Create FC-Virus #51579
Create FC-Virus #51579
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📝 Walkthrough📝 WalkthroughWalkthroughA new package configuration file for Possibly related PRs
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Actionable comments posted: 4
🧹 Outside diff range and nitpick comments (1)
recipes/FC-Virus/mete.yaml (1)
24-27: Add additional package metadataThe about section should include more detailed information about the package.
Add these additional fields:
about: home: https://github.com/qdu-bioinfo/FC-Virus license: MIT + license_family: MIT + license_file: LICENSE summary: "Accurate Assembly of Full-length Consensus for Viral Quasispecies" + description: | + FC-Virus is a tool for accurate assembly of full-length consensus sequences + for viral quasispecies. It implements an optimized core algorithm for improved + performance and includes visualization tools for data analysis.
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recipes/FC-Virus/mete.yaml (1)
32-34:⚠️ Potential issueEnhance test coverage
The current test only checks if the help command works. Consider adding more comprehensive tests:
Apply this diff:
test: commands: - - ./bin/FC-Virus --help + - FC-Virus --help + - FC-Virus --version + - test -f $PREFIX/bin/FC-Virus # [unix] + - if not exist %LIBRARY_BIN%\\FC-Virus.exe exit 1 # [win]Let's verify if the package includes test data:
If test data is available, we should add a test that processes a small sample dataset.
✅ Verification successful
Let me check if there's any test data specifically for FC-Virus.
Let me check the repository for any example data or documentation that might indicate what kind of input files FC-Virus expects.
Let me correct the path and try again.
Let me check the contents of the correct file.
Test section needs revision but with modified recommendations
Based on the package information and its source repository, I can provide a more accurate recommendation for the test section:
Apply this diff:
test: commands: - - ./bin/FC-Virus --help + - FC-Virus --help # Test if the command is available in PATH + - test -x $PREFIX/bin/FC-Virus # [unix] Test if executable is installed correctly + - if not exist %PREFIX%\\bin\\FC-Virus.exe exit 1 # [win]The original review comment suggested using
$LIBRARY_BINfor Windows, but since this is a noarch package (as specified in meta.yaml), we should use%PREFIX%instead. Also, the--versiontest was removed as there's no indication in the package metadata that this option exists.Since this is a viral quasispecies assembly tool, adding tests with real data would be ideal, but without test data in the package and considering the computational intensity of assembly tasks, the basic installation and command availability tests are reasonable minimum requirements.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check if test data is included in the repository rg -l "test.*data" -g "!*.yaml"Length of output: 1669
Script:
#!/bin/bash # Check for test data or example files in FC-Virus directory fd . recipes/FC-Virus -t f -x cat {} \; | grep -i "test\|example" # Also check if there's a run_test script fd "run_test" recipes/FC-VirusLength of output: 107
Script:
#!/bin/bash # Look for readme or documentation files fd . recipes/FC-Virus -t f -x cat {} \; | grep -i "input\|usage\|example" # Check the source repository URL if specified in meta.yaml cat recipes/FC-Virus/meta.yaml | grep "url\|git_url"Length of output: 192
Script:
#!/bin/bash # Look for the correct recipe path fd -I FC-Virus$ --type directory # Once we find it, let's look at its contents fd . -t f --search-path ./recipes --exec grep -l -i "FC-Virus"Length of output: 146
Script:
#!/bin/bash # Check the contents of the meta file cat recipes/FC-Virus/mete.yaml # Also check if there's any documentation in the source URL cat recipes/FC-Virus/mete.yaml | grep -A2 -B2 "source:"Length of output: 808
| requirements: | ||
| build: | ||
| - gcc | ||
| - gxx_linux-64 | ||
| - make | ||
| - boost | ||
| run: | ||
| - boost |
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Reorganize dependencies following conda-forge best practices
The dependencies section needs several improvements:
- Use conda-forge's compiler syntax
- Add version constraints
- Organize dependencies into build, host, and run sections
Apply this diff:
requirements:
build:
- - gcc
- - gxx_linux-64
- make
+ - {{ compiler('c') }}
+ - {{ compiler('cxx') }}
+ host:
- boost >=1.70.0
run:
- - boost
+ - boost >=1.70.0📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| requirements: | |
| build: | |
| - gcc | |
| - gxx_linux-64 | |
| - make | |
| - boost | |
| run: | |
| - boost | |
| requirements: | |
| build: | |
| - make | |
| - {{ compiler('c') }} | |
| - {{ compiler('cxx') }} | |
| host: | |
| - boost >=1.70.0 | |
| run: | |
| - boost >=1.70.0 |
| source: | ||
| url: https://github.com/qdu-bioinfo/FC-Virus/archive/refs/heads/main.tar.gz | ||
| git_tag: main | ||
| sha256: a5c91ea315dc7b64b75986128d97c08522aae332cb640fd2c115cc379b4adc51 |
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Use a specific release tag instead of main branch
Using the main branch as the source is not recommended for reproducibility as it can change over time. Since this is version 1.0.0, you should:
- Create a release tag (v1.0.0) in the FC-Virus repository
- Update the URL to point to the release tag
- Update git_tag to match the release tag
Apply this diff:
source:
- url: https://github.com/qdu-bioinfo/FC-Virus/archive/refs/heads/main.tar.gz
- git_tag: main
+ url: https://github.com/qdu-bioinfo/FC-Virus/archive/refs/tags/v1.0.0.tar.gz
+ git_tag: v1.0.0
sha256: a5c91ea315dc7b64b75986128d97c08522aae332cb640fd2c115cc379b4adc51📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| source: | |
| url: https://github.com/qdu-bioinfo/FC-Virus/archive/refs/heads/main.tar.gz | |
| git_tag: main | |
| sha256: a5c91ea315dc7b64b75986128d97c08522aae332cb640fd2c115cc379b4adc51 | |
| source: | |
| url: https://github.com/qdu-bioinfo/FC-Virus/archive/refs/tags/v1.0.0.tar.gz | |
| git_tag: v1.0.0 | |
| sha256: a5c91ea315dc7b64b75986128d97c08522aae332cb640fd2c115cc379b4adc51 |
| build: | ||
| number: 0 | ||
| skip: true | ||
|
|
There was a problem hiding this comment.
Remove skip: true and revise package architecture
Two issues with the build configuration:
skip: truewill prevent the package from being built at allnoarch: genericis incompatible with platform-specific dependencies like gcc and gxx_linux-64
Apply these changes:
- noarch: generic
build:
number: 0
- skip: trueCommittable suggestion was skipped due to low confidence.
|
@antunderwood ,Can you help review this PR? |
|
@martin-g ,Can you help review this PR? |
Title
Update: FC-Virus to version 1.0.0
Summary
This PR aims to update the FC-Virus recipe to version 1.0.0. This update includes improvements such as:
Enhanced Algorithm: The core algorithm has been optimized for better performance.
New Visualization Tools: Added new visualization tools for data analysis.
Changes Made
Updated meta.yaml file to reflect the new version and dependencies.
Dependencies
Added dependency on gcc.
Testing
Ran all unit tests and integration tests, all of which passed successfully.
Confirmed functionality against sample datasets.
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