| instanovo/cli.py |
main |
2 |
0 |
0 |
100% |
| instanovo/cli.py |
predict |
51 |
14 |
0 |
73% |
| instanovo/cli.py |
version |
6 |
0 |
0 |
100% |
| instanovo/cli.py |
instanovo_entrypoint |
1 |
1 |
0 |
0% |
| instanovo/cli.py |
(no function) |
27 |
0 |
2 |
100% |
| instanovo/common/dataset.py |
DataProcessor.metadata_columns |
1 |
0 |
0 |
100% |
| instanovo/common/dataset.py |
DataProcessor.__init__ |
1 |
0 |
0 |
100% |
| instanovo/common/dataset.py |
DataProcessor._get_expected_columns |
1 |
1 |
0 |
0% |
| instanovo/common/dataset.py |
DataProcessor.process_row |
1 |
1 |
0 |
0% |
| instanovo/common/dataset.py |
DataProcessor._collate_batch |
1 |
1 |
0 |
0% |
| instanovo/common/dataset.py |
DataProcessor.process_dataset |
3 |
0 |
0 |
100% |
| instanovo/common/dataset.py |
DataProcessor.collate_fn |
8 |
3 |
0 |
62% |
| instanovo/common/dataset.py |
DataProcessor.get_expected_columns |
1 |
0 |
0 |
100% |
| instanovo/common/dataset.py |
DataProcessor.add_metadata_columns |
1 |
0 |
0 |
100% |
| instanovo/common/dataset.py |
DataProcessor._pad_and_mask |
4 |
0 |
0 |
100% |
| instanovo/common/dataset.py |
DataProcessor.remove_modifications |
5 |
0 |
0 |
100% |
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(no function) |
25 |
0 |
0 |
100% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.s3 |
1 |
0 |
0 |
100% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.__init__ |
48 |
2 |
1 |
96% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.load_model |
1 |
1 |
0 |
0% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.setup_decoder |
1 |
1 |
0 |
0% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.setup_data_processor |
1 |
1 |
0 |
0% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.get_predictions |
1 |
1 |
0 |
0% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.postprocess_dataset |
1 |
0 |
0 |
100% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.load_dataset |
66 |
11 |
0 |
83% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.print_sample_batch |
10 |
0 |
0 |
100% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.setup_metrics |
1 |
0 |
0 |
100% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.setup_accelerator |
14 |
1 |
0 |
93% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.build_dataloader |
8 |
0 |
0 |
100% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.predict |
52 |
8 |
0 |
85% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor._tokens_to_string |
7 |
2 |
0 |
71% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.predictions_to_df |
15 |
0 |
0 |
100% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.postprocess_predictions |
1 |
0 |
0 |
100% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.calculate_metrics |
80 |
2 |
0 |
98% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.save_predictions |
21 |
3 |
0 |
86% |
| instanovo/common/predictor.py |
AccelerateDeNovoPredictor.save_encoder_outputs_to_parquet |
9 |
9 |
0 |
0% |
| instanovo/common/predictor.py |
(no function) |
55 |
0 |
0 |
100% |
| instanovo/common/scheduler.py |
FinetuneScheduler.__init__ |
12 |
12 |
0 |
0% |
| instanovo/common/scheduler.py |
FinetuneScheduler._get_schedule |
37 |
37 |
0 |
0% |
| instanovo/common/scheduler.py |
FinetuneScheduler._freeze_parameters |
8 |
8 |
0 |
0% |
| instanovo/common/scheduler.py |
FinetuneScheduler._unfreeze |
11 |
11 |
0 |
0% |
| instanovo/common/scheduler.py |
FinetuneScheduler.step |
6 |
6 |
0 |
0% |
| instanovo/common/scheduler.py |
WarmupScheduler.__init__ |
2 |
0 |
0 |
100% |
| instanovo/common/scheduler.py |
WarmupScheduler.get_lr |
2 |
0 |
0 |
100% |
| instanovo/common/scheduler.py |
WarmupScheduler.get_lr_factor |
4 |
0 |
0 |
100% |
| instanovo/common/scheduler.py |
CosineWarmupScheduler.__init__ |
2 |
0 |
0 |
100% |
| instanovo/common/scheduler.py |
CosineWarmupScheduler.get_lr |
2 |
0 |
0 |
100% |
| instanovo/common/scheduler.py |
CosineWarmupScheduler.get_lr_factor |
5 |
1 |
0 |
80% |
| instanovo/common/scheduler.py |
(no function) |
22 |
0 |
0 |
100% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.run_id |
1 |
0 |
0 |
100% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.s3 |
1 |
0 |
0 |
100% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.global_step |
1 |
0 |
0 |
100% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.epoch |
