Add recipe for mini3di.
#51211
Add recipe for mini3di.
#51211
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
recipes/mini3di/meta.yaml (3)
12-17: LGTM: Build configuration is well-defined with a minor suggestion.The build configuration is correctly set up:
- Build number is properly initialized to 0.
- Python 2 builds are appropriately skipped.
- The pip install script is used, which is standard for Python packages.
- The
run_exportssection ensures proper version pinning for downstream dependencies.Consider adding a
noarch: pythonfield if this package is compatible with all Python versions and platforms. This can simplify the build process and reduce the number of packages that need to be built and maintained.
19-26: LGTM: Requirements are well-defined with a suggestion for consideration.The host and run requirements are appropriately specified:
- Host requirements include necessary build tools (python, pip, setuptools).
- Run requirements correctly include numpy, which is likely needed for the package's functionality.
Consider adding a Python version constraint (e.g.,
python >=3.6) to ensure compatibility with the package's supported Python versions. This can help prevent potential issues with unsupported Python versions.
28-30: LGTM: Basic test is provided, with suggestions for improvement.The test section includes a basic import test, which is a minimum requirement for ensuring the package is installed correctly.
Consider enhancing the test section with more comprehensive tests:
- Add command-line interface (CLI) tests if the package provides any CLI tools.
- Include simple functional tests to verify core functionality.
- If available, consider running the package's own test suite as part of the conda build process.
These additions would provide greater confidence in the package's functionality within the conda environment.
📜 Review details
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Review profile: CHILL
📒 Files selected for processing (1)
- recipes/mini3di/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/mini3di/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/mini3di/meta.yaml (6)
1-6: LGTM: Package name and version are correctly defined.The package name and version are properly set using Jinja2 templating, which is a good practice in Conda recipes. 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)
8-10: LGTM: Source URL and checksum are correctly specified.The source URL is properly constructed using Jinja2 templating, pointing to the correct PyPI package. The SHA256 checksum is provided, which is crucial for verifying the integrity of the downloaded package.
32-36: LGTM: About section is comprehensive and informative.The about section provides all necessary metadata:
- The home page URL is correctly specified.
- The license (BSD-3-Clause) is clearly stated and appropriate for Bioconda.
- The license file is correctly referenced.
- The summary succinctly describes the package's functionality, highlighting its relevance to bioinformatics.
This information is valuable for users and maintainers of the package.
38-40: LGTM: Maintainer information is correctly provided.The extra section appropriately lists the recipe maintainer (althonos), which matches the PR submitter. This information is crucial for package management and future communications regarding the package.
1-1: Note on YAML linting warning: False positiveThe yamllint tool reported a syntax error for the '%' character at the beginning of the file. This is a false positive as the '%' is part of the Jinja2 templating syntax, which is correctly used in Conda recipe files. No action is required to address this warning.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
1-40: Overall assessment: Well-structured recipe ready for BiocondaThis recipe for
mini3diis well-constructed and adheres to Conda and Bioconda best practices. It provides all necessary information for building and distributing the package. The package's functionality, focusing on encoding protein structures, aligns well with Bioconda's bioinformatics scope.Key strengths:
- Proper use of Jinja2 templating
- Correct specification of build requirements and runtime dependencies
- Inclusion of a basic test
- Comprehensive metadata in the about section
- Clear maintainer information
Consider the minor suggestions provided in previous comments to further enhance the recipe. Once these are addressed (if deemed necessary), this recipe should be ready for inclusion in Bioconda.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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@BiocondaBot please add label |
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (3)
recipes/mini3di/meta.yaml (3)
12-17: LGTM: Build section is well-configured with a minor suggestion.The build section is correctly set up for a pure Python package (noarch). The pip install script and run_exports section are appropriately configured.
Consider adding a comment explaining the purpose of the run_exports section, as it's not commonly used in all recipes. This would help future maintainers understand its importance.
run_exports: # Ensure consistent versioning across the environment - {{ pin_subpackage(name, max_pin="x.x") }}
28-30: Consider adding more comprehensive tests.While the import test is a good start, it would be beneficial to include more comprehensive tests to ensure the package functions correctly.
