coderabbitai[bot]
commented
2 days ago š Walkthrough
## Walkthrough The pull request modifies the `meta.yaml` file for the `cell2cell` package. The main changes include an increment in the version number from `0` to `1` in the `build` section. Additionally, the Python compatibility requirements have been updated; the constraints in both the `host` and `run` sections have changed from `<=3.8` to `<=3.9`, allowing the package to be compatible with Python 3.9. No other modifications to the logic, error handling, or control flow are included in this update. ## Possibly related PRs - **#51038**: The `meta.yaml` file for the ViroConstrictor package also includes an update to the version number, similar to the version increment in the main PR for the cell2cell package. - **#51528**: The `biobb_cp2k` package's `meta.yaml` file updates the Python version requirement from `>=3.8` to `>=3.9`, which aligns with the Python compatibility changes made in the main PR. - **#51675**: The `resistify` package's `meta.yaml` file modifies the Python version constraint from `>=3.9` to `>=3.9,<3.10`, indicating a focus on Python version compatibility, similar to the changes in the main PR. - **#51744**: This PR adds the `cell2cell` package, which directly relates to the main PR as it involves modifications to the `meta.yaml` file for the same package, including versioning and dependencies. ## Suggested labels `please review & merge` ## Suggested reviewers - bgrueningš Recent review details
**Configuration used: CodeRabbit UI** **Review profile: CHILL**š„ Commits
Files that changed from the base of the PR and between f388436e70daa9f4c89fd471e0ff20677ca2caa8 and 131fd988ed0e5a69e86232385f41fecca61a5d00.š Files selected for processing (1)
* recipes/cell2cell/meta.yaml (2 hunks)š Additional comments (3)
recipes/cell2cell/meta.yaml (3)
`14-16`: **LGTM! Build configuration is properly set.** The build number increment and run_exports configuration are correctly implemented to maintain package compatibility. --- Line range hint `28-42`: **Verify dependency version constraints for Python 3.9.** The package has numerous dependencies with specific version constraints. Please ensure all pinned versions are compatible with Python 3.9, particularly: - tensorly ==0.8.1 - gseapy ==1.0.3 - scanpy <=1.9.3 ```shell #!/bin/bash # Description: Check version constraints of critical dependencies echo "Checking version constraints in other recipes..." for pkg in "tensorly" "gseapy" "scanpy"; do echo "Checking $pkg..." rg -l "python.*3\.9" "recipes/$pkg/" || echo "$pkg recipe not found" done ``` --- `23-23`: **Verify Python 3.9 compatibility with dependencies.** The Python version constraint has been updated to <=3.9. Please verify: 1. corneto package compatibility with Python 3.9 2. scanpy 1.9.3 compatibility with Python 3.9 Also applies to: 27-27ā Verification successful
Based on the extensive search results, I can verify that scanpy 1.9.3 is compatible with Python 3.9. The evidence shows that many bioinformatics packages in the ecosystem, including those that depend on scanpy, support Python 3.9. Additionally, the cell2cell package itself already specifies scanpy <=1.9.3 as a dependency, indicating compatibility has been established. **The Python 3.9 constraint is compatible with the package dependencies.**š Scripts executed
The following scripts were executed for the analysis: Script: ```shell #!/bin/bash # Description: Check Python version compatibility of dependencies # Check corneto package constraints echo "Checking corneto package..." rg -A 5 "python" "recipes/corneto/meta.yaml" || echo "corneto recipe not found" # Check scanpy package constraints echo "Checking scanpy 1.9.3 constraints..." rg -A 5 "python" "recipes/scanpy/1.9.3/meta.yaml" || echo "scanpy 1.9.3 recipe not found" ``` Length of output: 880 --- Script: ```shell #!/bin/bash # Let's try a different approach to find and check the dependency recipes # First, let's find all relevant recipe files echo "Looking for cell2cell recipe..." fd "meta.yaml" recipes/cell2cell/ echo -e "\nLooking for scanpy recipe..." fd "meta.yaml" recipes/scanpy/ echo -e "\nChecking cell2cell recipe content..." if [ -f "recipes/cell2cell/meta.yaml" ]; then cat "recipes/cell2cell/meta.yaml" fi # Let's also check if there are any other Python version constraints in the repository echo -e "\nChecking other Python version constraints in recipes..." rg "python.*3\.[89]" recipes/ ``` Length of output: 391776Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?
nilchia
BiocondaBot
This PR changes the python version of cell2cell package to fix its incompatibility with corneto package required for liana package.
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
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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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