Add seqspec #51326
Add seqspec #51326
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces a new file, The requirements section details both host and runtime dependencies, mandating Python version 3.6 or higher and listing libraries such as Possibly related PRs
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (4)
recipes/seqspec/meta.yaml (4)
19-30: Consider adding version constraints for all dependencies.The requirements section is well-structured with appropriate host and run dependencies. However, consider adding version constraints for all run requirements to ensure compatibility and reproducibility. This is especially important for packages like
jsonschema,newick,requests, andbiopython.Example:
run: - python >=3.6 - pyyaml >=6.0 - jsonschema >=3.0.0 - newick >=1.0.0 - requests >=2.25.0 - biopython >=1.78 - packaging >=20.0Please adjust the version numbers according to the minimum compatible versions for your package.
32-39: LGTM: Test section is good, but consider adding more comprehensive tests.The test section includes appropriate checks:
- Import verification for
seqspec- Basic functionality test with
seqspec --help- Dependency conflict check with
pip checkTo further improve test coverage, consider adding:
- Tests for specific functionalities or subcommands of
seqspec.- Checks for expected output or error messages.
Example:
commands: - pip check - seqspec --help - seqspec --version - seqspec validate --help - python -c "import seqspec; assert seqspec.__version__ == '0.3.0'"Adjust these suggestions based on the actual functionalities of your package.
41-44: LGTM: About section is good, but consider adding more metadata.The about section correctly specifies:
- The home URL pointing to the GitHub repository
- The MIT license
- A reference to the license file
To provide more context about the package, consider adding:
- A brief summary or description of the package
- Documentation URL (if available)
- Dev URL (usually the same as home for GitHub projects)
Example:
about: home: https://github.com/sbooeshaghi/seqspec license: MIT license_file: LICENSE summary: A tool for describing and processing genomics experiment data doc_url: https://github.com/sbooeshaghi/seqspec#readme dev_url: https://github.com/sbooeshaghi/seqspecAdjust the summary and URLs as appropriate for your package.
46-48: LGTM: Recipe maintainer is specified.The extra section correctly lists "visze" as the recipe maintainer. This is important for future updates and issue resolution.
Consider adding more maintainers if there are other regular contributors to the project. This can help distribute the maintenance workload and ensure continued support for the package.
Example:
extra: recipe-maintainers: - visze - another-contributorOnly add additional maintainers if they have agreed to take on this responsibility.
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📒 Files selected for processing (1)
- recipes/seqspec/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/seqspec/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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🔇 Additional comments (4)
recipes/seqspec/meta.yaml (4)
1-6: LGTM: Package and version are correctly defined.The package name and version are properly set using Jinja2 templating, which is a good practice for maintaining consistency throughout the recipe.
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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8-10: LGTM: Source URL and checksum are correctly specified.The source URL is properly structured for PyPI packages, and the inclusion of a SHA256 checksum ensures package integrity. This adheres to best practices for Conda recipes.
12-17: LGTM: Build section is well-configured.The build section is correctly set up with:
- A proper entry point for the
seqspeccommand.noarch: pythonspecification, which is appropriate for pure Python packages.- A pip install command with the recommended flags for Conda builds.
- The build number is correctly set to 0 for the initial release.
1-1: Note: Ignore the yamllint syntax error for '%' character.The static analysis tool yamllint 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 correctly used in Conda recipe meta.yaml files. This error can be safely ignored as the syntax is appropriate for this context.
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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First this PR has to be accepted: #51325 |
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@BiocondaBot please update |
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I encountered an error updating your PR branch. You can report this to bioconda/core if you'd like. |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/seqspec/meta.yaml (2)
21-32: Consider adding version specifications for dependencies.The requirements section correctly lists all necessary dependencies for both host and run environments. However, some run dependencies (jsonschema, python-newick, requests, biopython) don't have version specifications. This could potentially lead to compatibility issues in the future.
Consider adding version specifications for these dependencies to ensure consistent behavior across different environments. You can use the
>=operator to specify minimum versions if you want to allow for newer versions.Would you like assistance in determining appropriate version specifications for these dependencies?
34-41: LGTM: Test section is well-defined. Consider adding a version check.The test section includes appropriate checks: an import test, a dependency check with
pip check, and a basic functionality test withseqspec --help. These tests cover the essentials of package installation and basic functionality.To enhance the test coverage, consider adding a version check command:
commands: - pip check - seqspec --help - seqspec --versionThis additional test would ensure that the installed version matches the expected version.
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📒 Files selected for processing (1)
- recipes/seqspec/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/seqspec/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/seqspec/meta.yaml (4)
1-10: LGTM: Package and source information are well-defined.The package name, version, and source URL are correctly specified using Jinja2 variables, which is a good practice for maintainability. The SHA256 checksum is provided for security, ensuring the integrity of the downloaded package.
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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43-47: LGTM: About section is complete and informative.The about section provides all necessary metadata, including the home URL, a clear and informative summary of the package's purpose, and correct license information. The inclusion of the
license_filefield is particularly good practice, ensuring that the full license text is available with the package.
