Merge pull request #29 from EmoryUniversityTheoreticalBiophysics/py3

updating to python 3

.gitignore

@@ -78,3 +78,6 @@ wheels/
 .installed.cfg
 *.egg
 
+# backup files
+*.bak
+

Dockerfile

@@ -0,0 +1,38 @@
+FROM ubuntu:latest
+RUN apt-get update && apt-get -y update
+FROM python:2
+ARG DEBIAN_FRONTEND=noninteractive
+RUN mkdir app
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends sudo apt-utils && \
+    apt-get install -y --no-install-recommends openssh-server \
+        python-dev python-numpy python-pip python-virtualenv python-scipy \
+        gcc gfortran libopenmpi-dev openmpi-bin openmpi-common openmpi-doc binutils && \
+    apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+WORKDIR /app
+RUN useradd --create-home --home-dir /home/docker --shell /bin/bash docker
+RUN usermod -a -G sudo docker
+RUN echo "docker ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
+RUN wget http://www.open-mpi.org/software/ompi/v4.1/downloads/openmpi-4.1.1.tar.gz
+RUN tar xzvf openmpi-4.1.1.tar.gz
+WORKDIR openmpi-4.1.1
+RUN ./configure --prefix=/usr/local/openmpi4.1.1
+RUN make all
+RUN make install
+RUN MPI_DIR=/usr/local/openmpi4.1.1
+ENV LD_LIBRARY_PATH="${MPI_DIR}/lib:${LD_LIBRARY_PATH}"
+ENV PATH="/usr/local/openmpi4.1.1/bin:${PATH}"
+RUN git clone https://github.com/mpi4py/mpi4py.git ./mpi4py.git
+WORKDIR mpi4py.git
+RUN python setup.py build --mpicc=/usr/local/openmpi4.1.1/bin/mpicc
+RUN python setup.py install
+WORKDIR /app
+RUN apt-get -y update &&  apt -y install libopenmpi-dev
+
+RUN pip install numpy
+RUN pip install jupyter notebook
+RUN git clone -b mpi4py-convesion https://github.com/diging/SloppyCell.git
+RUN pip install -e SloppyCell/
+RUN git clone -b pypar-check  https://github.com/diging/SirIsaac.git
+RUN pip install -e SirIsaac/
+CMD ["jupyter", "notebook", "--port=8888", "--no-browser", "--ip=0.0.0.0", "--allow-root"]

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
@@ -20,15 +21,13 @@ 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
 version of SloppyCell, available on GitHub.
 In the simplest case, you can install with two steps.  First download the git repository by running
 
-    https://github.com/GutenkunstLab/SloppyCell.git
+    git clone https://github.com/GutenkunstLab/SloppyCell.git
 
 which will create a folder named `SloppyCell` in the current directory.  Next, install SloppyCell by running setup.py.  The easiest way to do this is using `pip`:
 
@@ -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:
@@ -68,5 +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
+
+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
+
 

README.md

@@ -28,7 +28,8 @@ https://doi.org/10.1371/journal.pone.0119821
 Dependencies
 ============
 
-Python 2.6 or later (not Python 3)  
+Python 3  
+Numpy  
 Scipy  
 Matplotlib  
 (One way to install the above is with Anaconda or Sage.  See Installation.md.)
@@ -49,9 +50,10 @@ ipython (for reading ipython notebook file describing example usage)
 Contributors
 ============
 
-Bryan Daniels, Ilya Nemenman
-
-
+Bryan Daniels  
+Ilya Nemenman  
+hashknot  
+sudheerad9