Merge pull request #82 from sasaray/master

Trying to update documentation

doc/conf.py

@@ -22,7 +22,7 @@
 #sys.path.insert(0, os.path.abspath('.'))
 
 #following line is from Peter's computer, should probably be removed
-sys.path.insert(0,os.path.abspath('/home/fripe/workspace/git/optimizer/'))
+sys.path.insert(0,os.path.abspath('/home/osboxes/Optimizer_sasaray/optimizer/'))
 
 # -- General configuration -----------------------------------------------------
 

doc/install.rst

@@ -8,7 +8,7 @@ Get a read only copy of optimizer
 Install `git` and type:
 
 
-    git clone https://github.com/pfriedrich/optimizer.git
+    git clone https://github.com/vellamike/optimizer.git
 
 More information on this here: http://rogerdudler.github.com/git-guide/
 
@@ -40,7 +40,8 @@ or
 You can get `matplotlib` with the following command:
 
 
-    apt-get install python-matplotlib
+    Debian / Ubuntu : sudo apt-get install python-matplotlib
+    Fedora / Redhat : sudo yum install python-matplotlib
 
 If you encounter any difficulties you can find a more detailed description at:
 
@@ -54,6 +55,8 @@ You can get `wxpython` with the following command:
 This command might not work if your OS has an earlier version in the standard software repository. If so, please follow the instructions at:
 
     http://wiki.wxpython.org/InstallingOnUbuntuOrDebian
+
+Currently, Optimizer works properly only with version 2.8 of wxpython. Some distributions (e.g., Ubuntu 16.04) may install version 3.0 instead (or in addition to) 2.8. In this case, please remove version 3.0 and make sure to install only version 2.8. Support for later versions of wxpython will be added to Optimizer in the future.
 
 You can get `pyelectro` from:
 
@@ -65,7 +68,7 @@ After cloning the repository you can install it by the standard installation met
     python setup.py install
 
 Installing Neuron as a python package is optional since Optimizer can use any executable to run the simulations.
-WARNING: Optimizer was built around Neuron so we reccomend to install it!
+WARNING: Many features of Optimizer are designed to work with Neuron, so we recommend that you install it!
 Installing Neuron as a python package is beyond the scope of this tutorial as it is somewhat complicated, but you can find a step-by-step guide at:
 
     http://www.davison.webfactional.com/notes/accessing-hoc-python/
@@ -82,7 +85,7 @@ Use the standard install method for Python packages:
 Run optimizer
 -------------------
 
-You can run optimizer directly from its installation folder with:
+You can run Optimizer (with a GUI) directly from its installation folder with:
 
     python optimizer.py -g
 
@@ -94,7 +97,7 @@ Or for the command line version (you must specify a configuration file as well):
 Build documentation
 -------------------
 
-To build a local copy of documentation you need a working install of
+If you should require a local copy of the Optimizer documentation, you need a working install of
 Sphinx, then run the command:
 
 
@@ -138,6 +141,16 @@ The package was tested on the following systems:
       - pyelectro
       - neuron 7.2
 
+    4. Ubuntu 14.04.4 LTS 
+      - Python 2.7.6
+      - numpy 1.8.2
+      - scipy 0.13.3
+      - matplotlib 1.3.1
+      - wxPython 2.8.12.1
+      - inspyred 1.0
+      - pyelectro 0.1.6
+      - neuron 7.4
+
 Notes
     - Since Neuron with the python interpreter is not working perfectly on Windows, we recommend to use Ubuntu (installing and setting up a virtual os is not hard).
     - inspyred requires a feature which is only included in python 2.7, but ther is a workaround for this problem: https://groups.google.com/forum/#!topic/inspyred/YwJb3ABVtL8
@@ -154,6 +167,9 @@ Lead Developer:
 
     - Peter Friedrich:
         p.friedrich.m@gmail.com
+
+    - Sára Sáray
+	saraysari@gmail.com
 
 Contributors:
 

doc/tutorial.rst

@@ -128,12 +128,13 @@ D     Delay of stimulus onset.
 E     Duration of stimulus.
 F     Section which receives stimulus.
 G     Point of stimulation inside the section.
-H     Initial membrane potential.
-I     Length of the recording.
-J     Integration step size.
-K     The parameter to be recorded.
-L     The section where the recordings takes place.
-M     Position inside the recording section.
+H     The parameter to be recorded.
+I     The section where the recordings takes place.
+J     Position inside the recording section.
+K     Initial membrane potential.
+L     Length of the recording.
+M     Integration step size.
+
 =     ======================================
 
 Layer 4
@@ -208,11 +209,7 @@ C     Fitness components: name of fitness function; fitness value;calculated by
 D     Displays the “state” of the population during the
       evolution. (only for inspyred algorithms)
 
-E     Displays the alleles (only for inspyred
-      algorithms ), only useful for single parameter
-      tasks.
-
-F     Displays the given proximity of the optimum.
+E     Displays the given proximity of the optimum.
 =     =============================================
 
 Other windows and layers
@@ -244,5 +241,6 @@ C     Specify the amplitude of the stimuli.
 A     The list of selected parameters.
 B     Lower bounds.
 C     Upper bounds.
-D     Boundaries are set, continue.
+D     Load boundaries from file.
+E     Boundaries are set, continue.
 =     ===============================================

html/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: ada5c503f92081fdc855486ed8cbeffa
+tags: 645f666f9bcd5a90fca523b33c5a78b7

html/_sources/index.txt

@@ -13,9 +13,9 @@ conductance based neuron models.
    :maxdepth: 2
 
    install
+   tutorial
    optimizer
 
-
 Indices and tables
 ==================
 

html/_sources/install.txt

@@ -1,49 +1,176 @@
+
 Installation
 ============
 
-A working version is installable via pip:
-----------------------------------------
+Get a read only copy of optimizer
+----------------------------------
 
