update doc 1

Author: Remi-Gau

.gitignore

@@ -3,6 +3,8 @@
 *.m~
 *octave-workspace
 
+.vscode/*
+
 # exclude content of logfiles folders
 *.tsv
 *.mat

.readthedocs.yml

@@ -23,4 +23,4 @@ formats:
 python:
   version: 3.7
   install:
-    - requirements: docs/requirements.txt
+    - requirements: requirements.txt

README.md

@@ -30,15 +30,8 @@
 <!-- TOC -->
 
 -   [CPP_PTB](#cpp_ptb)
-    -   [Requirements](#requirements)
     -   [Documentation](#documentation)
     -   [Content](#content)
-    -   [How to install](#how-to-install)
-        -   [Download with git](#download-with-git)
-        -   [Add as a submodule](#add-as-a-submodule)
-            -   [Example for submodule usage](#example-for-submodule-usage)
-        -   [Direct download](#direct-download)
-        -   [Add CPP_PTB globally to the matlab path](#add-cpp_ptb-globally-to-the-matlab-path)
     -   [Code style guide](#code-style-guide)
     -   [Unit tests](#unit-tests)
     -   [Contributors ✨](#contributors-)
@@ -53,30 +46,10 @@ toolbox.
 Those functions are mostly wrappers around some PTB functions to facilitate
 their use and their reuse (#DontRepeatYourself)
 
-## Requirements
-
-Make sure that the following toolboxes are installed and added to the matlab /
-octave path.
-
-For instructions see the following links:
-
-<!-- lint disable -->
-
-| Requirements                                             | Used version |
-| -------------------------------------------------------- | ------------ |
-| [PsychToolBox](http://psychtoolbox.org/)                 | >=3.0.14     |
-| [Matlab](https://www.mathworks.com/products/matlab.html) | >=2015b      |
-| or [Octave](https://www.gnu.org/software/octave/)        | 4.?          |
-
-<!-- lint enable -->
-
-Tested:
-
--   matlab 2015b or octave 4.2.2 and PTB 3.0.14.
-
 ## Documentation
 
-All the documentation is accessible [here](./docs/00-index.md).
+All the documentation and installtion information is accessible
+[here](https://cpp-ptb.readthedocs.io/en/stable/index.html#).
 
