Add pyhmmsearch #51419
Add pyhmmsearch #51419
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Caution Review failedThe pull request is closed. 📝 Walkthrough📝 WalkthroughWalkthroughThe pull request updates the In the Possibly related PRs
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (4)
recipes/pyhmmsearch/meta.yaml (4)
1-6: LGTM! Consider using a more conventional version format.The package name and version are correctly defined using Jinja2 templating. However, the version format (YYYY.MM.DD) is unconventional. While it's valid, consider using a more standard semantic versioning format (e.g., MAJOR.MINOR.PATCH) for better compatibility with tools and easier version comparison.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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23-31: LGTM! Consider version pinning for pandas and tqdm.The requirements section is well-defined with appropriate dependencies. The version pinning for pyhmmer is good for ensuring compatibility. However, consider adding version constraints for pandas and tqdm to prevent potential compatibility issues in the future.
Example:
run: - python - pyhmmer >=0.10.12 - pandas >=1.0.0 - tqdm >=4.0.0Replace the version numbers with the minimum versions that your package is known to work with.
33-37: LGTM! Consider adding more comprehensive tests.The current test commands verify that the entry point scripts are accessible and can run without errors, which is a good start. However, to ensure the package's functionality, consider adding more comprehensive tests. For example:
- Test with a small input file to verify the core functionality.
- Check if the package can handle edge cases (e.g., empty input, large input).
- Verify the output format of each script.
Example additional test:
commands: - pyhmmsearch.py -h - reformat_pyhmmsearch.py -h - serialize_hmm_models.py -h - pyhmmsearch.py --version - python -c "import pyhmmsearch; assert pyhmmsearch.__version__ == '{{ version }}'"
39-43: LGTM! Consider adding maintainer information.The about section provides essential information about the package, including the home URL, summary, license type, and license file reference. This is excellent for users and potential contributors. To further improve it, consider adding maintainer information:
about: home: https://github.com/new-atlantis-labs/pyhmmsearch-stable summary: Fast implementation of HMMSEARCH optimized for high-memory systems using PyHmmer license: MIT license_file: LICENSE maintainers: - your_github_usernameReplace
your_github_usernamewith the appropriate maintainer information.
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📒 Files selected for processing (1)
- recipes/pyhmmsearch/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/pyhmmsearch/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/pyhmmsearch/meta.yaml (3)
8-10: LGTM! Source URL and checksum are correctly defined.The source URL is properly constructed using Jinja2 templating, pointing to the correct PyPI package. The inclusion of the SHA256 checksum is excellent for ensuring package integrity during installation.
1-1: Ignore yamllint error for Jinja2 syntax.The yamllint tool reports a syntax error for the '%' character at the beginning of the file. This is a false positive as the '%' character is part of the Jinja2 templating syntax, which is correctly used in conda-forge recipes. No action is required.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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1-43: Overall, the meta.yaml file is well-structured and follows Bioconda guidelines.The package definition is comprehensive and adheres to best practices. Minor suggestions for improvement include:
- Considering a more conventional version format.
- Verifying the necessity of build script flags.
- Adding version constraints for pandas and tqdm.
- Implementing more comprehensive tests.
- Adding maintainer information.
These suggestions are not critical and the current implementation is acceptable. Great job on creating this recipe for pyhmmsearch!
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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recipes/pyhmmsearch/meta.yaml
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| build: | ||
| script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation | ||
| number: 0 | ||
| entry_points: | ||
| - pyhmmsearch.py=pyhmmsearch/pyhmmsearch.py | ||
| - reformat_pyhmmsearch.py=reformat_pyhmmsearch.py | ||
| - serialize_hmm_models.py=serialize_hmm_models.py | ||
| run_exports: | ||
| - {{ pin_subpackage("pyhmmsearch", max_pin="x.x") }} |
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💡 Codebase verification
Potential Issues with --no-deps --no-build-isolation Flags
The use of --no-deps --no-build-isolation in the build script may prevent necessary dependencies from being installed during the build process. Since setup.py specifies install_requires, omitting dependencies could lead to build failures or runtime issues if required packages are not already present in the environment.
🔗 Analysis chain
LGTM! Verify the necessity of build script flags.
The build section is well-defined, with correct entry points and run_exports implementation. However, please verify if the --no-deps --no-build-isolation flags in the build script are necessary for this package. These flags prevent pip from installing or building dependencies, which might lead to issues if the package requires any build-time dependencies.
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fd -e py -e toml '(setup|pyproject)' | xargs cat
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (1)
recipes/pyhmmsearch/meta.yaml (1)
40-44: LGTM! Consider adding maintainer information.The about section is well-defined with all necessary information. As an enhancement, consider adding maintainer information to make it easier for users to reach out with questions or issues.