-::
+Install `git` and type:
 
-    pip install optimizer
 
-This is always the latest (stable) branch corresponding to the master
-branch on github.
+    git clone https://github.com/vellamike/optimizer.git
 
+More information on this here: http://rogerdudler.github.com/git-guide/
+
+
+Dependencies
+-------------
+
+The following python libraries are required:
+  - python
+  - numpy 
+  - scipy 
+  - matplotlib 
+  - wxPython 
+  - inspyred 
+  - pyelectro
+
+The following libraries are recommended:
+  - neuron
+
+You can get `numpy`, `scipy` and `inspyred` with `easy_install` or `pip` with the following command (for numpy):
+
+
+    pip install numpy
+
+or
+
+    easy_install install numpy
+
+You can get `matplotlib` with the following command:
 
-Get a read only copy of libNeuroML
-----------------------------------
 
-Install `git`_ and type:
+    Debian / Ubuntu : sudo apt-get install python-matplotlib
+    Fedora / Redhat : sudo yum install python-matplotlib
 
-::
+If you encounter any difficulties you can find a more detailed description at:
+
+    http://matplotlib.org/users/installing.html
 
-    git clone git://github.com/vellamike/optimizer.git
+You can get `wxpython` with the following command:
 
-More information on this here:
-.. _Git: http://rogerdudler.github.com/git-guide/
 
+    apt-get install python-wxgtk2.8 python-wxtools wx2.8-i18n
+
+This command might not work if your OS has an earlier version in the standard software repository. If so, please follow the instructions at:
+
+    http://wiki.wxpython.org/InstallingOnUbuntuOrDebian
+
+Currently, Optimizer works properly only with version 2.8 of wxpython. Some distributions (e.g., Ubuntu 16.04) may install version 3.0 instead (or in addition to) 2.8. In this case, please remove version 3.0 and make sure to install only version 2.8. Support for later versions of wxpython will be added to Optimizer in the future.
+
+You can get `pyelectro` from:
+
+    https://github.com/vellamike/pyelectro.git
+
+After cloning the repository you can install it by the standard installation method:
+
+
+    python setup.py install
+
+Installing Neuron as a python package is optional since Optimizer can use any executable to run the simulations.
+WARNING: Many features of Optimizer are designed to work with Neuron, so we recommend that you install it!
+Installing Neuron as a python package is beyond the scope of this tutorial as it is somewhat complicated, but you can find a step-by-step guide at:
+
+    http://www.davison.webfactional.com/notes/accessing-hoc-python/
 
 Install optimizer
 ------------------
 
 Use the standard install method for Python packages:
 
 
-::
-
     sudo python setup.py install
 
+
+Run optimizer
+-------------------
+
+You can run Optimizer (with a GUI) directly from its installation folder with:
+
+    python optimizer.py -g
+
+Or for the command line version (you must specify a configuration file as well):
+
+    python optimizer.py -c example.xml
+
+
 Build documentation
 -------------------
 
-To build a local copy of documentation you need a working install of
+If you should require a local copy of the Optimizer documentation, you need a working install of
 Sphinx, then run the command:
 
-::
 
     sphinx-build ./doc <local build directory>
 
 from the top-level optimizer directory where <local build directory>
 should be replaced with a custom filepath.
+
+Test Platforms
+--------------
+
+The package was tested on the following systems:
+
+    1. Mandriva 2010.2 (kernel 2.6.33, glibc 2.11)
+      - python 2.6.5
+      - numpy 1.6.2
+      - scipy 0.7.2
+      - matplotlib 1.1.1
+      - wxPython 2.8.10.1
+      - inspyred 1.0
+      - pyelectro
+      - neuron 7.3
+
+    2. CentOS 6.4 (kernel 2.6.32, glibc 2.12)
+      - python 2.6.6
+      - numpy 1.6.1
+      - scipy 0.10.1
+      - matplotlib 1.3.1
+      - wxPython 2.8.12.0
+      - inspyred 1.0
+      - pyelectro
+      - neuron 7.2
+
+    3. Ubuntu 12.04.3 LTS (kernel 3.2.0-54-generic, glibc 2.15)
+      - Python 2.7.3
+      - numpy 1.7.0
+      - scipy 0.11.0
+      - matplotlib 1.1.1rc
+      - wxPython 2.8.12.1
+      - inspyred 1.0
+      - pyelectro
+      - neuron 7.2
+
+    4. Ubuntu 14.04.4 LTS 
+      - Python 2.7.6
+      - numpy 1.8.2
+      - scipy 0.13.3
+      - matplotlib 1.3.1
+      - wxPython 2.8.12.1
+      - inspyred 1.0
+      - pyelectro 0.1.6
+      - neuron 7.4
+
+Notes
+    - Since Neuron with the python interpreter is not working perfectly on Windows, we recommend to use Ubuntu (installing and setting up a virtual os is not hard).
+    - inspyred requires a feature which is only included in python 2.7, but ther is a workaround for this problem: https://groups.google.com/forum/#!topic/inspyred/YwJb3ABVtL8
+
+Developers
+----------
+
+Project Leader:
+
+    - Szabolcs Káli:
+        kali@koki.hu
+
+Lead Developer:
+
+    - Peter Friedrich:
+        p.friedrich.m@gmail.com
+
+    - Sára Sáray
+	saraysari@gmail.com
+
+Contributors:
+
+    - Mike Vella