perf: Update datavzrd wrapper to latest yte version #3537
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
utils/datavzrd/environment.linux-64.pin.txt (1)
1-48: Consider adding environment name and descriptionWhile the file follows the conda explicit environment format, it would be helpful to add a comment indicating the specific purpose of this environment (datavzrd wrapper) and any special requirements.
Consider adding these comments at the top of the file:
# This file may be used to create an environment using: # $ conda create --name <env> --file <this file> # platform: linux-64 +# Purpose: Environment for datavzrd wrapper +# Requirements: Python 3.13+
📜 Review details
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Review profile: CHILL
📒 Files selected for processing (2)
utils/datavzrd/environment.linux-64.pin.txt(1 hunks)utils/datavzrd/environment.yaml(1 hunks)
✅ Files skipped from review due to trivial changes (1)
- utils/datavzrd/environment.yaml
🔇 Additional comments (3)
utils/datavzrd/environment.linux-64.pin.txt (3)
16-16: Review system library updates
The addition of liblzma-5.6.3 and libmpdec-4.0.0 along with updates to core system libraries appears to be related to Python 3.13 requirements. These changes look appropriate for the Python version upgrade.
Also applies to: 23-23, 24-24
36-37: Verify version compatibility matrix
Notable changes:
- yte upgraded to 1.5.5 (aligns with PR objective)
- datavzrd updated to 2.44.4
- New dependencies added: pandas 2.2.3 and polars 1.17.1
The package versions look current and the addition of pandas and polars suggests enhanced data processing capabilities.
Also applies to: 41-48
✅ Verification successful
Package versions are compatible and properly constrained
The environment files show a well-structured dependency setup:
- The pinned file provides exact versions for all packages, including their dependencies
- The environment.yaml confirms the explicit version constraints for datavzrd and yte
- pandas and polars are flexibly specified in environment.yaml but properly pinned in the lock file
- All packages are from conda-forge channel, ensuring consistent builds
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for any known conflicts between these package versions
# Check if there are any reported issues with these specific versions
for pkg in "datavzrd 2.44.4" "yte 1.5.5" "pandas 2.2.3" "polars 1.17.1"; do
echo "Checking issues for $pkg..."
pkg_name=$(echo $pkg | cut -d' ' -f1)
pkg_version=$(echo $pkg | cut -d' ' -f2)
gh api graphql -f query='
query($pkg: String!, $version: String!) {
search(query: "is:issue repo:snakemake/snakemake-wrappers $pkg $version", type: ISSUE, first: 5) {
nodes {
... on Issue {
title
url
state
}
}
}
}' -F pkg="$pkg_name" -F version="$pkg_version"
done
Length of output: 4417
Script:
#!/bin/bash
# Let's check for any potential conflicts or dependencies between these packages in the environment file
# First, let's see the full environment file content to understand the complete dependency structure
cat utils/datavzrd/environment.linux-64.pin.txt
# Then, let's check if there are any other files that might define version constraints
fd -t f "environment" -x grep -l "datavzrd\|yte\|pandas\|polars" {}
Length of output: 8290
Script:
#!/bin/bash
# Let's check the datavzrd environment.yaml to see if there are any specific version constraints
cat utils/datavzrd/environment.yaml
# Also check if there are any known conflicts in the wrapper's documentation
cat utils/datavzrd/README.md 2>/dev/null || true
Length of output: 198
8-8: Verify Python 3.13 compatibility with all dependencies
The upgrade from Python 3.12 to 3.13 is significant. Python 3.13 is relatively new and might have compatibility issues with some packages.
Also applies to: 32-32
🤖 I have created a release \*beep\* \*boop\* --- ## [5.5.0](https://github.com/snakemake/snakemake-wrappers/compare/v5.4.0...v5.5.0) (2024-12-10) ### Features * NGSCheckMate ([#3498](https://github.com/snakemake/snakemake-wrappers/issues/3498)) ([df7fe5b](https://github.com/snakemake/snakemake-wrappers/commit/df7fe5bcb5fe737e4d4bd958caec4445ce1f6748)) ### Performance Improvements * Update datavzrd wrapper to latest yte version ([#3537](https://github.com/snakemake/snakemake-wrappers/issues/3537)) ([336079b](https://github.com/snakemake/snakemake-wrappers/commit/336079be7c46dad737227dd02bc6e3b498af87f5)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
QC
snakemake-wrappers.While the contributions guidelines are more extensive, please particularly ensure that:
test.pywas updated to call any added or updated example rules in aSnakefileinput:andoutput:file paths in the rules can be chosen arbitrarilyinput:oroutput:)tempfile.gettempdir()points tometa.yamlcontains a link to the documentation of the respective tool or command underurl:Summary by CodeRabbit
New Features
liblzma,libmpdec,numpy,pandas,polars, among others.Bug Fixes
ytedependency version to ensure stability and performance.