update cell2cell #51790
update cell2cell #51790
Conversation
📝 WalkthroughWalkthroughThe pull request modifies the Possibly related PRs
Suggested labels
Suggested reviewers
📜 Recent review detailsConfiguration used: CodeRabbit UI 📒 Files selected for processing (1)
🔇 Additional comments (3)recipes/cell2cell/meta.yaml (3)
The build number increment and run_exports configuration are correctly implemented to maintain package compatibility. Line range hint The package has numerous dependencies with specific version constraints. Please ensure all pinned versions are compatible with Python 3.9, particularly:
#!/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
The Python version constraint has been updated to <=3.9. Please verify:
Also applies to: 27-27 ✅ Verification successfulBased 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. 🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/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: #!/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: 391776 Thank 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? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (Invoked using PR comments)
Other keywords and placeholders
CodeRabbit Configuration File (
|
|
@BiocondaBot please fetch artifacts |
|
Package(s) built are ready for inspection:
|
|
it is also fixes the incompatibility of cell2cell with cylp. |
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).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...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
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
Please use the following BiocondaBot commands:
Everyone has access to the following BiocondaBot commands, which can be given in a comment:
@BiocondaBot please update@BiocondaBot please add labelplease review & mergelabel.@BiocondaBot please fetch artifactsYou can use this to test packages locally.
Note that the
@BiocondaBot please mergecommand is now depreciated. Please just squash and merge instead.Also, the bot watches for comments from non-members that include
@bioconda/<team>and will automatically re-post them to notify the addressed<team>.