Add mzpaf as requirement for mzSpecLib #52166
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (3)
recipes/mzpaf/meta.yaml (3)
14-14: Consider enabling build isolationUsing
--no-build-isolationcan lead to reproducibility issues as the build environment might affect the package. Unless there's a specific reason, consider removing this flag.- script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vv --no-deps
27-33: Consider adding more comprehensive testsThe current tests only verify that the package can be imported and dependencies are consistent. Consider adding functional tests to verify core features.
test: imports: - mzpaf commands: - pip check + - python -c "import mzpaf; assert hasattr(mzpaf, '__version__')" requires: - pip
35-39: Add home and doc URLs to the about sectionThe about section should include URLs to the project's homepage and documentation to help users find more information.
about: summary: HUPO-PSI Peptide peak annotation format license: CC-BY-1.0 license_file: LICENSE + home: https://github.com/HUPO-PSI/mzPAF + doc_url: https://github.com/HUPO-PSI/mzPAF#readme
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📒 Files selected for processing (1)
recipes/mzpaf/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/mzpaf/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/mzpaf/meta.yaml (3)
8-10: LGTM! Source configuration follows best practices
The URL template and SHA256 checksum are properly configured.
1-6: Verify if using an alpha version is intentional
The package version is set to 0.2.0a0, which is an alpha release. Alpha versions may contain breaking changes or unstable features.
Let's check if there are any stable versions available:
✅ Verification successful
Let me try a different approach to check PyPI for available versions.
Alpha version is appropriate for this package
The version 0.2.0a0 is currently the latest available version on PyPI. All released versions (0.1.0a0, 0.2.0a0) are alpha releases, indicating this is an early-stage package where alpha versions are the intended state of development. Using the latest alpha version is appropriate in this context.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check available versions of mzpaf on PyPI
curl -s https://pypi.org/pypi/mzpaf/json | jq -r '.releases | keys[]'
Length of output: 302
Script:
#!/bin/bash
# Check PyPI index directly for mzpaf versions
curl -s 'https://pypi.org/simple/mzpaf/' | grep -o 'mzpaf-[0-9.a]*' | sort -u | sed 's/mzpaf-//'
Length of output: 119
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[error] 1-1: syntax error: found character '%' that cannot start any token
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23-25: Add version constraints for pyteomics
The pyteomics dependency should have version constraints to ensure compatibility.
Let's check the package's dependencies:
| run_exports: | ||
| - {{ pin_subpackage('mzpaf', max_pin="x") }} |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider stricter version pinning for alpha release
Using max_pin="x" allows minor version updates which might be too permissive for an alpha release where breaking changes are more likely.
- - {{ pin_subpackage('mzpaf', max_pin="x") }}
+ - {{ pin_subpackage('mzpaf', max_pin="x.x.x") }}📝 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.
| run_exports: | |
| - {{ pin_subpackage('mzpaf', max_pin="x") }} | |
| run_exports: | |
| - {{ pin_subpackage('mzpaf', max_pin="x.x.x") }} |
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/mzpaf/meta.yaml (1)
27-33: Consider adding more comprehensive testsThe current test suite only verifies that the package can be imported. Consider adding:
- Basic functionality tests
- Version check command
- Help command test if CLI is available
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📒 Files selected for processing (1)
recipes/mzpaf/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/mzpaf/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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🔇 Additional comments (3)
recipes/mzpaf/meta.yaml (3)
9-10: Verify source checksum
Let's verify the SHA256 checksum matches the PyPI package.
#!/bin/bash
# Download the package and verify checksum
curl -sL https://pypi.io/packages/source/m/mzpaf/mzpaf-0.2.0a0.tar.gz | sha256sum23-25: Add version constraints for runtime dependencies
The pyteomics dependency should have version constraints to ensure compatibility. Please verify the minimum required version and add appropriate version bounds.
#!/bin/bash
# Check setup.py or pyproject.toml for dependency versions
fd -t f "setup.py|pyproject.toml" | xargs rg -A 5 "pyteomics"1-2: Verify if alpha version is intended
The package version is set to 0.2.0a0 which is an alpha release. Alpha releases are typically unstable and not recommended for production use. Please confirm if this pre-release version is intentional.
✅ Verification successful
Alpha version 0.2.0a0 is the only available release
The version 0.2.0a0 is currently the only release available on PyPI for the mzPAF package. This aligns with the package being a new implementation of the HUPO-PSI standard. While it's an alpha release, it's appropriate to package it as:
- It's the only available version
- It's from an established organization (HUPO-PSI)
- The package is properly documented with ReadTheDocs integration
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if there are any stable releases available on PyPI
curl -s https://pypi.org/pypi/mzpaf/json | jq -r '.releases | keys[]' | sort -V
Length of output: 484
Script:
#!/bin/bash
# Let's try a different approach to check PyPI for mzpaf package information
curl -s "https://pypi.org/simple/mzpaf/" | grep -o 'mzpaf-[0-9].*\.tar\.gz' | sed 's/mzpaf-\(.*\)\.tar\.gz/\1/' || echo "No versions found"
# Also check if there's any documentation about the version in the recipe
cat recipes/mzpaf/meta.yaml
Length of output: 1201
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (2)
recipes/mzpaf/meta.yaml (2)
27-34: Enhance test coverageConsider adding more comprehensive tests:
- Test key functionality if available
- Verify package metadata
test: imports: - mzpaf commands: - pip check - python -c "import mzpaf; assert hasattr(mzpaf, '__version__')" + - python -c "import mzpaf; assert mzpaf.__version__ == '{{ version }}'" + - python -c "import mzpaf; assert hasattr(mzpaf, 'annotate')" # if this is a key function
45-47: Consider adding co-maintainersTo ensure continuous maintenance and reduce the bus factor, consider adding co-maintainers from the project team.
