From eda0ab825e14c8679779aa00153305b4cab08d26 Mon Sep 17 00:00:00 2001
From: marcobarilari <marcobarilr@gmail.com>
Date: Sat, 31 Oct 2020 21:17:00 +0100
Subject: [PATCH 01/15] update function description for eyetarcker

---
 src/eyeTracker.m | 42 +++++++++++++++++++++++++-----------------
 1 file changed, 25 insertions(+), 17 deletions(-)

diff --git a/src/eyeTracker.m b/src/eyeTracker.m
index 7378bd3a..2705d658 100755
--- a/src/eyeTracker.m
+++ b/src/eyeTracker.m
@@ -1,29 +1,37 @@
 % (C) Copyright 2020 CPP_PTB developers
 
 function [el, cfg] = eyeTracker(input, cfg, varargin)
-    % [el] = eyeTracker(input, cfg, varargin)
     %
     % Wrapper function that deals with all the necessery actions to implement
-    %  Eye Tracker recording with eyelink.
+    % Eye Tracker recording with eyelink.
     %
-    % INPUT
+    % USAGE:
     %
-    % - action: Defines what we want the function to do
-    %  - Calibration: to initialize EyeLink and run calibration
-    %    -- 'default calibration' (default) will run a calibration with 6 points
-    %    -- 'custom calibration'  (cfg.eyeTracker.defaultCalibration = 'false') will run a
-    %        calibration with 6 points but the experimenter can choose their position on the screen
-    %  - StartRecording: to start eye movements recording
-    %  - Message: will add a tag (e.g. 'Block_n1') in the ET output file, the tag is a string and it
-    %        is input from `varargin`
-    %  - StopRecordings: to stop eye movements recornding
-    %  - Shutdown: to save the `.edf` file with BIDS compliant name, from cpp-lln-lab/CPP_BIDS, in
-    %    the output folder and shut the connection between the stimulation computer and the EyeLink
-    %    computer
+    %   function [el, cfg] = eyeTracker(input, cfg, [message])
     %
-    %  OUTPUT
+    % :param input: action: Defines what we want the function to do:
+    %               - Calibration: to initialize EyeLink and run calibration
+    %                 - 'default calibration' (default) will run a calibration with 6 points
+    %                 - 'custom calibration'  (cfg.eyeTracker.defaultCalibration = 'false') will run
+    %                   a calibration with 6 points but the experimenter can choose their position
+    %                   on the screen
     %
-    % `el` is a structure where are stored EyeLink setup variables
+    %               - StartRecording: to start eye movements recording
+    %               - Message: will add a tag (e.g. 'Block_n1') in the ET output file, the tag is a
+    %                 string and it is input from `varargin`
+    %               - StopRecordings: to stop eye movements recornding
+    %               - Shutdown: to save the `.edf` file with BIDS compliant name, from
+    %                 cpp-lln-lab/CPP_BIDS, in the output folder and shut the connection between the
+    %                 stimulation computer and the EyeLink computer
+    % :type input: string
+    % :param cfg: structure that stores any info regarding the experiment
+    % :type cfg: struct
+    % :param message: optional argument to pass in when you want to tag the output in a specific
+    %                 moment of the experiment (for example ``Experiment-start``)
+    % :type message: string
+    %
+    % :returns: - :el: (struct) stores info related to the Eye Tracker
+    %           - :cfg: (struct)
 
     if ~cfg.eyeTracker.do
 

From e891e46bc59738cbceaf02aa0d68ea9be50ce5f7 Mon Sep 17 00:00:00 2001
From: marcobarilari <marcobarilr@gmail.com>
Date: Sat, 31 Oct 2020 21:34:22 +0100
Subject: [PATCH 02/15] update function details

---
 src/eyeTracker.m | 62 ++++++++++++++++++++++++------------------------
 1 file changed, 31 insertions(+), 31 deletions(-)

diff --git a/src/eyeTracker.m b/src/eyeTracker.m
index 2705d658..62a6771b 100755
--- a/src/eyeTracker.m
+++ b/src/eyeTracker.m
@@ -1,37 +1,37 @@
 % (C) Copyright 2020 CPP_PTB developers
 
