Update meta.yaml #52080
Update meta.yaml #52080
Conversation
- pinning muscle to 5.1 because 5.2 and 5.3 (as of their release 10 days ago) currently have issues on mac-osx, even with osx-64 specified, leading to an "Illegal instruction" error whenever muscle is invoked - adding pyarrow, due to pandas stating it will be required next major version update (pandas-dev/pandas#54466)
📝 WalkthroughWalkthroughThe pull request introduces several modifications to the Possibly related PRs
Suggested labels
Suggested reviewers
📜 Recent review detailsConfiguration used: CodeRabbit UI 📒 Files selected for processing (1)
🔇 Additional comments (3)recipes/gtotree/meta.yaml (3)
The build number increment is correct as per conda packaging guidelines, given the dependency changes in this update.
The pin to Muscle 5.1 aligns with the reported macOS compatibility issues. However, let's verify this is the latest stable version that works across all platforms. #!/bin/bash
# Description: Check available Muscle versions in conda-forge and bioconda
# Check conda-forge
curl -s https://conda.anaconda.org/conda-forge/noarch/repodata.json | jq -r '.packages | to_entries[] | select(.key | contains("muscle-")) | .key'
# Check bioconda
curl -s https://conda.anaconda.org/bioconda/noarch/repodata.json | jq -r '.packages | to_entries[] | select(.key | contains("muscle-")) | .key'
Consider adding version constraint for pyarrow While adding pyarrow is proactive for future Pandas compatibility, consider adding a minimum version constraint based on Pandas' requirements to ensure compatibility. - - pyarrow
+ - pyarrow >=7.0.0Also, verify the minimum version requirement: 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 (
|
Describe your pull request here
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>.