Update meta.yaml #51670
Update meta.yaml #51670
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces significant modifications to the Possibly related PRs
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🧹 Outside diff range and nitpick comments (1)
recipes/phabox/meta.yaml (1)
Line range hint
19-21: Consider adding run_exports constraints for core dependencies.The
run_exportssection currently only pins the package itself. Given the extensive dependency list, consider adding constraints for core dependencies to prevent ABI incompatibilities.Example addition:
run_exports: - {{ pin_subpackage('phabox', max_pin="x.x") }} - biopython >={{ biopython_version }} - pytorch >={{ pytorch_version }}🧰 Tools
🪛 Gitleaks
289-289: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
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- recipes/phabox/meta.yaml (1 hunks)
🧰 Additional context used
🪛 Gitleaks
recipes/phabox/meta.yaml
289-289: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
🔇 Additional comments (3)
recipes/phabox/meta.yaml (3)
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301-304: LGTM: Test section is appropriately configured.The test command verifies the basic functionality of the package by checking if the CLI is accessible.
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🪛 Gitleaks
289-289: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
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306-316: LGTM: Package metadata is well-documented.The about section provides comprehensive information including license, documentation, and citation details.
🧰 Tools
🪛 Gitleaks
289-289: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
26-300:⚠️ Potential issueReview required: Significant changes to package dependencies may break functionality.
The changes to the requirements section raise several concerns:
- Core bioinformatics dependencies have been removed (biopython, datasets, kcounter, fasttree, mafft, etc.)
- New cloud-related dependencies (AWS/Azure SDKs) have been added
- Dependencies are pinned to very specific versions
These changes suggest a major shift in functionality that might not be intentional.
Let's verify the package's functionality requirements:
Consider the following recommendations:
- Restore the core bioinformatics dependencies if they are still required
- Use more flexible version constraints unless specific versions are absolutely required
- Document the rationale for adding cloud-related dependencies
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🪛 Gitleaks
289-289: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
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🧹 Outside diff range and nitpick comments (2)
recipes/phabox/meta.yaml (2)
26-300: Consider using conda-forge's run_exports feature for core dependencies.The current approach of explicitly pinning every dependency version might lead to maintenance overhead and potential compatibility issues. Consider leveraging conda-forge's
run_exportsfeature for core dependencies to automatically handle version constraints.🧰 Tools
🪛 Gitleaks
289-289: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
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19-21: Consider updating run_exports pinning.The current
run_exportssection usesx.xwhich might be too permissive given the extensive dependency changes. Consider using a more restrictive pin likex.x.xto ensure compatibility.run_exports: - - {{ pin_subpackage('phabox', max_pin="x.x") }} + - {{ pin_subpackage('phabox', max_pin="x.x.x") }}🧰 Tools
🪛 Gitleaks
289-289: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
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- recipes/phabox/meta.yaml (1 hunks)
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🪛 Gitleaks
recipes/phabox/meta.yaml
289-289: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
🔇 Additional comments (2)
recipes/phabox/meta.yaml (2)
26-300: Review cloud SDK dependencies.The addition of AWS and Azure SDK dependencies suggests new cloud functionality:
- AWS SDK components (aws-c-*, aws-sdk-cpp)
- Azure SDK components (azure-*)
Please ensure:
- These are actually required for core functionality
- They don't unnecessarily increase the package size
- They align with bioconda's guidelines for biological software
Let's verify the cloud SDK usage:
🧰 Tools
🪛 Gitleaks
289-289: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
26-300: Verify the impact of dependency changes on package functionality.The requirements section has undergone significant changes that raise concerns:
Core dependencies have been removed:
- biopython
- datasets
- pytorch
- transformers
- and other scientific computing libraries
New dependencies added:
- AWS SDK components
- Azure SDK components
- Various system-level libraries
These changes suggest a major architectural shift that might affect the package's functionality.
Let's verify if these changes align with the package's documentation:
✅ Verification successful
Dependencies are correctly specified in meta.yaml
The review comment raised concerns about dependency changes, but after verification:
All core dependencies are present in the meta.yaml:
- biopython (1.84)
- pytorch (2.4.0)
- transformers (4.11.3)
- datasets (3.0.2)
- numpy, pandas, and other scientific computing libraries
The AWS and Azure SDK dependencies are system-level requirements needed for the package's cloud integration features.
The package's metadata and documentation URLs confirm this is a bioinformatics tool for phage-related tasks, and all dependencies align with its functionality.