 function [el, cfg] = eyeTracker(input, cfg, varargin)
-    %
-    % Wrapper function that deals with all the necessery actions to implement
-    % Eye Tracker recording with eyelink.
-    %
-    % USAGE:
-    %
-    %   function [el, cfg] = eyeTracker(input, cfg, [message])
-    %
-    % :param input: action: Defines what we want the function to do:
-    %               - Calibration: to initialize EyeLink and run calibration
-    %                 - 'default calibration' (default) will run a calibration with 6 points
-    %                 - 'custom calibration'  (cfg.eyeTracker.defaultCalibration = 'false') will run
-    %                   a calibration with 6 points but the experimenter can choose their position
-    %                   on the screen
-    %
-    %               - StartRecording: to start eye movements recording
-    %               - Message: will add a tag (e.g. 'Block_n1') in the ET output file, the tag is a
-    %                 string and it is input from `varargin`
-    %               - StopRecordings: to stop eye movements recornding
-    %               - Shutdown: to save the `.edf` file with BIDS compliant name, from
-    %                 cpp-lln-lab/CPP_BIDS, in the output folder and shut the connection between the
-    %                 stimulation computer and the EyeLink computer
-    % :type input: string
-    % :param cfg: structure that stores any info regarding the experiment
-    % :type cfg: struct
-    % :param message: optional argument to pass in when you want to tag the output in a specific
-    %                 moment of the experiment (for example ``Experiment-start``)
-    % :type message: string
-    %
-    % :returns: - :el: (struct) stores info related to the Eye Tracker
-    %           - :cfg: (struct)
+  %
+  % Wrapper function that deals with all the necessery actions to implement
+  % Eye Tracker recording with eyelink.
+  %
+  % USAGE:
+  %
+  %   function [el, cfg] = eyeTracker(input, cfg, [message])
+  %
+  % :param input: Defines what we want the function to do
+  % :type input: string
+  % :param cfg: structure that stores any info regarding the experiment
+  % :type cfg: struct
+  % :param message: optional argument to pass in when you want to tag the output in a specific
+  %                 moment of the experiment (for example ``Experiment-start``)
+  % :type message: string
+  %
+  % :returns: - :el: (struct) stores info related to the Eye Tracker
+  %           - :cfg: (struct)
+  %
+  % - ``Calibration`` to initialize EyeLink and run calibration
+  % - ``default calibration`` (default) will run a calibration with 6 points
+  % - ``custom calibration`` (``cfg.eyeTracker.defaultCalibration = 'false'``) will run
+  %   a calibration with 6 points but the experimenter can choose their position
+  %   on the screen
+  % - ``StartRecording``: to start eye movements recording
+  % - ``Message``: will add a tag (e.g. ``Block_n1``) in the ET output file, the tag is a
+  %   string and it is input from `varargin`
+  % - ``StopRecordings``: to stop eye movements recording
+  % - ``Shutdown``: to save the ``.edf`` file with BIDS compliant name, from
+  %   cpp-lln-lab/CPP_BIDS, in the output folder and shut the connection between the
+  %   stimulation computer and the EyeLink computer
 
     if ~cfg.eyeTracker.do
 

From 2504eaef65dee5e762da32563b1e124742779cef Mon Sep 17 00:00:00 2001
From: marcobarilari <marcobarilr@gmail.com>
Date: Sat, 31 Oct 2020 21:46:15 +0100
Subject: [PATCH 03/15] fix ci

---
 src/eyeTracker.m | 62 ++++++++++++++++++++++++------------------------
 1 file changed, 31 insertions(+), 31 deletions(-)

diff --git a/src/eyeTracker.m b/src/eyeTracker.m
index 62a6771b..3e27016e 100755
--- a/src/eyeTracker.m
+++ b/src/eyeTracker.m
@@ -1,37 +1,37 @@
 % (C) Copyright 2020 CPP_PTB developers
 
 function [el, cfg] = eyeTracker(input, cfg, varargin)
-  %
-  % Wrapper function that deals with all the necessery actions to implement
-  % Eye Tracker recording with eyelink.
-  %
-  % USAGE:
-  %
-  %   function [el, cfg] = eyeTracker(input, cfg, [message])
-  %
-  % :param input: Defines what we want the function to do
-  % :type input: string
-  % :param cfg: structure that stores any info regarding the experiment
-  % :type cfg: struct
-  % :param message: optional argument to pass in when you want to tag the output in a specific
-  %                 moment of the experiment (for example ``Experiment-start``)
-  % :type message: string
-  %
-  % :returns: - :el: (struct) stores info related to the Eye Tracker
-  %           - :cfg: (struct)
-  %
-  % - ``Calibration`` to initialize EyeLink and run calibration
-  % - ``default calibration`` (default) will run a calibration with 6 points
-  % - ``custom calibration`` (``cfg.eyeTracker.defaultCalibration = 'false'``) will run
-  %   a calibration with 6 points but the experimenter can choose their position
-  %   on the screen
-  % - ``StartRecording``: to start eye movements recording
-  % - ``Message``: will add a tag (e.g. ``Block_n1``) in the ET output file, the tag is a
-  %   string and it is input from `varargin`
-  % - ``StopRecordings``: to stop eye movements recording
-  % - ``Shutdown``: to save the ``.edf`` file with BIDS compliant name, from
-  %   cpp-lln-lab/CPP_BIDS, in the output folder and shut the connection between the
-  %   stimulation computer and the EyeLink computer
+    %
+    % Wrapper function that deals with all the necessery actions to implement
+    % Eye Tracker recording with eyelink.
+    %
+    % USAGE:
+    %
+    %   function [el, cfg] = eyeTracker(input, cfg, [message])
+    %
+    % :param input: Defines what we want the function to do
+    % :type input: string
+    % :param cfg: structure that stores any info regarding the experiment
+    % :type cfg: struct
+    % :param message: optional argument to pass in when you want to tag the output in a specific
+    %                 moment of the experiment (for example ``Experiment-start``)
+    % :type message: string
+    %
+    % :returns: - :el: (struct) stores info related to the Eye Tracker
+    %           - :cfg: (struct)
+    %
+    % - ``Calibration`` to initialize EyeLink and run calibration
+    % - ``default calibration`` (default) will run a calibration with 6 points
+    % - ``custom calibration`` (``cfg.eyeTracker.defaultCalibration = 'false'``) will run
+    %   a calibration with 6 points but the experimenter can choose their position
+    %   on the screen
+    % - ``StartRecording``: to start eye movements recording
+    % - ``Message``: will add a tag (e.g. ``Block_n1``) in the ET output file, the tag is a
+    %   string and it is input from `varargin`
+    % - ``StopRecordings``: to stop eye movements recording
+    % - ``Shutdown``: to save the ``.edf`` file with BIDS compliant name, from
+    %   cpp-lln-lab/CPP_BIDS, in the output folder and shut the connection between the
+    %   stimulation computer and the EyeLink computer
 
     if ~cfg.eyeTracker.do
 

From 97ef11efbfd5966a4d3bd0317d82144cf4847ca8 Mon Sep 17 00:00:00 2001
From: marcobarilari <marcobarilr@gmail.com>
Date: Sat, 31 Oct 2020 23:00:33 +0100
Subject: [PATCH 04/15] fix part of sphynx warning in some functions