Consider adding additional tests, such as:
- Running the package's test suite if available.
- Testing specific functions or features of the package.
- Checking if any command-line scripts are installed and runnable.
Example addition:
test: imports: - {{ name }} commands: - python -c "import {{ name }}; {{ name }}.run_tests()" # If a test function exists - mini3di --version # If there's a CLI toolWould you like assistance in identifying and adding more specific tests for this package?
38-40: Consider adding more maintainers.While it's great to have a maintainer specified, it's often beneficial to have multiple maintainers for better long-term maintenance of the package.
Consider reaching out to other contributors or interested parties to add them as co-maintainers. This can help ensure the recipe stays up-to-date and well-maintained over time.
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Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/mini3di/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/mini3di/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/mini3di/meta.yaml (4)
1-6: LGTM: Package and version section looks good.The use of Jinja2 variables for the package name and version is a good practice, allowing for easier updates. Lowercasing the package name ensures consistency.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-10: LGTM: Source section is well-defined.The source URL is correctly constructed using Jinja2 variables, following the PyPI standard format. The inclusion of a SHA256 checksum ensures package integrity and security.
32-36: LGTM: About section is well-documented.The about section provides all necessary information including the home URL, license details, and a concise summary of the package's functionality. The inclusion of the license file path is particularly important for compliance.
1-2: Note on static analysis warning: False positive.The static analysis tool (yamllint) reported a syntax error for the '%' character at the start of the file. This is a false positive as the '%' is part of the Jinja2 templating syntax, which is valid and commonly used in Conda meta.yaml files.
No action is needed to address this warning.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
| requirements: | ||
| host: | ||
| - python | ||
| - pip | ||
| - setuptools | ||
| run: | ||
| - python | ||
| - numpy |
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💡 Codebase verification
Issues Found: Incomplete Dependency Specifications in meta.yaml
The meta.yaml file specifies only python and numpy as run requirements. However, additional dependencies are defined within individual setup.py files across various recipes. This discrepancy may lead to missing dependencies during package installation.
- Additional Dependencies Identified:
WTForms>=1.0.4six>=1.4.1validators>=0.5.0intervals>=0.6.0- ...and others as listed in the shell script output.
Ensure that all necessary dependencies from the setup.py files are included in the meta.yaml to maintain consistency and prevent potential installation issues.
🔗 Analysis chain
LGTM: Requirements section looks good, but verify dependencies.
The host and run requirements are appropriately specified. However, it's worth verifying if these are all the necessary dependencies for the package.
Please run the following script to check if there are any additional dependencies listed in the package's setup.py or pyproject.toml:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for additional dependencies in setup.py or pyproject.toml
# Test: Search for setup.py
if fd -t f "setup.py"; then
echo "Found setup.py. Checking for install_requires:"
rg -i "install_requires\s*=" setup.py -A 10
fi
# Test: Search for pyproject.toml
if fd -t f "pyproject.toml"; then
echo "Found pyproject.toml. Checking for dependencies:"
rg -i "dependencies\s*=" pyproject.toml -A 10
fi
Length of output: 1190
Script:
#!/bin/bash
# Description: Search for install_requires in all setup.py files within the repository
# Find all setup.py files and search for install_requires
fd -t f "setup.py" | while read -r file; do
echo "Checking $file for install_requires:"
rg -i "install_requires\s*=" "$file" -A 10
done
Length of output: 6170
This PR adds a recipe for
mini3di, a pure-Python package for computing the 3di encoding of a protein structure.Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
Please use the following BiocondaBot commands:
Everyone has access to the following BiocondaBot commands, which can be given in a comment:
@BiocondaBot please update@BiocondaBot please add labelplease review & mergelabel.@BiocondaBot please fetch artifactsYou can use this to test packages locally.
Note that the
@BiocondaBot please mergecommand is now depreciated. Please just squash and merge instead.Also, the bot watches for comments from non-members that include
@bioconda/<team>and will automatically re-post them to notify the addressed<team>.