1 |
1 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.training_state |
1 |
1 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.__init__ |
60 |
4 |
0 |
93% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.setup_model |
1 |
1 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.setup_optimizer |
1 |
1 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.setup_decoder |
1 |
1 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.setup_data_processors |
1 |
1 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.save_model |
1 |
1 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.forward |
1 |
1 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.get_predictions |
1 |
1 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.convert_interval_to_steps |
3 |
3 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.log_if_verbose |
10 |
9 |
0 |
10% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.setup_metrics |
1 |
0 |
0 |
100% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.setup_accelerator |
17 |
1 |
0 |
94% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.build_dataloaders |
15 |
1 |
0 |
93% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.setup_scheduler |
8 |
3 |
0 |
62% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.setup_neptune |
14 |
10 |
0 |
29% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.setup_tensorboard |
10 |
4 |
0 |
60% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer._is_main_process_on_aichor |
1 |
0 |
0 |
100% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer._add_commit_message_to_monitoring_platform |
9 |
6 |
0 |
33% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer._add_config_summary_to_monitoring_platform |
4 |
1 |
0 |
75% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.load_datasets |
73 |
25 |
0 |
66% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.print_sample_batch |
10 |
2 |
0 |
80% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.save_accelerator_state |
24 |
24 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.check_if_best_checkpoint |
13 |
13 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.load_accelerator_state |
24 |
24 |
1 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.load_model_state |
26 |
8 |
0 |
69% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.update_model_state |
1 |
0 |
0 |
100% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.update_vocab |
0 |
0 |
1 |
100% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer._update_vocab |
19 |
19 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.train |
21 |
21 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.prepare_batch |
5 |
5 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.train_epoch |
69 |
69 |
0 |
0% |
| instanovo/common/trainer.py |
AccelerateDeNovoTrainer.validate_epoch |
100 |
100 |
0 |
0% |
| instanovo/common/trainer.py |
(no function) |
94 |
0 |
0 |
100% |
| instanovo/common/utils.py |
TrainingState.__init__ |
2 |
0 |
0 |
100% |
| instanovo/common/utils.py |
TrainingState.global_step |
1 |
0 |
0 |
100% |
| instanovo/common/utils.py |
TrainingState.epoch |
1 |
1 |
0 |
0% |
| instanovo/common/utils.py |
TrainingState.state_dict |
1 |
1 |
0 |
0% |
| instanovo/common/utils.py |
TrainingState.load_state_dict |
2 |
2 |
0 |
0% |
| instanovo/common/utils.py |
TrainingState.step |
1 |
1 |
0 |
0% |
| instanovo/common/utils.py |
TrainingState.step_epoch |
1 |
1 |
0 |
0% |
| instanovo/common/utils.py |
TrainingState.unstep_epoch |
1 |
1 |
0 |
0% |
| instanovo/common/utils.py |
Timer.__init__ |
3 |
0 |
0 |
100% |
| instanovo/common/utils.py |
Timer.start |
2 |
2 |
0 |
0% |
| instanovo/common/utils.py |
Timer.step |
2 |
0 |
0 |
100% |
| instanovo/common/utils.py |
Timer.get_delta |
1 |
0 |
0 |
100% |
| instanovo/common/utils.py |
Timer.get_eta |
6 |
2 |
0 |
67% |
| instanovo/common/utils.py |
Timer.get_total_time |
3 |
3 |
0 |
0% |
| instanovo/common/utils.py |
Timer.get_rate |
2 |
2 |
0 |
0% |
| instanovo/common/utils.py |
Timer.get_step_time |
2 |
0 |
0 |
100% |
| instanovo/common/utils.py |
Timer.get_time_str |
1 |
0 |
0 |
100% |
| instanovo/common/utils.py |
Timer.get_eta_str |
2 |
0 |
0 |
100% |
| instanovo/common/utils.py |
Timer.get_total_time_str |
1 |
1 |
0 |
0% |
