Update fastq-dl to 3.0.0 #51506
Update fastq-dl to 3.0.0 #51506
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recipes/fastq-dl/meta.yaml (1)
1-33: Summary of major changes in fastq-dl 3.0.0This update introduces significant changes to the fastq-dl package:
- Major version update from 2.0.4 to 3.0.0
- Tightened Python version requirement (>=3.9,<4.0)
- Updated build process with
--no-build-isolationflag- Changed entry point
- Added run_exports for better integration with Conda
- Significant updates to dependencies, including new additions
These changes may have implications for users of the package, particularly the stricter Python version requirement and the potential for changes in functionality due to the major version update. Users should be advised to review the changelog and test their workflows with this new version.
Consider adding a note in the package documentation or README to highlight these changes, especially the Python version requirement and any potential breaking changes introduced in this major version update.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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recipes/fastq-dl/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (7)
recipes/fastq-dl/meta.yaml (7)
14-14: Build script update approved with a note on build isolation.The build script has been updated to include the
--no-build-isolationflag. This flag disables build isolation, which can be useful for reducing build times or when dealing with complex dependency situations. However, it's important to note that this might lead to less reproducible builds if the build environment is not carefully controlled.To ensure this change doesn't introduce any issues, consider running a test build of the package.
17-18: Run exports addition approved.A new
run_exportssection has been added, usingpin_subpackageto pin the package to the same major and minor version when used as a dependency. This ensures that packages depending onfastq-dlwill use a compatible version, reducing the risk of version conflicts.This addition improves the package's integration with the Conda ecosystem and helps maintain consistency across dependent packages.
9-9: Source URL and checksum update approved.The SHA256 checksum has been updated, which is consistent with the version change. Although not visible in the diff, ensure that the source URL has been updated to reflect the new version (fastq_dl-3.0.0.tar.gz).
To verify the source URL update and validate the checksum, run the following script:
#!/bin/bash # Description: Verify source URL update and validate checksum # Test: Check if the source URL is updated rg 'url:.*fastq_dl-3\.0\.0\.tar\.gz' --type yaml # Test: Validate the checksum URL=$(rg 'url:.*fastq_dl-3\.0\.0\.tar\.gz' --type yaml -o | awk '{print $2}') if [ -n "$URL" ]; then CHECKSUM=$(curl -sL "$URL" | sha256sum | awk '{print $1}') echo "Calculated checksum: $CHECKSUM" echo "Specified checksum: de85e3fcc60c2f2fb9313336df9706add440b0f89963f28a46fa75e5ff041a0a" if [ "$CHECKSUM" = "de85e3fcc60c2f2fb9313336df9706add440b0f89963f28a46fa75e5ff041a0a" ]; then echo "Checksum validation passed" else echo "Checksum validation failed" fi else echo "Source URL not found" fi
22-23: Host requirements update approved with a note on Python version.The host requirements have been updated:
- The Python version constraint has been tightened to
>=3.9,<4.0. This change may affect compatibility with systems running older Python versions.poetry-corehas been added as a host requirement, indicating a change in the build system.To ensure these changes don't introduce any issues, run the following script:
#!/bin/bash # Description: Verify host requirements # Test: Check if poetry-core is used in the build system rg 'build-system' pyproject.toml -A 5 # Test: Verify minimum Python version in the package rg 'python_requires' pyproject.toml
16-16: Entry point update approved.The entry point has been updated from
fastq_dl.fastq_dl:maintofastq_dl.cli.download:main, which suggests a restructuring of the package's internal organization. This change is consistent with the major version update.To ensure the new entry point is correct and functional, run the following script:
#!/bin/bash # Description: Verify the new entry point # Test: Check if the new entry point file exists fd 'cli/download.py' --type f # Test: Check if the main function is defined in the new entry point rg 'def main\(' cli/download.py
26-33: Run requirements update approved.The run requirements have been significantly updated with several new dependencies and specific version constraints:
- Python version constraint updated to
>=3.9.0,<4.0.0- New dependencies added: requests, pysradb, rich-click, executor, rich, markdown-it-py, and pandas
These changes suggest expanded functionality or changes in the package's implementation. The specific version constraints help ensure compatibility and reproducibility.