You could add:
dev_url: https://github.com/new-atlantis-labs/pyhmmsearch-stable doc_url: https://github.com/new-atlantis-labs/pyhmmsearch-stable#readme maintainers: - your_github_usernameReplace
your_github_usernamewith the appropriate maintainer's GitHub username.
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📒 Files selected for processing (1)
- recipes/pyhmmsearch/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/pyhmmsearch/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/pyhmmsearch/meta.yaml (3)
1-6: Verify the version format.The version "2024.7.29" uses a date-based format (YYYY.MM.DD). While this is not incorrect, it's uncommon and might not align with semantic versioning principles. Consider if this accurately represents the package's versioning scheme.
Can you confirm if this version format is intentional and aligns with the upstream project's versioning?
🧰 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, and the inclusion of a SHA256 checksum ensures package integrity.
16-19: Verify the correctness of entry points.The entry points seem to be defined correctly, but it's important to ensure they match the actual script locations in the package. Please verify that:
pyhmmsearch.pyis indeed located atpyhmmsearch/pyhmmsearch.pyreformat_pyhmmsearch.pyis in the root directoryserialize_hmm_models.pyis in the root directoryCan you confirm that these entry points correctly reflect the package structure?
recipes/pyhmmsearch/meta.yaml
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| sha256: 5134759a9053a9c3f52ab6c3d672094915292d431f734074d1d33021138c75ec | ||
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| build: | ||
| script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation |
There was a problem hiding this comment.
Reconsider the use of --no-deps --no-build-isolation flags.
The build script uses --no-deps --no-build-isolation flags, which may prevent necessary dependencies from being installed during the build process. This could lead to build failures or runtime issues if required packages are not present in the environment.
Consider removing these flags unless there's a specific reason for their inclusion. If they are necessary, please provide a justification in a comment.
- script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+ script: {{ PYTHON }} -m pip install . -vv📝 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.
| script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation | |
| script: {{ PYTHON }} -m pip install . -vv |
recipes/pyhmmsearch/meta.yaml
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| requirements: | ||
| host: | ||
| - python | ||
| - pip | ||
| run: | ||
| - python | ||
| - pyhmmer >=0.10.12 | ||
| - pandas | ||
| - tqdm |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider adding version constraints for pandas and tqdm.
While you've specified a version constraint for pyhmmer, the pandas and tqdm dependencies don't have any version specifications. To ensure compatibility and reproducibility, it's generally a good practice to specify version constraints for all dependencies.
Consider adding version constraints like this:
run:
- python
- pyhmmer >=0.10.12
- - pandas
- - tqdm
+ - pandas >=1.0.0
+ - tqdm >=4.0.0Please adjust the version numbers according to the minimum versions required by your package.
📝 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 | |
| - pip | |
| run: | |
| - python | |
| - pyhmmer >=0.10.12 | |
| - pandas | |
| - tqdm | |
| requirements: | |
| host: | |
| - python | |
| - pip | |
| run: | |
| - python | |
| - pyhmmer >=0.10.12 | |
| - pandas >=1.0.0 | |
| - tqdm >=4.0.0 |
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Actionable comments posted: 1
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📒 Files selected for processing (1)
- recipes/pyhmmsearch/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/pyhmmsearch/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/pyhmmsearch/meta.yaml (5)
1-10: LGTM: Package and source information are well-defined.The package name, version, source URL, and SHA256 checksum are correctly specified. This section adheres to the Bioconda recipe guidelines.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
40-44: LGTM: About section is complete and accurate.The about section includes all necessary information: home URL, summary, license type, and license file reference. This adheres to the Bioconda recipe guidelines and provides clear information about the package.
1-44: Overall, the recipe is well-structured with some areas for improvement.The
meta.yamlfile forpyhmmsearchfollows the Bioconda recipe guidelines and includes all necessary sections. The package metadata, build instructions, dependencies, and basic tests are defined. However, there are a few areas that could be improved:
- Reconsider the use of
--no-deps --no-build-isolationflags in the build script.- Add version constraints for pandas and tqdm in the run requirements.
- Enhance the test section with more comprehensive tests.
Addressing these points will improve the robustness and maintainability of the recipe. Once these changes are made, the recipe should be ready for inclusion in the Bioconda repository.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-13:⚠️ Potential issueReconsider the use of
--no-deps --no-build-isolationflags.The build script uses
--no-deps --no-build-isolationflags, which may prevent necessary dependencies from being installed during the build process. This could lead to build failures or runtime issues if required packages are not present in the environment.Consider removing these flags unless there's a specific reason for their inclusion. If they are necessary, please provide a justification in a comment.
- script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvLikely invalid or redundant comment.
24-32: 🛠️ Refactor suggestionConsider adding version constraints for pandas and tqdm.