| instanovo/common/utils.py |
Timer.get_rate_str |
2 |
2 |
0 |
0% |
| instanovo/common/utils.py |
Timer.get_step_time_rate_str |
2 |
0 |
0 |
100% |
| instanovo/common/utils.py |
Timer.get_step_time_str |
2 |
2 |
0 |
0% |
| instanovo/common/utils.py |
Timer._format_time |
2 |
0 |
0 |
100% |
| instanovo/common/utils.py |
NeptuneSummaryWriter.__init__ |
2 |
0 |
0 |
100% |
| instanovo/common/utils.py |
NeptuneSummaryWriter.add_scalar |
8 |
5 |
0 |
38% |
| instanovo/common/utils.py |
NeptuneSummaryWriter.add_text |
2 |
0 |
0 |
100% |
| instanovo/common/utils.py |
NeptuneSummaryWriter.add_hparams |
4 |
4 |
0 |
0% |
| instanovo/common/utils.py |
_set_author_neptune_api_token |
14 |
0 |
0 |
100% |
| instanovo/common/utils.py |
_get_filepath_mapping |
5 |
5 |
0 |
0% |
| instanovo/common/utils.py |
_flatten_dict_using_keypath |
9 |
9 |
0 |
0% |
| instanovo/common/utils.py |
(no function) |
47 |
0 |
0 |
100% |
| instanovo/constants.py |
(no function) |
43 |
0 |
0 |
100% |
| instanovo/diffusion/cli.py |
diffusion_train |
10 |
10 |
0 |
0% |
| instanovo/diffusion/cli.py |
diffusion_predict |
43 |
9 |
0 |
79% |
| instanovo/diffusion/cli.py |
(no function) |
15 |
0 |
0 |
100% |
| instanovo/diffusion/data.py |
DiffusionDataProcessor.__init__ |
4 |
0 |
0 |
100% |
| instanovo/diffusion/data.py |
DiffusionDataProcessor.process_row |
28 |
3 |
0 |
89% |
| instanovo/diffusion/data.py |
DiffusionDataProcessor._collate_batch |
6 |
3 |
0 |
50% |
| instanovo/diffusion/data.py |
(no function) |
13 |
0 |
0 |
100% |
| instanovo/diffusion/layers.py |
TransformerEncoder.__init__ |
11 |
2 |
0 |
82% |
| instanovo/diffusion/layers.py |
TransformerEncoder.forward |
12 |
3 |
0 |
75% |
| instanovo/diffusion/layers.py |
(no function) |
13 |
0 |
0 |
100% |
| instanovo/diffusion/model.py |
MassSpectrumTransformer.forward |
10 |
0 |
0 |
100% |
| instanovo/diffusion/model.py |
MassSpectrumTransFusion.__init__ |
14 |
0 |
0 |
100% |
| instanovo/diffusion/model.py |
MassSpectrumTransFusion.forward |
30 |
3 |
0 |
90% |
| instanovo/diffusion/model.py |
(no function) |
14 |
0 |
0 |
100% |
| instanovo/diffusion/multinomial_diffusion.py |
cosine_beta_schedule |
7 |
0 |
0 |
100% |
| instanovo/diffusion/multinomial_diffusion.py |
InstaNovoPlus.__init__ |
9 |
0 |
0 |
100% |
| instanovo/diffusion/multinomial_diffusion.py |
InstaNovoPlus.save |
35 |
35 |
0 |
0% |
| instanovo/diffusion/multinomial_diffusion.py |
InstaNovoPlus.save.save_file_local |
1 |
1 |
0 |
0% |
| instanovo/diffusion/multinomial_diffusion.py |
InstaNovoPlus.save.save_file_s3 |
2 |
2 |
0 |
0% |
| instanovo/diffusion/multinomial_diffusion.py |
InstaNovoPlus.load |
36 |
20 |
0 |
44% |
| instanovo/diffusion/multinomial_diffusion.py |
InstaNovoPlus.get_pretrained |
5 |
1 |
0 |
80% |
| instanovo/diffusion/multinomial_diffusion.py |
InstaNovoPlus.from_pretrained |
44 |
44 |
0 |
0% |
| instanovo/diffusion/multinomial_diffusion.py |
InstaNovoPlus.prepare_fine_tuning |
6 |
6 |
0 |
0% |
| instanovo/diffusion/multinomial_diffusion.py |
InstaNovoPlus.mixture_categorical |
1 |
0 |
0 |
100% |
| instanovo/diffusion/multinomial_diffusion.py |
InstaNovoPlus.forward |
6 |
0 |
0 |
100% |
| instanovo/diffusion/multinomial_diffusion.py |
InstaNovoPlus.reverse_distribution |
2 |
0 |
0 |
100% |
| instanovo/diffusion/multinomial_diffusion.py |
DiffusionLoss.__init__ |
4 |
0 |
0 |
100% |
| instanovo/diffusion/multinomial_diffusion.py |
DiffusionLoss.kl_divergence |
1 |
0 |
0 |
100% |
| instanovo/diffusion/multinomial_diffusion.py |
DiffusionLoss.forward |
7 |
7 |
0 |
0% |
| instanovo/diffusion/multinomial_diffusion.py |
DiffusionLoss._compute_loss |
9 |
0 |
0 |
100% |
| instanovo/diffusion/multinomial_diffusion.py |
(no function) |
47 |
0 |
0 |
100% |
| instanovo/diffusion/predict.py |
DiffusionPredictor.__init__ |
5 |
0 |
0 |
100% |
| instanovo/diffusion/predict.py |
DiffusionPredictor.load_model |
9 |
1 |
0 |
89% |
| instanovo/diffusion/predict.py |
DiffusionPredictor.postprocess_dataset |
52 |
15 |
0 |
71% |
| instanovo/diffusion/predict.py |
DiffusionPredictor.postprocess_dataset.add_predictions_column |
6 |
1 |
0 |
83% |
| instanovo/diffusion/predict.py |
DiffusionPredictor._clean_predictions |
5 |
1 |
0 |
80% |
| instanovo/diffusion/predict.py |
DiffusionPredictor.setup_data_processor |
4 |
0 |
0 |
100% |
