Add cell2cell #51744
Add cell2cell #51744
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recipes/cell2cell/meta.yaml
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| - python ==3.10.* | ||
| - cython | ||
| - pip | ||
| run: | ||
| - python ==3.10.* |
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| - python ==3.10.* | |
| - cython | |
| - pip | |
| run: | |
| - python ==3.10.* | |
| - python | |
| - cython | |
| - pip | |
| run: | |
| - python |
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It conflicts with python 3.12
Co-authored-by: Björn Grüning <[email protected]>
Co-authored-by: Björn Grüning <[email protected]>
Oo, this is not fun. |
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Yes :( |
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@BiocondaBot please fetch artifacts |
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Package(s) built are ready for inspection:
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📝 WalkthroughWalkthroughThe pull request introduces a new Possibly related PRs
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (2)
recipes/cell2cell/meta.yaml (2)
45-52: Enhance test coverage.
The current test section only verifies imports and dependencies. Consider adding specific functionality tests to ensure the package works as expected.
Consider adding:
commands:
- pip check
+ - python -c "import cell2cell; assert cell2cell.__version__ == '0.7.4'"
+ - python -c "from cell2cell import io, preprocessing"54-58: Add more package metadata.
The about section could be enhanced with additional metadata to help users understand the package better.
Consider adding:
about:
home: https://github.com/earmingol/cell2cell
summary: Inferring cell-cell interactions from transcriptomes with cell2cell
license: BSD-3-Clause
license_file: LICENSE.txt
+ doc_url: https://github.com/earmingol/cell2cell#readme
+ dev_url: https://github.com/earmingol/cell2cell
+ description: |
+ cell2cell is a framework for inferring cell-cell interactions from
+ transcriptomics data, supporting various interaction inference methods.📜 Review details
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📒 Files selected for processing (1)
- recipes/cell2cell/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/cell2cell/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (1)
recipes/cell2cell/meta.yaml (1)
15-16: 🛠️ Refactor suggestion
Consider relaxing the run_exports pin.
The current pinning strategy x.x.x is very strict and might cause unnecessary constraints on downstream packages. For Python packages, x.x is typically sufficient unless there are specific ABI compatibility requirements.
Consider using:
run_exports:
- - {{ pin_subpackage("cell2cell", max_pin="x.x.x") }}
+ - {{ pin_subpackage("cell2cell", max_pin="x.x") }}| - python <=3.8 | ||
| - cython |
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Python version constraint is too restrictive.
The Python version constraint <=3.8 is very restrictive and might prevent users from using newer Python versions. If there's a specific reason for not supporting Python 3.9+, please document it. Otherwise, consider supporting newer versions.
Consider:
- - python <=3.8
+ - python >=3.8,<3.12Also applies to: 27-28
| - openpyxl >=2.6.2 | ||
| - networkx >=2.3 | ||
| - matplotlib-base >=3.2.0,<3.7.3 | ||
| - seaborn >=0.11.0 |
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Resolve version conflicts between scanpy and seaborn.
There's a version conflict in the dependencies:
- scanpy 1.9.8 requires seaborn>=0.13.0
- Current recipe specifies seaborn >=0.11.0 and scanpy <=1.9.3
This needs to be resolved to ensure package compatibility.
Consider either:
- Updating seaborn to match scanpy's requirements:
- - seaborn >=0.11.0
+ - seaborn >=0.13.0- Or keeping scanpy at a version compatible with seaborn 0.11.0:
- - scanpy <=1.9.3
+ - scanpy <=1.9.2Also applies to: 42-42
| - tensorly ==0.8.1 | ||
| - kneed | ||
| - scanpy <=1.9.3 | ||
| - gseapy ==1.0.3 |
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🛠️ Refactor suggestion
Review strict version pins.
Several dependencies have exact version pins (==) which might be unnecessarily restrictive:
- tensorly ==0.8.1
- gseapy ==1.0.3
Unless there are specific compatibility requirements, consider allowing minor version updates.
Consider:
- - tensorly ==0.8.1
- - gseapy ==1.0.3
+ - tensorly >=0.8.1,<0.9
+ - gseapy >=1.0.3,<1.1📝 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.
| - tensorly ==0.8.1 | |
| - kneed | |
| - scanpy <=1.9.3 | |
| - gseapy ==1.0.3 | |
| - tensorly >=0.8.1,<0.9 | |
| - kneed | |
| - scanpy <=1.9.3 | |
| - gseapy >=1.0.3,<1.1 |
This PR adds cell2cell package required by liana+
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