[
  "tests/test__utils.py::TestCalculateLossSampleWeights::test_diseased",
  "tests/test__utils.py::TestCalculateLossSampleWeights::test_intervention",
  "tests/test__utils.py::TestCalculateLossSampleWeights::test_output",
  "tests/test__utils.py::TestCalculateLossSampleWeights::test_treated",
  "tests/test__utils.py::TestCalculateLossSampleWeights::test_wrong_kind",
  "tests/test__utils.py::TestDummyWriter::test_create",
  "tests/test__utils.py::TestDummyWriter::test_writing",
  "tests/test__utils.py::TestEarlyStopping::test_saving_loading",
  "tests/test__utils.py::TestGetThresholds::test_output",
  "tests/test__utils.py::TestGetThresholds::test_output_all",
  "tests/test__utils.py::TestGetThresholds::test_wrong_kind",
  "tests/test__utils.py::TestTestCondition::test_assertion_false",
  "tests/test__utils.py::TestTestCondition::test_assertion_true",
  "tests/test__utils.py::TestTicToc::test_output_basic_1",
  "tests/test__utils.py::TestTicToc::test_output_basic_2",
  "tests/test__utils.py::TestTicToc::test_output_custom",
  "tests/test__utils.py::TestTicToc::test_output_custom_format",
  "tests/test__utils.py::TestTicToc::test_output_wrapped",
  "tests/test__utils.py::TestTicToc::test_output_wrapped_custom",
  "tests/test__utils.py::TestTicToc::test_output_wrapped_custom_format",
  "tests/test__utils.py::TestTicToc::test_wrapped_wrong_format",
  "tests/test__utils.py::TestTicToc::test_wrong_format",
  "tests/test_causal_estimator.py::TestCausalAlignmentLoss::test_alpha_beta_weighting",
  "tests/test_causal_estimator.py::TestCausalAlignmentLoss::test_bce_only",
  "tests/test_causal_estimator.py::TestCausalAlignmentLoss::test_gradient_flows",
  "tests/test_causal_estimator.py::TestCausalAlignmentLoss::test_perfect_prediction_low_loss",
  "tests/test_causal_estimator.py::TestCausalAlignmentLoss::test_sampled_bce_different_neg_counts",
  "tests/test_causal_estimator.py::TestCausalAlignmentLoss::test_with_effect_magnitude",
  "tests/test_causal_estimator.py::TestCausalGPU::test_estimator_on_cuda",
  "tests/test_causal_estimator.py::TestCausalGPU::test_planner_on_cuda",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_build_co_occurrence_graph_basic",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_build_co_occurrence_graph_device",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_build_co_occurrence_graph_symmetric",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_co_occurrence_produces_different_scores",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_deterministic_with_seed",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_different_batch_sizes",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_gradient_flows",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_large_gene_set",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_no_nan_forward",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_output_has_variance",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_output_not_all_same",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_output_range_sigmoid",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_output_shape",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_with_co_occurrence_graph",
  "tests/test_causal_estimator.py::TestCausalGeneEstimator::test_without_co_occurrence_graph",
  "tests/test_causal_estimator.py::TestCausalPlanner::test_forward_output_shapes",
  "tests/test_causal_estimator.py::TestCausalPlanner::test_forward_with_co_occurrence",
  "tests/test_causal_estimator.py::TestCausalPlanner::test_gradient_flows",
  "tests/test_causal_estimator.py::TestCausalPlanner::test_no_nan",
  "tests/test_causal_estimator.py::TestCausalPlanner::test_output_range",
  "tests/test_causal_estimator.py::TestCausalSparsityLoss::test_gradient_flows",
  "tests/test_causal_estimator.py::TestCausalSparsityLoss::test_output_scalar",
  "tests/test_causal_estimator.py::TestCausalSparsityLoss::test_scales_with_mean_score",
