Add wsidicomizer recipe #52006
Add wsidicomizer recipe #52006
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
recipes/wsidicomizer/meta.yaml (1)
48-48: Fix typo in package summary.There's a duplicate word "to" in the summary.
- summary: Tool for reading WSI files from proprietary formats and optionally convert them to to DICOM + summary: Tool for reading WSI files from proprietary formats and optionally convert them to DICOM
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/wsidicomizer/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/wsidicomizer/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/wsidicomizer/meta.yaml (5)
1-8: LGTM! Package metadata is well-structured.
The package name, version, and source URL follow conda packaging best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-17: LGTM! Build configuration follows best practices.
The build configuration is well-structured with proper noarch Python package declaration and run_exports for ABI compatibility.
37-45: LGTM! Test section is comprehensive.
Good coverage of package imports and CLI functionality testing.
51-53: LGTM! Maintainer section is properly configured.
11-12: Verify bioformats CLI availability.
The recipe includes an entry point for bioformats functionality, but this appears to be optional based on the constrained dependencies. Let's verify the CLI's availability.
✅ Verification successful
Let me gather more information about the package structure and dependencies to verify if bioformats is properly handled.
Let me check for any conditional imports or optional dependencies in the package configuration.
Let me check for any package metadata that might indicate optional dependencies.
Based on the analysis of the package metadata and dependencies, I can now provide a final response:
The bioformats CLI entry point is properly configured and available
The package correctly includes the bioformats CLI entry point and tests its availability in the test section. The required dependencies (scyjava and ome-types) are listed under run_constrained requirements, which is the appropriate way to handle optional dependencies in conda recipes. The package structure with extras.bioformats indicates this is an optional feature that will work when the constrained dependencies are present.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if the bioformats CLI is conditionally imported
rg -A 5 "bioformats_cli" || echo "No direct references found"
# Check for any conditional imports of bioformats
rg -A 5 "extras.bioformats" || echo "No conditional imports found"
Length of output: 944
Script:
#!/bin/bash
# Check package dependencies and requirements
cat recipes/wsidicomizer/meta.yaml
# Check if bioformats is listed in optional dependencies
fd setup.py --exec cat {} \;
# Look for any conditional imports or optional dependencies related to bioformats
rg -l "bioformats" --type py
Length of output: 43294
Script:
#!/bin/bash
# Check for any pyproject.toml or setup.cfg that might define optional dependencies
fd "pyproject.toml|setup.cfg" --exec cat {} \;
# Look for any import statements or try-except blocks around bioformats
rg -A 5 "import.*bioformats|try:.*bioformats" --type py
Length of output: 559
Script:
#!/bin/bash
# Check for any package metadata files that might contain dependency information
cat recipes/wsidicomizer/meta.yaml
# Look for any extras or optional dependencies in the package
rg -A 5 "extras_require|optional-dependencies" || echo "No optional dependencies found"
Length of output: 4048
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
recipes/wsidicomizer/meta.yaml (3)
19-35: Consider Python version compatibility.The recipe requires Python >=3.10, which is relatively recent. Consider if supporting Python 3.9 is feasible to increase compatibility with older systems.
Also, some dependencies have very strict version pins (e.g., wsidicom, opentile). While this is good for stability, it might need frequent updates. Consider documenting the rationale for these strict pins.
36-44: Consider enhancing test coverage.While the basic import and help command tests are good, consider adding functional tests that verify the core conversion capabilities, perhaps with a small test file.
50-52: Consider adding co-maintainers.For better long-term maintenance, consider adding co-maintainers from the project team or bioconda community. This helps ensure timely updates and support.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
recipes/wsidicomizer/LICENCE(1 hunks)recipes/wsidicomizer/meta.yaml(1 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/wsidicomizer/LICENCE
🧰 Additional context used
🪛 yamllint
recipes/wsidicomizer/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (2)
recipes/wsidicomizer/meta.yaml (2)
1-8: LGTM: Package metadata is well-structured.
The package name, version, and source URL are correctly specified following conda packaging best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
10-12: Verify bioformats entry point dependencies.
The recipe includes a bioformats CLI entry point, but its dependencies might be optional. Consider documenting the additional dependencies required for the bioformats functionality.
✅ Verification successful
Let me gather more information about the bioformats dependencies by checking the package's source code and requirements.
Bioformats dependencies are properly constrained
The recipe already handles bioformats dependencies correctly through the run_constrained section, which includes scyjava and ome-types packages that are typically required for bioformats functionality. These optional dependencies are appropriately specified as constrained requirements, allowing users to install them only when needed for the bioformats CLI.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if bioformats dependencies are documented
rg -l "bioformats" "$(fd -t f "README.*")"
Length of output: 568
Script:
#!/bin/bash
# Check meta.yaml for bioformats dependencies
cat recipes/wsidicomizer/meta.yaml
# Check if there's a setup.py or pyproject.toml with optional dependencies
fd "setup.py|pyproject.toml" recipes/wsidicomizer/ --exec cat {}
# Look for bioformats imports and dependencies in the source
rg -l "bioformats" recipes/wsidicomizer/
Length of output: 1666
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Not sure how to resolve the dependency issues, this was built from greyskull, it resolves acceptably in pip.
but it uses a pillow version that's higher than |
This package enables converting a range of formats, losslessly into DICOM files. The optional dependencies enable converting an even large range of formats lossily.
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
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@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
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If not already present in the meta.yaml, make sure to specify
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