Add pyright #56
Add pyright #56
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WalkthroughThis update enhances the project's linting and static type checking capabilities by integrating Pyright into both the GitHub Actions workflow and the pre-commit configuration. Additionally, the Changes
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #56 +/- ##
===========================================
+ Coverage 26.09% 37.91% +11.82%
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Files 3 3
Lines 479 480 +1
===========================================
+ Hits 125 182 +57
+ Misses 354 298 -56 ☔ View full report in Codecov by Sentry. |
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Files ignored due to path filters (1)
pyproject.tomlis excluded by!**/*.toml
Files selected for processing (4)
- .github/workflows/pylint.yml (2 hunks)
- .gitignore (1 hunks)
- .pre-commit-config.yaml (1 hunks)
- agility/analysis.py (1 hunks)
Files skipped from review due to trivial changes (2)
- .gitignore
- .pre-commit-config.yaml
Additional Context Used
GitHub Check Runs (1)
codecov/patch failure (1)
agility/analysis.py: [warning] 714-714: agility/analysis.py#L714
Added line #L714 was not covered by tests
Additional comments not posted (2)
.github/workflows/pylint.yml (2)
34-35: Addition of thepyrightstep is a good enhancement for static type checking.
24-24: Ensure that thepyrighttool is compatible with the Python versions specified in the matrix.
| else: | ||
| NearestNeighborFinder = None # noqa: N806 |
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The addition of NearestNeighborFinder = None when nearest_n is not provided is a logical change for handling cases where no nearest neighbors are specified. However, this line is not covered by tests.
Would you like me to help by adding unit tests for this scenario?
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@ab5424, here's a unit test for the scenario where nearest_n is not provided in the expand_to_non_selected method. This test checks that NearestNeighborFinder is set to None when nearest_n is None.
import unittest
from unittest.mock import patch
from agility.analysis import GBStructure
class TestGBStructure(unittest.TestCase):
def test_expand_to_non_selected_without_nearest_n(self):
# Create an instance of GBStructure
gb_structure = GBStructure(backend='ovito', filename='testfile')
# Mock the data attribute to prevent actual file reading
gb_structure.data = unittest.mock.MagicMock()
# Patch the get_finder function to return a mock finder
with patch('agility.analysis.get_finder') as mock_get_finder:
# Set up the mock to return None for NearestNeighborFinder
mock_get_finder.return_value = None
# Call the method with nearest_n as None
result = gb_structure.expand_to_non_selected(nearest_n=None)
# Assert that NearestNeighborFinder was set to None
self.assertIsNone(result)
if __name__ == '__main__':
unittest.main()This test uses Python's unittest framework and includes mocking to isolate the test scenario. Let me know if you need further modifications or additional tests!
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Files selected for processing (1)
- .pre-commit-config.yaml (2 hunks)
Files skipped from review as they are similar to previous changes (1)
- .pre-commit-config.yaml
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Outside diff range and nitpick comments (1)
tests/analysis/test_analysis.py (1)
8-8: Ensure consistent import order.It's a good practice to keep imports grouped and ordered alphabetically. Consider moving
import numpy as npaboveimport pytest.
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Files selected for processing (1)
- tests/analysis/test_analysis.py (2 hunks)
Additional comments not posted (3)
tests/analysis/test_analysis.py (3)
56-84: Review of the new test classTestGBStructureOxide.The new test class
TestGBStructureOxideis well-structured and follows the established patterns in the existing test suite. The use ofpytest.mark.filterwarningsto ignore specific warnings is appropriate and helps focus the tests on the intended behaviours.
59-63: Proper setup for test instances.The
setUpmethod inTestGBStructureOxidecorrectly initialises the test instance and includes a safety check to ensure the instance is properly created. This is a good practice in unit testing.
65-84: Thorough testing of expansion logic.The
test_expand_to_non_selected_method inTestGBStructureOxideprovides a comprehensive test of the expansion logic to non-selected particles. The assertions are well-placed to verify the correctness of the functionality.
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