Update snapatac2 to v2.7.1 #51922
Update snapatac2 to v2.7.1 #51922
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/snapatac2/meta.yaml (1)
Dependencies need updates based on upstream requirements
The pyproject.toml from v2.7.1 shows some differences in dependency specifications compared to the recipe:
anndatashould be constrained to>=0.8.0, <0.11.0python-igraphshould be specified asigraphin requirementspython-kaleidoshould be justkaleidotypeguard >= 4.0is missing from the recipe- Python version requirement is
>=3.9, <3.13Please update the dependencies in meta.yaml to match the upstream requirements.
🔗 Analysis chain
Line range hint
31-53: Verify dependency requirements for version 2.7.1.The recipe has specific version constraints for several dependencies. Please ensure these constraints are still valid for version 2.7.1.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for dependency changes in the new version # Expected: No dependency requirement changes in v2.7.1 # Check setup.py/pyproject.toml in the release for dependency changes curl -sL https://github.com/kaizhang/SnapATAC2/archive/refs/tags/v2.7.1.tar.gz | tar xz -O "SnapATAC2-2.7.1/pyproject.toml"Length of output: 483
Script:
#!/bin/bash # Let's try a different approach to check the dependencies # First, let's check if there's a setup.py file curl -sL https://github.com/kaizhang/SnapATAC2/archive/refs/tags/v2.7.1.tar.gz | tar xz -O "SnapATAC2-2.7.1/setup.py" # Also check for any requirements.txt curl -sL https://github.com/kaizhang/SnapATAC2/archive/refs/tags/v2.7.1.tar.gz | tar xz -O "SnapATAC2-2.7.1/requirements.txt" # Let's also check the repository directly using GitHub API curl -sL "https://api.github.com/repos/kaizhang/SnapATAC2/contents/setup.py?ref=v2.7.1" | jq -r '.content' | base64 -d || trueLength of output: 668
Script:
#!/bin/bash # Let's try checking the repository contents first to locate the dependency files curl -sL "https://api.github.com/repos/kaizhang/SnapATAC2/git/trees/v2.7.1?recursive=1" | jq -r '.tree[].path' | grep -E 'setup.py|pyproject.toml|requirements.txt|environment.yml|meta.yaml' # Also check the release page description for any dependency changes curl -sL "https://api.github.com/repos/kaizhang/SnapATAC2/releases/tags/v2.7.1" | jq -r '.body'Length of output: 382
Script:
#!/bin/bash # Let's check the content of the pyproject.toml files we found curl -sL "https://raw.githubusercontent.com/kaizhang/SnapATAC2/v2.7.1/snapatac2-python/pyproject.toml" # Also check the content of the contrib pyproject.toml curl -sL "https://raw.githubusercontent.com/kaizhang/SnapATAC2/v2.7.1/snapatac2-contrib/pyproject.toml"Length of output: 2095
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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📒 Files selected for processing (1)
recipes/snapatac2/meta.yaml(1 hunks)
🔇 Additional comments (3)
recipes/snapatac2/meta.yaml (3)
Line range hint 19-20: Excellent compatibility handling!
The run_exports section with max_pin="x" correctly handles API/ABI compatibility by ensuring downstream packages are rebuilt only for major version changes.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
10-10: Source URL change looks good but needs verification.
The switch from PyPI to GitHub releases is valid, as this points to the official repository. However, we should verify that the archive contains the same build structure as the PyPI package.
#!/bin/bash
# Description: Compare repository URL with package metadata
# Expected: Repository URL in about section matches the source URL
# Extract repository URL from package metadata
grep -A 3 "about:" recipes/snapatac2/meta.yaml | grep "home"2-3: Verify version and checksum authenticity.
The version and checksum updates need verification against the official release.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/snapatac2/pyproject.toml.patch (1)
1-11: LGTM! Build configuration changes improve package distribution.The addition of
strip = trueandprofile = "release"are appropriate optimizations for a release build:
- Stripping debug symbols reduces the package size
- Release profile enables performance optimizations
These changes align well with distribution best practices for Bioconda packages.
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📒 Files selected for processing (3)
recipes/snapatac2/build.sh(1 hunks)recipes/snapatac2/meta.yaml(2 hunks)recipes/snapatac2/pyproject.toml.patch(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/snapatac2/meta.yaml
🔇 Additional comments (1)
recipes/snapatac2/build.sh (1)
9-9: Verify wheel path after source URL change.
The wheel installation path has been simplified, but we should verify it works with the new GitHub source layout.
Let's verify the path structure in the GitHub source:
Consider adding path validation before the pip install:
-${PYTHON} -m pip install target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv
+if [ ! -d "target/wheels" ]; then
+ echo "Error: Wheel directory not found at target/wheels"
+ exit 1
+fi
+${PYTHON} -m pip install target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv
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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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