To ensure these new dependencies are necessary and correctly specified, run the following script:
#!/bin/bash # Description: Verify new dependencies # Test: Check if new dependencies are imported in the package for dep in requests pysradb rich_click executor rich markdown_it_py pandas; do echo "Checking imports for $dep" rg "import.*$dep" --type python rg "from.*$dep" --type python done # Test: Verify dependency versions in pyproject.toml rg 'dependencies' pyproject.toml -A 15
1-1: Version update to 3.0.0 approved.The package version has been updated from 2.0.4 to 3.0.0, which is consistent with the PR objectives. Note that this is a major version update, which might indicate significant changes or potential breaking changes in the package.
To ensure the version update is consistent across the package, run the following script:
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/fastq-dl/meta.yaml (2)
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35-39: Consider updating test commands.The test commands have remained unchanged despite the significant version update and new dependencies. Consider reviewing and potentially updating the test commands to ensure they cover any new functionalities or changes introduced in version 3.0.0.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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41-45: Consider updating the about section.The about section has remained unchanged. Consider reviewing and potentially updating this section to reflect any changes in the package description, license, or summary that may have occurred with the update to version 3.0.0.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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🪛 yamllint
recipes/fastq-dl/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/fastq-dl/meta.yaml (5)
8-9: Source URL and checksum updates approved.The source URL has been correctly updated to reflect the new version 3.0.0. The SHA256 checksum has also been updated, which is necessary for the new version. These changes are consistent with the package update.
1-1: Note on static analysis warning.The static analysis tool (yamllint) reported a syntax error for the '%' character at the beginning of the file. This is a false positive as the '%' is part of a Jinja2 template syntax, which is commonly used in Conda recipes. No action is required to address this warning.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
14-18: Build section updates require attention.
- A new build script command has been added with
--no-build-isolation. This might affect the build process and dependencies resolution.- The entry point has changed from
fastq_dl.fastq_dl:maintofastq_dl.cli.download:main, indicating a restructuring of the package's internal organization.- A new
run_exportssection has been added, which may affect downstream dependencies.These changes should be carefully tested to ensure they don't introduce any unexpected behavior.
To verify the entry point change:
#!/bin/bash # Check for references to the old entry point rg "fastq_dl.fastq_dl:main" recipes/ # Check for references to the new entry point rg "fastq_dl.cli.download:main" recipes/
22-23: Host requirements updates need attention.
- The Python version requirement has been tightened from
>=3.7to>=3.9,<4.0. This change might affect compatibility with older Python versions.- The
poetrydependency has been replaced withpoetry-core. This change in build system might impact the package build process.Ensure that these changes are intentional and aligned with the package's compatibility goals.
To verify Python version usage:
#!/bin/bash # Check for Python version references grep -n "python" recipes/fastq-dl/meta.yaml
26-33: Run requirements have been significantly updated.
- The Python version requirement now matches the host requirement (
>=3.9,<4.0).- Several new dependencies have been added with specific version constraints:
- requests >=2.31.0,<3.0.0
- pysradb >=1.4.0,<2.0.0
- rich-click >=1.6.1,<2.0.0
- executor >=23.2.0,<24.0.0
- rich >=13.3.1,<14.0.0
- markdown-it-py 2.2.0
- pandas >=2.2.3,<3.0.0
These new dependencies might introduce new functionalities or address security issues. However, the specific version constraints might affect compatibility with other packages in the Bioconda ecosystem.
Ensure that these changes are necessary and aligned with the package's functionality goals. Consider if any of these version constraints can be relaxed to improve compatibility.
To verify the new dependencies:
#!/bin/bash # Check for usage of new dependencies in the package for dep in requests pysradb rich-click executor rich markdown-it-py pandas; do echo "Checking usage of $dep:" rg "$dep" recipes/fastq-dl/ echo "" done
Update
fastq-dl: 2.0.4 → 3.0.0recipes/fastq-dl(click to view/edit other files)This pull request was automatically generated (see docs).