---
 docs/source/function_description.rst |  3 +-
 src/dot/initDots.m                   |  3 +-
 src/keyboard/checkAbort.m            | 10 +--
 src/keyboard/getResponse.m           | 97 +++++++++++++---------------
 src/readAndFilterLogfile.m           | 31 +++++----
 src/utils/degToPix.m                 | 15 ++---
 src/waitForTrigger.m                 | 31 +++++----
 7 files changed, 91 insertions(+), 99 deletions(-)

diff --git a/docs/source/function_description.rst b/docs/source/function_description.rst
index a1de908f..5a897f5f 100644
--- a/docs/source/function_description.rst
+++ b/docs/source/function_description.rst
@@ -23,12 +23,13 @@ List of functions in the ``src`` folder.
 
 List of functions in the ``src/aperture`` folder.
 
+(to add saveAperture)
+
 .. module:: src.aperture
 
 .. autofunction:: apertureTexture
 .. autofunction:: eccenLogSpeed
 .. autofunction:: getApertureName
-.. autofunction:: saveAperture
 .. autofunction:: saveApertures
 .. autofunction:: smoothOval
 .. autofunction:: smoothRect
diff --git a/src/dot/initDots.m b/src/dot/initDots.m
index 32175b50..65a6c243 100644
--- a/src/dot/initDots.m
+++ b/src/dot/initDots.m
@@ -20,8 +20,7 @@
     % dots.isSignal : signal dots (1) and those are noise dots (0)
     % dots.directionAllDots
     % dots.lifeTime : in frames
-    % dots.speeds : [ndots, 2] ; horizontal and vertical speed ; in pixels per
-    %   frame
+    % dots.speeds : [ndots, 2] ; horizontal and vertical speed ; in pixels per frame
     % dots.speedPixPerFrame
 
     dots.direction = thisEvent.direction(1);
diff --git a/src/keyboard/checkAbort.m b/src/keyboard/checkAbort.m
index ed2e0dfb..c367274d 100644
--- a/src/keyboard/checkAbort.m
+++ b/src/keyboard/checkAbort.m
@@ -1,13 +1,15 @@
 % (C) Copyright 2020 CPP_PTB developers
 
 function checkAbort(cfg, deviceNumber)
-    % checkAbort(cfg, deviceNumber)
     %
-    % Check for experiment abortion from operator
-    % When no deviceNumber is set then it will check the default device
-    % When an abort key s detected this will set a global variable and throw a
+    % Check for experiment abortion from operator. When no deviceNumber is set then it will check
+    % the default device. When an abort key is detected this will set a global variable and throw a
     % specific error that can then be catched.
     %
+    % USAGE:
+    %
+    %   function checkAbort(cfg, deviceNumber)
+    %
     % Maint script
     % try
     %     % Your awesome experiment
diff --git a/src/keyboard/getResponse.m b/src/keyboard/getResponse.m
index 11aee4e1..11ee2f4f 100644
--- a/src/keyboard/getResponse.m
+++ b/src/keyboard/getResponse.m
@@ -1,60 +1,51 @@
 % (C) Copyright 2020 CPP_PTB developers
 
 function responseEvents = getResponse(action, deviceNumber, cfg, getOnlyPress)
-    % responseEvents = getResponse(action, deviceNumber, cfg, getOnlyPress)
     %
-    % Wrapper function to use KbQueue
-    %
-    % The queue will be listening to key presses on a keyboard device:
-    % cfg.keyboard.responseBox or cfg.keyboard.keyboard are 2 main examples.
-    %
-    % When no deviceNumber is set then it will listen to the default device.
-    %
-    % Check the CPP_getResponseDemo for a quick script on how to use it.
-    %
-    %
-    % INPUT
-    %
-    % - action: Defines what we want the function to do
-    %  - init: to initialise the queue
-    %  - start: to start listening to keypresses
-    %  - check: checks all the key presses events since 'start', or since last
-    %    'check' or 'flush' (whichever was the most recent)
-    %    -- can check for demand to abort if the escapeKey is listed in the
-    %       Keys of interest.
-    %    -- can only check for demands to abort when getResponse('check') is called:
-    %       so there will be a delay between the key press and the experiment stopping
-    %    -- abort errors send specific signals that allow the catch to get
-    %       them and allows us to "close" nicely
-    %  - flush: empties the queue of events in case you want to restart from a clean
-    %    queue
-    %  - stop: stops listening to key presses
-    %
-    % - getOnlyPress: if set to true the function will only return the key presses and
-    %    will not return when the keys were released (default=true)
-    %    See the section on OUTPUT below for more info
-    %
-    %
-    %
-    % OUTPUT
-    %
-    % responseEvents: returns all the keypresses and return them as a structure
-    % with field names that make it easier to save the output of in a BIDS
-    % format
-    %
-    % responseEvents.onset : this is an absolute value and you should
-    %   substract the "experiment start time" to get a value relative to when the
-    %   experiment was started.
-    %
-    % responseEvents.trial_type = 'response';
-    %
-    % responseEvents.duration = 0;
-    %
-    % responseEvents.keyName : the name of the key pressed
-    %
-    % responseEvents(iEvent,1).pressed : if
-    %   pressed == 1  --> the key was pressed
-    %   pressed == 0  --> the key was released
+    % Wrapper function to use KbQueue. The queue will be listening to key presses on a keyboard device:
+    % ``cfg.keyboard.responseBox`` or ``cfg.keyboard.keyboard`` are 2 main examples.When no deviceNumber
+    % is set then it will listen to the default device. Check the ``CPP_getResponseDemo`` for a quick
+    % script on how to use it.
+    %
+    % USAGE:
+    %
+    %   responseEvents = getResponse(action, deviceNumber, cfg, getOnlyPress)
+    %
+    % :param action: Defines what we want the function to do
+    % :param deviceNumber: device number of the keyboard or trigger box in MRI
+    % :type deviceNumber: integer
+    % :param cfg:
+    % :param getOnlyPress: if set to true the function will only return the key presses and will not
+    %                      return when the keys were released (default=true). See the section on
+    %                      `Returns` below for more info
+    %
+    % :returns: - :responseEvents: returns all the keypresses and return them as a structure with
+    %                              field names that make it easier to save the output of in a BIDS format
+    %
+    % - ``responseEvents.onset``: this is an absolute value and you should substract the
+    %                              "experiment start time" to get a value relative to when the
+    %                              experiment was started.
+    % - ``responseEvents.trial_type = response``;
+    % - ``responseEvents.duration = 0;``
+    % - ``responseEvents.keyName``: the name of the key pressed
+    % - ``responseEvents(iEvent,1).pressed``: if
+    %  - pressed == 1  --> the key was pressed
+    %  - pressed == 0  --> the key was released
+    %
+    % ``action`` options:
+    %
+    % - ``init``: to initialise the queue
+    % - ``start``: to start listening to keypresses
+    % - ``check``: checks all the key presses events since 'start', or since last 'check' or 'flush'
+    %   (whichever was the most recent)
+    %  - can check for demand to abort if the escapeKey is listed in the Keys of interest
+    %  - can only check for demands to abort when ``getResponse('check')`` is called so there will be
+    %    a delay between the key press and the experiment stopping
+    %  - abort errors send specific signals that allow the catch to get
+    %    them and allows us to "close" nicely
+    % - ``flush``: empties the queue of events in case you want to restart from a clean
+    %   queue
+    % - ``stop``: stops listening to key presses
 
