Merge branch 'master' into kMaster

.gitignore

@@ -1,6 +1,3 @@
 *.asv
-+neurostim/cic-MU00043185.m
-+neurostim/plugin-MU00043185.m
 *.m~
-
 *.mat

CONTRIBUTING.md

@@ -0,0 +1,33 @@
+# Contributing to Neurostim
+We love your input! We want to make contributing to this project as easy and transparent as possible, whether it's:
+
+* Reporting a bug
+* Submitting a fix
+* Proposing new features
+
+## We Develop with Github
+We use github to host code, to track issues and feature requests, as well as to review and accept pull requests.
+
+## We Use Github Flow, So All Code Changes Happen Through Pull Requests
+Pull requests are the best way to propose changes to the codebase (we use Github Flow). We actively welcome your pull requests:
+
+* Fork the repo and create your branch from master.
+* Add your code, add tests of your code.
+* Document your code.
+* Add a demo to illustrate the use of your code.
+* Issue that pull request!
+
+When you submit code changes, your submissions are understood to be under the same license that covers the project.
+
+## Report bugs using Github's issues
+We use GitHub issues to track public bugs. Report a bug by opening a new issue; it's that easy!
+
+## Write bug reports with detail, background, and sample code
+Great Bug Reports tend to have:
+
+* A quick summary and/or background
+* Specific steps to reproduce
+* Give sample code if you can.
+* What you expected would happen
+* What actually happens
+* Notes (possibly including why you think this might be happening, or stuff you tried that didn't work)

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 KLab GitHub
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,25 +1,8 @@
-# neurostim-ptb
-Psychophysics Toolbox Variant of Neurostim
-
-The goal of this Matlab project is to wrap code around the basic graphics functionality of the PTB to make 
+# Neurostim
+This project wraps object oriented Matlab code around the basic graphics functionality of the [Psychophysics Toolbox](http://psychtoolbox.org/) to make 
 experiments more reusable and reproducable. 
 
-
-There is no user guide, but there are demos that show how to setup experiments
-and how to achieve certain goals:
-
-Simple experimental design :
-behaviorDemo
-
-Using staircases, quest, or jittered parameters:
-adaptiveDemo
-
-Using calibrated CIE color
-xylDemo
+Documentation is available at [http://klabhub.github.io/neurostim/](http://klabhub.github.io/neurostim/)
 
 
-Using calibrated luminance 
-lumDemo
 
-Using high resolution devices (Bits++, ViewPixx)
-vpxDemo

demos/tae.m → demos/taeDemo.m

@@ -2,8 +2,9 @@
 %% 
 % Tilt AfterEffect Example
 % 
-% Data recorded with this experiment can be analyzed with the anaTae
-% script.
+% Data recorded with this experiment are analyzed with some simple analysis
+% code at the end of this script.
+% 
 %  The experiment starts once the subject fixates the red dot (use the
 %  mouse), and the task is to determine whether the second grating
 %  presented in a trial is clockwise (press 'l') or counterclockwise (press

docs/_config.yml

@@ -0,0 +1,3 @@
+theme: jekyll-theme-slate
+title: Neurostim
+show_downloads: true

doc/helptoc.xml → docs/helptoc.xml

@@ -3,7 +3,7 @@
 <toc version="2.0">
 <!-- First tocitem specifies top level in Help browser Contents pane -->
 <!-- This can be a roadmap page, as shown below, or a content page -->
-    <tocitem target="neurostim.html">Neurostim Toolbox
+    <tocitem >Neurostim Toolbox
         <!-- Nest tocitems to create hierarchical entries in  Contents-->
         <!-- To include icons, use the following syntax for tocitems: -->
         <!-- <tocitem target="foo.html" image="HelpIcon.NAME"> -->
@@ -17,18 +17,17 @@
         <tocitem target="GettingStarted.html" image="HelpIcon.GETTING_STARTED">
             Getting Started with the Neurostim Toolbox            
         </tocitem>
-        <!-- User Guide comes next -->
-        <tocitem target="nsGui.html" image="HelpIcon.USER_GUIDE">Using the GUI            
+
+
+        <tocitem target="nsGuiTutorial.html" image="HelpIcon.USER_GUIDE">Using the GUI            
         </tocitem>
-        <!-- Function reference next -->
-        <!-- First item is page describing function categories, if any -->
-        <!-- Optional List of Examples, with hyperlinks to examples in other files -->
-        <tocitem target="demos.html" 
-                 image="HelpIcon.HelpIcon.EXAMPLES">Neurostim Demos
-        </tocitem>
-        <!-- Optional link or links to your or other Web sites -->
-        <tocitem target="https://github.com/klabhub/neurostim-ptb">
+
+
+        <tocitem target="https://github.com/klabhub/neurostim">
         Neurostim on Github 
         </tocitem>
+        <tocitem target="http://klabhub.github.io/neurostim/">
+        Github Pages
+        </tocitem>
     </tocitem>
 </toc>

docs/index.md

@@ -0,0 +1,14 @@
+# What is Neurostim? 
+Neurostim is software to create experiments in (visual) neuroscience. It allows users to design and/or implement visual stimuli, feedback conditions, eye tracking systems and more.  The software harnesses the functions available in Psychtoolbox and packages them into reusable, modular classes. In this way, new experiments can be quickly assembled by instantiating pre-existing classes from the Neurostim library. 
+
+# Why should I use Neurostim? 
+Rather than create independent scripts for every new experiment – a time consuming process – Neurostim enables users to build their experiments from pre-existing, re-usable and tested components. This accelerates the software development phase and allows users to focus on what matters most, the actual experimentation.  
+
+
+# Getting Started
+The docs/ folder contains Matlab mlx files with instructions on how to get started, you can view their content here, or open the file inside Matlab to see "live" results.
+
+* [GettingStarted.mlx](GettingStarted.html)
+* [Using the Graphical User Interface: nsGuiTutorial.mlx](nsGuiTutorial.html)
+
+

info.xml

@@ -16,7 +16,7 @@
     <!-- but required to parse the file -->
     <icon></icon>
     <!-- (Required if you supply help) Relative path to help (HTML) folder -->
-    <help_location>doc</help_location>
+    <help_location>docs</help_location>
     <!-- (Required if you supply help) Icon used in the Help browser TOC -->
     <!-- Ignored in R2015a and later -->
     <help_contents_icon></help_contents_icon>