Add zamp #51309
Add zamp #51309
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request updates the Possibly related PRs
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (4)
recipes/zamp/meta.yaml (4)
8-10: LGTM: Source URL and checksum are correctly defined.The source URL and SHA256 checksum are properly set, ensuring package integrity. However, consider adding a comment with the full URL for better readability.
You could add a comment with the full URL for better readability:
source: # https://github.com/metagenlab/zamp/archive/refs/tags/v1.0.0.tar.gz url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz sha256: 366d1a1bdff60e1a8100298608f20ab2294ef476a1da1bee9c1975641c495f6e
12-19: LGTM: Build configuration is well-defined.The build section is correctly configured:
noarch: pythonis appropriate for this package.- The entry point for the
zampcommand is properly defined.- The pip installation script follows Bioconda best practices.
run_exportsis used for version pinning, which is good for consistency.Consider adding a comment explaining the purpose of the
run_exportssection for better maintainability:run_exports: # Ensure that the installed version is compatible with the build version - {{ pin_subpackage('zamp', max_pin="x.x") }}
37-40: LGTM: Basic tests are present, but consider adding more comprehensive tests.The current test commands check if the zamp command-line interface is working correctly by verifying the help output and version information. This is a good start, but more comprehensive tests could be beneficial.
Consider adding more thorough tests to ensure the package's functionality. For example:
- Test importing key modules
- Run a simple workflow with test data
- Check if specific output files are generated
Example additional tests:
test: commands: - zamp -h - zamp -v - python -c "from zamp import __version__" - zamp run --help # Add a small test dataset and a simple workflow # files: # - path/to/test_data # - path/to/test_workflow.yaml # commands: # - zamp run test_workflow.yaml # - test -f expected_output_file.txt
49-54: LGTM: Extra section is properly configured.The extra section is correctly set up:
- The container is configured to use an extended base, which might be necessary for this package.
- Two recipe maintainers are listed, including the PR submitter (vicasze).
Consider adding a comment explaining why the extended base container is required:
extra: container: # Explain why extended-base is needed, e.g., "Required for additional system libraries" extended-base: true recipe-maintainers: - farchaab - vicasze
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📒 Files selected for processing (1)
- recipes/zamp/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/zamp/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/zamp/meta.yaml (4)
1-6: LGTM: Package name and version are correctly defined.The package name "zamp" and version "1.0.0" are properly set using Jinja2 templating, which is a good practice for maintainability in meta.yaml files.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
42-47: LGTM: About section is complete and accurate.The about section provides all necessary information:
- The home URL is correctly set to the GitHub repository.
- The license (MIT) is properly specified, including the license family and file.
- The summary provides a concise description of the package's purpose.
This information matches the PR objectives and follows Bioconda guidelines.
1-54: Overall assessment: The meta.yaml file is well-structured and ready for inclusion in Bioconda.The meta.yaml file for the zamp package is comprehensive and follows Bioconda guidelines. It includes all necessary sections with appropriate information:
- Package name and version are correctly defined.
- Source URL and checksum are properly set.
- Build configuration is well-defined, including noarch setting and entry point.
- Dependencies are comprehensively listed with version constraints.
- Basic tests are included, though more comprehensive tests could be added.
- About section provides accurate package information.
- Extra section correctly specifies maintainers and container requirements.
Minor suggestions for improvements have been made throughout the review, but these are not blocking issues. The file is ready for inclusion in the Bioconda repository, pending verification of the Python version requirement.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
21-35: LGTM: Requirements are well-defined, but verify Python version constraint.The requirements section is comprehensive and includes appropriate version constraints for dependencies, which is excellent for reproducibility. However, the Python version requirement (>=3.11) is quite recent.
Please verify if Python 3.11 is strictly necessary for this package. If possible, consider supporting a wider range of Python versions to increase compatibility. Run the following script to check the Python version requirement in the package's setup.py or pyproject.toml:
If the package truly requires Python 3.11+, please add a comment explaining the reason for this requirement.