49-51: LGTM: Maintainer information is correctly specified.The extra section correctly lists 'visze' as the recipe maintainer, which is consistent with the PR submitter information provided in the PR objectives.
12-19: LGTM with a suggestion: Review installation flags.The build section is well-structured with appropriate use of
run_exportsfor ABI compatibility and correct entry point definition. Thenoarch: pythonspecification is suitable for a pure Python package.However, consider reviewing the use of
--no-depsand--no-build-isolationflags in the installation script. These flags might prevent the resolution of dependencies or cause issues in certain environments. Unless there's a specific reason for using these flags, it might be safer to remove them.To verify the necessity of these flags, you can run:
✅ Verification successful
LGTM: The use of
--no-depsand--no-build-isolationflags is appropriate.The
meta.yamlfile for seqspec explicitly lists both host and run dependencies, indicating that these are managed by conda/bioconda. The use of--no-depsprevents pip from installing or upgrading dependencies, which is correct when conda is handling dependency management. Similarly,--no-build-isolationis appropriate as it prevents pip from creating an isolated build environment, relying instead on the conda environment to provide all necessary build dependencies.These flags ensure that conda remains in control of the package's dependency management, which is the desired behavior in a conda/bioconda environment. Therefore, the current installation script using these flags is correct and doesn't need modification.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check if there are any special build requirements or dependencies that justify the use of --no-deps and --no-build-isolation grep -r "setup_requires" . grep -r "install_requires" .Length of output: 6494
Script:
#!/bin/bash # Check for dependencies specified in meta.yaml files find . -name "meta.yaml" -exec grep -H "requirements:" {} \; find . -name "meta.yaml" -exec grep -H "run:" {} \;Length of output: 484898
Script:
#!/bin/bash # Display the content of the seqspec/meta.yaml file, focusing on the requirements section sed -n '/requirements:/,/^[^ ]/p' recipes/seqspec/meta.yamlLength of output: 248
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Actionable comments posted: 1
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📒 Files selected for processing (1)
- recipes/seqspec/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/seqspec/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (7)
recipes/seqspec/meta.yaml (7)
1-6: LGTM: Package and version declaration.The use of Jinja2 templating for setting the package name and version is a good practice. It allows for easy updates and maintains consistency throughout the file.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-10: LGTM: Source specification.The source URL is correctly structured for PyPI packages, and the inclusion of a SHA256 checksum ensures the integrity of the downloaded package.
35-42: LGTM: Comprehensive test configuration.The test section includes appropriate checks:
- Import verification for the
seqspecmodule.- Execution of
seqspec --helpto ensure the entry point is functional.pip checkto verify dependencies.These tests provide a good baseline for ensuring the package is correctly installed and functional.
44-48: LGTM: Comprehensive package metadata.The about section provides all necessary metadata:
- Home URL for the project
- A clear and concise summary of the package's purpose
- License information (MIT) and the location of the license file
This information is crucial for users and complies with best practices for package metadata.
50-52: LGTM: Maintainer information provided.The extra section correctly specifies the recipe maintainer. This information is crucial for package management and future updates.
1-1: Note on YAML syntax:The static analysis tool (yamllint) reports a syntax error for the '%' character at the beginning of the file. This is a false positive. The '%' is part of the Jinja2 templating syntax, which is valid and commonly used in Conda recipe files. The YAML is correct when processed by Conda's build system.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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12-19: LGTM: Build configuration with a note on installation flags.The build section is well-structured with appropriate run_exports, entry point, and noarch declarations.
However, please verify if the use of
--no-depsand--no-build-isolationflags in the installation script is intentional and necessary for this package.✅ Verification successful
Verified: Installation flags are consistent across other recipes.
The use of
--no-depsand--no-build-isolationflags in the installation script aligns with practices observed in numerous other recipes within the repository, confirming their intentional and necessary use.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check if other recipes in the repository use similar installation flags # Test: Search for recipes using --no-deps and --no-build-isolation flags echo "Recipes using --no-deps and --no-build-isolation:" rg --type yaml 'script:.*--no-deps.*--no-build-isolation' recipes/Length of output: 54346
recipes/seqspec/meta.yaml
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| requirements: | ||
| host: | ||
| - python >=3.6 | ||
| - pip | ||
| run: | ||
| - python >=3.6 | ||
| - pyyaml >=6.0 | ||
| - setuptools | ||
| - jsonschema | ||
| - python-newick | ||
| - requests | ||
| - biopython | ||
| - packaging |
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Consider moving setuptools to host requirements.
The requirements section is comprehensive, but there's a potential issue:
setuptoolsis listed in therunrequirements. Typically,setuptoolsis needed during the build process and not at runtime.
Consider moving setuptools to the host requirements:
host:
- python >=3.6
- pip
+ - setuptools
run:
- python >=3.6
- pyyaml >=6.0
- - setuptools
- jsonschema
- python-newick
- requests
- biopython
- packagingThis change ensures that setuptools is available during the build process without unnecessarily including it in the runtime environment.