While you've specified a version constraint for pyhmmer, the pandas and tqdm dependencies don't have any version specifications. To ensure compatibility and reproducibility, it's generally a good practice to specify version constraints for all dependencies.
Consider adding version constraints like this:
run: - python - pyhmmer >=0.10.12 - - pandas - - tqdm + - pandas >=1.0.0 + - tqdm >=4.0.0Please adjust the version numbers according to the minimum versions required by your package.
Likely invalid or redundant comment.
recipes/pyhmmsearch/meta.yaml
Outdated
| test: | ||
| commands: | ||
| - pyhmmsearch.py -h | ||
| - reformat_pyhmmsearch.py -h | ||
| - serialize_hmm_models.py -h |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider adding more comprehensive tests.
The current test commands check if the scripts can be executed with the -h flag, which is a good basic check. However, more comprehensive tests could provide better assurance of package functionality.
Consider adding tests that:
- Execute the scripts with sample inputs
- Verify expected outputs
- Check for specific functionalities
For example, you could add:
commands:
- pyhmmsearch.py -h
- reformat_pyhmmsearch.py -h
- serialize_hmm_models.py -h
- python -c "import pyhmmsearch; assert pyhmmsearch.__version__ == '{{ version }}'"
# Add more specific functional tests hereThis addition checks if the package can be imported and if the version is correct. Add more specific tests based on the package's functionality.
There was a problem hiding this comment.
Actionable comments posted: 2
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📒 Files selected for processing (2)
- recipes/pyhmmsearch/meta.yaml (1 hunks)
- recipes/sopa/meta.yaml (3 hunks)
🧰 Additional context used
🪛 yamllint
recipes/pyhmmsearch/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (12)
recipes/pyhmmsearch/meta.yaml (6)
1-10: LGTM: Package and source sections are well-defined.The package name, version, source URL, and sha256 checksum are correctly specified. This follows the best practices for Bioconda recipes.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
16-19: Clarify the status of commented-out entry points.The entry points for
pyhmmsearch.py,reformat_pyhmmsearch.py, andserialize_hmm_models.pyare currently commented out. If these are intended to be executable scripts, they should be uncommented. Otherwise, if they are not needed, consider removing these lines entirely.Please clarify the intended use of these scripts and update the configuration accordingly.
41-48: LGTM: About section is comprehensive and well-defined.The about section provides all necessary information including the home URL, summary, license details, and additional URLs for development and documentation. This follows the best practices for Bioconda recipes and provides users with valuable information about the package.
1-1: Note: Ignore yamllint error for Jinja2 syntax.The static analysis tool yamllint reports a syntax error for the Jinja2 template syntax (
{% set ... %}). This is a false positive as Jinja2 template syntax is valid and commonly used in meta.yaml files for Conda recipes. No action is required to address this error.🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
1-48: Summary: meta.yaml is well-structured with some areas for improvement.Overall, the meta.yaml file for pyhmmsearch is well-structured and follows most Bioconda guidelines. Here's a summary of the review:
- Package and source sections are correctly defined.
- Build section needs attention regarding the use of
--no-deps --no-build-isolationflags and clarification on entry points.- Requirements section could benefit from adding version constraints for all dependencies.
- Test section could be enhanced with more comprehensive tests.
- About section is comprehensive and well-defined.
Please address the suggestions in the previous comments to improve the recipe. Once these changes are made, the package should be ready for inclusion in the Bioconda channel.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
23-31: 🛠️ Refactor suggestionConsider adding version constraints for pandas and tqdm.
While you've specified a version constraint for pyhmmer, the pandas and tqdm dependencies don't have any version specifications. To ensure compatibility and reproducibility, it's generally a good practice to specify version constraints for all dependencies.
Consider adding version constraints like this:
run: - python - pyhmmer >=0.10.12 - - pandas - - tqdm + - pandas >=1.0.0 + - tqdm >=4.0.0Please adjust the version numbers according to the minimum versions required by your package.
Likely invalid or redundant comment.
recipes/sopa/meta.yaml (6)
16-16: Build script improvements approved.The changes to the build script are beneficial:
- Adding
--no-cache-dirensures a clean build by preventing the use of cached packages.- Increasing verbosity from
-vvto-vvvprovides more detailed output during installation, which can be helpful for debugging.These modifications align with best practices for conda recipe builds.
61-61: Summary formatting improvement approved.The addition of a period at the end of the summary is a minor but welcome improvement to the formatting. It enhances the readability of the package metadata.