  "tests/test_causal_estimator.py::TestCausalSparsityLoss::test_weight_scaling",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDGPU::test_forward_on_cuda",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDGeneSpace::test_forward_keys",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDGeneSpace::test_forward_shapes",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDGeneSpace::test_gradient_flows",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDGeneSpace::test_loss_decreases_over_steps",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDGeneSpace::test_no_nan",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDGeneSpace::test_predict_targets",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDGeneSpace::test_recon_loss_zero",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDGeneSpaceGPU::test_forward_on_cuda",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDModel::test_causal_scores_informative",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDModel::test_different_batch_sizes",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDModel::test_forward_keys",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDModel::test_forward_shapes",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDModel::test_gradient_flows",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDModel::test_loss_components_nonzero",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDModel::test_loss_is_finite",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDModel::test_no_nan",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDModel::test_predict_targets",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDModel::test_predict_targets_no_topk",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDModel::test_without_co_occurrence",
  "tests/test_causal_flow_gid.py::TestCausalFlowGIDModel::test_without_true_perturbation",
  "tests/test_datasets.py::TestDataset::test_multiple_folds",
  "tests/test_datasets.py::TestDataset::test_single_fold",
  "tests/test_distributional_cycle_loss.py::TestDistributionalCycleLoss::test_de_loss_enabled",
  "tests/test_distributional_cycle_loss.py::TestDistributionalCycleLoss::test_de_zero_when_weight_zero",
  "tests/test_distributional_cycle_loss.py::TestDistributionalCycleLoss::test_differentiable",
  "tests/test_distributional_cycle_loss.py::TestDistributionalCycleLoss::test_gpu_if_available",
  "tests/test_distributional_cycle_loss.py::TestDistributionalCycleLoss::test_loss_lower_when_pred_equals_target",
  "tests/test_distributional_cycle_loss.py::TestDistributionalCycleLoss::test_no_nan",
  "tests/test_distributional_cycle_loss.py::TestDistributionalCycleLoss::test_output_keys",
  "tests/test_distributional_cycle_loss.py::TestDistributionalCycleLoss::test_with_masks",
  "tests/test_distributional_cycle_loss.py::TestMMDRBF::test_distant_distributions_high_mmd",
  "tests/test_distributional_cycle_loss.py::TestMMDRBF::test_identical_distributions_low_mmd",
  "tests/test_distributional_cycle_loss.py::TestMMDRBF::test_mmd_differentiable",
  "tests/test_distributional_cycle_loss.py::TestMMDRBF::test_mmd_fixed_sigma",
  "tests/test_distributional_cycle_loss.py::TestMMDRBF::test_mmd_shape",
  "tests/test_distributional_cycle_loss.py::TestMMDRBF::test_mmd_with_mask",
  "tests/test_distributional_cycle_loss.py::TestMaskedStats::test_masked_mean_no_mask",
  "tests/test_distributional_cycle_loss.py::TestMaskedStats::test_masked_mean_with_mask",
  "tests/test_distributional_cycle_loss.py::TestMaskedStats::test_masked_var_shape",
  "tests/test_distributional_cycle_loss.py::TestMaskedStats::test_masked_var_with_mask",
  "tests/test_drug_modules.py::TestDoseConsistencyLoss::test_consistent_predictions",
  "tests/test_drug_modules.py::TestDoseConsistencyLoss::test_inconsistent_predictions",
  "tests/test_drug_modules.py::TestDoseConsistencyLoss::test_no_duplicates",
  "tests/test_drug_modules.py::TestDrugAlignmentLoss::test_forward_with_targets",
  "tests/test_drug_modules.py::TestDrugAlignmentLoss::test_forward_without_dose",
