fixed bug AllenInstitute#7, and added dockerfiles for ubuntu and fedora

.gitignore

@@ -1,3 +1,5 @@
+.idea
+.cache
 update.sh
 doc
 .DS_Store

dipde/internals/externalpopulation.py

@@ -16,6 +16,7 @@
 import sympy.parsing.sympy_parser as symp
 from sympy.utilities.lambdify import lambdify
 from sympy.abc import t as sym_t
+from sympy import Piecewise
 
 
 class ExternalPopulation(object):
@@ -48,7 +49,7 @@ class ExternalPopulation(object):
     def __init__(self, firing_rate, record=False, **kwargs):
 
         self.firing_rate_string = str(firing_rate)
-        self.closure = lambdify(sym_t,symp.parse_expr(self.firing_rate_string))
+        self.closure = lambdify(sym_t, symp.parse_expr(self.firing_rate_string, local_dict={'Heaviside': lambda x: Piecewise((0, x < 0), (1, x > 0), (.5, True))}))
 
         self.record = record
         self.type = "external"

docker/README

@@ -0,0 +1,12 @@
+This version of dipde supports docker images for Fedora 24 and Ubuntu 16.  Other OS versions may work, but are not currently tested; if you need a docker image that is not supported email the MAINTAINER for help.
+
+To build the docker images:
+   1) Install docker: https://docs.docker.com/engine/installation/
+   2) cd to the dipde docker directory
+   3) Run: 
+      3a) Fedora: docker build --tag alleninstitute/dipde:fedora24 -f ./fedora_24_python.dockerfile .
+      3b) Ubuntu: docker build --tag alleninstitute/dipde:ubuntu16 -f ./ubuntu_16.04_python.dockerfile .
+   4) Run the dipde tests to validate the installation:
+      export DIPDEDIR=`pwd`'/../'
+      4a) Fedora: docker run -v $DIPDEDIR:/python/dipde -t -i alleninstitute/dipde:fedora24 python setup.py test
+      4b) Ubuntu: docker run -v $DIPDEDIR:/python/dipde -t -i alleninstitute/dipde:ubuntu16 python setup.py test

docker/fedora_24_python.dockerfile

@@ -0,0 +1,14 @@
+FROM fedora:24
+
+MAINTAINER Nicholas Cain <[email protected]>
+
+RUN dnf -y install \
+           python \
+	   python-matplotlib \
+	   python-pip \
+	   python-scipy \
+	   python-pytest
+
+RUN pip install sympy
+ENV PYTHONPATH /python/dipde
+WORKDIR /python/dipde

docker/ubuntu_16.04_python.dockerfile

@@ -0,0 +1,10 @@
+FROM ubuntu:16.04
+
+MAINTAINER Nicholas Cain <[email protected]>
+
+RUN apt-get update
+RUN apt-get -y install python python-pip python-scipy python-pytest python-matplotlib
+
+RUN pip install sympy
+ENV PYTHONPATH /python/dipde
+WORKDIR /python/dipde