From c1ea03b473f81532b3f0439d9a205c1789a7dfda Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 13 Nov 2017 14:33:57 -0500
Subject: [PATCH] Update README with conda instructions. Closes #110
---
README.md | 28 ++++++++++++++++++-
.../class1_neural_network.py | 2 +-
requirements.txt | 2 +-
setup.py | 6 ++--
4 files changed, 32 insertions(+), 6 deletions(-)
diff --git a/README.md b/README.md
index 99945648..8bfc7c72 100644
--- a/README.md
+++ b/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
diff --git a/mhcflurry/class1_affinity_prediction/class1_neural_network.py b/mhcflurry/class1_affinity_prediction/class1_neural_network.py
index fe8de016..8e2a638e 100644
--- a/mhcflurry/class1_affinity_prediction/class1_neural_network.py
+++ b/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
diff --git a/requirements.txt b/requirements.txt
index 67444843..8d31007f 100644
--- a/requirements.txt
+++ b/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
diff --git a/setup.py b/setup.py
index 5eeec1c5..6f45d037 100644
--- a/setup.py
+++ b/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',
--
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