  "tests/test_drug_modules.py::TestDrugEncoder::test_different_emb_dims",
  "tests/test_drug_modules.py::TestDrugEncoder::test_embedding_cache",
  "tests/test_drug_modules.py::TestDrugEncoder::test_empty_input",
  "tests/test_drug_modules.py::TestDrugEncoder::test_morgan_encoding_frozen",
  "tests/test_drug_modules.py::TestDrugEncoder::test_morgan_encoding_shape",
  "tests/test_drug_modules.py::TestDrugEncoder::test_morgan_encoding_trainable",
  "tests/test_drug_modules.py::TestDrugEncoder::test_similarity",
  "tests/test_drug_modules.py::TestDrugGeneBridge::test_forward_shape_with_gene_emb",
  "tests/test_drug_modules.py::TestDrugGeneBridge::test_forward_shape_without_gene_emb",
  "tests/test_drug_modules.py::TestDrugGeneBridge::test_gene_aware_attention",
  "tests/test_drug_modules.py::TestDrugTargetAlignmentLoss::test_perfect_prediction",
  "tests/test_drug_modules.py::TestDrugTargetAlignmentLoss::test_wrong_prediction",
  "tests/test_flow_response.py::TestFlowMatchingGPU::test_forward_on_cuda",
  "tests/test_flow_response.py::TestFlowMatchingGPU::test_sample_on_cuda",
  "tests/test_flow_response.py::TestFlowMatchingGeneSpace::test_different_gene_dims",
  "tests/test_flow_response.py::TestFlowMatchingGeneSpace::test_forward_loss_no_nan",
  "tests/test_flow_response.py::TestFlowMatchingGeneSpace::test_forward_loss_scalar",
  "tests/test_flow_response.py::TestFlowMatchingGeneSpace::test_gradient_flows",
  "tests/test_flow_response.py::TestFlowMatchingGeneSpace::test_loss_zero_when_source_equals_target",
  "tests/test_flow_response.py::TestFlowMatchingGeneSpace::test_no_encoder_decoder",
  "tests/test_flow_response.py::TestFlowMatchingGeneSpace::test_reconstruction_loss_zero",
  "tests/test_flow_response.py::TestFlowMatchingGeneSpace::test_sample_is_different_from_source",
  "tests/test_flow_response.py::TestFlowMatchingGeneSpace::test_sample_no_nan",
  "tests/test_flow_response.py::TestFlowMatchingGeneSpace::test_sample_shape",
  "tests/test_flow_response.py::TestFlowMatchingGeneSpace::test_variable_cell_count",
  "tests/test_flow_response.py::TestFlowMatchingGeneSpaceGPU::test_forward_on_cuda",
  "tests/test_flow_response.py::TestFlowMatchingGeneSpaceGPU::test_sample_on_cuda",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_batch_size_one",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_deterministic_with_seed",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_different_gene_dims",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_forward_loss_no_nan",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_forward_loss_scalar",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_loss_lower_for_similar_targets",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_loss_zero_when_source_equals_target",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_more_steps_better",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_sample_gradient_does_not_flow",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_sample_no_nan",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_sample_shape",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_t_at_extremes",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_target_cells_required",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_training_gradient_flows",
  "tests/test_flow_response.py::TestFlowMatchingResponseModel::test_variable_cell_count",
  "tests/test_flow_response.py::TestSinusoidalTimeEmbedding::test_different_for_different_t",
  "tests/test_flow_response.py::TestSinusoidalTimeEmbedding::test_differentiable",
  "tests/test_flow_response.py::TestSinusoidalTimeEmbedding::test_output_shape",
  "tests/test_flow_response.py::TestSinusoidalTimeEmbedding::test_output_shape_odd_dim",
  "tests/test_gene_graph_encoder.py::TestGIDModelWithGeneGraph::test_forward_shapes",
  "tests/test_gene_graph_encoder.py::TestGIDModelWithGeneGraph::test_gcn_off_matches_no_graph",
  "tests/test_gene_graph_encoder.py::TestGIDModelWithGeneGraph::test_gradient_flows_through_gcn",
