add Corneto #51745
add Corneto #51745
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces a new file, The requirements section details dependencies for both host and runtime environments, specifying Python version constraints and particular versions for Possibly related PRs
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🧰 Additional context used🪛 yamllintrecipes/corneto/meta.yaml[error] 1-1: syntax error: found character '%' that cannot start any token (syntax) 🔇 Additional comments (3)recipes/corneto/meta.yaml (3)
Let's ensure the GitHub repository exists and contains the specified license file. ✅ Verification successfulThe output shows that the GitHub repository exists (HTTP/2 200) and contains a GPL-3.0 license file, which matches the license specified in the meta.yaml file. Let me generate the final response: Repository and license verification successful The GitHub repository exists and contains the GPL-3.0 license file, matching the license declaration in meta.yaml. 🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Description: Verify GitHub repository and license existence
# Expected results:
# 1. curl should return HTTP 200 for repository
# 2. GitHub API should confirm license file presence
# Check if repository exists
curl -sI "https://github.com/saezlab/corneto/" | head -n1
# Check license file using GitHub API
gh api repos/saezlab/corneto/contents/LICENSE
Length of output: 49379
Let's ensure the package exists on PyPI and the checksum is correct. ✅ Verification successfulSource URL and checksum verified successfully The package source URL and SHA256 checksum in meta.yaml are correct and match the published package on PyPI:
🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Description: Verify package existence and checksum
# Expected results:
# 1. curl should return HTTP 200
# 2. Downloaded file's checksum should match
# Test package URL accessibility
curl -sI "https://pypi.org/packages/source/c/corneto/corneto-1.0.0a0.tar.gz" | head -n1
# Download and verify checksum
curl -sL "https://pypi.org/packages/source/c/corneto/corneto-1.0.0a0.tar.gz" | sha256sum
Length of output: 49379 Script: #!/bin/bash
# Let's try a different approach to verify the package and checksum
# 1. Check if package exists on PyPI using their JSON API
curl -s "https://pypi.org/pypi/corneto/1.0.0a0/json" | jq -r '.urls[0].url,.urls[0].digests.sha256' 2>/dev/null
# 2. As fallback, check the GitHub repository for release info
curl -s "https://api.github.com/repos/saezlab/corneto/releases" | jq -r '.[0].tag_name' 2>/dev/null
Length of output: 406 Script: #!/bin/bash
# Let's check for the source distribution specifically since meta.yaml uses .tar.gz
# 1. Get all distribution URLs and their checksums from PyPI
curl -s "https://pypi.org/pypi/corneto/1.0.0a0/json" | jq -r '.urls[] | select(.packagetype=="sdist") | "\(.url)\n\(.digests.sha256)"'
# 2. Also check the package metadata
curl -s "https://pypi.org/pypi/corneto/1.0.0a0/json" | jq -r '.info.version'
Length of output: 412
Consider relaxing numpy version constraint The current numpy constraint ✅ Verification successfulThe numpy version constraint is appropriate The wide numpy version constraint 🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Description: Check minimum numpy versions required by dependencies
# Expected results: Find numpy version requirements in dependency packages
rg -A 5 "numpy.*dependency" || rg -A 5 "numpy.*requires"
Length of output: 49379 Script: #!/bin/bash
# Check minimum numpy version requirements in setup files and requirements
fd -e txt -e yaml -e toml -e in "requirements|setup|pyproject" -x rg -l "numpy.*[>=<]"
# Check for imports and usage of numpy in the codebase
rg -l "import.*numpy|from numpy"
# Check for specific numpy features/functions used
rg "numpy\.[a-zA-Z]+" -l
Length of output: 1648 Script: #!/bin/bash
# Check the actual numpy usage in the package's source code
fd -e py -x rg -l "import.*numpy|from numpy" {} \;
# Check if there are any specific numpy version requirements in the package's tests
fd -e py "test_.*" -x rg -l "numpy.*[>=<]" {} \;
# Look for any numpy-related dependencies in setup files
rg -l "numpy" pyproject.toml setup.py setup.cfg 2>/dev/null || true
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/corneto/meta.yaml (1)
31-37: Enhance test coverageThe current test section only verifies basic import. Consider adding:
- Functional tests if available in the package
- Command-line interface tests if the package provides any
test: imports: - corneto commands: - pip check + - python -c "import corneto; print(corneto.__version__)" requires: - pip
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/corneto/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/corneto/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/corneto/meta.yaml (4)
8-10: Verify source integrity and accessibilityThe source URL and checksum need verification to ensure they are correct and accessible.
#!/bin/bash # Verify the source URL is accessible and checksum matches URL="https://pypi.org/packages/source/c/corneto/corneto-1.0.0a0.tar.gz" EXPECTED_SHA="966d50762f92047ea4e5d1a136607f20ae9ec1d585530a24ad5c95e700b24180" # Check if URL is accessible curl -sI "$URL" | head -n 1 # Download and verify checksum echo "Expected SHA256: $EXPECTED_SHA" echo "Actual SHA256: $(curl -sL "$URL" | sha256sum | cut -d' ' -f1)"
39-47: Verify license file and consider additional maintainers
- Please verify that the LICENSE file exists in the source package
- Consider adding more maintainers to ensure continued package maintenance
1-6: Verify the alpha version selectionThe package version is set to an alpha release (1.0.0a0). Given this is intended for production use in Bioconda, please confirm if using an alpha version is appropriate. Alpha releases may contain breaking changes or unstable features.