     if nargin < 2 || isempty(deviceNumber)
         deviceNumber = -1;
diff --git a/src/readAndFilterLogfile.m b/src/readAndFilterLogfile.m
index 9049b444..e6b6980b 100644
--- a/src/readAndFilterLogfile.m
+++ b/src/readAndFilterLogfile.m
@@ -1,27 +1,26 @@
 % (C) Copyright 2020 CPP_PTB developers
 
-function outputFiltered = readAndFilterLogfile(columnName, filterBy, varargin)
-    % outputFiltered = readOutputFilter(filterHeader, filterContent, varargin)
+function [outputFiltered] = readAndFilterLogfile(columnName, filterBy, varargin)
     %
     % It will display in the command window the content of the `output.tsv' filtered by one element
-    % of a target column.
+    % of a target column. Dependecies: bids_matlab (from CPP_BIDS)
     %
-    % DEPENDENCIES:
-    %  - bids_matlab (from CPP_BIDS)
+    % USAGE:
     %
-    % INPUT:
+    %   [outputFiltered] = readOutputFilter(filterHeader, filterContent, varargin)
     %
-    %  - columnName: string, the header of the column where the content of insterest is stored
-    %    (e.g., for 'trigger' will be 'trial type')
-    %  - filterBy: string, the content of the column you want to filter out. It can take just
-    %    part of the content name (e.g., you want to display the triggers and you have
-    %    'trigger_motion' and 'trigger_static', 'trigger' as input will do)
-    %  - varargin: either cfg (to display the last run output) or the file path as string
+    % :param columnName: the header of the column where the content of insterest is stored
+    %                    (e.g., for 'trigger' will be 'trial type')
+    % :type columnName: string
+    % :param filterBy: the content of the column you want to filter out. It can take just
+    %                   part of the content name (for example, you want to display the triggers and
+    %                   you have ``trigger_motion`` and ``trigger_static``, ``trigger``' as input
+    %                   will do)
+    % :type filterBy: string
+    % :param varargin: either ``cfg`` (to display the last run output) or the file path as string
     %
-    % OUTPUT:
-    %
-    %  - outputFiltered: dataset with only the specified content, to see it in the command window
-    %    use display(outputFiltered)
+    % :returns: - outputFiltered: dataset with only the specified content, to see it in the command
+    %             window use display(outputFiltered)
 
     % Checke if input is cfg or the file path
     if ischar(varargin{1})
diff --git a/src/utils/degToPix.m b/src/utils/degToPix.m
index a2a1c09e..92fdc64d 100644
--- a/src/utils/degToPix.m
+++ b/src/utils/degToPix.m
@@ -1,24 +1,21 @@
 % (C) Copyright 2020 CPP_PTB developers
 
 function structure = degToPix(fieldName, structure, cfg)
-    % structure = degToPix(fieldName, structure, cfg)
+    % For a given field value in degrees of visual angle in the structure, this computes its value
+    % in pixel using the pixel per degree value of the cfg structure and returns a structure with
+    % an additional field with Pix suffix holding that new value.
     %
-    % For a given field value in degrees of visual angle in the structure,
-    % this computes its value in pixel using the pixel per degree value of the cfg structure
-    % and returns a structure with an additional field with Pix suffix holding that new value.
+    % USAGE:
     %
+    %   structure = degToPix(fieldName, structure, cfg)
     %
-    % USAGE:
-    % ------
     % fixation.width = 2;
     % cfg.screen.ppd = 10;
     %
     % fixation = degToPix('width', fixation, cfg);
     %
-    % Returns:
-    % -------
+    % - Returns:
     % fixation.widthPix = 20;
-    %
 
     deg = getfield(structure, fieldName); %#ok<GFLD>
 
diff --git a/src/waitForTrigger.m b/src/waitForTrigger.m
index a8c8bace..147fe895 100644
--- a/src/waitForTrigger.m
+++ b/src/waitForTrigger.m
@@ -1,10 +1,23 @@
 % (C) Copyright 2020 CPP_PTB developers
 