| instanovo/diffusion/predict.py |
DiffusionPredictor.setup_decoder |
1 |
0 |
0 |
100% |
| instanovo/diffusion/predict.py |
DiffusionPredictor.get_predictions |
27 |
8 |
0 |
70% |
| instanovo/diffusion/predict.py |
CombinedPredictor.__init__ |
8 |
0 |
0 |
100% |
| instanovo/diffusion/predict.py |
CombinedPredictor.load_model |
14 |
3 |
0 |
79% |
| instanovo/diffusion/predict.py |
CombinedPredictor.setup_decoder |
5 |
1 |
0 |
80% |
| instanovo/diffusion/predict.py |
CombinedPredictor._tokenize_and_pad |
10 |
0 |
0 |
100% |
| instanovo/diffusion/predict.py |
CombinedPredictor.get_predictions |
14 |
1 |
0 |
93% |
| instanovo/diffusion/predict.py |
(no function) |
36 |
0 |
0 |
100% |
| instanovo/diffusion/train.py |
DiffusionTrainer.__init__ |
2 |
0 |
0 |
100% |
| instanovo/diffusion/train.py |
DiffusionTrainer.setup_model |
5 |
0 |
0 |
100% |
| instanovo/diffusion/train.py |
DiffusionTrainer.setup_optimizer |
1 |
0 |
0 |
100% |
| instanovo/diffusion/train.py |
DiffusionTrainer.setup_decoder |
1 |
0 |
0 |
100% |
| instanovo/diffusion/train.py |
DiffusionTrainer.setup_data_processors |
3 |
0 |
0 |
100% |
| instanovo/diffusion/train.py |
DiffusionTrainer.add_checkpoint_state |
1 |
1 |
0 |
0% |
| instanovo/diffusion/train.py |
DiffusionTrainer.save_model |
24 |
24 |
0 |
0% |
| instanovo/diffusion/train.py |
DiffusionTrainer.update_vocab |
1 |
1 |
0 |
0% |
| instanovo/diffusion/train.py |
DiffusionTrainer.update_model_state |
6 |
6 |
0 |
0% |
| instanovo/diffusion/train.py |
DiffusionTrainer.forward |
2 |
2 |
0 |
0% |
| instanovo/diffusion/train.py |
DiffusionTrainer.get_predictions |
3 |
3 |
0 |
0% |
| instanovo/diffusion/train.py |
main |
3 |
3 |
0 |
0% |
| instanovo/diffusion/train.py |
(no function) |
33 |
0 |
2 |
100% |
| instanovo/inference/beam_search.py |
BeamSearchDecoder.__init__ |
29 |
6 |
0 |
79% |
| instanovo/inference/beam_search.py |
BeamSearchDecoder.decode |
168 |
27 |
1 |
84% |
| instanovo/inference/beam_search.py |
BeamSearchDecoder._get_top_n_beams |
9 |
1 |
0 |
89% |
| instanovo/inference/beam_search.py |
(no function) |
14 |
0 |
0 |
100% |
| instanovo/inference/diffusion.py |
DiffusionDecoder.__init__ |
5 |
0 |
0 |
100% |
| instanovo/inference/diffusion.py |
DiffusionDecoder.decode |
75 |
25 |
1 |
67% |
| instanovo/inference/diffusion.py |
DiffusionDecoder._extract_predictions |
8 |
1 |
0 |
88% |
| instanovo/inference/diffusion.py |
(no function) |
13 |
0 |
0 |
100% |
| instanovo/inference/greedy_search.py |
GreedyDecoder.__init__ |
28 |
5 |
0 |
82% |
| instanovo/inference/greedy_search.py |
GreedyDecoder.decode |
96 |
15 |
1 |
84% |
| instanovo/inference/greedy_search.py |
(no function) |
13 |
0 |
0 |
100% |
| instanovo/inference/interfaces.py |
Decodable.residue_set |
1 |
1 |
0 |
0% |
| instanovo/inference/interfaces.py |
Decodable.init |
1 |
1 |
0 |
0% |
| instanovo/inference/interfaces.py |
Decodable.score_candidates |
1 |
1 |
0 |
0% |
| instanovo/inference/interfaces.py |
Decodable.get_residue_masses |
1 |
1 |
0 |
0% |
| instanovo/inference/interfaces.py |
Decodable.decode |
1 |
1 |
0 |
0% |
| instanovo/inference/interfaces.py |
Decodable.get_eos_index |
1 |
1 |
0 |
0% |
| instanovo/inference/interfaces.py |
Decodable.get_empty_index |
1 |
1 |
0 |
0% |
| instanovo/inference/interfaces.py |
Decoder.__init__ |
1 |
0 |
0 |
100% |
| instanovo/inference/interfaces.py |
Decoder.decode |
1 |
1 |
0 |
0% |
| instanovo/inference/interfaces.py |
(no function) |
34 |
0 |
0 |
100% |
| instanovo/inference/knapsack.py |
Knapsack.save |
7 |
0 |
0 |
100% |
| instanovo/inference/knapsack.py |
Knapsack.construct_knapsack |
39 |
4 |
0 |
90% |
| instanovo/inference/knapsack.py |
Knapsack.from_file |
4 |
0 |
0 |
100% |
| instanovo/inference/knapsack.py |
Knapsack.get_feasible_masses |
6 |
0 |
0 |
100% |
| instanovo/inference/knapsack.py |
(no function) |
26 |
0 |
0 |
100% |
| instanovo/inference/knapsack_beam_search.py |
KnapsackBeamSearchDecoder.__init__ |
31 |
6 |
0 |
81% |
| instanovo/inference/knapsack_beam_search.py |
KnapsackBeamSearchDecoder.from_file |
2 |
0 |
0 |
100% |
| instanovo/inference/knapsack_beam_search.py |
KnapsackBeamSearchDecoder._filter_knapsack |
17 |
0 |
0 |
100% |
| instanovo/inference/knapsack_beam_search.py |
KnapsackBeamSearchDecoder.decode |
170 |
28 |
1 |
84% |