The dependencies haven't been removed but rather specified with exact versions, which is a good practice for conda packages to ensure reproducibility.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check if removed dependencies are still required # by examining imports in the source code # Get the source code echo "Checking imports in Python files..." rg -t py "^import|^from.*import" # Specifically check for removed core dependencies echo "Checking for core dependency usage..." rg -t py "import (biopython|torch|datasets|transformers|numpy|pandas|scipy)"Length of output: 415
Script:
#!/bin/bash # Let's try a different approach to check dependencies # Check if any Python files exist echo "Finding Python files..." fd -e py # Check imports one by one to avoid syntax issues echo -e "\nChecking for torch imports..." rg -l "import torch|from torch" echo -e "\nChecking for transformers imports..." rg -l "import transformers|from transformers" echo -e "\nChecking for biopython imports..." rg -l "from Bio|import Bio" echo -e "\nChecking for datasets imports..." rg -l "import datasets|from datasets" echo -e "\nChecking for numpy/pandas imports..." rg -l "import numpy|import pandas|from numpy|from pandas" # Check for AWS/Azure SDK usage echo -e "\nChecking for cloud SDK imports..." rg -l "import boto3|import azure|from boto3|from azure" # Look for setup.py or requirements.txt echo -e "\nChecking for dependency files..." fd "setup.py|requirements.txt|environment.yml"Length of output: 10144
Script:
#!/bin/bash # Let's check the actual package's source code and requirements # Check if there's a phabox directory or similar echo "Looking for package source..." fd -t d "phabox|PhaBOX" -I # Check meta.yaml in parent directories for package info echo -e "\nChecking parent meta.yaml files..." fd "meta.yaml" -d 2 # If we find the source, let's examine its requirements echo -e "\nChecking package's meta.yaml content..." cat recipes/phabox/meta.yaml # Look for any build or requirements files in the package echo -e "\nChecking for requirement files in package directory..." fd "setup.py|requirements.txt|environment.yml" recipes/phabox/Length of output: 11189
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🪛 Gitleaks
289-289: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/phabox/meta.yaml (1)
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301-304: Consider enhancing test coverage.The current test only verifies the help command. Consider adding tests for core functionality to ensure the package works as expected after dependency updates.
Example additional test commands:
test: commands: - phabox2 --help + - phabox2 --version + - python -c "import phabox2; print(phabox2.__version__)"🧰 Tools
🪛 Gitleaks
288-288: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
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📒 Files selected for processing (1)
- recipes/phabox/meta.yaml (2 hunks)
🧰 Additional context used
🪛 Gitleaks
recipes/phabox/meta.yaml
288-288: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
🔇 Additional comments (3)
recipes/phabox/meta.yaml (3)
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13-19: LGTM! Build configuration looks good.The build number increment and run_exports configuration are appropriate for this package update.
26-51: Consider making cloud dependencies optional.The addition of AWS and Azure SDK dependencies suggests new cloud integration features. However, these dependencies might significantly increase the package size and add unnecessary dependencies for users who don't need cloud features. Consider:
- Making cloud features optional through separate dependency groups
- Moving cloud-specific dependencies to a separate package (e.g., phabox-cloud)
Let's verify the necessity of these dependencies:
#!/bin/bash # Check if cloud features are used in the codebase echo "Searching for AWS SDK usage..." rg -l "boto3|aws-sdk|aws-crt" echo "Searching for Azure SDK usage..." rg -l "azure.storage|azure.identity"
52-299: Verify the impact of dependency updates.The dependencies have been updated with specific versions and builds. Please ensure that these versions are compatible with the package's functionality.
Let's check for potential compatibility issues:
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🪛 Gitleaks
288-288: Detected a Generic API Key, potentially exposing access to various services and sensitive operations.
(generic-api-key)
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/phabox/meta.yaml (1)
27-29: Consider consistent version constraint style.The new dependencies use inconsistent version constraints:
diamond =0.9.14(exact)blast =2.16.0(exact)mcl >= 22(minimum)Consider using consistent version constraint style across dependencies.
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📒 Files selected for processing (1)
- recipes/phabox/meta.yaml (4 hunks)
🔇 Additional comments (3)
recipes/phabox/meta.yaml (3)
13-13: LGTM: Build number increment is appropriate.The build number increment is justified due to the significant dependency changes.
56-56: LGTM: Summary update reflects broader scope.The change from "phage-related" to "virus-related" appropriately reflects a broader scope of functionality.
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27-45: Verify the extensive dependency changes.The changes show a significant shift in dependencies:
- Removal of ML-related packages (pytorch, transformers)
- Removal of data processing packages (pandas, numpy, scipy)
- Addition of new bioinformatics tools (diamond, blast, mcl)
Please verify:
- That these changes align with the new version's functionality
- That removing core dependencies won't break the package
Let's check the package's setup.py for required dependencies:
✅ Verification successful
Let me analyze the dependencies in the codebase further by searching for import statements and requirements files:
Let me search for Python files to analyze the code dependencies more thoroughly:
Let me try one final search to look for any documentation or README files that might explain the package's functionality and dependencies:
Based on the gathered information, I can now provide a final response:
Dependencies are correctly aligned with package functionality
The dependency changes in
meta.yamlare valid and necessary for PhaBOX 2.1.0:
The package is a bioinformatics tool for virus-related tasks (as stated in the package summary), which explains the addition of bioinformatics tools like diamond, blast, and mcl.
