0.5.4 some model args and ESM2 args are suppressed

senseppi/__init__.py

-__version__ = "0.5.3"
+__version__ = "0.5.4"
 __author__ = "Konstantin Volzhenin"
 
 from . import model, commands, esm2_model, dataset, utils, network_utils

senseppi/esm2_model.py

 #!/usr/bin/env python3 -u
 # Copyright (c) Meta Platforms, Inc. and affiliates.
+# Modified by Konstantin Volzhenin, Sorbonne University, 2023
 
 import argparse
 import pathlib
@@ -20,8 +21,9 @@ def add_esm_args(parent_parser):
     parser.add_argument(
         "--model_location_esm",
         type=str, default="esm2_t36_3B_UR50D",
-        help="PyTorch model file OR name of pretrained model to download. If not default, "
-             "the number of encoder_features has to be modified according to the embedding dimensionality. "
+        # help="PyTorch model file OR name of pretrained model to download. If not default, "
+        #      "the number of encoder_features has to be modified according to the embedding dimensionality. "
+        help=argparse.SUPPRESS
     )
     parser.add_argument(
         "--output_dir_esm",
@@ -35,13 +37,15 @@ def add_esm_args(parent_parser):
         type=int,
         default=[-1],
         nargs="+",
-        help="layers indices from which to extract representations (0 to num_layers, inclusive)",
+        # help="layers indices from which to extract representations (0 to num_layers, inclusive)",
+        help=argparse.SUPPRESS
     )
     parser.add_argument(
         "--truncation_seq_length_esm",
         type=int,
         default=1022,
-        help="truncate sequences longer than the given value",
+        # help="truncate sequences longer than the given value",
+        help=argparse.SUPPRESS
     )
 
 

senseppi/model.py

+import argparse
 import torch
 import torch.nn.functional as F
 from torch.utils.data import DataLoader
 import pytorch_lightning as pl
 import torch.utils.data as data
 from torch.utils.data import Subset
-from torchmetrics import AUROC, ROC, Accuracy, Precision, Recall, F1Score, MatthewsCorrCoef, AveragePrecision
+from torchmetrics import AUROC, Accuracy, Precision, Recall, F1Score, MatthewsCorrCoef, AveragePrecision
 from torchmetrics.collections import MetricCollection
 from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
 import torch.optim as optim
@@ -206,9 +207,10 @@ class BaselineModel(pl.LightningModule):
                                                                    "Cosine warmup will be applied.")
         parser.add_argument("--batch_size", type=int, default=32, help="Batch size for training/testing.")
         parser.add_argument("--encoder_features", type=int, default=2560,
-                            help="Number of features in the encoder "
-                                 "(Corresponds to the dimentionality of per-token embedding of ESM2 model.) "
-                                 "If not a 3B version of ESM2 is chosen, this parameter needs to be set accordingly.")
+                            # help="Number of features in the encoder "
+                            #      "(Corresponds to the dimentionality of per-token embedding of ESM2 model.) "
+                            #      "If not a 3B version of ESM2 is chosen, this parameter needs to be set accordingly."
+                            help=argparse.SUPPRESS)
         return parent_parser
 
 

senseppi/network_utils.py

 import json
 from Bio import SeqIO
-from itertools import permutations, product
+from itertools import permutations
 import pandas as pd
-import numpy as np
 import os
 import urllib.request
-import time
-from tqdm import tqdm
-from copy import deepcopy
 import requests
 import gzip
 import shutil

senseppi/utils.py

@@ -15,7 +15,8 @@ def add_general_args(parser):
                              "considered and will be deleted from the fasta file.")
     parser.add_argument("--device", type=str, default=determine_device(), choices=['cpu', 'gpu', 'mps'],
                         help="Device to used for computations. Options include: cpu, gpu, mps (for MacOS)."
-                             "If not selected the device is set by torch automatically.")
+                             "If not selected the device is set by torch automatically. WARNING: mps is temporarily "
+                             "disabled, if it is chosen, cpu will be used instead.")
 
     return parser