update Hsdecipher #51021
update Hsdecipher #51021
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📝 Walkthrough📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces a new Changes
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/hsdecipher/meta.yaml (2)
19-24: Consider adding build-time dependencies.The runtime dependencies look appropriate for a data analysis and visualization package. However, there are no build-time dependencies specified. Consider adding a
hostsection with at leastpythonas a dependency to ensure the package is built with the correct Python version.Add a
hostsection to specify build-time dependencies:requirements: host: - python >=3.7 run: - python >=3.7 - pandas - seaborn - matplotlib-base
25-27: Consider adding more comprehensive tests.The current test command verifies that the package is installed and can be executed, which is good. However, consider adding more comprehensive tests to ensure the package's functionality. This could include running a simple analysis or checking for the presence of key functions or modules.
Add more test commands, for example:
test: commands: - hsdecipher -h - python -c "import hsdecipher; print(hsdecipher.__version__)" - hsdecipher --version
📜 Review details
Configuration used: CodeRabbit UI
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📒 Files selected for processing (1)
- recipes/hsdecipher/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/hsdecipher/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/hsdecipher/meta.yaml (3)
1-6: LGTM: Package metadata is correctly defined.The package name and version are properly set using Jinja2 templating. The lowercase conversion for the package name is a good practice.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-17: Verify the custom build script.The build settings look good overall. The use of
noarch: pythonandrun_exportswithpin_subpackageare appropriate. However, please ensure that theconda_build_package.shscript exists and contains the correct build commands.#!/bin/bash # Check if the build script exists and display its contents if [ -f conda_build_package.sh ]; then echo "Build script found. Contents:" cat conda_build_package.sh else echo "Build script not found in the repository root." fi
8-10: Verify the source repository URL.The source URL and checksum look good. However, please confirm that
https://github.com/zx0223winner/hsdecipher_condais the correct repository for the source code.✅ Verification successful
Source URL is accessible and build script is present.
- The source URL
https://github.com/zx0223winner/hsdecipher_conda/archive/refs/tags/v1.0.0.tar.gzreturned HTTP status 200.- The
conda_build_package.shscript is included in the archive athsdecipher_conda-1.0.0/conda_build_package.sh.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Verify if the source URL is accessible and contains the expected content curl -sI https://github.com/zx0223winner/hsdecipher_conda/archive/refs/tags/v1.0.0.tar.gz | grep -i "HTTP/2 200"Length of output: 138
Script:
#!/bin/bash # Check if the source URL is accessible curl -s -o /dev/null -w "%{http_code}" https://github.com/zx0223winner/hsdecipher_conda/archive/refs/tags/v1.0.0.tar.gz # Search for conda_build_package.sh in the repository fd "conda_build_package.sh"Length of output: 152
Script:
#!/bin/bash # Follow redirects and check the final HTTP status code final_status=$(curl -s -o /dev/null -w "%{http_code}" -L https://github.com/zx0223winner/hsdecipher_conda/archive/refs/tags/v1.0.0.tar.gz ) echo "Final HTTP Status: $final_status" # Download the tar.gz archive curl -s -L -o v1.0.0.tar.gz https://github.com/zx0223winner/hsdecipher_conda/archive/refs/tags/v1.0.0.tar.gz # List contents of the tar.gz archive to verify the presence of conda_build_package.sh tar -tzf v1.0.0.tar.gz | grep "conda_build_package.sh"Length of output: 411
recipes/hsdecipher/meta.yaml
Outdated
| about: | ||
| home: https://github.com/zx0223winner/HSDecipher | ||
| summary: Pipeline for the downstream analysis of highly similar duplicate genes | ||
| description: "Many tools have been developed to measure the degree of similarity between gene duplicates within and between species. Here, we present HSDecipher, a bioinformatics pipeline to assist users in the analysis and visualization of highly similar duplicate genes (HSDs). We describe the steps for analysis of HSDs statistics, expanding HSD gene set, and visualizing the results of comparative genomic analyses. HSDecipher represents a useful tool for researchers exploring the evolution of duplicate genes in select eukaryotic species." | ||
| license: GPL-3.0-or-later | ||
| license_file: licence |
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💡 Codebase verification
License file 'license' not found.
The license_file is specified as license in the about section, but no such file exists in the repository.
Please add a license file named license to the repository.
🔗 Analysis chain
Fix the license file name typo.
The about section provides comprehensive information about the package, which is excellent. However, there's a typo in the license file name.
Please correct the license file name:
- license_file: licence
+ license_file: licenseAlso, verify that the license file exists in the repository with the correct name.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check for the existence of the license file
if [ -f license ]; then
echo "License file 'license' found."
elif [ -f licence ]; then
echo "License file 'licence' found (with British spelling)."
else
echo "No license file found. Please add a license file named 'license'."
fi
Length of output: 188
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Describe your pull request here
update Hsdecipher description
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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@bioconda/<team>and will automatically re-post them to notify the addressed<team>.Summary by CodeRabbit
New Features
HSDecipherpackage for analyzing highly similar duplicate genes.Documentation