Update Hsdfinder #51092
Update Hsdfinder #51092
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📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThe pull request includes updates to the Changes
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Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/hsdfinder/meta.yaml (2 hunks)
🔇 Additional comments (3)
recipes/hsdfinder/meta.yaml (3)
2-2: LGTM: Version update looks good.The version has been correctly updated from 1.1.0 to 1.1.1, which aligns with the PR objective of updating the Hsdfinder package. This minor version update follows semantic versioning principles.
3-3: Verify the updated SHA256 checksum.The SHA256 checksum has been updated, which is necessary for the new version. However, we should verify that this checksum corresponds to the correct source package.
Please run the following script to verify the SHA256 checksum:
#!/bin/bash # Description: Verify the SHA256 checksum of the source package # Extract version and checksum from meta.yaml version=$(grep 'version = ' recipes/hsdfinder/meta.yaml | cut -d'"' -f2) checksum=$(grep 'sha256 = ' recipes/hsdfinder/meta.yaml | cut -d'"' -f2) # Download the package and calculate its checksum url="https://github.com/zx0223winner/hsdfinder_conda/archive/refs/tags/hsdfinder.tar.gz" downloaded_checksum=$(curl -sL "$url" | sha256sum | cut -d' ' -f1) # Compare the checksums if [ "$checksum" = "$downloaded_checksum" ]; then echo "Checksum verification passed." else echo "Checksum verification failed." echo "Expected: $checksum" echo "Got: $downloaded_checksum" fi
Line range hint
1-33: Overall assessment: Changes look good, with minor verifications needed.The updates to the meta.yaml file are consistent with a minor version update (1.1.0 to 1.1.1) of the HSDFinder package. The changes include:
- Updated version number
- Updated SHA256 checksum
- Added new test command for
hsd_to_keggThe
run_exportssection is correctly maintained, which aligns with the PR description's emphasis on preventing API, ABI, and CLI breakage issues. Thenoarch: pythonspecification is appropriate for a Python package without compiled extensions.To complete the review:
- Verify the SHA256 checksum (see previous comment).
- Provide information about the new
hsd_to_keggfunctionality (see previous comment).- Confirm that no changes to the build number are necessary for this update.
Please run the following script to check if any changes to the build number are necessary:
If the script output shows significant changes to setup.py, requirements.txt, or any compiled components, consider incrementing the build number.
| @@ -24,6 +24,7 @@ requirements: | |||
| test: | |||
| commands: | |||
| - hsdfinder -h | |||
| - hsd_to_kegg -h | |||
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💡 Codebase verification
Missing documentation for the new test command hsd_to_kegg -h.
The new test command hsd_to_kegg -h has been added, but there are no corresponding entries in the changelog or documentation.
Please ensure that:
- The new feature is mentioned in the package's changelog.
- Documentation is updated to include usage and details about
hsd_to_kegg.
🔗 Analysis chain
New test command added: Please provide more information.
The addition of the new test command hsd_to_kegg -h is a good practice to ensure the package is working correctly. This suggests that a new functionality has been added in this version.
Could you please provide more information about this new functionality? It would be helpful to:
- Confirm if this new feature is mentioned in the package's changelog or release notes.
- Verify if any documentation updates are needed for this new feature.
To help verify the new command, please run the following script:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the new hsd_to_kegg command
# Clone the repository
git clone https://github.com/zx0223winner/hsdfinder_conda.git
cd hsdfinder_conda
# Check for mentions of hsd_to_kegg in recent commits or changelog
git log -n 10 --pretty=format:"%h - %s" | grep -i "hsd_to_kegg"
if [ -f CHANGELOG.md ]; then
grep -i "hsd_to_kegg" CHANGELOG.md
fi
# Check for documentation updates
grep -r "hsd_to_kegg" docs/ || echo "No mentions of hsd_to_kegg found in docs/"
Length of output: 663
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@BiocondaBot please add label |
Describe your pull request here
update hsdfinder fixing bugs
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:
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@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>.Summary by CodeRabbit
New Features
hsd_to_kegg -hfor enhanced testing capabilities.Bug Fixes