Update tbtamr dependencies #51140
Update tbtamr dependencies #51140
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📝 Walkthrough📝 WalkthroughWalkthroughThe changes in this pull request involve the addition of a GNU General Public License (GPL) Version 3 text to the Changes
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (2)
recipes/mutamr/meta.yaml (2)
13-20: LGTM: Build section is well-defined, with a suggestion for run_exports.The build section is correctly set up for a Python package. The noarch setting, entry point, and installation script are all appropriate.
Consider adjusting the run_exports pin for better flexibility:
- - {{ pin_subpackage('mutamr', max_pin="x.x") }} + - {{ pin_subpackage('mutamr', max_pin="x.x.x") }}This change allows for more granular version control, which is beneficial for a package in its early stages (0.0.1).
35-35: Remove trailing spaces.There are trailing spaces on this line. Please remove them to improve code cleanliness.
Apply this change:
- +🧰 Tools
🪛 yamllint
[error] 35-35: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (3)
- recipes/mutamr/LICENSE (1 hunks)
- recipes/mutamr/meta.yaml (1 hunks)
- recipes/tbtamr/meta.yaml (2 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/mutamr/LICENSE
🧰 Additional context used
🪛 yamllint
recipes/mutamr/meta.yaml
[error] 35-35: trailing spaces
(trailing-spaces)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (7)
recipes/tbtamr/meta.yaml (3)
Line range hint
20-21: The run_exports section looks good.The use of
run_exportswithpin_subpackageandmax_pin="x.x"aligns with the PR description's suggestion for ensuring compatibility. This pinning strategy allows updates to patch versions but not to minor or major versions.Please verify if this pinning strategy (x.x) is appropriate for the tbtamr package. Consider the following:
- Does the package follow semantic versioning?
- Are there any plans for breaking changes in minor versions?
You can check the package's version history to inform this decision:
#!/bin/bash # Fetch version history from PyPI curl -s https://pypi.org/pypi/tbtamr/json | jq -r '.releases | keys[]' | sort -V🧰 Tools
🪛 yamllint
[error] 29-29: trailing spaces
(trailing-spaces)
2-3: Version and checksum update looks good.The version bump from 0.0.4 to 1.0.2 indicates significant changes, which aligns with the PR objective of updating tbtamr dependencies.
Please verify the SHA256 checksum to ensure it matches the source tarball:
24-24: Please justify the increased Python version requirement.The Python version requirement has been raised from >=3.8 to >=3.10. This change might break compatibility with Python 3.8 and 3.9.
Could you please provide justification for this change? Also, ensure this aligns with Bioconda's Python support policy.
To verify the minimum supported Python version in the package:
Also applies to: 27-27
✅ Verification successful
Python version requirement successfully updated to >=3.10.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check the package's setup.py or pyproject.toml for Python version requirement rg -i 'python_requires' $(fd -t f -e py -e toml setup pyproject)Length of output: 218
Script:
#!/bin/bash # Check the package's setup.py or pyproject.toml for Python version requirement rg -i 'python_requires' $(fd -t f -e py -e toml -e setup.py -e pyproject.toml)Length of output: 6035
Script:
#!/bin/bash # Search for Python version requirements in meta.yaml rg -i 'python.*>=\s*3\.(8|9|10)' recipes/tbtamr/meta.yamlLength of output: 99
recipes/mutamr/meta.yaml (4)
1-11: LGTM: Package and source information are correctly defined.The package name, version, SHA256 checksum, and source URL are properly set up using Jinja2 variables. This ensures consistency and ease of updating in the future.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
36-40: LGTM: Test section provides basic package validation.The test section includes both an import test and a command-line test, which are sufficient for initial package validation.
42-47: LGTM: About section is complete and informative.The about section provides all necessary information, including the home URL, license details, and a concise summary of the package's purpose.
49-51: LGTM: Extra section correctly specifies the recipe maintainer.The extra section properly lists the recipe maintainer.
| - bedtools | ||
| - delly | ||
| - python >=3.10 | ||
| - mutamr |
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💡 Codebase verification
Dependencies Not Fully Removed
References to the following dependencies were found in the codebase:
pandasinrecipes/hap.py/meta.yaml,recipes/velocyto.py/meta.yaml, etc.bcftoolsinrecipes/hap.py/meta.yaml,recipes/hap.py/build.sh, etc.samtoolsinrecipes/hap.py/meta.yaml,recipes/hap.py/build.sh, etc.psutil,csvtk,bwa,snpeff,samclip,freebayes,bedtools,dellyacross various scripts.
This indicates that the removal of dependencies was incomplete, which may affect the package's functionality.