✅ Verification successful
Verified: Python version requirement (>=3.11) is consistently enforced across the codebase.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check Python version requirement in setup.py or pyproject.toml # Test: Search for Python version specification in setup.py echo "Checking setup.py:" rg --type python 'python_requires' setup.py # Test: Search for Python version specification in pyproject.toml echo "Checking pyproject.toml:" rg 'requires-python' pyproject.tomlLength of output: 271
Script:
#!/bin/bash # Description: Search for Python version specifications in common configuration files and identify Python 3.11-specific syntax in code files. # Check for Python version in environment.yml echo "Checking environment.yml for Python version specification:" if [ -f environment.yml ]; then rg 'python\s*:\s*3\.11' environment.yml else echo "environment.yml not found." fi # Check for Python version in Dockerfile echo "Checking Dockerfile for Python base image version:" if [ -f Dockerfile ]; then rg 'FROM python:3\.11' Dockerfile else echo "Dockerfile not found." fi # Search for Python 3.11-specific syntax in .py files echo "Searching for Python 3.11-specific syntax in .py files:" rg --type python 'def\s+\w+\(.*\)\s*->\s*\w+' . # Optionally, search for newly introduced modules or functions in Python 3.11 echo "Searching for Python 3.11-specific modules or functions in .py files:" rg --type python 'from\s+tomllib\s+import\s+' .Length of output: 838
Script:
#!/bin/bash # Description: Comprehensive search for Python version specifications in the codebase. # Search for Python version constraints in all files echo "Searching for Python version specifications in all files:" rg -i 'python\s*[><=~]{1,2}\s*3\.11' . # Search for explicit Python 3.11 usage echo "Searching for explicit Python 3.11 usage:" rg -i 'python3\.11' . # Search in tox.ini for Python version specifications echo "Searching in tox.ini for Python version specifications:" if [ -f tox.ini ]; then rg -i 'python_version' tox.ini else echo "tox.ini not found." fi # Search in Pipfile for Python version specifications echo "Searching in Pipfile for Python version specifications:" if [ -f Pipfile ]; then rg -i 'python_version' Pipfile else echo "Pipfile not found." fi # Search for version checks in Python code echo "Searching for version checks in Python code:" rg -i 'sys\.version_info' .Length of output: 27043
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I'd like to reopen the pull request after fixing the version needed for a required package |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
recipes/zamp/meta.yaml (3)
1-10: LGTM! Consider using a Jinja2 variable for the GitHub repository name.The package and source sections are well-defined. Good job on using Jinja2 variables for the package name and version, and providing the SHA256 checksum for integrity verification.
Consider using a Jinja2 variable for the GitHub repository name to improve maintainability:
{% set github_repo = "zAMP" %} source: url: https://github.com/metagenlab/{{ github_repo }}/archive/refs/tags/v{{ version }}.tar.gz🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-19: LGTM! Consider adding a comment explaining the run_exports section.The build section is well-configured for a Python package. The use of
noarch: pythonis appropriate, and the installation script ensures a clean build environment.Consider adding a comment to explain the purpose of the
run_exportssection:run_exports: # This ensures that packages depending on zamp will use a compatible version - {{ pin_subpackage('zamp', max_pin="x.x") }}
37-40: LGTM! Consider adding more comprehensive tests.The test section includes basic checks for the package installation.
While the current tests verify that the package is installed and accessible, consider adding more comprehensive tests to ensure the package's core functionality works as expected. For example:
test: commands: - zamp -h - zamp -v - zamp --version | grep {{ version }} - python -c "import zamp; assert zamp.__version__ == '{{ version }}'"
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📒 Files selected for processing (1)
- recipes/zamp/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/zamp/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/zamp/meta.yaml (4)
42-47: LGTM! The about section is well-defined.The about section provides all the necessary metadata for the package, including the homepage, license information, and a concise summary of the package's purpose.
49-54: LGTM! The extra section is properly configured.The extra section correctly specifies the extended-base container, which is appropriate for bioinformatics tools. The recipe maintainers are also listed, which is important for package maintenance.
1-1: Ignore the yamllint error for Jinja2 syntax.The yamllint error reported for the '%' character is a false positive. The '%' characters are part of the Jinja2 templating syntax, which is valid and commonly used in Bioconda recipe files.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
21-35: LGTM! Verify the Python version requirement.The requirements section is well-defined with appropriate host and run dependencies.
The Python version requirement (>=3.11) is quite recent. Please verify that this is intentional and necessary for the package. If possible, consider supporting a wider range of Python versions to increase compatibility.
To check the minimum required Python version, you can run:
✅ Verification successful
Python version requirement verified as >=3.11.
The
meta.yamlfile correctly specifiespython >=3.11with no additional Python version constraints found.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check the minimum required Python version in the package's setup.py or pyproject.toml # Test: Look for Python version specification in setup.py echo "Checking setup.py:" rg 'python_requires' setup.py # Test: Look for Python version specification in pyproject.toml echo "Checking pyproject.toml:" rg '^\[project\]' -A 10 pyproject.toml | rg 'requires-python'Length of output: 301
Script:
#!/bin/bash # Description: Extract all Python version specifications from meta.yaml echo "Extracting Python version requirements from recipes/zamp/meta.yaml:" rg -i 'python\s*>=\s*3\.11' recipes/zamp/meta.yaml echo "" echo "Checking for any additional Python version constraints in recipes/zamp/meta.yaml:" rg -i 'python\s*[<>=!]' recipes/zamp/meta.yaml | grep -v '>=\s*3\.11'Length of output: 516
recipes/zamp/meta.yaml
Outdated
| - zamp=zamp.__main__:main | ||
| script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv | ||
| run_exports: | ||
| - {{ pin_subpackage('zamp', max_pin="x.x") }} |
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Usually versions 1.+ should use max_pin="x". Are you sure about "x.x" ?