-function lastTriggerTimeStamp = waitForTrigger(varargin)
-    % waitForTrigger(cfg, deviceNumber, quietMode, nbTriggersToWait)
-    %
+function [lastTriggerTimeStamp] = waitForTrigger(varargin)
     % Counts a certain number of triggers coming from the scanner before returning.
     %
+    % USAGE:
+    %
+    %   [lastTriggerTimeStamp] = waitForTrigger([cfg,] [deviceNumber,] [quietMode,] [nbTriggersToWait])
+    %
+    % :param cfg:
+    % :type cfg: struct
+    % :param deviceNumber: device number of the keyboard or trigger box in MRI
+    % :type deviceNumber: integer
+    % :param quietMode: a boolean to make sure nothing is printed on the screen or the prompt
+    % :type quietMode: boolean
+    % :param nbTriggersToWait: number of triggers to wait
+    % :type nbTriggersToWait: integer
+    %
+    % :returns: - :lastTriggerTimeStamp: (optional) it can be used as experimentStart timestamp (``cfg.experimentStart``)
+    %
     % If you are not using the quietMode, it flips and waits for half a TR before starting to
     % check for the next trigger (unless this was the last trigger to wait for and in
     % this case it returns immediately).
@@ -12,23 +25,13 @@
     % Will print the count down in the command line and on the PTB window if one is
     % opened.
     %
-    % If the fMRI sequence RT is provided (cgf.MRI.repetitionTime) then it will wait
+    % If the fMRI sequence RT is provided (``cgf.MRI.repetitionTime``) then it will wait
     % for half a RT before starting to check for next trigger, otherwise it will
     % wait 500 ms.
     %
     % When no deviceNumber is set then it will check the default device: this is
     % probably only useful in debug as you will want to make sure you get the
     % triggers coming from the scanner in a real case scenario.
-    %
-    % INPUTS
-    % - varargin{1} = cfg
-    %
-    % - varargin{2} = deviceNumber
-    %
-    % - varargin{3} = quietMode: a boolean to make sure nothing is printed on the screen or
-    % the prompt
-    %
-    % - nvarargin{4} = nbTriggersToWait
 
     [cfg, nbTriggersToWait, deviceNumber, quietMode] = checkInputs(varargin);
 

From ffd4154425aee3758ec0d258c965f808a81d6518 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 31 Oct 2020 23:35:28 +0100
Subject: [PATCH 05/15] partial fix help section readAndFilter

---
 src/readAndFilterLogfile.m | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/src/readAndFilterLogfile.m b/src/readAndFilterLogfile.m
index e6b6980b..4f647780 100644
--- a/src/readAndFilterLogfile.m
+++ b/src/readAndFilterLogfile.m
@@ -2,8 +2,8 @@
 
 function [outputFiltered] = readAndFilterLogfile(columnName, filterBy, varargin)
     %
-    % It will display in the command window the content of the `output.tsv' filtered by one element
-    % of a target column. Dependecies: bids_matlab (from CPP_BIDS)
+    % It will display in the command window the content of the `output.tsv` filtered 
+    % by one element of a target column. Dependecies: bids_matlab (from CPP_BIDS)
     %
     % USAGE:
     %
@@ -13,14 +13,18 @@
     %                    (e.g., for 'trigger' will be 'trial type')
     % :type columnName: string
     % :param filterBy: the content of the column you want to filter out. It can take just
-    %                   part of the content name (for example, you want to display the triggers and
-    %                   you have ``trigger_motion`` and ``trigger_static``, ``trigger``' as input
-    %                   will do)
+    %                  part of the content name (for example, you want to display the triggers and
+    %                  you have ``trigger_motion`` and ``trigger_static``, ``trigger`` as input
+    %                  will do)
     % :type filterBy: string
-    % :param varargin: either ``cfg`` (to display the last run output) or the file path as string
+    % :param varargin: either ``cfg`` (to display the last run output) or 
+    %                  the file path as string
     %
-    % :returns: - outputFiltered: dataset with only the specified content, to see it in the command
-    %             window use display(outputFiltered)
+    % :returns: - :outputFiltered: dataset with only the specified content
+    %             to see it in the command window use display(outputFiltered)
+    %
+    %
+    
 
     % Checke if input is cfg or the file path
     if ischar(varargin{1})

From 2cd37c24e7a835c5cf34c19d36e7a0521c6879e5 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 31 Oct 2020 23:51:16 +0100
Subject: [PATCH 06/15] fix readAndFilter

---
 src/readAndFilterLogfile.m | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/readAndFilterLogfile.m b/src/readAndFilterLogfile.m
index 4f647780..153d70cd 100644
--- a/src/readAndFilterLogfile.m
+++ b/src/readAndFilterLogfile.m
@@ -17,11 +17,9 @@
     %                  you have ``trigger_motion`` and ``trigger_static``, ``trigger`` as input
     %                  will do)
     % :type filterBy: string
-    % :param varargin: either ``cfg`` (to display the last run output) or 
-    %                  the file path as string
+    % :param varargin: either ``cfg`` (to display the last run output) or the file path as string
     %
-    % :returns: - :outputFiltered: dataset with only the specified content
-    %             to see it in the command window use display(outputFiltered)
+    % :returns: - :outputFiltered: dataset with only the specified content to see it in the command window use display(outputFiltered)
     %
     %
     