 ## Content
 
@@ -95,111 +68,6 @@ All the documentation is accessible [here](./docs/00-index.md).
 └── tests # all the tests that that can be run by github actions
 ```
 
-## How to install
-
-The easiest way to use this repository is to create a new repository by using
-the
-[template PTB experiment repository](https://github.com/cpp-lln-lab/template_PTB_experiment):
-this creates a new repository on your github account with all the basic folders,
-files and submodules already set up. You only have to then clone the repository
-and you are good to go.
-
-### Download with git
-
-```bash
-cd fullpath_to_directory_where_to_install
-# use git to download the code
-git clone https://github.com/cpp-lln-lab/CPP_PTB.git
-# move into the folder you have just created
-cd CPP_PTB
-```
-
-Then get the latest commit to stay up to date:
-
-```bash
-# from the directory where you downloaded the code
-git pull origin master
-```
-
-To work with a specific version, create a branch at a specific version tag
-number
-
-```bash
-# creating and checking out a branch that will be called version1 at the version tag v1.0.0
-git checkout -b version1 v1.0.0
-```
-
-### Add as a submodule
-
-Add it as a submodule in the repo you are working on.
-
-```bash
-cd fullpath_to_directory_where_to_install
-# use git to download the code
-git submodule add https://github.com/cpp-lln-lab/CPP_PTB.git
-```
-
-To get the latest commit you then need to update the submodule with the
-information on its remote repository and then merge those locally.
-
-```bash
-git submodule update --remote --merge
-```
-
-Remember that updates to submodules need to be committed as well.
-
-#### Example for submodule usage
-
-So say you want to clone a repo that has some nested submodules, then you would
-type this to get the content of all the submodules at once (here with my
-experiment repo):
-
-```bash
-git clone --recurse-submodules https://github.com/user_name/yourExperiment.git
-```
-
-This would be the way to do it "by hand"
-
-```bash
-# clone the repo
-git clone https://github.com/user_name/yourExperiment.git
-
-# go into the directory
-cd yourExperiment
-
-# initialize and get the content of the first level of submodules  (CPP_PTB and CPP_BIDS)
-git submodule init
-git submodule update
-
-# get the nested submodules JSONio and BIDS-matlab for CPP_BIDS
-git submodule foreach --recursive 'git submodule init'
-git submodule foreach --recursive 'git submodule update'
-```
-
-### Direct download
-
-Download the code. Unzip. And add to the matlab path.
-
-Pick a specific version from
-[here](https://github.com/cpp-lln-lab/CPP_PTB/releases).
-
-Or take
-[the latest commit](https://github.com/cpp-lln-lab/CPP_PTB/archive/master.zip) -
-NOT RECOMMENDED.
-
-### Add CPP_PTB globally to the matlab path
-
-This is NOT RECOMMENDED as this might create conflicts if you use different
-versions of CPP_PTB as sub-modules.
-
-Also note that this might not work at all if you have not set a command line
-alias to start Matlab from a terminal window by just typing `matlab`. :wink:
-
-```bash
-# from within the CPP_PTB folder
-matlab -nojvm -nosplash -r "addpath(genpath(fullfile(pwd, 'src'))); savepath(); path(); exit();"
-```
-
 ## Code style guide
 
 We use the `camelCase` to more easily differentiates our functions from the ones

docs/00-index.md

@@ -110,23 +110,15 @@ cfg.audio.initVolume = 1;
 cfg.audio.repeat = 1;
 cfg.audio.startCue = 0;
 cfg.audio.waitForDevice = 1;
+# Main changes
 
-%% -------------------------------------------------------------------------- %%
-% eyetracker
-cfg.eyeTracker.do = false; % set to true if you are using an eyelink eyetracker
-cfg.eyeTracker.defaultCalibration = true;
-cfg.eyeTracker.backgroundColor = [192 192 192];
-cfg.eyeTracker.fontColor = [0 0 0];
-cfg.eyeTracker.calibrationTargetColor = [0 0 0];
-cfg.eyeTracker.calibrationTargetSize = 1;
-cfg.eyeTracker.calibrationTargetWidth = 0.5;
-cfg.eyeTracker.displayCalResults = 1;
+- update documentation using sphinx and RTD
+- change the API for creating and events.tsv and stim.tsv
+- update jupyter notebooks
 
-%% -------------------------------------------------------------------------- %%
-% cfg.mri
-cfg.bids.mri.repetitionTime
+# Minor changes
 
-%% -------------------------------------------------------------------------- %%
+- refactor and add tests-------------- %%
 								SET BY initPTB
 %% -------------------------------------------------------------------------- %%
 
@@ -200,9 +192,6 @@ The main functions of the toolbox are described
 
 ## Annexes
 
-### Experiment template  {WIP}
-
-Will be moved to a different repository
 
 ### devSandbox (stand-alone)
 

docs/10-functions-description.md

@@ -49,6 +49,7 @@ any other functions of CPP_PTB.
 -   set some defaults
 
 -   set the screen details
+
     -   the window opened takes the whole screen by default
     -   set in debug mode with window transparency if necessary
     -   can skip synch test if you ask for it (nicely)

docs/source/function_description.rst

@@ -15,7 +15,6 @@ List of functions in the ``src`` folder.
 .. autofunction:: getExperimentEnd
 .. autofunction:: getExperimentStart
 .. autofunction:: isOctave
-.. autofunction:: readAndFilterLogfile
 .. autofunction:: waitForTrigger
 .. autofunction:: waitFor
 

docs/source/installation.rst

@@ -41,8 +41,10 @@ Download with git
    :linenos:
 
     cd fullpath_to_directory_where_to_install
+
     # use git to download the code
     git clone https://github.com/cpp-lln-lab/CPP_PTB.git
+
     # move into the folder you have just created
     cd CPP_PTB
 
@@ -74,6 +76,7 @@ Add it as a submodule in the repo you are working on.
    :linenos:
 
    cd fullpath_to_directory_where_to_install
+   
    # use git to download the code
    git submodule add https://github.com/cpp-lln-lab/CPP_PTB.git
 

src/drawFieldOfVIew.m

@@ -1,13 +1,24 @@
 % (C) Copyright 2020 CPP_PTB developers
 
 function fov = drawFieldOfVIew(cfg, centerOnScreen)
-    % drawFieldOfVIew(cfg)
-    %
-    % draws a red rectangle on the screen to materialize the field of view of
+    % 
+    % Draws a red rectangle on the screen to materialize the field of view of
     % the participant. This can be used during debugging to help design the
     % stimuli if you know the FOV of the participant will be obstructed by
     % something
-
+    %
+    % USAGE::
+    %
+    %   fov = drawFieldOfVIew(cfg, centerOnScreen)
+    %
+    % :param cfg: 
+    % :type cfg: structure
+    % :param centerOnScreen: 
+    % :type centerOnScreen: boolean
+    %
+    % :returns: - :fov: (array) PTB rectangle
+    %
+    
     if nargin < 2
         centerOnScreen = true;
     end

src/templates/templateFunctionNumpy.m

@@ -1,7 +1,13 @@
 % (C) Copyright 2020 CPP_PTB developers
 
 function checkPtbVersion()
+    %
     % Checks that the right dependencies are installed.
+    %
+    % USAGE::
+    %
+    %   checkPtbVersion()
+    %
 
     printCreditsCppPtb();