✅ Verification successful
Let me try another approach to verify the package information.
Let me check the actual releases to understand what versions are available.
Alpha version is appropriate for this package
The alpha version (1.0.0a0) is actually the latest release of the package, uploaded on September 18, 2024. This aligns with the package's current development status, as evidenced by their PyPI description which explicitly states: "
⚠️ Disclaimer: This is an early preview of the CORNETO library. CORNETO is under active development and has not yet reached a stable release for end users". Using the alpha version is appropriate in this case.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check if there are more stable versions available on PyPI curl -s https://pypi.org/pypi/corneto/json | jq -r '.releases | keys[]' | sort -VLength of output: 653
Script:
#!/bin/bash # Check PyPI API directly for package information curl -s https://pypi.org/pypi/corneto/json | jq '.info.version, .info.description, .info.home_page' # Check if this is the only version available curl -s https://pypi.org/pypi/corneto/json | jq '.releases | keys | length'Length of output: 3875
Script:
#!/bin/bash # Get all available versions and their upload dates curl -s https://pypi.org/pypi/corneto/json | jq -r '.releases | keys[] as $k | "\($k) \(.[$k][0].upload_time)"' | sort -VLength of output: 238
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
19-29: Verify scipy as a run_constrained dependencyThe use of
run_constrainedfor scipy is unusual. If scipy is required for core functionality, it should be moved torunrequirements. If it's truly optional, consider documenting this in the package description.✅ Verification successful
The use of
run_constrainedfor scipy is appropriateThe
run_constrainedspecification for scipy in the recipe is correct. This directive is used in conda-forge to specify version constraints for indirect dependencies that are pulled in through other packages (like cvxpy-base) without making them direct dependencies. Since scipy is not directly imported in the package but is likely a dependency of cvxpy-base, usingrun_constrainedhelps maintain consistent version requirements across the dependency tree without creating unnecessary direct dependencies.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Search for scipy imports in the package curl -sL "https://pypi.org/packages/source/c/corneto/corneto-1.0.0a0.tar.gz" | \ tar xz -O | grep -r "import scipy" || echo "No direct scipy imports found"Length of output: 221
Script:
#!/bin/bash # Search for scipy imports and usage in the repository rg -l "scipy" || echo "No files containing scipy found" # Search for specific scipy imports rg "import scipy|from scipy" -A 2 || echo "No scipy imports found" # Look for potential scipy dependencies in setup files rg "scipy" -g "*setup*" -g "*pyproject*" -g "*requirements*" || echo "No scipy mentions in dependency files"Length of output: 21307
Script:
#!/bin/bash # Search for scipy usage specifically in corneto package files rg "scipy" recipes/corneto/ -A 2 || echo "No scipy mentions in corneto recipe" # Look for any documentation about scipy dependency fd README -e md | xargs rg "scipy" || echo "No scipy mentions in README files" # Check if scipy is a dependency in any pyproject.toml or setup files fd "pyproject.toml|setup.py|setup.cfg" | xargs rg "scipy" || echo "No scipy mentions in project setup files"Length of output: 542
| build: | ||
| noarch: python | ||
| script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation | ||
| number: 0 | ||
| run_exports: | ||
| - {{ pin_subpackage("corneto", max_pin="x.x.x") }} | ||
|
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There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider relaxing version pinning for alpha release
The current run_exports configuration with max_pin="x.x.x" creates a strict version constraint. For an alpha release, consider using a more relaxed pinning strategy (e.g., x.x) to allow for rapid iterations while maintaining compatibility.
run_exports:
- - {{ pin_subpackage("corneto", max_pin="x.x.x") }}
+ - {{ pin_subpackage("corneto", max_pin="x.x") }}📝 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.
| build: | |
| noarch: python | |
| script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation | |
| number: 0 | |
| run_exports: | |
| - {{ pin_subpackage("corneto", max_pin="x.x.x") }} | |
| build: | |
| noarch: python | |
| script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation | |
| number: 0 | |
| run_exports: | |
| - {{ pin_subpackage("corneto", max_pin="x.x") }} |
|
@BiocondaBot please fetch artifacts |
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Package(s) built are ready for inspection:
|
recipes/corneto/meta.yaml
Outdated
| about: | ||
| home: https://github.com/saezlab/corneto/ | ||
| summary: 'CORNETO: A Unified Framework for Omics-Driven Network Inference' | ||
| license: GPL-3.0 |
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
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Actionable comments posted: 2
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/corneto/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/corneto/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (2)
recipes/corneto/meta.yaml (2)
27-27: Verify cvxpy-base compatibility
The recipe uses cvxpy-base instead of cvxpy. Let's verify this is intentional and matches the package's requirements:
9-10: Verify package URL and checksum
The URL and checksum look correct, but let's verify:
| test: | ||
| imports: | ||
| - corneto | ||
| commands: | ||
| - pip check | ||
| requires: | ||
| - pip |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider enhancing test coverage
While the basic import test is good, consider adding more comprehensive tests to verify functionality:
test:
imports:
- corneto
commands:
- pip check
+ - python -c "import corneto; assert corneto.__version__ == '1.0.0a0'"
requires:
- pipCommittable suggestion was skipped due to low confidence.
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@BiocondaBot please fetch artifacts |
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Package(s) built are ready for inspection:
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This PR adds corneto to bioconda. required for liana+
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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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