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Noble-Lab · Nov 1, 2023 · 9b4d06c · 9b4d06c
1 parent 9ffbc97
commit 9b4d06c
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Showing 3 changed files with 6 additions and 2 deletions.
diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py
@@ -357,6 +357,7 @@ def setup_model(
         try:
             model = _get_model_weights()
         except github.RateLimitExceededException:
+
             logger.error(
                 "GitHub API rate limit exceeded while trying to download the "
                 "model weights. Please download compatible model weights "

diff --git a/casanovo/denovo/model.py b/casanovo/denovo/model.py
@@ -137,7 +137,9 @@ def __init__(
             max_charge=max_charge,
         )
         self.softmax = torch.nn.Softmax(2)
-        self.celoss = torch.nn.CrossEntropyLoss(ignore_index=0, label_smoothing=train_label_smoothing)
+        self.celoss = torch.nn.CrossEntropyLoss(
+            ignore_index=0, label_smoothing=train_label_smoothing
+        )
         self.val_celoss = torch.nn.CrossEntropyLoss(ignore_index=0)
         # Optimizer settings.
         self.warmup_iters = warmup_iters
@@ -727,7 +729,7 @@ def training_step(
         """
         pred, truth = self._forward_step(*batch)
         pred = pred[:, :-1, :].reshape(-1, self.decoder.vocab_size + 1)
-        if mode=="train":
+        if mode == "train":
             loss = self.celoss(pred, truth.flatten())
         else:
             loss = self.val_celoss(pred, truth.flatten())

diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py
@@ -50,6 +50,7 @@ def __init__(
         self.trainer = None
         self.model = None
         self.loaders = None
+
         self.writer = None
 
         # Configure checkpoints.