From 46bd905355adca45f6aefbd8220b9e161ff21215 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 26 Feb 2018 10:11:11 -0500
Subject: [PATCH] Update downloads.yml to include models_class1_minimal
---
.../models_class1_minimal/README.md | 13 +++++++++++++
mhcflurry/downloads.yml | 4 ++++
test/test_train_and_related_commands.py | 2 +-
3 files changed, 18 insertions(+), 1 deletion(-)
create mode 100644 downloads-generation/models_class1_minimal/README.md
diff --git a/downloads-generation/models_class1_minimal/README.md b/downloads-generation/models_class1_minimal/README.md
new file mode 100644
index 00000000..ddf90f67
--- /dev/null
+++ b/downloads-generation/models_class1_minimal/README.md
@@ -0,0 +1,13 @@
+# 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
diff --git a/mhcflurry/downloads.yml b/mhcflurry/downloads.yml
index 6ca5cfb6..09930b7a 100644
--- a/mhcflurry/downloads.yml
+++ b/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
diff --git a/test/test_train_and_related_commands.py b/test/test_train_and_related_commands.py
index 513c95dd..a43b6d2f 100644
--- a/test/test_train_and_related_commands.py
+++ b/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,
--
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