Update downloads.yml to include models_class1_minimal

downloads-generation/models_class1_minimal/README.md

+# Class I allele-specific models (minimal: ensemble size of 1)
+
+This download contains "minimal" MHC Class I MHCflurry predictors consisting
+of a single model per allele. These predictors are expected to have slightly
+lower accuracy than the standard ensembles (models_class1) but are small and
+fast. Useful for testing.
+
+To download these models and set them as the default predictor, run:
+
+```
+$ mhcflurry-downloads fetch models_class1_minimal
+$ export MHCFLURRY_DEFAULT_CLASS1_MODELS=$(mhcflurry-downloads path models_class1_minimal)/models
+```
\ No newline at end of file

mhcflurry/downloads.yml

@@ -32,6 +32,10 @@ releases:
               url: https://github.com/openvax/mhcflurry/releases/download/pre-1.2/models_class1_unselected.20180221.tar.bz2
               default: false
 
+            - name: models_class1_minimal
+              url: https://github.com/openvax/mhcflurry/releases/download/pre-1.2/models_class1_minimal.20180226.tar.bz2
+              default: false
+
             - name: models_class1_consensus
               url: https://github.com/openvax/mhcflurry/releases/download/pre-1.2/models_class1_consensus.tar.bz2
               default: false

test/test_train_and_related_commands.py

@@ -18,7 +18,7 @@ HYPERPARAMETERS = [
     {
         "n_models": 2,
         "max_epochs": 500,
-        "patience": 10,
+        "patience": 5,
         "minibatch_size": 128,
         "early_stopping": True,
         "validation_split": 0.2,