| instanovo/inference/knapsack_beam_search.py |
KnapsackBeamSearchDecoder._get_top_n_beams |
9 |
0 |
0 |
100% |
| instanovo/inference/knapsack_beam_search.py |
(no function) |
18 |
0 |
0 |
100% |
| instanovo/scripts/convert_to_sdf.py |
convert |
11 |
0 |
0 |
100% |
| instanovo/scripts/convert_to_sdf.py |
(no function) |
17 |
0 |
2 |
100% |
| instanovo/scripts/get_zenodo_record.py |
get_zenodo |
12 |
0 |
0 |
100% |
| instanovo/scripts/get_zenodo_record.py |
unzip_zenodo |
8 |
0 |
0 |
100% |
| instanovo/scripts/get_zenodo_record.py |
main |
18 |
2 |
0 |
89% |
| instanovo/scripts/get_zenodo_record.py |
(no function) |
16 |
0 |
2 |
100% |
| instanovo/scripts/set_gcp_credentials.py |
to_base64 |
3 |
3 |
0 |
0% |
| instanovo/scripts/set_gcp_credentials.py |
set_credentials |
16 |
1 |
0 |
94% |
| instanovo/scripts/set_gcp_credentials.py |
(no function) |
9 |
0 |
2 |
100% |
| instanovo/scripts/update_ipc_format.py |
update_ipc |
8 |
0 |
0 |
100% |
| instanovo/scripts/update_ipc_format.py |
main |
7 |
0 |
0 |
100% |
| instanovo/scripts/update_ipc_format.py |
(no function) |
9 |
0 |
2 |
100% |
| instanovo/transformer/cli.py |
transformer_train |
10 |
10 |
0 |
0% |
| instanovo/transformer/cli.py |
transformer_predict |
35 |
3 |
0 |
91% |
| instanovo/transformer/cli.py |
(no function) |
16 |
0 |
0 |
100% |
| instanovo/transformer/data.py |
TransformerDataProcessor.__init__ |
12 |
0 |
0 |
100% |
| instanovo/transformer/data.py |
TransformerDataProcessor._process_spectrum |
42 |
10 |
0 |
76% |
| instanovo/transformer/data.py |
TransformerDataProcessor.process_row |
15 |
1 |
0 |
93% |
| instanovo/transformer/data.py |
TransformerDataProcessor._get_expected_columns |
4 |
0 |
0 |
100% |
| instanovo/transformer/data.py |
TransformerDataProcessor._collate_batch |
19 |
2 |
0 |
89% |
| instanovo/transformer/data.py |
(no function) |
19 |
0 |
0 |
100% |
| instanovo/transformer/layers.py |
PositionalEncoding.__init__ |
8 |
0 |
0 |
100% |
| instanovo/transformer/layers.py |
PositionalEncoding.forward |
2 |
0 |
0 |
100% |
| instanovo/transformer/layers.py |
MultiScalePeakEmbedding.__init__ |
9 |
1 |
0 |
89% |
| instanovo/transformer/layers.py |
MultiScalePeakEmbedding.forward |
5 |
0 |
0 |
100% |
| instanovo/transformer/layers.py |
MultiScalePeakEmbedding.encode_mass |
3 |
0 |
0 |
100% |
| instanovo/transformer/layers.py |
ConvPeakEmbedding.__init__ |
3 |
3 |
0 |
0% |
| instanovo/transformer/layers.py |
ConvPeakEmbedding.forward |
2 |
2 |
0 |
0% |
| instanovo/transformer/layers.py |
(no function) |
17 |
0 |
0 |
100% |
| instanovo/transformer/model.py |
InstaNovo.__init__ |
19 |
2 |
0 |
89% |
| instanovo/transformer/model.py |
InstaNovo.residue_set |
1 |
0 |
0 |
100% |
| instanovo/transformer/model.py |
InstaNovo._get_causal_mask |
4 |
1 |
0 |
75% |
| instanovo/transformer/model.py |
InstaNovo.get_pretrained |
5 |
1 |
0 |
80% |
| instanovo/transformer/model.py |
InstaNovo.load |
21 |
6 |
0 |
71% |
| instanovo/transformer/model.py |
InstaNovo.from_pretrained |
27 |
27 |
0 |
0% |
| instanovo/transformer/model.py |
InstaNovo.forward |
8 |
3 |
0 |
62% |
| instanovo/transformer/model.py |
InstaNovo.init |
7 |
3 |
0 |
57% |
| instanovo/transformer/model.py |
InstaNovo.score_candidates |
4 |
1 |
0 |
75% |
| instanovo/transformer/model.py |
InstaNovo.get_residue_masses |
5 |
0 |
0 |
100% |
| instanovo/transformer/model.py |
InstaNovo.get_eos_index |
1 |
0 |
0 |
100% |
| instanovo/transformer/model.py |
InstaNovo.get_empty_index |
1 |
0 |
0 |
100% |
| instanovo/transformer/model.py |
InstaNovo.decode |
1 |
0 |
0 |
100% |
| instanovo/transformer/model.py |
InstaNovo.idx_to_aa |
9 |
9 |
0 |
0% |
| instanovo/transformer/model.py |
InstaNovo.batch_idx_to_aa |
1 |
1 |
0 |
0% |
| instanovo/transformer/model.py |
InstaNovo.score_sequences |
30 |
30 |
0 |
0% |
| instanovo/transformer/model.py |
InstaNovo._encoder |
19 |
2 |
0 |
89% |
| instanovo/transformer/model.py |
InstaNovo._decoder |
15 |
0 |
0 |
100% |
| instanovo/transformer/model.py |
InstaNovo._flash_encoder |
17 |
17 |
0 |
0% |
| instanovo/transformer/model.py |
InstaNovo._flash_decoder |
15 |
15 |
0 |
0% |
| instanovo/transformer/model.py |
_whitelist_torch_omegaconf |
6 |
0 |
0 |
100% |
| instanovo/transformer/model.py |
(no function) |
48 |
0 |
0 |
100% |
| instanovo/transformer/predict.py |