The ML-related packages (pytorch, transformers) and data processing packages (pandas, numpy, scipy) are not being removed - they are still present in the requirements. The review comment incorrectly interpreted these as removals.
All dependencies are properly pinned with version constraints and align with the package's purpose as a virus analysis toolkit.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify dependency changes against setup.py # Look for setup.py or pyproject.toml in the package source fd -t f "setup.py|pyproject.toml" | xargs catLength of output: 42133
Script:
#!/bin/bash # Look for requirements files and imports fd -t f "requirements.txt|environment.yml" | xargs cat # Search for Python imports related to the removed packages rg "^import (pytorch|pandas|numpy|scipy|transformers)" -A 2 rg "^from (pytorch|pandas|numpy|scipy|transformers)" -A 2 # Search for Python imports related to the new bioinformatics packages rg "^import (diamond|blast|mcl)" -A 2 rg "^from (diamond|blast|mcl)" -A 2Length of output: 510
Script:
#!/bin/bash # Find all Python files and look for imports fd -e py | xargs cat | rg "^(import|from) (torch|pandas|numpy|scipy|transformers|diamond|blast|mcl)" -A 2 # Look for main script or entry point files fd -e py "main.py|__main__.py|run.py|cli.py"Length of output: 405
Script:
#!/bin/bash # Look for documentation files fd -t f "README|DESCRIPTION|CHANGELOG" -i | xargs cat # Look specifically in the phabox directory for any documentation fd -t f . recipes/phabox/ | xargs catLength of output: 8096
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📒 Files selected for processing (1)
- recipes/phabox/meta.yaml (3 hunks)
🔇 Additional comments (3)
recipes/phabox/meta.yaml (3)
13-13: LGTM: Build number increment is appropriate.The build number increment is correct for package updates with dependency changes.
30-30: Fix duplicate prodigal-gv dependency entries.The issue with duplicate prodigal-gv entries still exists. Please keep only one entry with the most specific version constraint.
Also applies to: 39-39
56-56: Verify the scope change in package description.The summary changed from "phage-related" to "virus-related" tasks, which suggests a broader scope. Please verify if this change accurately reflects the package's current functionality and purpose.
#!/bin/bash # Check the upstream repository for related changes gh api repos/KennthShang/PhaBOX/releases/tags/2.1.0 --jq '.body' || true
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🧹 Outside diff range and nitpick comments (1)
recipes/phabox/meta.yaml (1)
27-45: Consider standardizing version constraint style.The recipe mixes exact pins (=) and minimum version constraints (>=). Consider standardizing to:
- Use exact pins (=) for tools with potential CLI/API changes (diamond, blast, mcl)
- Use minimum version constraints (>=) for Python libraries
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📒 Files selected for processing (1)
- recipes/phabox/meta.yaml (3 hunks)
🔇 Additional comments (4)
recipes/phabox/meta.yaml (4)
13-13: LGTM: Build number increment is appropriate.The build number increment is correct for the dependency updates being made.
30-30: Remove duplicate prodigal-gv dependency.The recipe lists prodigal-gv twice with different version constraints:
- Line 30:
prodigal-gv =2.11.0- Line 39:
prodigal-gv >=2.11.0Also applies to: 39-39
56-56: LGTM: Summary update accurately reflects tool's scope.The updated summary better represents the tool's capabilities for virus-related tasks.
32-44: Verify compatibility with updated dependency versions.Several dependencies have been updated to newer major versions:
- datasets >=3.0.2
- pandas >=2.2.3
- pytorch >=2.4.0
- transformers >=4.11.3
Please ensure these updates have been tested with the package.
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📒 Files selected for processing (1)
- recipes/phabox/meta.yaml (4 hunks)
🔇 Additional comments (2)
recipes/phabox/meta.yaml (2)
13-13: LGTM! Build number increment is appropriate.The build number increment is correct for the dependency updates being made.
56-56: LGTM! Summary update is appropriate.The broader description "virus-related tasks" better reflects the package's capabilities.
