add flexiformatter version 1.0.2 #51633
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (3)
recipes/meta.yaml (3)
18-19: Consider removing run_exports section.The
run_exportssection is typically used for compiled libraries (C/C++) to ensure ABI compatibility. For a pure Python package marked asnoarch: python, this section is unnecessary and can be removed.- run_exports: - - {{ pin_subpackage(name|lower, max_pin='x.x') }}
32-41: Enhance test coverage.While basic import and help command tests are good, consider adding functional tests to verify the core functionality:
commands: - flexiformatter --help - samtools --help + - flexiformatter --version + # Add a test with minimal input data if possible requires: - pip
42-50: Add recommended metadata fields.Consider adding these additional fields to the
aboutsection as per Bioconda guidelines:about: home: "https://github.com/ljwharbers/flexiformatter" summary: Moving flexiplex barcode and UMI to bam tags license: MIT license_file: LICENSE + doc_url: "https://github.com/ljwharbers/flexiformatter#readme" + dev_url: "https://github.com/ljwharbers/flexiformatter" + description: | + Flexiformatter is a tool for processing flexiplex output files, + moving barcode and UMI information to BAM tags.
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Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (1)
recipes/meta.yaml (1)
8-10: Verify package source URL and checksum.The source URL follows the PyPI convention, but let's verify its accessibility and integrity.
✅ Verification successful
The previous attempt showed a 301 redirect and missing sha256sum command. Let's try to:
- Verify the package information directly from PyPI's JSON API
- Compare it with our meta.yaml content
- This will help us confirm both the correct URL pattern and SHA256 hash
Source URL and checksum are correct and verified
The verification confirms that:
- The package version (1.0.2) matches
- The SHA256 checksum in meta.yaml (4afde5aa4318b663d348bfe35845f911dc7770b107ae2eddc69b588f979638ab) matches the PyPI source distribution's checksum
- While the URL pattern in meta.yaml uses pypi.io, this redirects to files.pythonhosted.org which is the canonical PyPI storage, so this is correct and follows conda-forge conventions
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify package source URL and checksum # Expected: URL should be accessible and checksum should match # Test source URL accessibility curl -sI "https://pypi.io/packages/source/f/flexiformatter/flexiformatter-1.0.2.tar.gz" | head -n 1 # Download and verify checksum curl -sL "https://pypi.io/packages/source/f/flexiformatter/flexiformatter-1.0.2.tar.gz" | sha256sumLength of output: 289
Script:
#!/bin/bash # Let's try a different approach using Python's pip to get package info # and verify the package existence on PyPI # Check if the package exists on PyPI and get its information curl -s "https://pypi.org/pypi/flexiformatter/json" | jq -r '.info.version, .urls[].url, .urls[].digests.sha256' 2>/dev/null # Also let's check the actual meta.yaml content to compare cat recipes/meta.yamlLength of output: 1599
recipes/meta.yaml
Outdated
| requirements: | ||
| host: | ||
| - python >=3 | ||
| - pip | ||
| - setuptools | ||
| run: | ||
| - python >=3 | ||
| - typer | ||
| - simplesam | ||
| - samtools |
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🛠️ Refactor suggestion
Add specific version constraints for dependencies.
While the requirements are correct, consider adding more specific version constraints for better reproducibility and to prevent potential compatibility issues:
host:
- - python >=3
+ - python >=3.7
- pip
- setuptools
run:
- - python >=3
- - typer
+ - python >=3.7
+ - typer >=0.9.0
- simplesam
- samtools📝 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: | |
| host: | |
| - python >=3 | |
| - pip | |
| - setuptools | |
| run: | |
| - python >=3 | |
| - typer | |
| - simplesam | |
| - samtools | |
| requirements: | |
| host: | |
| - python >=3.7 | |
| - pip | |
| - setuptools | |
| run: | |
| - python >=3.7 | |
| - typer >=0.9.0 | |
| - simplesam | |
| - samtools |
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/meta.yaml (1)
32-40: Consider adding functional tests.While basic import and help command tests are good, consider adding tests that verify core functionality:
- Testing actual file processing
- Verifying tag manipulation in BAM files
Consider adding these test commands:
commands: - flexiformatter --help - samtools --help + - flexiformatter --version + - flexiformatter convert --help
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Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/meta.yaml (5)
1-6: LGTM! Package metadata is correctly defined using Jinja2 templating.🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
48-50: LGTM! Recipe maintainer correctly set to the package author.