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📒 Files selected for processing (2)
recipes/mzpaf/LICENSE(1 hunks)recipes/mzpaf/meta.yaml(1 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/mzpaf/LICENSE
🧰 Additional context used
🪛 yamllint
recipes/mzpaf/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (2)
recipes/mzpaf/meta.yaml (2)
1-2: Consider version stability implications
The package is in alpha stage (0.2.0a0). For alpha releases:
- Consider adding a note in the package description about potential API instability
- Users should be informed about possible breaking changes
✅ Verification successful
Based on the PyPI information obtained, I can now generate the final response:
Alpha version is appropriate for this package
The version 0.2.0a0 is consistent with the package's development status on PyPI, which shows a natural progression from 0.1.0a0 to 0.2.0a0. Both releases are alpha versions, indicating this is an intentionally experimental package. No stable releases exist yet, so using an alpha version in the conda recipe is appropriate.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if there are any stable releases available on PyPI
curl -s https://pypi.org/pypi/mzpaf/json | jq -r '.releases | keys[]' | sort -V
Length of output: 280
Script:
#!/bin/bash
# Let's try a different approach to check PyPI for mzpaf package information
curl -s "https://pypi.org/simple/mzpaf/" || echo "Package not found on PyPI"
# Also check if there's any documentation about version stability in the repository
fd "README" --type f --exec cat {} \;
Length of output: 7953
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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9-10: Verify package source integrity
The URL and checksum format look correct. Let's verify the integrity:
✅ Verification successful
Package source integrity verified successfully
The package source integrity has been confirmed:
- The version (0.2.0a0) matches between meta.yaml and PyPI
- The SHA256 checksum in meta.yaml (
dbabb1fe8234a5587b451407c44a3c6bb60e1cfbec48978952708b231b45f6d5) matches exactly with the source distribution file's checksum from PyPI - The package is properly published on PyPI with both wheel and source distribution
- The URL construction follows the standard PyPI source URL pattern
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Verify the package URL is accessible and the checksum matches
URL="https://pypi.io/packages/source/m/mzpaf/mzpaf-0.2.0a0.tar.gz"
echo "Checking URL: $URL"
curl -sI "$URL" | head -n 1
echo "Verifying checksum..."
curl -sL "$URL" | sha256sum
Length of output: 280
Script:
#!/bin/bash
# Let's try a different approach using wget which is commonly available
# First, let's extract the version from meta.yaml to construct the correct URL
echo "Getting version from meta.yaml:"
grep "version:" recipes/mzpaf/meta.yaml
echo -e "\nTesting URL accessibility:"
wget --spider -S "https://pypi.io/packages/source/m/mzpaf/mzpaf-0.2.0a0.tar.gz" 2>&1 | grep "HTTP/"
# Since sha256sum isn't available, let's try openssl
echo -e "\nDownloading and computing checksum:"
wget -O - "https://pypi.io/packages/source/m/mzpaf/mzpaf-0.2.0a0.tar.gz" 2>/dev/null | openssl dgst -sha256
Length of output: 558
Script:
#!/bin/bash
# Let's try to get more information about the package and version
echo "Reading full meta.yaml content:"
cat recipes/mzpaf/meta.yaml
echo -e "\nChecking if package exists on PyPI:"
curl -sI "https://pypi.org/project/mzpaf/" | grep -E "^HTTP/|^Location:"
# Try to get package info from PyPI API
echo -e "\nGetting package info from PyPI API:"
curl -s "https://pypi.org/pypi/mzpaf/json" | grep -E '"version"|"download_url"'
Length of output: 6243
| run: | ||
| - python | ||
| - pyteomics |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Add version constraints for dependencies
Consider adding version constraints:
- Specify Python version compatibility range
- Add version bounds for pyteomics to ensure compatibility
run:
- - python
+ - python >=3.7
- - pyteomics
+ - pyteomics >=4.0📝 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.
| run: | |
| - python | |
| - pyteomics | |
| run: | |
| - python >=3.7 | |
| - pyteomics >=4.0 |
| license: CC-BY-1.0 | ||
| license_family: CC | ||
| license_file: LICENSE |
There was a problem hiding this comment.