See https://github.com/bioconda/bioconda-recipes/blob/master/.github/PULL_REQUEST_TEMPLATE.md#instructions-for-avoiding-api-abi-and-cli-breakage-issues
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Thank you. I modified meta.yaml to max_pin="x" as suggested.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/zamp/meta.yaml (1)
37-40: LGTM: Basic test commands are provided.The test section includes basic functionality checks for the
zampCLI:
- Verifying the help output (
zamp -h)- Checking the version information (
zamp -v)These tests are good for ensuring the package is installed correctly and the CLI is accessible.
Consider adding more comprehensive tests to verify key functionalities of the zamp package. For example:
- Test a simple workflow execution
- Verify the presence and functionality of important subcommands
Would you like assistance in generating additional test commands?
📜 Review details
Configuration used: CodeRabbit UI
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📒 Files selected for processing (1)
- recipes/zamp/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/zamp/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (7)
recipes/zamp/meta.yaml (7)
1-6: LGTM: Package name and version are correctly defined.The use of Jinja2 templating for the package name and version is a good practice, allowing for easy updates and maintainability.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-19: LGTM: Build configuration is correct and follows best practices.The build section is well-configured:
noarch: pythonis appropriate for a Python package.- The entry point for the
zampcommand is correctly defined.- The build script uses the recommended approach for installing Python packages.
- The
run_exportssection correctly usespin_subpackagewithmax_pin="x", addressing the previous review comment.
42-47: LGTM: About section is complete and informative.The about section provides all necessary metadata:
- Home page URL is correctly specified.
- License information is consistent (MIT license and license family).
- The summary provides a clear and concise description of the package's purpose.
- License file location is specified.
1-54: Summary: The zamp recipe is well-structured and follows Bioconda guidelines.Overall, the
meta.yamlfile for the zamp package is well-written and adheres to Bioconda best practices. Here's a summary of the review:
- Package metadata is correctly defined.
- Source URL and checksum are properly specified.
- Build configuration is appropriate for a Python package.
- Dependencies are well-defined, but the
apptainerdependency should be verified.- Basic test commands are provided, but more comprehensive tests could be added.
- About section provides all necessary information.
- Extra section is complete, but the need for an extended base container should be verified.
Please address the verification points mentioned in the individual comments to ensure the recipe is fully optimized and compliant with Bioconda standards.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
21-35: LGTM: Requirements are well-defined, but verify apptainer dependency.The requirements section is comprehensive and well-structured:
- Host requirements are correct for a Python package.
- Run requirements list all necessary dependencies with appropriate version constraints.
Please verify if the
apptainerdependency is necessary and available in the Bioconda channel. You can check its availability using:#!/bin/bash # Description: Check if apptainer is available in the Bioconda channel conda search -c bioconda apptainerIf it's not available in Bioconda, consider adding it as a dependency from another channel (e.g., conda-forge) or removing it if it's not strictly necessary for the package functionality.
49-54: LGTM: Extra section is well-defined, but verify extended base container requirement.The extra section provides additional metadata:
- Recipe maintainers are correctly listed.
- The container is set to use an extended base.
Please verify if the extended base container is necessary for this package. If it's not required, consider removing the
extended-base: trueline to use the standard base container, which may be more efficient.You can check if any of the package's dependencies require an extended base container by running:
#!/bin/bash # Description: Check if any dependencies require an extended base container # List all dependencies deps=$(sed -n '/^requirements:/,/^test:/p' recipes/zamp/meta.yaml | grep '^\s*-' | awk '{print $2}' | sort -u) # Check each dependency's meta.yaml for extended-base: true for dep in $deps; do if grep -q "extended-base: true" recipes/$dep/meta.yaml 2>/dev/null; then echo "$dep requires extended base container" fi doneIf none of the dependencies require an extended base container, consider removing the
extended-base: trueline.
8-10: LGTM: Source URL and checksum are correctly defined.The source URL is well-formatted and uses the GitHub release tag. The SHA256 checksum is provided for integrity verification.
To ensure the integrity of the source, you can verify the checksum using the following script:
Hello,
this PR is to add zAMP to bioconda.
zAMP is a snakemake CLI pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics.
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:
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