Coverage report: 38.94%

Files Functions Classes

coverage.py v7.9.1, created at 2025-08-12 04:23 +0000

File function statements missing excluded coverage
barbet/__init__.py (no function) 4 0 0 100.00%
barbet/apps.py ImageFormat.__str__ 1 1 0 0.00%
barbet/apps.py ImageFormat.__bool__ 1 1 0 0.00%
barbet/apps.py Barbet.setup 35 35 0 0.00%
barbet/apps.py Barbet.model 2 2 0 0.00%
barbet/apps.py Barbet.loss_function 2 2 0 0.00%
barbet/apps.py Barbet.metrics 4 4 0 0.00%
barbet/apps.py Barbet.data 2 2 0 0.00%
barbet/apps.py Barbet.module_class 2 2 0 0.00%
barbet/apps.py Barbet.extra_hyperparameters 9 9 0 0.00%
barbet/apps.py Barbet.prediction_dataloader 26 0 0 100.00%
barbet/apps.py Barbet.node_to_str 1 1 0 0.00%
barbet/apps.py Barbet.predict 41 4 0 90.24%
barbet/apps.py Barbet.predict_memmap 28 28 0 0.00%
barbet/apps.py Barbet.prediction_dataloader_memmap 22 22 0 0.00%
barbet/apps.py Barbet.monitor 3 3 0 0.00%
barbet/apps.py Barbet.checkpoint 9 9 0 0.00%
barbet/apps.py (no function) 52 6 0 88.46%
barbet/data.py read_memmap 6 6 0 0.00%
barbet/data.py gene_id_from_accession 1 1 0 0.00%
barbet/data.py choose_k_from_n 7 7 0 0.00%
barbet/data.py BarbetStack.__post_init__ 1 0 0 100.00%
barbet/data.py BarbetPredictionDataset.__post_init__ 33 2 0 93.94%
barbet/data.py BarbetPredictionDataset.add_stack 4 0 0 100.00%
barbet/data.py BarbetPredictionDataset.__len__ 1 0 0 100.00%
barbet/data.py BarbetPredictionDataset.__getitem__ 8 0 0 100.00%
barbet/data.py BarbetTrainingDataset.__len__ 1 1 0 0.00%
barbet/data.py BarbetTrainingDataset.__getitem__ 13 13 0 0.00%
barbet/data.py BarbetDataModule.__init__ 11 11 0 0.00%
barbet/data.py BarbetDataModule.setup 14 14 0 0.00%
barbet/data.py BarbetDataModule.create_dataset 1 1 0 0.00%
barbet/data.py BarbetDataModule.train_dataloader 1 1 0 0.00%
barbet/data.py BarbetDataModule.val_dataloader 1 1 0 0.00%
barbet/data.py (no function) 58 0 0 100.00%
barbet/embedding.py _open 4 4 0 0.00%
barbet/embedding.py set_validation_rank_to_treedict 11 11 0 0.00%
barbet/embedding.py get_key 2 2 0 0.00%
barbet/embedding.py get_node 10 10 0 0.00%
barbet/embedding.py generate_overlapping_intervals 41 8 0 80.49%
barbet/embedding.py Embedding.__post_init__ 1 0 0 100.00%
barbet/embedding.py Embedding.embed 1 1 0 0.00%
barbet/embedding.py Embedding.reduce 4 0 0 100.00%
barbet/embedding.py Embedding.__call__ 21 0 0 100.00%
barbet/embedding.py Embedding.setup 1 1 0 0.00%
barbet/embedding.py Embedding.build_treedict 14 14 0 0.00%
barbet/embedding.py Embedding.test_lengths 11 11 0 0.00%
barbet/embedding.py Embedding.test_lengths.random_amino_acid_sequence 2 2 0 0.00%
barbet/embedding.py Embedding.build_gene_array 68 68 0 0.00%
barbet/embedding.py Embedding.set_validation_rank 4 4 0 0.00%
barbet/embedding.py Embedding.preprocess 54 54 0 0.00%
barbet/embedding.py Embedding.prune_to_representatives 29 29 0 0.00%
barbet/embedding.py (no function) 44 0 0 100.00%
barbet/embeddings/__init__.py (no function) 0 0 0 100.00%
barbet/embeddings/esm.py ESMLayers.from_value 4 4 0 0.00%
barbet/embeddings/esm.py ESMLayers.__int__ 1 1 0 0.00%
barbet/embeddings/esm.py ESMLayers.__str__ 1 1 0 0.00%
barbet/embeddings/esm.py ESMLayers.model_name 13 13 0 0.00%
barbet/embeddings/esm.py ESMLayers.get_model_alphabet 1 1 0 0.00%
barbet/embeddings/esm.py ESMEmbedding.setup 13 13 0 0.00%
barbet/embeddings/esm.py ESMEmbedding.__getstate__ 1 1 0 0.00%
barbet/embeddings/esm.py ESMEmbedding.__setstate__ 7 7 0 0.00%
barbet/embeddings/esm.py ESMEmbedding.load 4 4 0 0.00%
barbet/embeddings/esm.py ESMEmbedding.embed 17 17 0 0.00%
barbet/embeddings/esm.py (no function) 26 26 0 0.00%
barbet/markers.py read_fasta 16 16 0 0.00%
barbet/markers.py run_prodigal 12 2 0 83.33%
barbet/markers.py parse_domtblout_top_hits 20 3 0 85.00%
barbet/markers.py _process_single_genome 39 39 0 0.00%
barbet/markers.py extract_markers_genes 51 3 0 94.12%
barbet/markers.py (no function) 16 0 0 100.00%
barbet/models.py BarbetModel.__init__ 13 13 0 0.00%
barbet/models.py BarbetModel.forward 10 10 0 0.00%
barbet/models.py (no function) 7 7 0 0.00%
barbet/modules.py BarbetLightningModule.__init__ 1 1 0 0.00%
barbet/modules.py BarbetLightningModule.setup_prediction 12 12 0 0.00%
barbet/modules.py BarbetLightningModule.on_predict_batch_end 20 20 0 0.00%
barbet/modules.py BarbetLightningModule.on_predict_epoch_end 57 57 0 0.00%
barbet/modules.py (no function) 12 0 0 100.00%
barbet/output.py print_polars_df 12 2 0 83.33%
barbet/output.py (no function) 4 1 0 75.00%
Total   1117 682 0 38.94%

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