update Installation.md

Installation.md

@@ -5,13 +5,14 @@ Installing SirIsaac
 
 SirIsaac depends on the following packages:
 
-- Python 2.6 or later (not Python 3)
+- Python 3
 - Scipy
+- Numpy
 - Matplotlib
 - SloppyCell (https://github.com/GutenkunstLab/SloppyCell)
 
 There exist several relatively simple ways to install
-the first three packages above at once, including
+the first four packages above at once, including
 
 - Anaconda: http://www.anaconda.com
 - Sage: http://www.sagemath.org
@@ -20,8 +21,6 @@ These systems also have the added benefit of coming
 prepackaged with other useful software such as
 iPython and Jupyter.
 
-Note: As of June 2020, SirIsaac does not support Python 3 (we are working on it).  Installing Python 2 using the above package managers is likely no longer the default option as it is now officially out of date.
-
 ### Install SloppyCell
 
 SirIsaac depends on the latest
@@ -46,18 +45,22 @@ which will create a folder named `SirIsaac` in the current directory.  Next, ins
 
 ## Test installation
 
-A basic test of the SirIsaac and SloppyCell installation can be
-run by descending into the `SirIsaac/SirIsaac/` directory and running
+A basic suite of unit tests can be run by moving into the SirIsaac directory and running
+
+    python -m unittest
 
-    python SloppyCellTest.py
+This should take about a minute to run.  Note that there may be lots of warnings and compiler optimization messages (we're working on it...), but if you see something like the following then all tests have passed: 
 
-More comprehensive tests are found in the `test` subfolder, and can be run using, e.g., `nosetests`.
+	---------------------------------------------
+	Ran 9 tests in 56.687s
+
+	OK
 
 To further help you get up and running, 
 code to fit and analyze a simple example dataset 
 using SirIsaac is provided in two formats: 
-Python (simpleExample.py) and a Jupyter iPython 
-notebook (simpleExample.ipynb).  The 
+a Jupyter iPython 
+notebook (simpleExample.ipynb) and a simple Python script (simpleExample.py).  The 
 iPython notebook opens in a web browser and 
 includes plots in an interactive format.  To 
 open the .ipynb file, run:
@@ -68,35 +71,39 @@ To run the .py file in iPython at the command line, run:
 
     ipython --pylab
     %run simpleExample.py
-    show()
+    plt.show()
 
 ## Running in parallel
 
-OpenMPI Installation
-
-Download the latest version(4.1.1) from https://www.open-mpi.org/software/ompi/v4.1/
-Refer the Building MPI from sources section for the installation.
-
-Another source for OpenMPI Installation - https://gist.github.com/mrosemeier/088115b2e34f319b913a
-
-Other Installations that were done for Ubuntu
-
-pip install mpi4py
-
-sudo apt-get install python-dev  \
-     build-essential libssl-dev libffi-dev \
-     libxml2-dev libxslt1-dev zlib1g-dev \
-
-
-sudo apt install libopenmpi-dev
-
-sudo apt-get install python2.7-dev
-sudo apt-get install build-essential
-sudo apt-get install gcc
-sudo apt-get install python-dev gcc
-sudo apt-get install python2-dev build-essential gcc libpq-dev
-sudo apt-get install libblas-dev libatlas-base-dev
-sudo apt-get install build-essential gcc gfortran git
-sudo apt install gfortran
+To run parameter fitting in parallel, you will need to install mpi4py, which further depends on an installation of mpi (often OpenMPI, depending on your operating system).  For more information about installing mpi4py, see here: https://pypi.org/project/mpi4py/
+
+Following are notes from one user detailing OpenMPI installation—these are somewhat outdated (using Python 2.7) but could potentially be useful:
+
+	OpenMPI Installation
+
+	Download the latest version(4.1.1) from https://www.open-mpi.org/software/ompi/v4.1/
+	Refer the Building MPI from sources section for the installation.
+
+	Another source for OpenMPI Installation - https://gist.github.com/mrosemeier/088115b2e34f319b913a
+
+	Other Installations that were done for Ubuntu
+
+	pip install mpi4py
+
+	sudo apt-get install python-dev  \
+	     build-essential libssl-dev libffi-dev \
+	     libxml2-dev libxslt1-dev zlib1g-dev \
+	     
+
+	sudo apt install libopenmpi-dev
+
+	sudo apt-get install python2.7-dev
+	sudo apt-get install build-essential
+	sudo apt-get install gcc
+	sudo apt-get install python-dev gcc
+	sudo apt-get install python2-dev build-essential gcc libpq-dev
+	sudo apt-get install libblas-dev libatlas-base-dev
+	sudo apt-get install build-essential gcc gfortran git
+	sudo apt install gfortran