From 3829f81e04d0eafc320bc44dfbc5fe823335b3b1 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 13 Nov 2017 13:46:39 -0500
Subject: [PATCH] Bump version, upgrade to Keras 2.0.9
* Switch from JSON to YAML for hyperparameters
* Pin tensorflow (hoping will help with #110)
---
mhcflurry/__init__.py | 2 +-
.../train_allele_specific_models_command.py | 6 +++---
requirements.txt | 7 ++++---
setup.py | 5 +++--
4 files changed, 11 insertions(+), 9 deletions(-)
diff --git a/mhcflurry/__init__.py b/mhcflurry/__init__.py
index ab21634e..cf13e1e6 100644
--- a/mhcflurry/__init__.py
+++ b/mhcflurry/__init__.py
@@ -17,7 +17,7 @@ from .class1_affinity_prediction.class1_neural_network import (
from .class1_affinity_prediction.class1_affinity_predictor import (
Class1AffinityPredictor)
-__version__ = "0.9.2"
+__version__ = "0.9.3"
__all__ = [
"Class1NeuralNetwork",
diff --git a/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py b/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py
index 6f0aa975..1128ca99 100644
--- a/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py
+++ b/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py
@@ -5,7 +5,7 @@ Train Class1 single allele models.
import os
import sys
import argparse
-import json
+import yaml
import pandas
@@ -31,7 +31,7 @@ parser.add_argument(
"--hyperparameters",
metavar="FILE.json",
required=True,
- help="JSON of hyperparameters")
+ help="JSON or YAML of hyperparameters")
parser.add_argument(
"--allele",
default=None,
@@ -61,7 +61,7 @@ def run(argv=sys.argv[1:]):
configure_logging(verbose=args.verbosity > 1)
- hyperparameters_lst = json.load(open(args.hyperparameters))
+ hyperparameters_lst = yaml.load(open(args.hyperparameters))
assert isinstance(hyperparameters_lst, list)
print("Loaded hyperparameters list: %s" % str(hyperparameters_lst))
diff --git a/requirements.txt b/requirements.txt
index 51a6f3a0..67444843 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,9 +1,10 @@
six
-numpy>= 1.11
+numpy>=1.11
pandas>=0.13.1
-Keras==2.0.8
+Keras==2.0.9
+tensorflow>=1.4.0
appdirs
-tensorflow
scikit-learn
typechecks
mhcnames
+pyyaml
diff --git a/setup.py b/setup.py
index ae7b0a20..5eeec1c5 100644
--- a/setup.py
+++ b/setup.py
@@ -51,12 +51,13 @@ if __name__ == '__main__':
'six',
'numpy>=1.11',
'pandas>=0.13.1',
- 'Keras==2.0.8',
+ 'Keras==2.0.9',
'appdirs',
- 'tensorflow',
+ 'tensorflow>=1.4.0',
'scikit-learn',
'typechecks',
'mhcnames',
+ 'pyyaml',
]
if PY2:
# concurrent.futures is a standard library in Py3 but Py2
--
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