Add phenograph package #51795
Add phenograph package #51795
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
recipes/phenograph/meta.yaml (1)
32-34: Consider adding more comprehensive tests.
While the basic import test is good, consider adding:
- Command-line interface tests if any exist
- Basic functionality tests to ensure the package works as expected
Would you like help generating additional test cases?
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/phenograph/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/phenograph/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/phenograph/meta.yaml (5)
1-6: LGTM! Package metadata is properly configured.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
44-46: LGTM! Maintainer information is correctly specified.
12-17: Consider if run_exports is necessary for this pure Python package.
The run_exports section is typically used for compiled extensions where ABI compatibility matters. Since PhenoGraph appears to be a pure Python package, this section might not be necessary.
#!/bin/bash
# Description: Check if package has compiled extensions
# Expected: No setup.py with extension modules
# Look for potential C extensions in setup.py
rg -l "Extension|setup.*\(.*ext_modules" 37-38: Verify package's relevance to biological sciences.
The package summary mentions "single-cell data", suggesting biological relevance. However, let's verify its primary use case to ensure it belongs in Bioconda rather than conda-forge.
✅ Verification successful
Package confirmed as biologically relevant - suitable for Bioconda
The verification results strongly confirm this package's biological relevance:
- Published in Cell journal (a premier biological sciences journal)
- Specifically designed for single-cell data analysis
- Used for phenotypic analysis of AML (Acute Myeloid Leukemia)
- Developed by dpeerlab (Dana Pe'er's lab, known for computational biology research)
- Focuses on biological phenotype detection and cell population analysis
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check package's biological relevance
# Expected: Find references to biological/single-cell analysis
# Check PyPI description for biological terms
curl -s "https://pypi.org/pypi/PhenoGraph/1.5.7/json" | jq -r '.info.description' | grep -iE "cell|rna|gene|bio|sequence|protein"
# Check GitHub repository description and topics
curl -s "https://api.github.com/repos/dpeerlab/PhenoGraph" | jq -r '.description, .topics[]'
Length of output: 923
36-42: Verify LICENSE file existence in the source package.
The recipe references a LICENSE file, but we should verify it exists in the source package.
✅ Verification successful
Let me try a different approach to verify the LICENSE file existence.
LICENSE file is present and correctly referenced
The LICENSE file exists in the repository root and contains the MIT license text, which matches the license metadata specified in the recipe. The license_file field in the recipe correctly references this file.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if LICENSE file exists in the package
# Expected: Find LICENSE file in package contents
curl -sL "https://pypi.org/pypi/PhenoGraph/1.5.7/json" | jq -r '.urls[0].filename' | xargs -I{} curl -sL "https://pypi.org/packages/source/p/phenograph/{}" | tar -tz | grep -i license
Length of output: 923
Script:
#!/bin/bash
# Try to fetch the LICENSE file directly from the GitHub repository
curl -sL "https://raw.githubusercontent.com/dpeerlab/PhenoGraph/master/LICENSE"
# Also check if there are any other license files in the repository
gh api repos/dpeerlab/PhenoGraph/contents | jq -r '.[].name' | grep -i license
Length of output: 1244
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/phenograph/meta.yaml (1)
32-34: Consider enhancing test coverage.
The current test only verifies basic import. Consider adding:
- Additional module imports
- Command-line interface tests if available
- Basic functionality tests
Would you like me to help generate additional test cases based on the package documentation?
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/phenograph/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/phenograph/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/phenograph/meta.yaml (6)
1-6: LGTM: Package metadata is well-structured.
The package name and version are properly defined using Jinja2 variables, with correct lowercasing of the package name.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
44-46: LGTM: Maintainer section is properly configured.
The recipe maintainer is correctly specified.
8-10: Verify source URL and checksum.
The URL format is correct, but let's verify the accessibility and checksum.
#!/bin/bash
# Description: Verify package URL accessibility and checksum
# Expected: URL should be accessible and checksum should match
# Verify URL accessibility
curl -sI "https://files.pythonhosted.org/packages/75/97/c1077df94cb0e1ebd201d67e52c438810fdaa393dc4c663b3bc651e497b8/PhenoGraph-1.5.7.tar.gz" | head -n1
# Download and verify checksum
curl -sL "https://files.pythonhosted.org/packages/75/97/c1077df94cb0e1ebd201d67e52c438810fdaa393dc4c663b3bc651e497b8/PhenoGraph-1.5.7.tar.gz" | sha256sum12-17: Verify run_exports configuration.
The build configuration looks good, but the run_exports section needs attention:
- Ensure the pinning strategy aligns with the package's versioning scheme.
- Verify if the package actually provides any shared libraries that need pinning.
#!/bin/bash
# Description: Check if package contains shared libraries
# Expected: Should show any .so files if present
# Search for setup.py to check for extensions
fd -t f "setup.py" | xargs rg -l "Extension|setup.*ext_modules"19-30: Verify dependency versions against PyPI metadata.
The requirements look well-structured, but let's verify the version constraints against the package's actual requirements.
#!/bin/bash
# Description: Verify dependency versions against PyPI metadata
# Expected: Version constraints should match package requirements
# Get package metadata from PyPI
curl -s "https://pypi.org/pypi/phenograph/1.5.7/json" | jq -r '.info.requires_dist[]'36-42: Verify license file and URLs.
The about section is well-documented. Let's verify:
- License file existence in the source package
- URL accessibility
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@BiocondaBot please fetch artifacts |
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No artifacts found on the most recent builds. Either the builds failed, the artifacts have been removed due to age, or the recipe was blacklisted/skipped. |
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
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