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bayesDREAM Tests

This directory contains test scripts for bayesDREAM functionality.

Current Test Suite (16 Essential Tests)

Core Integration Tests

  • test_multimodal_fitting.py - Core multi-modal fitting infrastructure test
  • test_per_modality_fitting.py - Per-modality technical fitting with different distributions
  • test_trans_all_distributions.py - Comprehensive trans fitting test for all distributions

Compatibility Tests

  • test_negbinom_compat.py - Backward compatibility test for negative binomial distribution
  • test_technical_compat.py - Backward compatibility test for fit_technical() with negbinom

Feature-Specific Tests

  • test_atac_modality.py - Tests ATAC-seq modality integration
  • test_cell_names_numpy.py - Tests cell_names parameter for numpy arrays
  • test_exon_skip_aggregation.py - Tests exon skipping aggregation methods (min vs mean)
  • test_filtering_simple.py - Distribution-specific filtering at modality creation
  • test_gene_meta.py - Gene metadata handling and auto-creation
  • test_high_moi.py - High MOI (multiplicity of infection) workflows
  • test_matrix_types.py - Matrix type handling (sparse/dense)
  • test_modality_save_load.py - Modality save/load functionality

Export and Summary Tests

  • test_summary_export.py - Full pipeline summary export (runs complete pipeline)
  • test_summary_export_simple.py - Summary export with mock posterior data (fast)

Quick Validation

  • test_imports.py - Quick smoke test for package imports

Running Tests

Tests require the pyroenv conda environment:

# Set PYTHONPATH to repository root
cd "/Users/lrosen/Library/Mobile Documents/com~apple~CloudDocs/Documents/Postdoc/bayesDREAM code/bayesDREAM_forClaude"
export PYTHONPATH="."

# Run a specific test
/opt/anaconda3/envs/pyroenv/bin/python tests/test_multimodal_fitting.py

# Run multiple tests
/opt/anaconda3/envs/pyroenv/bin/python tests/test_filtering_simple.py
/opt/anaconda3/envs/pyroenv/bin/python tests/test_per_modality_fitting.py
/opt/anaconda3/envs/pyroenv/bin/python tests/test_trans_all_distributions.py

Archived Tests

The archive/ subdirectory contains older test scripts organized by category:

  • archive/debug_scripts/ - One-off debugging scripts (debug_alpha_.py, quick_test_.py, verify_extraction.py)
  • archive/bug_fix_tests/ - Tests for specific bug fixes (sparse sum flatten, cis extraction)
  • archive/plotting_tests/ - Old plotting validation tests
  • archive/redundant_tests/ - Tests superseded by more comprehensive versions

These archived tests are kept for historical reference but are no longer actively maintained.

Test Organization Principles

Essential tests (kept in main tests/ directory):

  • Core integration tests for main functionality
  • Backward compatibility tests
  • Feature-specific tests for actively maintained features
  • Export and summary functionality tests

Archived tests (moved to tests/archive/):

  • One-off debugging scripts
  • Tests for specific historical bugs
  • Redundant tests superseded by more comprehensive versions
  • Development-phase validation scripts