  "tests/test_gene_graph_encoder.py::TestGIDModelWithGeneGraph::test_no_nan",
  "tests/test_gene_graph_encoder.py::TestGIDModelWithGeneGraph::test_predict_targets_shape",
  "tests/test_gene_graph_encoder.py::TestGIDModelWithGeneGraph::test_with_protein_features_and_graph",
  "tests/test_gene_graph_encoder.py::TestGeneGraphEncoder::test_different_graphs_give_different_embeddings",
  "tests/test_gene_graph_encoder.py::TestGeneGraphEncoder::test_gradient_through_embedding",
  "tests/test_gene_graph_encoder.py::TestGeneGraphEncoder::test_no_nan",
  "tests/test_gene_graph_encoder.py::TestGeneGraphEncoder::test_output_shape",
  "tests/test_gene_graph_encoder.py::TestGeneGraphEncoder::test_real_pdgrapher_graph",
  "tests/test_gene_graph_encoder.py::TestGeneGraphEncoder::test_set_graph_raises_before_forward",
  "tests/test_gene_graph_encoder.py::TestGeneGraphEncoder::test_with_protein_features",
  "tests/test_gene_graph_encoder.py::TestGraphUtils::test_adjacency_nonneg_and_diagonal_positive",
  "tests/test_gene_graph_encoder.py::TestGraphUtils::test_adjacency_row_sum_le_1",
  "tests/test_gene_graph_encoder.py::TestGraphUtils::test_adjacency_symmetric_and_positive",
  "tests/test_gene_graph_encoder.py::TestGraphUtils::test_adjacency_undirected_is_symmetric",
  "tests/test_gene_graph_encoder.py::TestGraphUtils::test_build_normalized_adjacency_shape",
  "tests/test_gene_graph_encoder.py::TestGraphUtils::test_extract_subgraph_correct_remapping",
  "tests/test_gene_graph_encoder.py::TestGraphUtils::test_extract_subgraph_reduces_edges",
  "tests/test_gene_graph_encoder.py::TestGraphUtils::test_load_pdgrapher_edge_index",
  "tests/test_package.py::TestPackage::test_multiple_folds",
  "tests/test_package.py::TestPackage::test_single_fold",
  "tests/test_population_batch.py::TestPopulationCollateFn::test_dataloader_integration",
  "tests/test_population_batch.py::TestPopulationCollateFn::test_mask_values",
  "tests/test_population_batch.py::TestPopulationCollateFn::test_max_cells_truncation",
  "tests/test_population_batch.py::TestPopulationCollateFn::test_output_type",
  "tests/test_population_batch.py::TestPopulationCollateFn::test_padded_shapes",
  "tests/test_population_batch.py::TestPopulationCollateFn::test_padding_is_zero",
  "tests/test_population_batch.py::TestPopulationCollateFn::test_perturbation_stacked_correctly",
  "tests/test_population_batch.py::TestPopulationPerturbationBatch::test_optional_fields_default_none",
  "tests/test_population_batch.py::TestPopulationPerturbationBatch::test_shapes",
  "tests/test_population_batch.py::TestPopulationPerturbationBatch::test_to_device_cpu",
  "tests/test_population_batch.py::TestSyntheticPopulationPerturbationDataset::test_cell_counts_in_range",
  "tests/test_population_batch.py::TestSyntheticPopulationPerturbationDataset::test_different_seeds_differ",
  "tests/test_population_batch.py::TestSyntheticPopulationPerturbationDataset::test_gene_dim",
  "tests/test_population_batch.py::TestSyntheticPopulationPerturbationDataset::test_item_keys",
  "tests/test_population_batch.py::TestSyntheticPopulationPerturbationDataset::test_length",
  "tests/test_population_batch.py::TestSyntheticPopulationPerturbationDataset::test_perturbation_is_multihot",
  "tests/test_population_batch.py::TestSyntheticPopulationPerturbationDataset::test_reproducible",
  "tests/test_population_response.py::TestSimplePopulationResponseModel::test_batch_size_1",
  "tests/test_population_response.py::TestSimplePopulationResponseModel::test_different_n_per_call",
  "tests/test_population_response.py::TestSimplePopulationResponseModel::test_gpu_if_available",
  "tests/test_population_response.py::TestSimplePopulationResponseModel::test_gradient_flows",
  "tests/test_population_response.py::TestSimplePopulationResponseModel::test_mask_accepted",
  "tests/test_population_response.py::TestSimplePopulationResponseModel::test_no_nan",
  "tests/test_population_response.py::TestSimplePopulationResponseModel::test_output_shape",
