fix

mhcflurry/train_pan_allele_models_command.py

@@ -406,7 +406,7 @@ def train_model(
     if pretrain_data_filename:
         iterator = pretrain_data_iterator(pretrain_data_filename, allele_encoding)
         original_hyperparameters = dict(model.hyperparameters)
-        model.hyperparameters['minibatch_size'] = len(next(iterator)[-1])
+        model.hyperparameters['minibatch_size'] = int(len(next(iterator)[-1]) / 100)
         model.hyperparameters['max_epochs'] = 1
         model.hyperparameters['validation_split'] = 0.0
         model.hyperparameters['random_negative_rate'] = 0.0
@@ -443,7 +443,7 @@ def train_model(
             print(
                 progress_preamble,
                 "PRETRAIN epoch %d [%d values, %0.2f sec]. "
-                "Score [%0.2f sec.]: %f" % (
+                "Score [%0.2f sec.]: %10f" % (
                     epoch, len(affinities), fit_time, score_time, score))
             scores.append(score)
 
@@ -464,8 +464,8 @@ def train_model(
 
 
     model.fit(
-        train_peptides,
-        train_data.measurement_value,
+        peptides=train_peptides,
+        affinities=train_data.measurement_value.values,
         allele_encoding=train_alleles,
         inequalities=(
             train_data.measurement_inequality.values
@@ -476,9 +476,18 @@ def train_model(
 
     predictor.class1_pan_allele_models.append(model)
     predictor.clear_cache()
-    return predictor
 
+    if save_to:
+        predictor.save(save_to)
+
+    return predictor
 
 
 if __name__ == '__main__':
-    run()
+    try:
+        run()
+    except Exception as e:
+        print(e)
+        import ipdb ; ipdb.set_trace()
+        raise
+