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🧹 Outside diff range and nitpick comments (1)
recipes/phabox/meta.yaml (1)
59-59: Remove extra blank lines at end of file.For consistent YAML formatting, remove the extra blank lines at the end of the file.
identifiers: - doi:10.1093/bioadv/vbad101 - biotools:phabox -🧰 Tools
🪛 yamllint
[warning] 59-59: too many blank lines
(1 > 0) (empty-lines)
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- recipes/phabox/meta.yaml (4 hunks)
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🪛 yamllint
recipes/phabox/meta.yaml
[warning] 59-59: too many blank lines
(1 > 0) (empty-lines)
🔇 Additional comments (2)
recipes/phabox/meta.yaml (2)
13-13: LGTM: Build number increment is appropriate.The build number increment is correct for the dependency updates. The existing
run_exportssection helps prevent ABI/API breakage issues as recommended in the PR guidelines.
49-49: LGTM: Summary update reflects broader scope.The updated summary better reflects the tool's capabilities by expanding from phage-specific to virus-related tasks.
| - scipy >=1.14 | ||
| - pandas >=2.2.3 | ||
| - pyarrow >=16.1.0 | ||
| - pytorch >=2.4.0 |
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Update package versions to available releases.
Several specified package versions are not currently available in conda-forge:
- PyTorch 2.4.0 is not yet released
- Some version constraints are too strict
Consider using these available versions:
- - pytorch >=2.4.0
+ - pytorch >=2.1.0
- - transformers >=4.11.3
- - triton >=2.0.0
+ - transformers >=4.11.3,<5.0
+ - triton >=2.0.0,<3.0Also applies to: 37-38
| - python >=3.8 | ||
| - setuptools | ||
| run: | ||
| - python >=3.8 | ||
| - python >=3.10 |
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Fix Python version mismatch between host and run requirements.
The host section specifies python >=3.8 while the run section requires python >=3.10. This mismatch could cause build issues.
host:
- - python >=3.8
+ - python >=3.10Committable suggestion was skipped due to low confidence.
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🧹 Outside diff range and nitpick comments (1)
recipes/phabox/meta.yaml (1)
65-65: Remove extra blank lines at the end of the file.There are too many blank lines at the end of the file. YAML files should end with a single newline.
identifiers: - doi:10.1093/bioadv/vbad101 - biotools:phabox -🧰 Tools
🪛 yamllint
[warning] 65-65: too many blank lines
(1 > 0) (empty-lines)
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Review profile: CHILL
📒 Files selected for processing (1)
- recipes/phabox/meta.yaml (4 hunks)
🧰 Additional context used
🪛 yamllint
recipes/phabox/meta.yaml
[warning] 65-65: too many blank lines
(1 > 0) (empty-lines)
🔇 Additional comments (2)
recipes/phabox/meta.yaml (2)
13-13: LGTM: Build number increment is appropriate.The build number increment is correct for the dependency updates. The existing
run_exportssection helps prevent ABI/API breakage issues as recommended.
55-55: Verify if the scope change is intentional.The summary changed from "phage-related" to "virus-related" tasks. Please verify if this reflects actual changes in functionality, as phages are specifically viruses that infect bacteria.
✅ Verification successful
The scope change appears to be intentional and accurate
The change from "phage-related" to "virus-related" in the summary reflects the package's evolution. Looking at the git history, this change was part of a larger update (version 2.1.0) that included significant dependency updates and a complete overhaul of the package's functionality. The package's homepage (phage.ee.cityu.edu.hk) still maintains its phage focus, suggesting that phages remain a core part of its functionality while the scope has been broadened to include virus-related tasks in general.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check if there are corresponding changes in functionality # Look for changes in documentation or code that indicate broader virus support # Check documentation for scope changes rg -i "virus|phage" "$(fd -t f -e md)" # Check Python files for new virus-related functionality rg -i "virus|phage" "$(fd -t f -e py)"Length of output: 13685
Script:
#!/bin/bash # Let's check the package's source code and documentation specifically # First, find the package's source files fd -t f . recipes/phabox/ # Then search for content about functionality scope rg -i "phage|virus" recipes/phabox/Length of output: 245
Script:
#!/bin/bash # Let's check the git history of this file to see the context of the change git log -p recipes/phabox/meta.yaml # Also check if there's a package homepage or documentation curl -I https://phage.ee.cityu.edu.hkLength of output: 54423
| - scipy >=1.14 | ||
| - pandas >=2.2.3 | ||
| - pyarrow >=16.1.0 | ||
| - pytorch >=2.4.0 |
There was a problem hiding this comment.
PyTorch 2.4.0 is not yet released.
The specified PyTorch version 2.4.0 is a future version that hasn't been released yet. This will cause package installation failures.
Use the latest stable version instead:
- pytorch >=2.4.0
+ pytorch >=2.1.0📝 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.
| - pytorch >=2.4.0 | |
| - pytorch >=2.1.0 |
|
Is this PR a duplicate of #51687? |
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Hi @mencian , Sorry, it seems I opened it twice by accident. This is a duplicate indeed. |
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All good! |
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