From f0f3e1c47550c4d90325dd302881db6f3c24622e Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 31 Oct 2020 23:51:32 +0100
Subject: [PATCH 07/15] fix help section getResponse

---
 src/keyboard/getResponse.m | 50 +++++++++++++++++++++-----------------
 1 file changed, 28 insertions(+), 22 deletions(-)

diff --git a/src/keyboard/getResponse.m b/src/keyboard/getResponse.m
index 11ee2f4f..93805a77 100644
--- a/src/keyboard/getResponse.m
+++ b/src/keyboard/getResponse.m
@@ -3,7 +3,7 @@
 function responseEvents = getResponse(action, deviceNumber, cfg, getOnlyPress)
     %
     % Wrapper function to use KbQueue. The queue will be listening to key presses on a keyboard device:
-    % ``cfg.keyboard.responseBox`` or ``cfg.keyboard.keyboard`` are 2 main examples.When no deviceNumber
+    % ``cfg.keyboard.responseBox`` or ``cfg.keyboard.keyboard`` are 2 main examples. When no deviceNumber
     % is set then it will listen to the default device. Check the ``CPP_getResponseDemo`` for a quick
     % script on how to use it.
     %
@@ -19,33 +19,39 @@
     %                      return when the keys were released (default=true). See the section on
     %                      `Returns` below for more info
     %
-    % :returns: - :responseEvents: returns all the keypresses and return them as a structure with
-    %                              field names that make it easier to save the output of in a BIDS format
+    % :returns: - :responseEvents: returns all the keypresses and return them as a structure with field names that make it easier to save the output of in a BIDS format
+    %
+    % - ``responseEvents.onset`` this is an absolute value and you should substract the "experiment start time" to get a value relative to when the experiment was started.
+    %
+    % - ``responseEvents.trial_type = response``
+    %
+    % - ``responseEvents.duration = 0``
+    %
+    % - ``responseEvents.keyName`` the name of the key pressed
+    %
+    % - ``responseEvents(iEvent,1).pressed`` if
     %
-    % - ``responseEvents.onset``: this is an absolute value and you should substract the
-    %                              "experiment start time" to get a value relative to when the
-    %                              experiment was started.
-    % - ``responseEvents.trial_type = response``;
-    % - ``responseEvents.duration = 0;``
-    % - ``responseEvents.keyName``: the name of the key pressed
-    % - ``responseEvents(iEvent,1).pressed``: if
     %  - pressed == 1  --> the key was pressed
     %  - pressed == 0  --> the key was released
     %
+    % ---
+    %
     % ``action`` options:
     %
-    % - ``init``: to initialise the queue
-    % - ``start``: to start listening to keypresses
-    % - ``check``: checks all the key presses events since 'start', or since last 'check' or 'flush'
-    %   (whichever was the most recent)
-    %  - can check for demand to abort if the escapeKey is listed in the Keys of interest
-    %  - can only check for demands to abort when ``getResponse('check')`` is called so there will be
-    %    a delay between the key press and the experiment stopping
-    %  - abort errors send specific signals that allow the catch to get
-    %    them and allows us to "close" nicely
-    % - ``flush``: empties the queue of events in case you want to restart from a clean
-    %   queue
-    % - ``stop``: stops listening to key presses
+    % - ``init`` to initialise the queue
+    %
+    % - ``start`` to start listening to keypresses
+    %
+    % - ``check`` checks all the key presses events since 'start', or since last 'check' or 'flush' (whichever was the most recent)
+    %
+    %  - can check for demand to abort if the ``escapeKey`` is listed in the Keys of interest
+    %  - can only check for demands to abort when ``getResponse('check')`` is called so there will be a delay between the key press and the experiment stopping
+    %  - abort errors send specific signals that allow the catch to get them and allows us to "close" nicely
+    %
+    % - ``flush`` empties the queue of events in case you want to restart from a clean queue
+    %
+    % - ``stop`` stops listening to key presses
+    %
 
     if nargin < 2 || isempty(deviceNumber)
         deviceNumber = -1;

From 91bdd7142aac0275d08353fe0a839ef16991e62e Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 31 Oct 2020 23:57:53 +0100
Subject: [PATCH 08/15] fix help section pix to deg

---
 src/utils/pixToDeg.m | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/utils/pixToDeg.m b/src/utils/pixToDeg.m
index 728d558d..c5d32dcd 100644
--- a/src/utils/pixToDeg.m
+++ b/src/utils/pixToDeg.m
@@ -10,14 +10,14 @@
     % 'Pix' suffix removed and replaced with the 'DegVA' suffix .
     %
     % USAGE:
-    % ------
+    % 
     % fixation.widthPix = 20;
     % cfg.screen.ppd = 10;
     %
     % fixation = degToPix('widthPix', fixation, cfg);
     %
     % Returns:
-    % -------
+    %  
     % fixation.widthDegVA = 2;
     %
 

From d4adc6b7a562894c1783da98726d5bdfbe523b42 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 31 Oct 2020 23:59:05 +0100
Subject: [PATCH 09/15] fix help section deg to pix

---
 src/utils/degToPix.m | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/utils/degToPix.m b/src/utils/degToPix.m
index 92fdc64d..b694ea48 100644
--- a/src/utils/degToPix.m
+++ b/src/utils/degToPix.m
@@ -15,7 +15,8 @@
     % fixation = degToPix('width', fixation, cfg);
     %
     % - Returns:
-    % fixation.widthPix = 20;
+    %   fixation.widthPix = 20;
+    %
 
     deg = getfield(structure, fieldName); %#ok<GFLD>
 

From e85321f15d4232b73673586de395d5b4bdda70aa Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 1 Nov 2020 00:12:13 +0100
Subject: [PATCH 10/15] fix checkAbort