  "tests/test_population_response.py::TestSimplePopulationResponseModel::test_perturbation_changes_output",
  "tests/test_real_data.py::TestGeneSelection::test_hvg_fewer_than_requested",
  "tests/test_real_data.py::TestGeneSelection::test_hvg_shape",
  "tests/test_real_data.py::TestGeneSelection::test_normalize_log1p",
  "tests/test_real_data.py::TestGeneSelection::test_normalize_no_log",
  "tests/test_real_data.py::TestPDGrapherPseudobulkDataset::test_collate_fn_integration",
  "tests/test_real_data.py::TestPDGrapherPseudobulkDataset::test_item_shapes",
  "tests/test_real_data.py::TestPDGrapherPseudobulkDataset::test_length",
  "tests/test_real_data.py::TestPDGrapherPseudobulkDataset::test_no_nan",
  "tests/test_real_data.py::TestPDGrapherPseudobulkDataset::test_num_genes",
  "tests/test_real_data.py::TestPDGrapherPseudobulkDataset::test_perturbation_nonzero",
  "tests/test_real_data.py::TestScPerturbPopulationDataset::test_collate_fn_integration",
  "tests/test_real_data.py::TestScPerturbPopulationDataset::test_item_shapes",
  "tests/test_real_data.py::TestScPerturbPopulationDataset::test_most_perts_in_gene_space",
  "tests/test_real_data.py::TestScPerturbPopulationDataset::test_num_conditions",
  "tests/test_real_data.py::TestScPerturbPopulationDataset::test_perturbation_is_multihot",
  "tests/test_real_data.py::TestScPerturbPopulationDataset::test_reproducibility",
  "tests/test_real_data.py::TestScPerturbPopulationDataset::test_source_target_differ",
  "tests/test_sparse_planner.py::TestGapEncoder::test_gradient_flows",
  "tests/test_sparse_planner.py::TestGapEncoder::test_output_shape",
  "tests/test_sparse_planner.py::TestMMDProjected::test_different_dist_higher_mmd",
  "tests/test_sparse_planner.py::TestMMDProjected::test_same_dist_low_mmd",
  "tests/test_sparse_planner.py::TestMMDProjected::test_shape",
  "tests/test_sparse_planner.py::TestPerturbationEval::test_compute_all_returns_keys",
  "tests/test_sparse_planner.py::TestPerturbationEval::test_de_direction_agreement_perfect",
  "tests/test_sparse_planner.py::TestPerturbationEval::test_pearson_r_good_better_than_random",
  "tests/test_sparse_planner.py::TestPerturbationEval::test_pearson_r_perfect",
  "tests/test_sparse_planner.py::TestPerturbationEval::test_pearson_r_topk_de",
  "tests/test_sparse_planner.py::TestPopulationEncoder::test_gradient_flows",
  "tests/test_sparse_planner.py::TestPopulationEncoder::test_mask_accepted",
  "tests/test_sparse_planner.py::TestPopulationEncoder::test_output_shape_no_var",
  "tests/test_sparse_planner.py::TestPopulationEncoder::test_output_shape_with_var",
  "tests/test_sparse_planner.py::TestPopulationGIDModel::test_end_to_end_gradient",
  "tests/test_sparse_planner.py::TestPopulationGIDModel::test_forward_keys",
  "tests/test_sparse_planner.py::TestPopulationGIDModel::test_no_nan",
  "tests/test_sparse_planner.py::TestPopulationGIDModel::test_predict_targets_shape",
  "tests/test_sparse_planner.py::TestPopulationGIDModel::test_shapes",
  "tests/test_sparse_planner.py::TestPopulationGIDModel::test_teacher_forcing",
  "tests/test_sparse_planner.py::TestSparsePlanner::test_score_shape",
  "tests/test_sparse_planner.py::TestSparsePlanner::test_soft_mask_range",
  "tests/test_sparse_planner.py::TestSparsePlanner::test_ste_mask_is_binary",
  "tests/test_sparse_planner.py::TestSparsePlanner::test_ste_topk_gradient",
  "tests/test_sparse_planner.py::TestSparsePlanner::test_topk_mask_binary",
  "tests/test_sparse_planner.py::TestTargetMetrics::test_compute_all_returns_keys",
  "tests/test_sparse_planner.py::TestTargetMetrics::test_mrr_perfect",
  "tests/test_sparse_planner.py::TestTargetMetrics::test_ndcg_perfect_vs_random",
  "tests/test_sparse_planner.py::TestTargetMetrics::test_recall_at_k_perfect",
  "tests/test_sparse_planner.py::TestTargetMetrics::test_recall_at_k_random",
  "tests/test_train.py::TestTrainer::test_trainer",
  "tests/test_train.py::TestTrainer::test_trainer_args",
  "tests/test_train.py::TestTrainer::test_trainer_unknown_kwargs"
]