Add comprehensive test suite and coverage utilities #60

rhoadesScholar · 2025-07-22T21:14:20Z

Introduced coverage_utils.py for managing test coverage, including cleaning up coverage files and running tests with coverage reporting.
Created a new test dataset in Zarr format under tests/dummy.zarr to facilitate testing.
Implemented run_tests.py as a test runner script for executing the test suite with detailed coverage analysis and reporting.
Added extensive unit tests for data utilities, global state management, input normalization, processing, and serialization functionalities.
Refactored existing tests to improve coverage and reliability, including the removal of flaky integration tests.
Enhanced coverage reporting to include HTML, XML, and JSON formats, with a minimum coverage threshold.

- Introduced `coverage_utils.py` for managing test coverage, including cleaning up coverage files and running tests with coverage reporting. - Created a new test dataset in Zarr format under `tests/dummy.zarr` to facilitate testing. - Implemented `run_tests.py` as a test runner script for executing the test suite with detailed coverage analysis and reporting. - Added extensive unit tests for data utilities, global state management, input normalization, processing, and serialization functionalities. - Refactored existing tests to improve coverage and reliability, including the removal of flaky integration tests. - Enhanced coverage reporting to include HTML, XML, and JSON formats, with a minimum coverage threshold.

…ions

github-actions · 2025-07-24T15:44:23Z

Coverage report

This PR does not seem to contain any modification to coverable code.

codecov · 2025-07-24T16:27:01Z

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Copilot

Pull Request Overview

This PR introduces a comprehensive test suite and coverage utilities to the cellmap-flow package. The implementation adds extensive unit tests across core functionality areas while removing flaky integration tests and establishing proper coverage tracking infrastructure.

Key changes:

Added comprehensive unit test coverage for data utilities, global state management, input normalization, and processing functionality
Implemented coverage tracking utilities and test runner scripts for automated testing workflows
Replaced flaky integration tests with focused unit tests that properly mock external dependencies

Reviewed Changes

Copilot reviewed 21 out of 33 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tests/test_script.py	Replaced flaky integration test with explanation comment
tests/test_processing.py	Added comprehensive unit tests for inference pipeline and postprocessing
tests/test_input_normalize.py	Added extensive tests for normalization classes and utility functions
tests/test_globals.py	Added tests for singleton Flow class and global state management
tests/test_data_utils.py	Added tests for model configuration classes and validation
tests/run_tests.py	Added comprehensive test runner script with multiple execution modes
tests/coverage_utils.py	Added utilities for coverage tracking and cleanup
tests/conftest.py	Added pytest configuration and shared fixtures
tests/TESTING_SUMMARY.md	Added comprehensive documentation of test implementation
tests/README.md	Added test structure overview and usage documentation
pyproject.toml	Updated test dependencies and added pytest configuration
.coveragerc	Added coverage configuration with appropriate exclusions

Copilot · 2025-07-24T17:05:05Z

tests/test_processing.py

+        mock_model_config.config.model = Mock()
+
+        inferencer = Inferencer(mock_model_config)
+        expected_context = Coordinate([8, 8, 8])


The expected context calculation should be derived from the mock data rather than hardcoded. Consider calculating it as (read_shape - write_shape) / 2 to make the test more maintainable and self-documenting.

Suggested change

expected_context = Coordinate([8, 8, 8])

expected_context = Coordinate(

(np.array(mock_model_config.config.read_shape) - np.array(mock_model_config.config.write_shape)) // 2

)

Copilot · 2025-07-24T17:05:05Z

tests/test_input_normalize.py

+        np.testing.assert_array_almost_equal(
+            result, expected, decimal=2
+        )  # Reduced precision for floating point tolerance


The reduced precision (decimal=2) in the assertion suggests potential floating point precision issues. Consider using a more robust comparison method or documenting why reduced precision is necessary.

Suggested change

np.testing.assert_array_almost_equal(

result, expected, decimal=2

) # Reduced precision for floating point tolerance

np.testing.assert_allclose(

result, expected, atol=1e-2

) # Use absolute tolerance for floating point comparison

Copilot · 2025-07-24T17:05:06Z

tests/test_data_utils.py

+        # Fix the datasplit mock to be properly indexable
+        mock_train_data = Mock()
+        mock_train_data.raw.voxel_size = [1, 1, 1]
+        mock_run.datasplit.train = [mock_train_data]  # Make it a list


The inline comment explaining why this needs to be a list suggests the mock structure might not accurately reflect the real API. Consider creating a more realistic mock structure that doesn't require explanatory comments.

Suggested change

mock_run.datasplit.train = [mock_train_data] # Make it a list

mock_run.datasplit.train = [mock_train_data] # Assuming the real API returns a list

tests/coverage_utils.py

Copilot · 2025-07-24T17:05:06Z

cellmap_flow/dashboard/app.py

-        "~/Desktop/cellmap/cellmap-flow/example/example_norm",
-    )
-)
+CustomCodeFolder = "/Users/zouinkhim/Desktop/cellmap/cellmap-flow/example/example_norm"


Hardcoded absolute path contains a username which could expose sensitive information and will not work in different environments. This should use environment variables or relative paths.

Suggested change

CustomCodeFolder = "/Users/zouinkhim/Desktop/cellmap/cellmap-flow/example/example_norm"

CustomCodeFolder = os.getenv("CUSTOM_CODE_FOLDER", "./example/example_norm")

Copilot · 2025-07-24T17:05:07Z

tests/run_tests.py

+                    response = input("\nOpen HTML coverage report in browser? (y/N): ")
+                    if response.lower() in ["y", "yes"]:
+                        webbrowser.open(f"file://{html_report.absolute()}")


Using input() in a test utility script could cause issues in automated environments. Consider adding a --no-interactive flag or checking if running in a non-interactive environment.

Suggested change

response = input("\nOpen HTML coverage report in browser? (y/N): ")

if response.lower() in ["y", "yes"]:

webbrowser.open(f"file://{html_report.absolute()}")

if args.no_interactive or not sys.stdin.isatty():

print("\nSkipping prompt to open HTML coverage report (non-interactive mode).")

else:

response = input("\nOpen HTML coverage report in browser? (y/N): ")

if response.lower() in ["y", "yes"]:

webbrowser.open(f"file://{html_report.absolute()}")

rhoadesScholar requested review from Copilot, mzouink and davidackerman July 22, 2025 21:14

Merge branch 'main' into test_coverage

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rhoadesScholar requested a review from Copilot July 22, 2025 21:16

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rhoadesScholar added 2 commits July 23, 2025 18:03

Add initial files for test coverage improvement and analysis

592742e

Refactor coverage configuration and testing strategies for GPU operat…

fc727a7

…ions

rhoadesScholar added 2 commits July 24, 2025 12:05

Update test-coverage.yml

c9589e8

Update test-coverage.yml

efe4e8d

Merge branch 'main' into test_coverage

91519f6

rhoadesScholar requested a review from Copilot July 24, 2025 17:03

Copilot AI reviewed Jul 24, 2025

View reviewed changes

Merge branch 'main' into test_coverage

e889ad9

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	mock_run.datasplit.train = [mock_train_data] # Make it a list
	mock_run.datasplit.train = [mock_train_data] # Assuming the real API returns a list

	CustomCodeFolder = "/Users/zouinkhim/Desktop/cellmap/cellmap-flow/example/example_norm"
	CustomCodeFolder = os.getenv("CUSTOM_CODE_FOLDER", "./example/example_norm")

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Coverage report

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Welcome to Codecov 🎉

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Pull Request Overview

Reviewed Changes

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