TransformerPredictor.__init__ |
3 |
0 |
0 |
100% |
| instanovo/transformer/predict.py |
TransformerPredictor.load_model |
9 |
1 |
0 |
89% |
| instanovo/transformer/predict.py |
TransformerPredictor.setup_data_processor |
2 |
0 |
0 |
100% |
| instanovo/transformer/predict.py |
TransformerPredictor.setup_decoder |
19 |
6 |
0 |
68% |
| instanovo/transformer/predict.py |
TransformerPredictor.get_predictions |
7 |
0 |
0 |
100% |
| instanovo/transformer/predict.py |
_setup_knapsack |
5 |
0 |
0 |
100% |
| instanovo/transformer/predict.py |
(no function) |
22 |
0 |
0 |
100% |
| instanovo/transformer/train.py |
TransformerTrainer.__init__ |
2 |
0 |
0 |
100% |
| instanovo/transformer/train.py |
TransformerTrainer.setup_model |
3 |
0 |
0 |
100% |
| instanovo/transformer/train.py |
TransformerTrainer.update_vocab |
1 |
1 |
0 |
0% |
| instanovo/transformer/train.py |
TransformerTrainer.setup_optimizer |
1 |
0 |
0 |
100% |
| instanovo/transformer/train.py |
TransformerTrainer.setup_decoder |
1 |
0 |
0 |
100% |
| instanovo/transformer/train.py |
TransformerTrainer.setup_data_processors |
3 |
0 |
0 |
100% |
| instanovo/transformer/train.py |
TransformerTrainer.add_checkpoint_state |
1 |
1 |
0 |
0% |
| instanovo/transformer/train.py |
TransformerTrainer.save_model |
24 |
24 |
0 |
0% |
| instanovo/transformer/train.py |
TransformerTrainer.forward |
4 |
4 |
0 |
0% |
| instanovo/transformer/train.py |
TransformerTrainer.get_predictions |
3 |
3 |
0 |
0% |
| instanovo/transformer/train.py |
main |
3 |
3 |
0 |
0% |
| instanovo/transformer/train.py |
(no function) |
31 |
0 |
2 |
100% |
| instanovo/types.py |
(no function) |
21 |
0 |
0 |
100% |
| instanovo/utils/cli_utils.py |
compose_config |
5 |
0 |
0 |
100% |
| instanovo/utils/cli_utils.py |
(no function) |
6 |
0 |
0 |
100% |
| instanovo/utils/colorlogging.py |
DynamicRankFormatter.__init__ |
1 |
0 |
0 |
100% |
| instanovo/utils/colorlogging.py |
DynamicRankFormatter.format |
4 |
1 |
0 |
75% |
| instanovo/utils/colorlogging.py |
ColorLog.__init__ |
10 |
1 |
0 |
90% |
| instanovo/utils/colorlogging.py |
(no function) |
12 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.__init__ |
88 |
9 |
0 |
90% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._create_filter_series |
2 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._shuffle_df |
2 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._sanitise_peptide |
7 |
1 |
0 |
86% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._ensure_experiment_name |
13 |
4 |
0 |
69% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._map_columns |
3 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._cast_columns |
1 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._is_glob |
1 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._convert_file_paths |
10 |
1 |
0 |
90% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._concat_dataframes |
10 |
10 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.get_data_shards |
26 |
10 |
0 |
62% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.check_values |
12 |
5 |
0 |
58% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.filter_rows |
11 |
3 |
0 |
73% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._log |
2 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.reset_filter |
5 |
5 |
1 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._update_file_indices |
9 |
1 |
0 |
89% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._preshuffle_files |
45 |
41 |
0 |
9% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._reset_current_file |
6 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._shuffle_file_order |
1 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._load_parquet_data |
6 |
1 |
0 |
83% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._load_next_file |
16 |
16 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._start_preload_next |
2 |
2 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._preload_next_file |
5 |
5 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.__len__ |
4 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.__getitem__ |
39 |
25 |
0 |
36% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.is_annotated |
1 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.has_predictions |
1 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.is_lazy |
