
- recipes/mess/meta.yaml (2 hunks)
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🔇 Additional comments (7)
recipes/mess/meta.yaml (5)
29-37: Run requirements updates look goodThe changes to the run requirements are in line with the PR objectives:
- Python version requirement has been updated to >=3.11.
- apptainer >=1.3.2 has been added.
- pandas version has been updated to >=2.2.3.
- rich-click version has been updated to >=1.8.3.
These updates are appropriate and align with the package's needs.
To verify the removal of mamba from run requirements, run the following command:
#!/bin/bash # Description: Check for the presence of mamba in run requirements grep -n 'mamba' recipes/mess/meta.yaml
Line range hint
1-67: Verify all changes mentioned in the PR summaryThe overall structure of the meta.yaml file is correct and follows the standard Conda recipe format. However, there are some discrepancies between the changes mentioned in the AI summary and the visible code changes:
- The version update from 0.9.0 to 0.9.1 is not visible in the provided code.
- The removal of mamba from the dependencies is not visible.
Please ensure that all intended changes have been applied correctly throughout the file.
To verify all changes, run the following command:
#!/bin/bash # Description: Display the entire contents of the meta.yaml file for a manual review cat recipes/mess/meta.yaml
13-13: Verify version number and build number consistencyThe build number has been correctly incremented to 1. However, according to the AI summary, the version number should have been updated from 0.9.0 to 0.9.1, but this change is not reflected in the provided code. Please ensure that the version number is updated consistently throughout the file.
To verify the version number, run the following command:
#!/bin/bash # Description: Check for the correct version number in the meta.yaml file grep -n 'version = ' recipes/mess/meta.yaml
24-26: Host requirements updates look goodThe Python version requirement has been correctly updated to >=3.11, and setuptools has been added as a host requirement. These changes are in line with the PR objectives and follow good practices.
To verify the removal of mamba from host requirements, run the following command:
✅ Verification successful
Host requirements updates verified
The Python version requirement has been correctly updated to >=3.11, setuptools has been added as a host requirement, and mamba has been successfully removed from the host requirements. These changes are in line with the PR objectives and follow good practices.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for the presence of mamba in host requirements grep -n 'mamba' recipes/mess/meta.yamlLength of output: 169
Script:
#!/bin/bash # Description: Check for the presence of mamba in host requirements grep -n 'mamba' recipes/mess/meta.yamlLength of output: 38
Script:
#!/bin/bash # Description: Check for the presence of mamba in host requirements grep -n 'mamba' recipes/mess/meta.yamlLength of output: 38
Line range hint
1-67: Verify adherence to Bioconda guidelinesThe recipe structure and metadata appear to follow Bioconda guidelines. However, please ensure that:
- The package is directly related to biological sciences, as per Bioconda requirements.
- All dependency versions are appropriately specified to avoid API, ABI, and CLI breakage issues.
- Consider adding a
run_exportssection in the meta.yaml file to specify dependency versioning, as mentioned in the PR objectives.To verify the package's relevance to biological sciences, please review the package description and documentation:
recipes/assembly_finder/meta.yaml (2)
13-13: Build number increment looks good.The build number has been correctly incremented from 0 to 1, which is appropriate when updating the package.
27-33: Run requirements updates look good.The following changes have been made correctly:
- Python version requirement updated to >=3.11
- pyyaml version updated to >=6.0.1
- rich-click version updated to >=1.8.3
These updates align with the PR objectives.
Please verify the compatibility of these updated versions with the package:
PR to update recipe dependencies:
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
Please use the following BiocondaBot commands:
Everyone has access to the following BiocondaBot commands, which can be given in a comment:
@BiocondaBot please update@BiocondaBot please add labelplease review & mergelabel.@BiocondaBot please fetch artifactsYou can use this to test packages locally.
Note that the
@BiocondaBot please mergecommand is now depreciated. Please just squash and merge instead.Also, the bot watches for comments from non-members that include
@bioconda/<team>and will automatically re-post them to notify the addressed<team>.