Adding Unit Tests for next release

[ramosv]

Draft PR while I finish Unit Test for remaining classes
todo:
-smccnet
-metrics

For louvain and pagerank I am considering not adding unittest since hybrid calls both of these and is not unlikely that users will use them independently. We can either extend test_hybrid.py or add independent tests for both pagerank and louvain.

[Copilot]

Pull Request Overview

Adds and reorganizes unit tests for core modules while cleaning up outdated commented tests.

• Introduces new test suites for graph generation (gen_*), hybrid clustering, GNN embeddings, downstream task (DPMON), and subject representation.
• Removes old commented-out tests for utilities, SMCCNet, metrics, and correlated clustering (to be re-added later).
• Updates test package imports, temporary directory handling, and adapts code to new logging/error behaviors.

Reviewed Changes

Copilot reviewed 18 out of 18 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/test_utils.py	Removed obsolete commented-out tests for data summary utilities.
tests/test_subject_representation.py	Reformatted and extended SubjectRepresentation unit tests.
tests/test_smccnet.py	Deleted entire test file (coverage to be restored later).
tests/test_metrics.py	Deleted entire test file (coverage to be restored later).
tests/test_hybrid_louvain.py	Refactored setup and added mocks for HybridLouvain.
tests/test_graph_gen.py	New test suite covering graph generation utilities.
tests/test_gnn_embedding.py	Updated GNNEmbedding tests with patch-based embed/fitting scenarios.
tests/test_dpmon.py	Extended DPMON tests with temporary directories and warnings handling.
tests/test_correlated_pagerank.py	Deleted entire test file (coverage to be restored later).
tests/test_correlated_louvain.py	Deleted entire test file (coverage to be restored later).
tests/init.py	Adjusted test imports to include new modules and comment out obsolete.
docs/source/index.rst	Updated project title formatting.
bioneuralnet/utils/graph.py	Added logger import, warnings, and improved exception handling.
bioneuralnet/network_embedding/gnn_embedding.py	Changed empty clinical_data behavior from error to warning.
bioneuralnet/downstream_task/subject_representation.py	Enhanced embeddings validation and type checks.
README.md	Updated project title wording.

Comments suppressed due to low confidence (6)

tests/test_utils.py:1

• All tests in tests/test_utils.py have been removed, leaving core utility functions untested. Consider restoring or writing new tests to cover data_summary utilities.

-# import unittest

tests/test_smccnet.py:1

• The entire SMCCNet test file has been deleted. SMCCNet functionality is now untested—add or restore tests to ensure coverage.

-import unittest

tests/test_metrics.py:1

• The metrics test suite was removed entirely, leaving metrics functions unverified. Please reintroduce tests for omics_correlation, evaluate_rf, plotting, etc.

-import unittest

tests/test_correlated_pagerank.py:1

• CorrelatedPageRank tests have been deleted; its behavior is no longer covered by CI. Consider adding back tests for run validity and empty-seed errors.

-import unittest

tests/test_correlated_louvain.py:1

• CorrelatedLouvain tests were removed, removing coverage for quality and DFS outputs. Add tests to ensure clustering correctness.

-import unittest

tests/test_gnn_embedding.py:58

• Missing import for torch at the top of this test file leads to NameError when referencing torch.Tensor. Add import torch.

self.assertIsInstance(embeddings, torch.Tensor)

[Copilot]

Pull Request Overview

This PR adds a suite of new unit tests and updates core utility/error handling, logging, documentation, and CI configurations to prepare for the next release. Key changes include:

• Adding tests for graph generation, data utilities, DPMON downstream task, and dataset loading; updating hybrid-louvain and GNN embedding tests.
• Removing legacy tests for metrics, CorrelatedLouvain, and CorrelatedPageRank, and updating imports in tests/__init__.py.
• Enhancing graph utils with logging, improving GNNEmbedding and subject_representation error handling, and refining pre-commit/CI scripts.

Reviewed Changes

Copilot reviewed 25 out of 25 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/test_metrics.py	Entire file deleted—metrics functions now lack dedicated tests
tests/test_hybrid_louvain.py	Removed basic test_run, added more focused partition/DFS tests
tests/test_graph_gen.py	New tests covering all gen_*_graph utilities
tests/test_gnn_embedding.py	Refactored tests, patched embed, removed model params
tests/test_dpmon.py	New tests for DPMON, warnings filter, temporary output dir
tests/test_dataset_loader.py	New tests for DatasetLoader including error cases
tests/test_data_utils.py	New tests for summaries and explore_data_stats output
tests/test_correlation_metrics.py	New dedicated tests for omics_correlation, cluster_correlation
tests/init.py	Updated imports to include new tests, removed legacy imports
bioneuralnet/utils/graph.py	Added logging, improved k bounds, error fallback for Lasso
bioneuralnet/network_embedding/gnn_embedding.py	Warn instead of error on empty clinical data
bioneuralnet/downstream_task/subject_representation.py	Strengthened embedding/type checks
.pre-commit-config.yaml	Tweaked pre-commit hooks for coverage cleanup and test runs
docs/source/index.rst	Updated project title
.github/workflows/pre-commit.yml	Enabled caching and running pre-commit checks

Comments suppressed due to low confidence (6)

tests/test_metrics.py:1

• Dedicated unit tests for the metrics module were removed. Consider re-adding tests for omics_correlation, cluster_correlation, louvain_to_adjacency, evaluate_rf, and all plotting functions to maintain coverage.

-import unittest

tests/test_hybrid_louvain.py:1

• [nitpick] The original test_run method was removed, which reduces coverage for basic HybridLouvain behavior. Consider keeping a simple smoke test to cover default .run() output.

import unittest

tests/test_correlated_pagerank.py:1

• Tests for CorrelatedPageRank were deleted. Add back unit tests to cover valid runs and empty-seed error handling.

import unittest

tests/test_correlated_louvain.py:1

• Tests for CorrelatedLouvain were deleted. Reintroduce tests to ensure both partition (as_dfs=False) and DataFrame (as_dfs=True) paths are covered.

import unittest

tests/test_gnn_embedding.py:61

• In test_empty_adjacency_matrix, the instantiation of GNNEmbedding expecting a ValueError isn't wrapped in with self.assertRaises(ValueError), so the test will error instead of catching the exception.

empty_adj = pd.DataFrame()

.github/workflows/pre-commit.yml:56

• [nitpick] There’s a duplicate commented-out block at the bottom of this workflow. Consider removing the outdated comments to keep the CI config clean.

#      - name: Cache pre-commit hooks

[Copilot]

The decorator order for patching run_standard_training and run_hyperparameter_tuning is inverted; the function parameters mock_tune and mock_standard are reversed. Swap the decorator order or adjust the parameter order to match.

Suggested change

	@patch("bioneuralnet.downstream_task.dpmon.run_standard_training")
	@patch("bioneuralnet.downstream_task.dpmon.run_hyperparameter_tuning")
	@patch("bioneuralnet.downstream_task.dpmon.run_hyperparameter_tuning")
	@patch("bioneuralnet.downstream_task.dpmon.run_standard_training")

[ramosv]

I believe this is mostly semantic. I fixed regardless

[ramosv]

Actually, I applied the suggestion and it broke the test. So I put it back how it was.
leaving this open for records

[ramosv]

Stacked another branch on this branch to update the version number to v1.0.9

[abdelhafizm]

nice

[ramosv]

All checks passed. Merging to main.