🔗 Analysis chain
Please clarify the significant changes in dependencies.
Most of the previous dependencies have been removed, leaving only 'mutamr'. While this aligns with the PR objective of updating to reflect a new structure, it's a significant change that might affect the package's functionality.
Could you please provide more information on these changes?
- Does 'mutamr' now include or replace the functionality of the removed dependencies?
- Have you verified that the package still functions correctly with these changes?
To check for any remaining references to removed dependencies:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Search for references to removed dependencies in Python files
rg -i 'psutil|pandas|csvtk|bwa|samtools|snpeff|samclip|freebayes|bcftools|bedtools|delly' $(fd -e py)
Length of output: 218
Script:
#!/bin/bash
# Corrected search for references to removed dependencies in Python files
rg -i 'psutil|pandas|csvtk|bwa|samtools|snpeff|samclip|freebayes|bcftools|bedtools|delly' $(fd -e py)
Length of output: 7272
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mutamr has the required tools as dependencies.
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Yes - i have tested that the package functions
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@kristyhoran, thank you for the clarification. It's good to know that mutamr includes all the required tools as dependencies. I've noted this information for future reviews.
（・・？）
✏️ Learnings added
Learnt from: kristyhoran
PR: bioconda/bioconda-recipes#51140
File: recipes/tbtamr/meta.yaml:28-28
Timestamp: 2024-10-06T22:18:24.856Z
Learning: The `mutamr` package includes `psutil`, `pandas`, `csvtk`, `bwa`, `samtools`, `snpeff`, `samclip`, `freebayes`, `bcftools`, `bedtools`, and `delly` as dependencies, so these do not need to be specified separately in `tbtamr`'s `meta.yaml`.
Note: Learnings are effective only in the context of similar code segments. To apply general coding guidelines, please configure review instructions. You can manage existing learnings in the app.
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@kristyhoran, thank you for confirming that mutamr includes the necessary dependencies and that you've tested the package to ensure it functions correctly.
(^‿^)
✏️ Learnings added
Learnt from: kristyhoran
PR: bioconda/bioconda-recipes#51140
File: recipes/tbtamr/meta.yaml:28-28
Timestamp: 2024-10-06T22:18:39.282Z
Learning: The `mutamr` package includes all the required tools as dependencies, replacing the previously separate dependencies in `tbtamr`.
Note: Learnings are effective only in the context of similar code segments. To apply general coding guidelines, please configure review instructions. You can manage existing learnings in the app.
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/mutamr/meta.yaml (1)
22-35: LGTM: Requirements are well-defined, with a minor formatting issue.The host and run requirements are appropriately specified, ensuring compatibility and reproducibility. The bcftools package name is correctly spelled, addressing the past review comment.
There's a trailing space on line 35. Please remove it to adhere to YAML best practices:
- +🧰 Tools
🪛 yamllint
[error] 35-35: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/mutamr/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/mutamr/meta.yaml
[error] 35-35: trailing spaces
(trailing-spaces)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/mutamr/meta.yaml (6)
1-11: LGTM: Package and source sections are well-defined.The package name, version, and source URL are correctly specified using Jinja2 variables, which is good for maintainability. The SHA256 checksum is provided for integrity verification.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-20: LGTM: Build section is well-configured.The build section is correctly defined with appropriate settings:
- Architecture-independent (noarch: python)
- Build number set to 0
- Entry point defined for the main function
- run_exports section included for compatibility
- Installation script uses pip with appropriate flags
36-40: LGTM: Test section is well-defined.The test section includes both an import test for the mutamr package and a command test to run
mutamr --help. This combination ensures basic functionality and accessibility of the package.
42-47: LGTM: About section provides comprehensive metadata.The about section includes all necessary information:
- Project homepage
- License details (GPL-3.0-or-later)
- License file specification
- Brief summary of the package's functionality
49-51: LGTM: Extra section correctly specifies the recipe maintainer.The extra section properly identifies kristyhoran as the recipe maintainer.
1-1: Note: YAML syntax error is a false positive.The static analysis tool reported 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 template syntax, which is commonly used in Conda recipe files. The YAML parser used by the static analysis tool might not be aware of the Jinja2 syntax. This error can be safely ignored.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
Updated tbtamr dependencies to reflect new stucture.
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...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
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@bioconda/<team>and will automatically re-post them to notify the addressed<team>.Summary by CodeRabbit
New Features
mutamrpackage, ensuring user freedoms for software usage and distribution.mutamrpackage with version0.0.1, including key dependencies for enhanced functionality.Updates
tbtamrpackage version to1.0.2and raised the Python version requirement to 3.10.mutamrpackage as a dependency for improved performance.