1 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.save |
11 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._to_parquet_chunks |
20 |
8 |
0 |
60% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.write_csv |
1 |
1 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.write_ipc |
4 |
4 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.write_mgf |
9 |
9 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.write_pointnovo |
0 |
0 |
1 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.write_mzxml |
0 |
0 |
1 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.write_mzml |
0 |
0 |
1 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.to_pandas |
1 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.to_polars |
16 |
6 |
0 |
62% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._get_unified_schema |
38 |
19 |
0 |
50% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.to_dataset |
5 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.to_matchms |
2 |
2 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.export_predictions |
2 |
2 |
1 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.load |
5 |
1 |
0 |
80% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._df_from_any |
16 |
5 |
0 |
69% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.load_mgf |
2 |
2 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._df_from_mgf |
2 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.load_pointnovo |
0 |
0 |
1 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.load_csv |
3 |
3 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.load_mzxml |
2 |
2 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._df_from_mzxml |
1 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.load_mzml |
2 |
2 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._df_from_mzml |
1 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.from_huggingface |
3 |
3 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.from_pandas |
2 |
2 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.from_polars |
1 |
1 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.load_ipc |
2 |
2 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._df_from_ipc |
4 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._df_from_csv |
4 |
4 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._df_from_parquet |
4 |
4 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.from_matchms |
2 |
2 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._parse_scan_number |
6 |
1 |
0 |
83% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._df_from_dict |
2 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._df_from_matchms |
12 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._df_to_matchms |
8 |
8 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._check_type_spec |
28 |
2 |
0 |
93% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._check_type_spec.check_columns |
2 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._check_type_spec.check_annotations |
1 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.concatenate |
1 |
1 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.get_unique_sequences |
10 |
1 |
0 |
90% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.get_vocabulary |
7 |
1 |
0 |
86% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.validate_precursor_mass |
15 |
15 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.sample_subset |
14 |
14 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.validate_data |
0 |
0 |
1 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.__del__ |
4 |
0 |
0 |
100% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._strip_shape_info |
2 |
2 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._truncate_list_repr |
3 |
3 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._truncate_list_repr.process_list |
6 |
6 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame._display_string_preview |
7 |
7 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.__str__ |
6 |
6 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.__repr__ |
6 |
6 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.__repr__.adjust_indentation |
6 |
6 |
0 |
0% |
| instanovo/utils/data_handler.py |
SpectrumDataFrame.__repr__.pretty |
10 |
