Coverage report: 71%

Files Functions Classes

coverage.py v7.11.0, created at 2025-12-08 07:26 +0000

File class statements missing excluded coverage
instanovo/cli.py (no class) 87 15 2 83%
instanovo/common/dataset.py DataProcessor 27 6 0 78%
instanovo/common/dataset.py (no class) 25 0 0 100%
instanovo/common/predictor.py AccelerateDeNovoPredictor 338 42 1 88%
instanovo/common/predictor.py (no class) 55 0 0 100%
instanovo/common/scheduler.py FinetuneScheduler 74 74 0 0%
instanovo/common/scheduler.py WarmupScheduler 8 0 0 100%
instanovo/common/scheduler.py CosineWarmupScheduler 9 1 0 89%
instanovo/common/scheduler.py (no class) 22 0 0 100%
instanovo/common/trainer.py AccelerateDeNovoTrainer 549 361 2 34%
instanovo/common/trainer.py (no class) 94 0 0 100%
instanovo/common/utils.py TrainingState 10 7 0 30%
instanovo/common/utils.py Timer 33 14 0 58%
instanovo/common/utils.py NeptuneSummaryWriter 16 9 0 44%
instanovo/common/utils.py (no class) 75 14 0 81%
instanovo/constants.py PrecursorDimension 0 0 0 100%
instanovo/constants.py SpecialTokens 0 0 0 100%
instanovo/constants.py MSColumns 0 0 0 100%
instanovo/constants.py (no class) 43 0 0 100%
instanovo/diffusion/cli.py (no class) 68 19 0 72%
instanovo/diffusion/data.py DiffusionDataProcessor 38 6 0 84%
instanovo/diffusion/data.py (no class) 13 0 0 100%
instanovo/diffusion/layers.py TransformerEncoder 23 5 0 78%
instanovo/diffusion/layers.py (no class) 13 0 0 100%
instanovo/diffusion/model.py MassSpectrumTransformer 10 0 0 100%
instanovo/diffusion/model.py MassSpectrumTransFusion 44 3 0 93%
instanovo/diffusion/model.py (no class) 14 0 0 100%
instanovo/diffusion/multinomial_diffusion.py InstaNovoPlus 147 109 0 26%
instanovo/diffusion/multinomial_diffusion.py DiffusionLoss 21 7 0 67%
instanovo/diffusion/multinomial_diffusion.py (no class) 54 0 0 100%
instanovo/diffusion/predict.py DiffusionPredictor 109 26 0 76%
instanovo/diffusion/predict.py CombinedPredictor 51 5 0 90%
instanovo/diffusion/predict.py (no class) 36 0 0 100%
instanovo/diffusion/train.py DiffusionTrainer 49 37 0 24%
instanovo/diffusion/train.py (no class) 36 3 2 92%
instanovo/inference/beam_search.py BeamSearchDecoder 206 34 1 83%
instanovo/inference/beam_search.py (no class) 14 0 0 100%
instanovo/inference/diffusion.py DiffusionDecoder 88 26 1 70%
instanovo/inference/diffusion.py (no class) 13 0 0 100%
instanovo/inference/greedy_search.py GreedyDecoder 124 20 1 84%
instanovo/inference/greedy_search.py (no class) 13 0 0 100%
instanovo/inference/interfaces.py ScoredSequence 0 0 0 100%
instanovo/inference/interfaces.py Decodable 7 7 0 0%
instanovo/inference/interfaces.py Decoder 2 1 0 50%
instanovo/inference/interfaces.py (no class) 34 0 0 100%
instanovo/inference/knapsack.py Knapsack 56 4 0 93%
instanovo/inference/knapsack.py (no class) 26 0 0 100%
instanovo/inference/knapsack_beam_search.py KnapsackBeamSearchDecoder 229 34 1 85%
instanovo/inference/knapsack_beam_search.py (no class) 18 0 0 100%
instanovo/scripts/convert_to_sdf.py Partition 0 0 0 100%
instanovo/scripts/convert_to_sdf.py (no class) 28 0 2 100%
instanovo/scripts/get_zenodo_record.py (no class) 54 2 2 96%
instanovo/scripts/set_gcp_credentials.py (no class) 28 4 2 86%
instanovo/scripts/update_ipc_format.py (no class) 24 0 2 100%
instanovo/transformer/cli.py (no class) 61 13 0 79%
instanovo/transformer/data.py TransformerDataProcessor 92 13 0 86%
instanovo/transformer/data.py (no class) 19 0 0 100%
instanovo/transformer/layers.py PositionalEncoding 10 0 0 100%
instanovo/transformer/layers.py MultiScalePeakEmbedding 17 1 0 94%
instanovo/transformer/layers.py ConvPeakEmbedding 5 5 0 0%
instanovo/transformer/layers.py (no class) 17 0 0 100%
instanovo/transformer/model.py InstaNovo 210 118 0 44%
instanovo/transformer/model.py (no class) 54 0 0 100%
instanovo/transformer/predict.py TransformerPredictor 40 7 0 82%
instanovo/transformer/predict.py (no class) 27 0 0 100%
instanovo/transformer/train.py TransformerTrainer 43 33 0 23%
instanovo/transformer/train.py (no class) 34 3 2 91%
instanovo/types.py (no class) 21 0 0 100%
instanovo/utils/cli_utils.py (no class) 11 0 0 100%
instanovo/utils/colorlogging.py DynamicRankFormatter 5 1 0 80%
instanovo/utils/colorlogging.py ColorLog 10 1 0 90%
instanovo/utils/colorlogging.py (no class) 12 0 0 100%
instanovo/utils/data_handler.py SpectrumDataFrame 650 312 7 52%
instanovo/utils/data_handler.py (no class) 148 3 0 98%
instanovo/utils/device_handler.py (no class) 57 1 0 98%
instanovo/utils/file_downloader.py (no class) 20 12 0 40%
instanovo/utils/metrics.py Metrics 104 4 0 96%
instanovo/utils/metrics.py (no class) 20 0 0 100%
instanovo/utils/msreader.py (no class) 47 11 0 77%
instanovo/utils/residues.py ResidueSet 51 3 0 94%
instanovo/utils/residues.py (no class) 17 0 0 100%
instanovo/utils/s3.py S3FileHandler 87 28 0 68%
instanovo/utils/s3.py (no class) 32 0 0 100%
Total   5076 1464 28 71%

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