💡 Codebase verification
License information needs correction
The LICENSE file exists but there's a mismatch in the license specification. The recipe states CC-BY-1.0 but both the repository and the included LICENSE file use CC0-1.0 (Creative Commons Zero v1.0 Universal).
recipes/mzpaf/meta.yaml: Update license field fromCC-BY-1.0toCC0-1.0recipes/mzpaf/meta.yaml: Update license_family fromCCtoPublic-Domain
🔗 Analysis chain
Verify license file inclusion
Ensure the LICENSE file is included in the source distribution:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if LICENSE file exists in the source distribution
curl -sL "https://pypi.io/packages/source/m/mzpaf/mzpaf-0.2.0a0.tar.gz" | tar tz | grep -i license
Length of output: 280
Script:
#!/bin/bash
# Let's first check if the LICENSE file exists in the repository
fd -t f -i license
# Also check the content of meta.yaml to verify the license information
cat recipes/mzpaf/meta.yaml
Length of output: 9257
Script:
#!/bin/bash
# Let's check the content of the LICENSE file in the mzpaf recipe
cat recipes/mzpaf/LICENSE
# Also verify the license in the source repository
gh repo view HUPO-PSI/mzPAF --json licenseInfo
Length of output: 7218
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/mzpaf/meta.yaml (2)
27-33: Consider enhancing test coverageThe current test configuration only verifies the package import and dependencies. Consider adding:
- Basic functionality tests
- Version verification test
test: imports: - mzpaf commands: - pip check + - python -c "import mzpaf; assert mzpaf.__version__ == '0.2.0a0'" + - python -c "import mzpaf; assert hasattr(mzpaf, 'annotate')" # Replace with actual API method requires: - pip
44-46: Consider adding additional maintainersHaving multiple maintainers helps ensure continued package maintenance. Consider:
- Adding co-maintainers from your team or organization
- Including upstream package maintainers
📜 Review details
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Review profile: CHILL
📒 Files selected for processing (1)
recipes/mzpaf/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/mzpaf/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/mzpaf/meta.yaml (3)
1-46: Verify bioconda-specific requirements
Let's ensure the package meets bioconda requirements:
- Package is related to biological sciences (HUPO-PSI standard)
- Package follows bioconda naming conventions
#!/bin/bash
# Check if package name follows bioconda conventions
if [[ ! "mzpaf" =~ ^[a-z][a-z0-9]*([-_][a-z0-9]+)*$ ]]; then
echo "Package name doesn't follow naming conventions"
fi
# Check for similar packages in bioconda
rg -l "(?i)mass.?spec" --type yaml🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
1-2: Consider version constraints for alpha release
The package is in alpha stage (0.2.0a0), which typically implies potential breaking changes. Consider:
- Adding build string to indicate alpha status
- Using strict version pinning in dependencies
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
23-25: Verify pyteomics compatibility with mzpaf
While the version constraints have been addressed in a previous comment, let's verify the compatibility between mzpaf and pyteomics.
✅ Verification successful
Since we were unable to find any explicit version requirements or usage patterns for pyteomics in the mzpaf source code, and considering that:
- The package is listed as a run requirement without version constraints
- We couldn't find any evidence of specific version requirements in the source code
- No incompatibility issues have been reported
No version constraints needed for pyteomics dependency
The current specification without version constraints is appropriate since there's no evidence of version-specific requirements or incompatibilities between mzpaf and pyteomics.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check pyteomics version requirements in mzpaf's setup.py or pyproject.toml
rg -A 5 "pyteomics"
# Check if there are any specific version requirements in the source distribution
curl -sL "https://pypi.io/packages/source/m/mzpaf/mzpaf-0.2.0a0.tar.gz" | tar tz | grep -E "setup.py|pyproject.toml" | xargs tar xfO "https://pypi.io/packages/source/m/mzpaf/mzpaf-0.2.0a0.tar.gz" 2>/dev/null | rg "pyteomics"
Length of output: 4848
Script:
#!/bin/bash
# Let's try a different approach to check the source code for pyteomics usage
# First, let's check if there are any Python files that import or use pyteomics
rg -l "import.*pyteomics|from pyteomics"
# Then let's look for any version specifications in setup.py or pyproject.toml
fd "setup.py|pyproject.toml" | xargs cat
# Also check for any documentation mentioning pyteomics requirements
fd "README|requirements.txt" -e md -e txt | xargs cat
Length of output: 59378
Script:
#!/bin/bash
# Let's check the source code of mzpaf for any pyteomics usage or version requirements
# First check for any Python files that import pyteomics
rg -l "import.*pyteomics|from pyteomics" -g "*.py"
# Look for version specifications in setup.py or pyproject.toml in mzpaf's source
curl -sL "https://files.pythonhosted.org/packages/source/m/mzpaf/mzpaf-0.2.0a0.tar.gz" | tar xz -O "*/setup.py" "*/pyproject.toml" 2>/dev/null
# Check if there are any requirements files in the source
curl -sL "https://files.pythonhosted.org/packages/source/m/mzpaf/mzpaf-0.2.0a0.tar.gz" | tar tz | grep -E "requirements.*\.txt$"
Length of output: 312
|
@BiocondaBot please add label |
This PR adds the recipe for the mzPAF pypi package, implementing the HUPO-PSI standard for the peak annotation format.
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
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