| [ |
| "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" |
| ] |