---
 src/keyboard/checkAbort.m | 34 ++++++++++++++++++++++------------
 1 file changed, 22 insertions(+), 12 deletions(-)

diff --git a/src/keyboard/checkAbort.m b/src/keyboard/checkAbort.m
index c367274d..25836dec 100644
--- a/src/keyboard/checkAbort.m
+++ b/src/keyboard/checkAbort.m
@@ -6,22 +6,32 @@ function checkAbort(cfg, deviceNumber)
     % the default device. When an abort key is detected this will set a global variable and throw a
     % specific error that can then be catched.
     %
-    % USAGE:
+    % USAGE::
     %
-    %   function checkAbort(cfg, deviceNumber)
+    %   checkAbort(cfg, deviceNumber)
     %
-    % Maint script
-    % try
-    %     % Your awesome experiment
-    % catch ME % when something goes wrong
-    %     switch ME.identifier
+    % Examples::
+    %
+    %   try
+    %
+    %   % Your awesome experiment
+    %
+    %   catch ME % when something goes wrong
+    %
+    %       switch ME.identifier
+    %         
     %         case 'checkAbort:abortRequested'
-    %             % stuff to do when an abort is requested (save data...)
+    %         
+    %         % stuff to do when an abort is requested (save data...)
+    %          
     %         otherwise
-    %             % stuff to do otherwise
-    %             rethrow(ME) % display the error
-    %     end
-    % end
+    %
+    %          % stuff to do otherwise
+    %          rethrow(ME) % display the error
+    %
+    %       end
+    %   end
+    %
 
     if nargin < 1 || isempty(cfg)
         error('I need at least one input.');

From 12e8c8a9b2273d44ef17a57e5fd9f3f277bdc0fc Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 1 Nov 2020 00:13:20 +0100
Subject: [PATCH 11/15] mh fix

---
 src/keyboard/checkAbort.m  | 6 +++---
 src/readAndFilterLogfile.m | 3 +--
 src/utils/pixToDeg.m       | 4 ++--
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/src/keyboard/checkAbort.m b/src/keyboard/checkAbort.m
index 25836dec..c1201ae3 100644
--- a/src/keyboard/checkAbort.m
+++ b/src/keyboard/checkAbort.m
@@ -19,11 +19,11 @@ function checkAbort(cfg, deviceNumber)
     %   catch ME % when something goes wrong
     %
     %       switch ME.identifier
-    %         
+    %
     %         case 'checkAbort:abortRequested'
-    %         
+    %
     %         % stuff to do when an abort is requested (save data...)
-    %          
+    %
     %         otherwise
     %
     %          % stuff to do otherwise
diff --git a/src/readAndFilterLogfile.m b/src/readAndFilterLogfile.m
index 153d70cd..338e1fe5 100644
--- a/src/readAndFilterLogfile.m
+++ b/src/readAndFilterLogfile.m
@@ -2,7 +2,7 @@
 
 function [outputFiltered] = readAndFilterLogfile(columnName, filterBy, varargin)
     %
-    % It will display in the command window the content of the `output.tsv` filtered 
+    % It will display in the command window the content of the `output.tsv` filtered
     % by one element of a target column. Dependecies: bids_matlab (from CPP_BIDS)
     %
     % USAGE:
@@ -22,7 +22,6 @@
     % :returns: - :outputFiltered: dataset with only the specified content to see it in the command window use display(outputFiltered)
     %
     %
-    
 
     % Checke if input is cfg or the file path
     if ischar(varargin{1})
diff --git a/src/utils/pixToDeg.m b/src/utils/pixToDeg.m
index c5d32dcd..3eb29d05 100644
--- a/src/utils/pixToDeg.m
+++ b/src/utils/pixToDeg.m
@@ -10,14 +10,14 @@
     % 'Pix' suffix removed and replaced with the 'DegVA' suffix .
     %
     % USAGE:
-    % 
+    %
     % fixation.widthPix = 20;
     % cfg.screen.ppd = 10;
     %
     % fixation = degToPix('widthPix', fixation, cfg);
     %
     % Returns:
-    %  
+    %
     % fixation.widthDegVA = 2;
     %
 

From e9b886b99d2d7bcc9072d43ef296e2127283c9c2 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 1 Nov 2020 00:15:34 +0100
Subject: [PATCH 12/15] add template functions

---
 src/templates/templateFunction.m        | 29 +++++++++++++++++
 src/templates/templateFunctionExample.m | 42 +++++++++++++++++++++++++
 src/templates/templateFunctionNumpy.m   | 21 +++++++++++++
 3 files changed, 92 insertions(+)
 create mode 100644 src/templates/templateFunction.m
 create mode 100644 src/templates/templateFunctionExample.m
 create mode 100644 src/templates/templateFunctionNumpy.m

