updated documentation

docs/source/Installation.rst

@@ -0,0 +1,53 @@
+**Installation**  
+===================================================
+
+Installation on MAC OS
+----------------------
+
+1. Download and install Anaconda <http://docs.continuum.io/anaconda/install> 
+
+2. Clone these two repositories *in the same folder*:
+
+    a. `git clone https://github.com/agiovann/Constrained_NMF.git`
+
+    b. `git clone https://github.com/epnev/SPGL1_python_port.git`
+
+3.     
+    1. Go into the cloned folder and type `conda create --name CNMF --file requirements.txt`
+
+    2. type `source activate CNMF` (this activates the environment, remember to do this every time you want to use the software)
+
+    3. type `pip install tifffile picos` 
+
+    4. type `conda install joblib` 
+
+B. Use this in case 3. does not work. Type the following
+
+        a. `git clone https://github.com/agiovann/Constrained_NMF.git`
+
+        b. `git clone https://github.com/epnev/SPGL1_python_port.git`
+
+        c. `conda create -n CNMF --no-deps ipython`
+
+        d. `source activate CNMF`
+
+        e. `conda install spyder numpy scipy ipyparallel matplotlib bokeh jupyter scikit-image scikit-learn joblib cvxopt`      
+
+        f. `pip install picos`
+
+        g. `pip install tifffile`
+
+Test the system
+----------------------
+
+A. Using the Spyder IDE. 
+
+    1. Open the file demo.py 
+
+    2. Run the cells one by one inspecting the output
+
+B. Using notebook. 
+
+    1. type `ipython notebook`
+
+    2. open the notebook called demoCNMF.ipynb and run cell by cell inspecting the result

docs/source/index.rst

@@ -11,7 +11,8 @@ Contents:
 .. toctree::
    :maxdepth: 2
 
-   Overview	      
+   Overview
+   Installation	      
    Tutorial	      
    core_functions
    API reference