diff --git a/src/ms_pred/autoregr_gen/hyperopt.py b/src/ms_pred/autoregr_gen/hyperopt.py index d8559000..78dc3264 100644 --- a/src/ms_pred/autoregr_gen/hyperopt.py +++ b/src/ms_pred/autoregr_gen/hyperopt.py @@ -37,7 +37,7 @@ def score_function(config, base_args, orig_dir=""): kwargs = copy.deepcopy(base_args) kwargs.update(config) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Get dataset # Load smiles dataset and split into 3 subsets diff --git a/src/ms_pred/autoregr_gen/predict.py b/src/ms_pred/autoregr_gen/predict.py index 912b3957..75fa9870 100644 --- a/src/ms_pred/autoregr_gen/predict.py +++ b/src/ms_pred/autoregr_gen/predict.py @@ -56,7 +56,7 @@ def predict(): save_dir = kwargs["save_dir"] common.setup_logger(save_dir, log_name="autoregr_pred.log", debug=kwargs["debug"]) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Dump args yaml_args = yaml.dump(kwargs) diff --git a/src/ms_pred/autoregr_gen/train.py b/src/ms_pred/autoregr_gen/train.py index a74e619f..01059af2 100644 --- a/src/ms_pred/autoregr_gen/train.py +++ b/src/ms_pred/autoregr_gen/train.py @@ -83,7 +83,7 @@ def train_model(): save_dir = kwargs["save_dir"] common.setup_logger(save_dir, log_name="autoregr_train.log", debug=kwargs["debug"]) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Dump args yaml_args = yaml.dump(kwargs) diff --git a/src/ms_pred/ffn_pred/ffn_hyperopt.py b/src/ms_pred/ffn_pred/ffn_hyperopt.py index 5c7f34f0..e48101bb 100644 --- a/src/ms_pred/ffn_pred/ffn_hyperopt.py +++ b/src/ms_pred/ffn_pred/ffn_hyperopt.py @@ -40,7 +40,7 @@ def score_function(config, base_args, orig_dir=""): kwargs = copy.deepcopy(base_args) kwargs.update(config) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Get dataset # Load smiles dataset and split into 3 subsets diff --git a/src/ms_pred/ffn_pred/predict.py b/src/ms_pred/ffn_pred/predict.py index 7b23d9fe..0bd589d7 100644 --- a/src/ms_pred/ffn_pred/predict.py +++ b/src/ms_pred/ffn_pred/predict.py @@ -58,7 +58,7 @@ def predict(): save_dir = kwargs["save_dir"] common.setup_logger(save_dir, log_name="ffn_pred.log", debug=kwargs["debug"]) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Dump args yaml_args = yaml.dump(kwargs) diff --git a/src/ms_pred/glacier/predict_inten_joint.py b/src/ms_pred/glacier/predict_inten_joint.py index 4079c8d8..e18591c1 100644 --- a/src/ms_pred/glacier/predict_inten_joint.py +++ b/src/ms_pred/glacier/predict_inten_joint.py @@ -54,7 +54,7 @@ def predict(): save_dir = kwargs["save_dir"] common.setup_logger(save_dir, log_name="inten_pred.log", debug=kwargs["debug"]) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) binned_out = kwargs["binned_out"] # Dump args diff --git a/src/ms_pred/gnn_pred/gnn_hyperopt.py b/src/ms_pred/gnn_pred/gnn_hyperopt.py index b349dace..c7753fe4 100644 --- a/src/ms_pred/gnn_pred/gnn_hyperopt.py +++ b/src/ms_pred/gnn_pred/gnn_hyperopt.py @@ -40,7 +40,7 @@ def score_function(config, base_args, orig_dir=""): kwargs = copy.deepcopy(base_args) kwargs.update(config) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Get dataset # Load smiles dataset and split into 3 subsets diff --git a/src/ms_pred/gnn_pred/predict.py b/src/ms_pred/gnn_pred/predict.py index 24d41f0a..7e880449 100644 --- a/src/ms_pred/gnn_pred/predict.py +++ b/src/ms_pred/gnn_pred/predict.py @@ -59,7 +59,7 @@ def predict(): save_dir = kwargs["save_dir"] common.setup_logger(save_dir, log_name="gnn_pred.log", debug=kwargs["debug"]) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Dump args yaml_args = yaml.dump(kwargs) diff --git a/src/ms_pred/graff_ms/graff_ms_hyperopt.py b/src/ms_pred/graff_ms/graff_ms_hyperopt.py index 1f8e3188..87226c33 100644 --- a/src/ms_pred/graff_ms/graff_ms_hyperopt.py +++ b/src/ms_pred/graff_ms/graff_ms_hyperopt.py @@ -40,7 +40,7 @@ def score_function(config, base_args, orig_dir=""): kwargs = copy.deepcopy(base_args) kwargs.update(config) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Get dataset # Load smiles dataset and split into 3 subsets diff --git a/src/ms_pred/graff_ms/predict.py b/src/ms_pred/graff_ms/predict.py index 22d6cac3..f0bf546a 100644 --- a/src/ms_pred/graff_ms/predict.py +++ b/src/ms_pred/graff_ms/predict.py @@ -59,7 +59,7 @@ def predict(): save_dir = kwargs["save_dir"] common.setup_logger(save_dir, log_name="graff_ms_pred.log", debug=kwargs["debug"]) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Dump args yaml_args = yaml.dump(kwargs) diff --git a/src/ms_pred/iceberg/gen_hyperopt.py b/src/ms_pred/iceberg/gen_hyperopt.py index 98a3bb41..337ce8f4 100644 --- a/src/ms_pred/iceberg/gen_hyperopt.py +++ b/src/ms_pred/iceberg/gen_hyperopt.py @@ -40,7 +40,7 @@ def score_function(config, base_args, orig_dir=""): kwargs = copy.deepcopy(base_args) kwargs.update(config) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Get dataset # Load smiles dataset and split into 3 subsets diff --git a/src/ms_pred/iceberg/iceberg_elucidation.py b/src/ms_pred/iceberg/iceberg_elucidation.py index db4b8c32..d43ac665 100644 --- a/src/ms_pred/iceberg/iceberg_elucidation.py +++ b/src/ms_pred/iceberg/iceberg_elucidation.py @@ -334,7 +334,7 @@ def iceberg_prediction( df.to_csv(save_dir / f'cands_df_{exp_name}.tsv', sep='\t', index=False) # run iceberg to generate in-silico spectrum - cmd = (f'''{python_path} src/ms_pred/iceberg/predict_smis.py \\ + cmd = (f'''{python_path} {Path(__file__).resolve().parent / "predict_smis.py"} \\ --batch-size {batch_size} \\ --num-gpu-workers {num_gpu_workers} \\ --num-cpu-workers {num_cpu_workers} \\ diff --git a/src/ms_pred/iceberg/inten_hyperopt.py b/src/ms_pred/iceberg/inten_hyperopt.py index 7748b8b1..66983a21 100644 --- a/src/ms_pred/iceberg/inten_hyperopt.py +++ b/src/ms_pred/iceberg/inten_hyperopt.py @@ -40,7 +40,7 @@ def score_function(config, base_args, orig_dir=""): kwargs = copy.deepcopy(base_args) kwargs.update(config) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Get dataset # Load smiles dataset and split into 3 subsets diff --git a/src/ms_pred/iceberg/predict_inten.py b/src/ms_pred/iceberg/predict_inten.py index f060b26c..c261f7cf 100644 --- a/src/ms_pred/iceberg/predict_inten.py +++ b/src/ms_pred/iceberg/predict_inten.py @@ -58,7 +58,7 @@ def predict(): save_dir = kwargs["save_dir"] common.setup_logger(save_dir, log_name="inten_pred.log", debug=kwargs["debug"]) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) binned_out = kwargs["binned_out"] # Dump args diff --git a/src/ms_pred/marason/gen_hyperopt.py b/src/ms_pred/marason/gen_hyperopt.py index 861a6a25..fedff3bb 100644 --- a/src/ms_pred/marason/gen_hyperopt.py +++ b/src/ms_pred/marason/gen_hyperopt.py @@ -40,7 +40,7 @@ def score_function(config, base_args, orig_dir=""): kwargs = copy.deepcopy(base_args) kwargs.update(config) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Get dataset # Load smiles dataset and split into 3 subsets diff --git a/src/ms_pred/marason/inten_hyperopt.py b/src/ms_pred/marason/inten_hyperopt.py index 2e186f55..444d6aa2 100644 --- a/src/ms_pred/marason/inten_hyperopt.py +++ b/src/ms_pred/marason/inten_hyperopt.py @@ -44,7 +44,7 @@ def score_function(config, base_args, orig_dir=""): kwargs = copy.deepcopy(base_args) kwargs.update(config) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Get dataset # Load smiles dataset and split into 3 subsets diff --git a/src/ms_pred/marason/predict_inten.py b/src/ms_pred/marason/predict_inten.py index 3920e8c2..62ee1f4d 100644 --- a/src/ms_pred/marason/predict_inten.py +++ b/src/ms_pred/marason/predict_inten.py @@ -70,7 +70,7 @@ def predict(): save_dir = kwargs["save_dir"] common.setup_logger(save_dir, log_name="inten_pred.log", debug=kwargs["debug"]) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) binned_out = kwargs["binned_out"] # Dump args diff --git a/src/ms_pred/massformer_pred/massformer_hyperopt.py b/src/ms_pred/massformer_pred/massformer_hyperopt.py index 67eea91a..e9ece002 100644 --- a/src/ms_pred/massformer_pred/massformer_hyperopt.py +++ b/src/ms_pred/massformer_pred/massformer_hyperopt.py @@ -40,7 +40,7 @@ def score_function(config, base_args, orig_dir=""): kwargs = copy.deepcopy(base_args) kwargs.update(config) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Get dataset # Load smiles dataset