Line range hint
1-69: Overall review: Changes approved with verification stepsAll changes in this update to the
soparecipe have been reviewed and approved. The modifications include:
- Version update to 1.1.5
- Build script improvements for cleaner builds and better debugging
- Dependency optimization by switching to snakemake-minimal
- Minor formatting improvement in the summary
- Addition of dev_url for better package information
These changes collectively improve the package recipe and metadata. However, please ensure to complete the suggested verification steps:
- Confirm version consistency across the recipe and source URL
- Verify that snakemake-minimal provides all necessary functionality
- Check the accessibility of the provided dev_url
Once these verifications are complete, the recipe update should be ready for merging.
64-64: Addition of dev_url approved.The inclusion of the
dev_urlfield is a valuable addition to the package metadata. It provides users with a direct link to the project's documentation or development page, making it easier to find more information about the project.Please verify that the URL "https://gustaveroussy.github.io/sopa" is correct and accessible. You can use the following command to check:
#!/bin/bash # Verify dev_url accessibility curl -sI https://gustaveroussy.github.io/sopa | head -n 1This command will return the HTTP status code of the URL. Ensure it returns a 200 OK status.
Line range hint
2-2: Version update looks good.The version has been updated to 1.1.5. This change is straightforward and appropriate.
Please ensure that this version matches the one in the source URL and the package's actual release. You can verify this with the following command:
✅ Verification successful
Version update verified.
The version is correctly set to 1.1.5 and matches the source URL.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Verify version consistency grep -n "version = " recipes/sopa/meta.yaml grep -n "sopa-" recipes/sopa/meta.yamlLength of output: 207
40-40: Dependency change to snakemake-minimal approved.The change from
snakemaketosnakemake-minimalis a good optimization that can reduce the package's footprint and dependencies. The version constraints remain the same, which maintains consistency.Please verify that
snakemake-minimalprovides all the necessary functionality for the package. You can check this by running:If the search returns any results, please review them to ensure that
snakemake-minimalis sufficient for these use cases.✅ Verification successful
Dependency change to snakemake-minimal verified.
No direct usage of
snakemakewas found in thesopacodebase. The existing references tosnakemake-minimalensure that all necessary functionalities are maintained.🏁 Scripts executed
The following scripts were executed for the analysis:
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#!/bin/bash # Check if sopa uses any features specific to full snakemake rg -i 'snakemake' --type pythonLength of output: 149
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#!/bin/bash # Corrected script to check if 'sopa' uses any features specific to full snakemake rg -i 'snakemake' --type pythonLength of output: 62
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#!/bin/bash # Search for 'snakemake' usage in all Python files using a glob pattern rg -i 'snakemake' --glob '*.py'Length of output: 280
recipes/pyhmmsearch/meta.yaml
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| test: | ||
| imports: | ||
| - pyhmmsearch | ||
| commands: | ||
| #- pyhmmsearch.py -h | ||
| #- reformat_pyhmmsearch.py -h | ||
| #- serialize_hmm_models.py -h |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Enhance test coverage with more comprehensive tests.
The current test configuration only checks if the package can be imported. While this is a good start, more comprehensive tests could provide better assurance of package functionality. Consider adding tests that:
- Execute the scripts with sample inputs
- Verify expected outputs
- Check for specific functionalities
For example, you could add:
commands:
- pyhmmsearch.py -h
- reformat_pyhmmsearch.py -h
- serialize_hmm_models.py -h
- python -c "import pyhmmsearch; assert pyhmmsearch.__version__ == '{{ version }}'"
# Add more specific functional tests hereThis addition checks if the scripts can be executed and if the package version is correct. Add more specific tests based on the package's functionality.
| sha256: 5134759a9053a9c3f52ab6c3d672094915292d431f734074d1d33021138c75ec | ||
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| build: | ||
| script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir |
There was a problem hiding this comment.
Reconsider the use of --no-deps --no-build-isolation flags.
The build script uses --no-deps --no-build-isolation flags, which may prevent necessary dependencies from being installed during the build process. This could lead to build failures or runtime issues if required packages are not present in the environment.
Consider removing these flags unless there's a specific reason for their inclusion. If they are necessary, please provide a justification in a comment.
- script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
+ script: {{ PYTHON }} -m pip install . -vvv📝 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.
| script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir | |
| script: {{ PYTHON }} -m pip install . -vvv |
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Yea definitely! I'll look into these tomorrow morning and try to implement them by the end of the week. Thanks for getting the ball rolling on the bioconda push. |
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Thanks!! |
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@apcamargo I had never heard of entry points. Thanks for introducing me to this best practice. I just updated PyHMMSearch to v2024.10.18 which uses this. Can you try to build again? I'll update pykofamsearch and kegg_pathway_profiler next. |
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@apcamargo do you have any suggestions on how I can get this to work? The structure is a little different. I tried bringing the executables into the python package directory. Here's my error: |
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I think that's because the |
This PR adds
pyhmmsearch, by @jolespin.Please read the guidelines for Bioconda recipes before opening a pull request (PR).
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