perf: autobump bio/gdc-client/download #2031
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Sequence Diagram(s)sequenceDiagram
participant User
participant System
participant GDCClient
User->>System: Create conda environment
System->>GDCClient: Install dependencies from environment file
GDCClient-->>System: Dependencies installed
User->>GDCClient: Run download command
GDCClient-->>User: Download MAF file
GDCClient-->>User: Download BAM file
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Files selected for processing (4)
- bio/gdc-client/download/environment.linux-64.pin.txt (1 hunks)
- bio/gdc-client/download/environment.yaml (1 hunks)
- bio/gdc-client/download/meta.yaml (1 hunks)
- test.py (1 hunks)
Additional context used
Path-based instructions (1)
test.py (1)
Pattern
**/*.py: Do not suggest to add trailing commas.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Additional comments not posted (4)
bio/gdc-client/download/environment.yaml (1)
6-6: Verify compatibility and check for breaking changes.The
gdc-clientversion has been upgraded from1.6.1to2.0. Ensure that this upgrade is compatible with other dependencies and check the documentation for any breaking changes or new features.bio/gdc-client/download/meta.yaml (1)
3-3: Addition of URL improves metadata.The addition of a
urlentry provides a direct link to the GDC website, enhancing the usability and documentation of the tool.bio/gdc-client/download/environment.linux-64.pin.txt (1)
1-61: Ensure compatibility of pinned dependencies.The new file lists explicit package URLs for creating a conda environment. Verify that all listed dependencies are compatible and up-to-date to ensure a stable environment.
test.py (1)
3195-3198: Enhance test coverage by including BAM file download.The addition of a BAM file download command in
test_gdc_downloadbroadens the test coverage to validate the functionality for both MAF and BAM file types. Ensure that the BAM file path and options are correct.
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Files selected for processing (1)
- bio/gdc-client/download/environment.linux-64.pin.txt (1 hunks)
Additional comments not posted (5)
bio/gdc-client/download/environment.linux-64.pin.txt (5)
1-1: Good documentation.The comment provides clear instructions on how to use the file to create a conda environment.
2-2: Correct command usage.The command for creating a conda environment is correctly formatted.
3-3: Platform specification is correct.The platform is correctly specified as
linux-64, ensuring compatibility with the intended system.
4-4: Appropriate use of@EXPLICIT.The
@EXPLICITdirective is correctly used to indicate that the file contains exact package specifications.
5-61: Verify package URLs and relevance.The file lists specific package URLs, which should be checked for correctness and relevance to the environment's purpose. Ensure that each URL points to a valid package and that the packages are necessary for the intended use of the environment.
Verification successful
All package URLs are valid in format and domain.
The URLs listed in the file are correctly formatted and belong to recognized domains (conda-forge and bioconda). However, this does not confirm the actual accessibility or relevance of the packages. Manual verification of these aspects may be necessary to ensure the environment's functionality.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the validity of package URLs and relevance of packages in the conda environment file. # Test: Check if the URLs are accessible and valid. # Note: This script does not execute the URLs but checks their format and potential accessibility. for url in $(grep -o 'https://[^ ]*' bio/gdc-client/download/environment.linux-64.pin.txt); do echo "Checking URL: $url" # Check URL format and domain if [[ $url =~ ^https://conda\.anaconda\.org/conda-forge/ ]] || [[ $url =~ ^https://conda\.anaconda\.org/bioconda/ ]]; then echo "URL format and domain are valid." else echo "Invalid URL format or domain." fi doneLength of output: 34742
Automatic bump of bio/gdc-client/download.
Summary by CodeRabbit
New Features
environment.linux-64.pin.txtfile for streamlined conda environment setup on Linux 64-bit systems, ensuring consistency in package dependencies.gdc-clientdependency from version1.6.1to2.0, which may enhance functionality and performance.meta.yamlfile for direct access to the GDC website, improving user documentation and resource accessibility.Bug Fixes