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hyanwong / giglib

MIT License
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Use ruff for linting #125

Closed hyanwong closed 3 months ago

hyanwong commented 3 months ago

Summary by CodeRabbit

coderabbitai[bot] commented 3 months ago

[!WARNING]

Review failed

The pull request is closed.

Walkthrough

The overall changes involve updating import statements, reorganizing code for better readability, refactoring hooks in the .pre-commit-config.yaml, and refining bitwise operations in flag constants. These modifications improve code maintainability, readability, and standardize the project configuration.

Changes

File Change Summary
.pre-commit-config.yaml Replaced reorder-python-imports, pyupgrade, black, flake8, and blacken-docs hooks with ruff and ruff-format from a new repository.
GeneticInheritanceGraphLibrary/__init__.py Reorganized imports, updated package version handling, and adjusted constants import.
GeneticInheritanceGraphLibrary/constants.py Reorganized imports, simplified bitwise operations within ValidFlags class, and updated np.dtype usage.
GeneticInheritanceGraphLibrary/graph.py Reorganized imports, clarified exception messages, and improved formatting.
GeneticInheritanceGraphLibrary/tables.py Refactored imports, revised data structure initialization, and updated class definitions and validation logic.
docs/Makefile Changed Python command from python3 to python for version extraction.
tests/conftest.py Reordered and removed unused import statements, and adjusted function calls for readability.
tests/gigutil.py Reordered imports, removed unnecessary whitespace, and simplified list comprehensions.
tests/sim.py Added import statement for DTWF_no_recombination_sim from gigutil module.
tests/test_gigutil.py Rearranged imports and made minor formatting changes.
tests/test_graph.py Moved import statement for GeneticInheritanceGraphLibrary and updated @pytest.mark.parametrize syntax.
tests/test_tables.py Consolidated imports from GeneticInheritanceGraphLibrary and adjusted method calls for consistency.
tests/test_util.py Added import statement for pytest and reordered existing imports.

Sequence Diagram(s)

No sequence diagrams are provided as the changes primarily involve code restructuring, import reordering, and minor functional adjustments without significant control flow alterations.

Poem

In the code where imports take their stand,
Hooks from Ruff now grace our land.
Constants now flow with less disruption,
Enhancements made for better function.
Our project's paths are more aligned,
With changes small, but well-defined. 🐇✨

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hyanwong commented 3 months ago

Failing because of numpy 2 issues with msprime. Should be fixed later today.