Add newick #51325
Add newick #51325
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📝 Walkthrough📝 WalkthroughWalkthroughThis pull request introduces a new file, Possibly related PRs
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/newick/meta.yaml (2)
8-10: LGTM: Source information is correctly specified.The source URL and SHA256 checksum are properly defined. The use of a checksum is a good security practice for ensuring package integrity.
Consider adding a comment with the direct URL for easier manual verification:
source: url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/newick-{{ version }}.tar.gz # https://pypi.org/packages/source/n/newick/newick-1.9.0.tar.gz sha256: 9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf
25-31: LGTM: Test section is well-defined, consider adding a functional test.The test section includes appropriate checks:
- Import test for the
newickmodule.pip checkcommand to verify package compatibility.- Correct inclusion of pip in test requirements.
Consider adding a simple functional test to ensure basic functionality. For example:
test: imports: - newick commands: - pip check - python -c "import newick; assert newick.loads('(A,B)C;'), 'Failed to parse a simple Newick tree'" requires: - pip
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/newick/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/newick/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/newick/meta.yaml (6)
1-6: LGTM: Package metadata is correctly defined.The package name and version are properly set using Jinja2 templating, which is a good practice for maintaining consistency across the recipe.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-15: LGTM: Build configuration is well-defined.The build section is correctly configured:
noarch: pythonis appropriate for a pure Python package.- The installation script follows best practices by using
--no-depsand--no-build-isolation.- The build number is correctly set to 0 for an initial release.
33-37: LGTM: About section provides comprehensive metadata.The about section is well-defined:
- The home URL correctly points to the GitHub repository.
- The summary concisely describes the package's functionality.
- License information is properly specified, including the license type and file reference.
39-41: LGTM: Recipe maintainer is correctly specified.The recipe maintainer is properly set to "visze", which matches the PR submitter mentioned in the PR objectives.
1-41: Overall assessment: The meta.yaml file is well-structured and follows Conda packaging best practices.The recipe for the
newickpackage is correctly defined, including all necessary sections such as package metadata, source, build instructions, requirements, tests, and about information. The use of Jinja2 templating and the inclusion of a SHA256 checksum are good practices.A few minor suggestions for improvement:
- Add a comment with the direct PyPI URL for easier manual verification.
- Verify if there are any additional run dependencies for the
newickpackage.- Consider adding a simple functional test to ensure basic functionality.
These suggestions are optional and do not affect the overall quality of the recipe. Great job on creating this Conda recipe!
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
17-23: LGTM: Requirements are properly specified, but verify run dependencies.The host and run requirements are correctly defined. However, it's worth verifying if there are any additional run dependencies for the
newickpackage.Please run the following script to check for any potential missing run requirements:
|
@BiocondaBot please add label |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/newick/meta.yaml (2)
8-10: LGTM: Source definition is correct.The source URL and SHA256 checksum are properly defined. The use of Jinja2 templating in the URL is good for maintainability.
Consider adding a comment with the actual URL for easier reading and debugging. For example:
source: url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/newick-{{ version }}.tar.gz # https://pypi.org/packages/source/n/newick/newick-1.9.0.tar.gz sha256: 9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf
27-33: LGTM: Test configuration is good, but consider adding a functional test.The test section is well-defined:
- The import check for the newick module is essential.
- The pip check command is a good practice to ensure all dependencies are correctly installed.
- Including pip as a test requirement is correct for running the pip check command.
Consider adding a simple functional test to ensure the package works as expected. For example:
test: imports: - newick commands: - pip check - python -c "import newick; tree = newick.loads('(A,B,(C,D)E)F;'); assert tree.name == 'F'" requires: - pipThis additional test creates a simple tree and checks if it's parsed correctly.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/newick/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/newick/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/newick/meta.yaml (6)
1-6: LGTM: Package and version definition looks good.The use of Jinja2 templating for the package name and version is a good practice for maintainability. The package name is correctly lowercased in the package section.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-17: LGTM: Build configuration is well-defined.The build section is correctly configured:
- The
noarch: pythonsetting is appropriate for a pure Python package.- The
run_exportssection is correctly implemented as per the PR objectives, ensuring compatibility with downstream recipes.- The build script follows the recommended approach for pip installation without dependencies or build isolation.
- The build number is correctly set to 0 for a new package.
35-39: LGTM: About section is complete and accurate.The about section contains all the required metadata:
- The home URL points to the correct GitHub repository.
- The summary is concise and accurately describes the package's functionality.
- The license is correctly specified as Apache-2.0, matching the information in the PR objectives.
- The license file is correctly referenced.
41-43: LGTM: Maintainer information is correct.The extra section correctly lists 'visze' as the recipe maintainer, which matches the PR submitter mentioned in the PR objectives.
1-1: Note: Ignore the yamllint syntax error for '%' character.The yamllint tool reported a syntax error for the '%' character at the beginning of the file. This is a false positive. The '%' character is part of the Jinja2 templating syntax, which is commonly used and valid in Bioconda recipes. The YAML file is correctly formatted and follows the Bioconda recipe guidelines.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
19-25: LGTM: Requirements are defined, but verify run dependencies.The requirements section is well-structured:
- Python version requirement (>=3.7) is consistent between host and run environments.
- Host requirements appropriately include setuptools and pip.
Please verify if there are any additional run requirements for the newick package. You can check this by running the following script:
If any dependencies are found, please update the run requirements accordingly.
✅ Verification successful
Verified: Run dependencies are correctly defined.
The requirements section is comprehensive, and no additional run dependencies were found for the newick package based on the verification.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for any dependencies in setup.py or pyproject.toml # Test: Search for install_requires in setup.py echo "Checking setup.py for dependencies:" fd -t f setup.py | xargs rg "install_requires" # Test: Search for dependencies in pyproject.toml echo "Checking pyproject.toml for dependencies:" fd -t f pyproject.toml | xargs rg "dependencies" # Test: Check if there's a requirements.txt file echo "Checking for requirements.txt:" fd -t f requirements.txtLength of output: 1332
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| {% set name = "newick" %} | |||
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should we maybe also call this package python-newick?
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OH! it is already there and it is called python-newick. thank you! Will clos ethe PR
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python is already there. called |
python package to read and write the Newick format.
This package will be used for seqspec
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