and split into 3 subsets diff --git a/src/ms_pred/massformer_pred/predict.py b/src/ms_pred/massformer_pred/predict.py index 91a6b348..f0b4e52d 100644 --- a/src/ms_pred/massformer_pred/predict.py +++ b/src/ms_pred/massformer_pred/predict.py @@ -58,7 +58,7 @@ def predict(): save_dir = kwargs["save_dir"] common.setup_logger(save_dir, log_name="massformer_pred.log", debug=kwargs["debug"]) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Dump args yaml_args = yaml.dump(kwargs) diff --git a/src/ms_pred/molnetms/molnetms_hyperopt.py b/src/ms_pred/molnetms/molnetms_hyperopt.py index b3100429..ce5d1ff9 100644 --- a/src/ms_pred/molnetms/molnetms_hyperopt.py +++ b/src/ms_pred/molnetms/molnetms_hyperopt.py @@ -40,7 +40,7 @@ def score_function(config, base_args, orig_dir=""): kwargs = copy.deepcopy(base_args) kwargs.update(config) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Get dataset # Load smiles dataset and split into 3 subsets diff --git a/src/ms_pred/molnetms/predict.py b/src/ms_pred/molnetms/predict.py index 9865fbf3..589bff16 100644 --- a/src/ms_pred/molnetms/predict.py +++ b/src/ms_pred/molnetms/predict.py @@ -59,7 +59,7 @@ def predict(): save_dir = kwargs["save_dir"] common.setup_logger(save_dir, log_name="molnetms_pred.log", debug=kwargs["debug"]) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Dump args yaml_args = yaml.dump(kwargs) diff --git a/src/ms_pred/nn_utils/base_hyperopt.py b/src/ms_pred/nn_utils/base_hyperopt.py index f08c5d60..3ba6a30d 100644 --- a/src/ms_pred/nn_utils/base_hyperopt.py +++ b/src/ms_pred/nn_utils/base_hyperopt.py @@ -65,7 +65,7 @@ def run_hyperopt( common.setup_logger( save_dir, log_name="hyperopt.log", debug=kwargs.get("debug", False) ) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Define score function trainable = tune.with_parameters( diff --git a/src/ms_pred/scarf_pred/gen_hyperopt.py b/src/ms_pred/scarf_pred/gen_hyperopt.py index a345bd15..7703a26a 100644 --- a/src/ms_pred/scarf_pred/gen_hyperopt.py +++ b/src/ms_pred/scarf_pred/gen_hyperopt.py @@ -38,7 +38,7 @@ def score_function(config, base_args, orig_dir=""): kwargs = copy.deepcopy(base_args) kwargs.update(config) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Get dataset # Load smiles dataset and split into 3 subsets diff --git a/src/ms_pred/scarf_pred/inten_hyperopt.py b/src/ms_pred/scarf_pred/inten_hyperopt.py index ecd7d870..1393b603 100644 --- a/src/ms_pred/scarf_pred/inten_hyperopt.py +++ b/src/ms_pred/scarf_pred/inten_hyperopt.py @@ -38,7 +38,7 @@ def score_function(config, base_args, orig_dir=""): kwargs = copy.deepcopy(base_args) kwargs.update(config) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Get dataset # Load smiles dataset and split into 3 subsets diff --git a/src/ms_pred/scarf_pred/predict_gen.py b/src/ms_pred/scarf_pred/predict_gen.py index 2e0c53d3..a63b8cdc 100644 --- a/src/ms_pred/scarf_pred/predict_gen.py +++ b/src/ms_pred/scarf_pred/predict_gen.py @@ -57,7 +57,7 @@ def predict(): save_dir = kwargs["save_dir"] common.setup_logger(save_dir, log_name="scarf_pred.log", debug=kwargs["debug"]) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Dump args yaml_args = yaml.dump(kwargs) diff --git a/src/ms_pred/scarf_pred/predict_inten.py b/src/ms_pred/scarf_pred/predict_inten.py index d7c6b2c7..40bac65f 100644 --- a/src/ms_pred/scarf_pred/predict_inten.py +++ b/src/ms_pred/scarf_pred/predict_inten.py @@ -61,7 +61,7 @@ def predict(): save_dir = kwargs["save_dir"] common.setup_logger(save_dir, log_name="inten_pred.log", debug=kwargs["debug"]) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Dump args yaml_args = yaml.dump(kwargs) diff --git a/src/ms_pred/scarf_pred/predict_smis.py b/src/ms_pred/scarf_pred/predict_smis.py index f759c6d8..bed5a952 100644 --- a/src/ms_pred/scarf_pred/predict_smis.py +++ b/src/ms_pred/scarf_pred/predict_smis.py @@ -74,7 +74,7 @@ def predict(): common.setup_logger( save_dir, log_name="scarf_pred_binned.log", debug=kwargs["debug"] ) - pl.utilities.seed.seed_everything(kwargs.get("seed")) + pl.seed_everything(kwargs.get("seed")) # Dump args yaml_args = yaml.dump(kwargs)