10 |
0 |
0% |
| instanovo/utils/data_handler.py |
_format_time |
2 |
2 |
0 |
0% |
| instanovo/utils/data_handler.py |
(no function) |
146 |
1 |
0 |
99% |
| instanovo/utils/device_handler.py |
get_device_capabilities |
1 |
0 |
0 |
100% |
| instanovo/utils/device_handler.py |
detect_device |
6 |
0 |
0 |
100% |
| instanovo/utils/device_handler.py |
get_device_config_updates |
10 |
0 |
0 |
100% |
| instanovo/utils/device_handler.py |
apply_device_config |
10 |
0 |
0 |
100% |
| instanovo/utils/device_handler.py |
validate_and_configure_device |
15 |
1 |
0 |
93% |
| instanovo/utils/device_handler.py |
check_device |
3 |
0 |
0 |
100% |
| instanovo/utils/device_handler.py |
(no function) |
12 |
0 |
0 |
100% |
| instanovo/utils/file_downloader.py |
download_file |
12 |
12 |
0 |
0% |
| instanovo/utils/file_downloader.py |
(no function) |
8 |
0 |
0 |
100% |
| instanovo/utils/metrics.py |
Metrics.__init__ |
8 |
1 |
0 |
88% |
| instanovo/utils/metrics.py |
Metrics.matches_precursor |
5 |
1 |
0 |
80% |
| instanovo/utils/metrics.py |
Metrics.compute_aa_er |
3 |
0 |
0 |
100% |
| instanovo/utils/metrics.py |
Metrics.compute_precision_recall |
29 |
1 |
0 |
97% |
| instanovo/utils/metrics.py |
Metrics.calc_auc |
7 |
0 |
0 |
100% |
| instanovo/utils/metrics.py |
Metrics.find_recall_at_fdr |
12 |
0 |
0 |
100% |
| instanovo/utils/metrics.py |
Metrics._split_sequences |
1 |
0 |
0 |
100% |
| instanovo/utils/metrics.py |
Metrics._split_peptide |
3 |
0 |
0 |
100% |
| instanovo/utils/metrics.py |
Metrics._get_pr_curve |
9 |
0 |
0 |
100% |
| instanovo/utils/metrics.py |
Metrics._mass |
2 |
0 |
0 |
100% |
| instanovo/utils/metrics.py |
Metrics._calc_mass_error |
1 |
0 |
0 |
100% |
| instanovo/utils/metrics.py |
Metrics._novor_match |
15 |
0 |
0 |
100% |
| instanovo/utils/metrics.py |
Metrics._get_peptide_matches |
9 |
1 |
0 |
89% |
| instanovo/utils/metrics.py |
(no function) |
20 |
0 |
0 |
100% |
| instanovo/utils/msreader.py |
read_mgf |
11 |
11 |
0 |
0% |
| instanovo/utils/msreader.py |
read_mzml |
15 |
0 |
0 |
100% |
| instanovo/utils/msreader.py |
read_mzxml |
13 |
0 |
0 |
100% |
| instanovo/utils/msreader.py |
_initialize_data_dict |
1 |
0 |
0 |
100% |
| instanovo/utils/msreader.py |
(no function) |
7 |
0 |
0 |
100% |
| instanovo/utils/residues.py |
ResidueSet.__init__ |
10 |
0 |
0 |
100% |
| instanovo/utils/residues.py |
ResidueSet.update_remapping |
1 |
0 |
0 |
100% |
| instanovo/utils/residues.py |
ResidueSet.get_mass |
3 |
0 |
0 |
100% |
| instanovo/utils/residues.py |
ResidueSet.get_sequence_mass |
4 |
0 |
0 |
100% |
| instanovo/utils/residues.py |
ResidueSet.tokenize |
5 |
1 |
0 |
80% |
| instanovo/utils/residues.py |
ResidueSet.detokenize |
1 |
0 |
0 |
100% |
| instanovo/utils/residues.py |
ResidueSet.encode |
10 |
0 |
0 |
100% |
| instanovo/utils/residues.py |
ResidueSet.decode |
12 |
0 |
0 |
100% |
| instanovo/utils/residues.py |
ResidueSet.__len__ |
1 |
0 |
0 |
100% |
| instanovo/utils/residues.py |
ResidueSet.__eq__ |
3 |
1 |
0 |
67% |
| instanovo/utils/residues.py |
ResidueSet.__contains__ |
1 |
1 |
0 |
0% |
| instanovo/utils/residues.py |
(no function) |
17 |
0 |
0 |
100% |
| instanovo/utils/s3.py |
S3FileHandler.__init__ |
3 |
0 |
0 |
100% |
| instanovo/utils/s3.py |
S3FileHandler.s3_enabled |
1 |
0 |
0 |
100% |
| instanovo/utils/s3.py |
S3FileHandler._create_s3fs |
15 |
0 |
0 |
100% |
| instanovo/utils/s3.py |
S3FileHandler._log_if_verbose |
2 |
0 |
0 |
100% |
| instanovo/utils/s3.py |
S3FileHandler._download_from_s3 |
8 |
8 |
0 |
0% |
| instanovo/utils/s3.py |
S3FileHandler.download |
9 |
1 |
0 |
89% |
| instanovo/utils/s3.py |
S3FileHandler.get_local_path |
9 |
0 |
0 |
100% |
| instanovo/utils/s3.py |
S3FileHandler.upload |
6 |
1 |
0 |
83% |
| instanovo/utils/s3.py |
S3FileHandler.upload_to_s3_wrapper |
8 |
4 |
0 |
50% |
| instanovo/utils/s3.py |
S3FileHandler.listdir |
5 |
5 |
0 |
0% |
| instanovo/utils/s3.py |
S3FileHandler._aichor_enabled |
4 |
2 |
0 |
50% |
| instanovo/utils/s3.py |
S3FileHandler.register_tb |
7 |
5 |
0 |
29% |
| instanovo/utils/s3.py |
S3FileHandler.convert_to_s3_output |
8 |
2 |
0 |
75% |
| instanovo/utils/s3.py |
S3FileHandler.cleanup |
1 |
0 |
0 |
100% |
| instanovo/utils/s3.py |
S3FileHandler.__del__ |
1 |
0 |
0 |
100% |
| instanovo/utils/s3.py |
(no function) |
32 |
0 |
0 |
100% |