12-20: 🛠️ Refactor suggestionReview build configuration flags and run_exports.
Using both
--no-depsand--no-build-isolationmight cause build issues. Consider removing--no-build-isolationto ensure proper dependency resolution during build time.The
run_exportssection is typically used for compiled packages with ABI compatibility concerns. For a pure Python package, this might be unnecessary.#!/bin/bash # Description: Check if this is a pure Python package # Expected: Should find only Python files, no compiled extensions # Look for any potential compiled extensions in the package rg -l "setup\(.*ext_modules.*\)" rg -l "Extension\(.*\)"Consider this simplified build section:
build: entry_points: - flexiformatter = flexiformatter.reformat_flexiplex_tags:app noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vv --no-deps number: 0 - run_exports: - - {{ pin_subpackage(name|lower, max_pin='x.x') }}
42-46: Verify repository and license information.#!/bin/bash # Description: Verify GitHub repository and license # Expected: Repository should exist and contain LICENSE file # Test 1: Check if the GitHub repository exists curl -sI "https://github.com/ljwharbers/flexiformatter" | head -n 1 # Test 2: Check for LICENSE file in the repository curl -sI "https://raw.githubusercontent.com/ljwharbers/flexiformatter/main/LICENSE" | head -n 1
21-30: Verify samtools package availability in Bioconda.#!/bin/bash # Description: Check if samtools is available in Bioconda # Expected: Should find samtools in conda-forge or bioconda # Search for samtools package in meta.yaml files rg "name:\s*samtools"
recipes/meta.yaml
Outdated
| source: | ||
| url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/flexiformatter-{{ version }}.tar.gz | ||
| sha256: 4afde5aa4318b663d348bfe35845f911dc7770b107ae2eddc69b588f979638ab |
There was a problem hiding this comment.
💡 Codebase verification
Package source integrity verification failed
The source verification revealed discrepancies between the recipe and PyPI:
- Version matches (1.0.2), but:
- SHA256 checksums don't match:
- Recipe:
4afde5aa4318b663d348bfe35845f911dc7770b107ae2eddc69b588f979638ab - PyPI:
fc117809168051e2ba4bfe83c69065de7f65efff7e3941e94552c88e4c6cb3a2
- Recipe:
- URL structure in recipe differs from PyPI's actual URL pattern
Please update the recipe with:
- The correct SHA256 checksum from PyPI:
fc117809168051e2ba4bfe83c69065de7f65efff7e3941e94552c88e4c6cb3a2 - Consider using PyPI's actual URL pattern:
https://files.pythonhosted.org/packages/...
🔗 Analysis chain
Verify package source integrity.
Let me try a different approach to verify the package source integrity.
The previous attempt failed because the URL structure was incorrect and some commands weren't available. Using PyPI's JSON API will give us more reliable information about the package's source URL and checksums.
Let me try one more verification to get the actual version number from the meta.yaml file.
This will help us verify if the version and checksum in the recipe match the ones from PyPI.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the PyPI package URL and checksum
# Expected: URL should be accessible and checksum should match
# Test 1: Check if the URL is accessible
curl -sI "https://pypi.io/packages/source/f/flexiformatter/flexiformatter-1.0.2.tar.gz" | head -n 1
# Test 2: Download and verify checksum
curl -sL "https://pypi.io/packages/source/f/flexiformatter/flexiformatter-1.0.2.tar.gz" | sha256sum
Length of output: 921
Script:
#!/bin/bash
# Let's verify the package information using PyPI's JSON API
curl -s "https://pypi.org/pypi/flexiformatter/json" | jq -r '.urls[] | select(.packagetype=="sdist") | {url, digests}'
# Also get the version from meta.yaml for reference
cat recipes/meta.yaml | grep "version:"
Length of output: 568
Script:
#!/bin/bash
# Get the complete content of meta.yaml to see the version and source information
cat recipes/meta.yaml
Length of output: 1083
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Hi @ljwharbers, I see that there's already a package named |
Hi, Sorry for the confusion. Should I also update it if I actually intend to change the package name (also some of the internal things have changed). The old named package has already been deleted from PyPi. |
Add flexiformatter version 1.0.2
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