Update README with conda instructions. Closes #110

README.md

@@ -22,7 +22,7 @@ If you find MHCflurry useful in your research please cite:
 
 > O'Donnell, T. et al., 2017. MHCflurry: open-source class I MHC binding affinity prediction. bioRxiv. Available at: http://www.biorxiv.org/content/early/2017/08/09/174243.
 
-## Setup
+## Setup (pip)
 
 Install the package:
 
@@ -56,6 +56,32 @@ export KERAS_BACKEND=theano
 
 You may also needs to `pip install theano`.
 
+## Setup (conda)
+
+You can alternatively get up and running with a [conda](https://conda.io/docs/)
+environment as follows:
+
+```
+conda create -q -n mhcflurry-env python=3.6 'tensorflow>=1.1.0'
+source activate mhcflurry-env
+```
+
+Then continue as above:
+
+```
+pip install mhcflurry
+mhcflurry-downloads fetch
+```
+
+If you wish to test your installation, you can install `nose` and run the tests
+from a checkout:
+
+```
+pip install nose
+nosetests .
+```
+
+
 
 ## Making predictions from the command-line
 

mhcflurry/class1_affinity_prediction/class1_neural_network.py

@@ -9,7 +9,7 @@ import keras.models
 import keras.layers.pooling
 import keras.regularizers
 from keras.layers import Input
-import keras.layers.merge
+import keras.layers
 from keras.layers.core import Dense, Flatten, Dropout
 from keras.layers.embeddings import Embedding
 from keras.layers.normalization import BatchNormalization

requirements.txt

@@ -2,7 +2,7 @@ six
 numpy>=1.11
 pandas>=0.13.1
 Keras==2.0.9
-tensorflow>=1.4.0
+tensorflow>=1.1.0
 appdirs
 scikit-learn
 typechecks

setup.py

@@ -30,14 +30,14 @@ try:
     with open(readme_filename, 'r') as f:
         readme = f.read()
 except:
-    logging.warn("Failed to load %s" % readme_filename)
+    logging.warning("Failed to load %s" % readme_filename)
     readme = ""
 
 try:
     import pypandoc
     readme = pypandoc.convert(readme, to='rst', format='md')
 except:
-    logging.warn("Conversion of long_description from MD to RST failed")
+    logging.warning("Conversion of long_description from MD to RST failed")
     pass
 
 with open('mhcflurry/__init__.py', 'r') as f:
@@ -53,7 +53,7 @@ if __name__ == '__main__':
         'pandas>=0.13.1',
         'Keras==2.0.9',
         'appdirs',
-        'tensorflow>=1.4.0',
+        'tensorflow>=1.1.0',
         'scikit-learn',
         'typechecks',
         'mhcnames',