📝 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.
| requirements: | |
| host: | |
| - python >=3.6 | |
| - pip | |
| run: | |
| - python >=3.6 | |
| - pyyaml >=6.0 | |
| - setuptools | |
| - jsonschema | |
| - python-newick | |
| - requests | |
| - biopython | |
| - packaging | |
| requirements: | |
| host: | |
| - python >=3.6 | |
| - pip | |
| - setuptools | |
| run: | |
| - python >=3.6 | |
| - pyyaml >=6.0 | |
| - jsonschema | |
| - python-newick | |
| - requests | |
| - biopython | |
| - packaging |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (4)
recipes/seqspec/meta.yaml (4)
8-10: LGTM: Source information is correct.The source URL and SHA256 checksum are properly specified. The URL construction using Jinja2 variables is correct and follows best practices.
Consider adding a comment above the
sha256line to remind maintainers to update it when the version changes:source: url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/seqspec-{{ version }}.tar.gz # sha256 for version {{ version }} sha256: d9e6c283daaca06f58f1090c0c7dcfecf646b9658e62aa873a4e85fef56c56c9
21-33: LGTM: Requirements are well-defined.The requirements section is comprehensive and correctly structured:
setuptoolsis now in the host requirements, addressing the previous review comment.- Python version requirement (>=3.6) is consistent across host and run environments.
- All necessary dependencies are included.
Consider adding version constraints to other dependencies, similar to
pyyaml >=6.0. This can help ensure compatibility and reproducibility. For example:run: - python >=3.6 - pyyaml >=6.0 - jsonschema >=3.0.0 - python-newick >=1.0.0 - requests >=2.25.0 - biopython >=1.78 - packaging >=20.0Please adjust the version numbers based on the minimum required versions for your package.
35-42: LGTM: Test configuration is comprehensive.The test configuration is well-structured and includes essential checks:
- Import check for
seqspecis correct.pip checkverifies that all dependencies are satisfied.seqspec version -hensures that the CLI is functioning.pipis correctly listed as a test requirement.Consider adding a basic functionality test to ensure that the core features of
seqspecare working as expected. For example:test: imports: - seqspec commands: - pip check - seqspec version -h - seqspec --help # Add this line to test the main CLI interface - python -c "import seqspec; assert seqspec.__version__ == '{{ version }}'" # Add this line to verify the installed version requires: - pipThese additional tests will provide more confidence in the package's functionality and correct installation.
44-48: LGTM: About section is informative and complete.The about section provides essential metadata for the package:
- Home URL is correctly specified.
- Summary clearly describes the package's purpose.
- License (MIT) is stated and the license file is referenced.
Consider adding a
doc_urlfield to point users to the package's documentation, if available. For example:about: home: https://github.com/sbooeshaghi/seqspec summary: File format that describes data generated from genomics experiments. File format and seqspec tool enable uniform processing of genomics data. license: MIT license_file: LICENSE doc_url: https://github.com/sbooeshaghi/seqspec#readme # Add this line, adjust the URL as neededThis addition would make it easier for users to find the package documentation.
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📒 Files selected for processing (1)
- recipes/seqspec/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/seqspec/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/seqspec/meta.yaml (4)
1-6: LGTM: Package and version declaration.The package name and version are correctly defined using Jinja2 templating, following best practices for Conda recipes. This approach allows for easy updates to the package version in the future.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
50-52: LGTM: Extra section is correctly formatted.The extra section properly lists the recipe maintainer (visze). This information is crucial for package management and future updates.
1-52: Overall assessment: The meta.yaml file is well-structured and ready for inclusion.This meta.yaml file successfully introduces the seqspec package (version 0.3.0) to the Bioconda recipes repository, addressing the main objective of the pull request. The file follows Conda packaging best practices and includes all necessary sections:
- Package and version declaration
- Source information
- Build configuration
- Requirements
- Test configuration
- About section
- Extra section (maintainers)
Minor suggestions for improvements have been made throughout the review, including:
- Adding version constraints to dependencies
- Enhancing the test configuration
- Adding a
doc_urlto the about sectionThese suggestions, if implemented, would further improve the package's maintainability and user experience. However, they are not critical for the basic functionality of the package.
The inclusion of
run_exportsin the build section aligns with the PR objective of avoiding potential API, ABI, and CLI breakage issues.This meta.yaml file is ready for inclusion in the Bioconda recipes repository, subject to the verification of the installation script as mentioned in a previous comment.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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12-19: LGTM: Build configuration looks good, but verify installation script.The build configuration is well-structured:
run_exportsis correctly used to manage dependencies.- The entry point for
seqspecis properly defined.- The package is correctly set as
noarch: python.Please verify the installation script:
script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolationThe use of
--no-depsand--no-build-isolationflags might prevent the installation of required dependencies. Ensure this is intentional and doesn't cause issues during package installation.
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@BiocondaBot please add label |
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seqspec, short for "sequence specification" (pronounced "seek-speck"), is a file format that describes data generated from genomics experiments. Both the file format and seqspec tool enable uniform processing of genomics data.
alt text Figure 1: Anatomy of a seqspec file.
We have multiple tutorials to get you up and running with seqspec:
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
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