diff --git a/src/templates/templateFunction.m b/src/templates/templateFunction.m
new file mode 100644
index 00000000..a0437c67
--- /dev/null
+++ b/src/templates/templateFunction.m
@@ -0,0 +1,29 @@
+% (C) Copyright 2020 CPP_PTB developpers
+
+function [argout1, argout2] = templateFunction(argin1, argin2, argin3)
+  %
+  % Short description of what the function does goes here.
+  %
+  % USAGE::
+  %
+  %   [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3])
+  %
+  % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet,
+  %                consectetur adipiscing elit. Ut congue nec est ac lacinia.
+  % :type argin1: type
+  % :param argin2: optional argument and its default value. And some of the
+  %               options can be shown in litteral like ``this`` or ``that``.
+  % :type argin2: string
+  % :param argin3: (dimension) optional argument
+  %
+  % :returns: - :argout1: (type) (dimension)
+  %           - :argout2: (type) (dimension)
+  %
+  % .. todo:
+  %
+  %    - item 1
+  %    - item 2
+
+  % The code goes below
+
+end
diff --git a/src/templates/templateFunctionExample.m b/src/templates/templateFunctionExample.m
new file mode 100644
index 00000000..3c247b2a
--- /dev/null
+++ b/src/templates/templateFunctionExample.m
@@ -0,0 +1,42 @@
+% (C) Copyright 2020 CPP_PTB developpers
+
+function templateFunctionExample()
+  % This function illustrates a documentation test defined for MOdox.
+  % Other than that it does absolutely nothinghort description of what
+  % the function does goes here.
+  %
+  % Examples:
+  %   a=2;
+  %   disp(a)
+  %   % Expected output is prefixed by '%||' as in the following line:
+  %   %|| 2
+  %   %
+  %   % The test continues because no interruption through whitespace,
+  %   % as the previous line used a '%' comment character;
+  %   % thus the 'a' variable is still in the namespace and can be
+  %   % accessed.
+  %   b=3+a;
+  %   disp(a+[3 4])
+  %   %|| [5 6]
+  %
+  %   % A new test starts here because the previous line was white-space
+  %   % only. Thus the 'a' and 'b' variables are not present here anymore.
+  %   % The following expression raises an error because the 'b' variable
+  %   % is not defined (and does not carry over from the previous test).
+  %   % Because the expected output indicates an error as well,
+  %   % the test passes
+  %   disp(b)
+  %   %|| error('Some error')
+  %
+  %   % A set of expressions is ignored if there is no expected output
+  %   % (that is, no lines starting with '%||').
+  %   % Thus, the following expression is not part of any test,
+  %   % and therefore does not raise an error.
+  %   error('this is never executed)
+  %
+  %
+  % % tests end here because test indentation has ended
+
+  % The code goes below
+
+end
diff --git a/src/templates/templateFunctionNumpy.m b/src/templates/templateFunctionNumpy.m
new file mode 100644
index 00000000..4ae9a956
--- /dev/null
+++ b/src/templates/templateFunctionNumpy.m
@@ -0,0 +1,21 @@
+% (C) Copyright 2020 CPP_PTB developpers
+
+function [argout] = templateFunctionNumpy(argin1, argin2, argin3)
+  %
+  % Short description of what the function does goes here.
+  %
+  %  y = templateFunction(argin1, argin2, argin3)
+  %
+  % Parameters:
+  %    argin1: The first input value
+  %
+  %    argin2: The second input value
+  %
+  %    argin3: The third input value
+  %
+  % Returns:
+  %    The input value multiplied by two
+
+  % The code goes below
+
+end

From e75246021068e54b21a720335640a44be5931ffe Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 1 Nov 2020 06:23:56 +0100
Subject: [PATCH 13/15] mh fix

---
 src/readAndFilterLogfile.m              |  5 +-
 src/templates/templateFunction.m        | 48 ++++++++--------
 src/templates/templateFunctionExample.m | 74 ++++++++++++-------------
 src/templates/templateFunctionNumpy.m   | 32 +++++------
 src/waitForTrigger.m                    | 10 +++-
 5 files changed, 89 insertions(+), 80 deletions(-)

diff --git a/src/readAndFilterLogfile.m b/src/readAndFilterLogfile.m
index 338e1fe5..a1735b12 100644
--- a/src/readAndFilterLogfile.m
+++ b/src/readAndFilterLogfile.m
@@ -19,7 +19,10 @@
     % :type filterBy: string
     % :param varargin: either ``cfg`` (to display the last run output) or the file path as string
     %
-    % :returns: - :outputFiltered: dataset with only the specified content to see it in the command window use display(outputFiltered)
+    % :returns: 
+    %
+    % - :outputFiltered: dataset with only the specified content to see it in the 
+    %                    command window use display(outputFiltered)
     %
     %
 
diff --git a/src/templates/templateFunction.m b/src/templates/templateFunction.m
index a0437c67..e71713b0 100644
--- a/src/templates/templateFunction.m
+++ b/src/templates/templateFunction.m
@@ -1,29 +1,29 @@
-% (C) Copyright 2020 CPP_PTB developpers
+% (C) Copyright 2020 CPP_PTB developers
 
 function [argout1, argout2] = templateFunction(argin1, argin2, argin3)
-  %
-  % Short description of what the function does goes here.
-  %
-  % USAGE::
-  %
-  %   [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3])
-  %
-  % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet,
-  %                consectetur adipiscing elit. Ut congue nec est ac lacinia.
-  % :type argin1: type
-  % :param argin2: optional argument and its default value. And some of the
-  %               options can be shown in litteral like ``this`` or ``that``.
-  % :type argin2: string
-  % :param argin3: (dimension) optional argument
-  %
-  % :returns: - :argout1: (type) (dimension)
-  %           - :argout2: (type) (dimension)
-  %
-  % .. todo:
-  %
-  %    - item 1
-  %    - item 2
+    %
+    % Short description of what the function does goes here.
+    %
+    % USAGE::
+    %
+    %   [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3])
+    %
+    % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet,
+    %                consectetur adipiscing elit. Ut congue nec est ac lacinia.
+    % :type argin1: type
+    % :param argin2: optional argument and its default value. And some of the
+    %               options can be shown in litteral like ``this`` or ``that``.
+    % :type argin2: string
+    % :param argin3: (dimension) optional argument
+    %
+    % :returns: - :argout1: (type) (dimension)
+    %           - :argout2: (type) (dimension)
+    %
+    % .. todo:
+    %
+    %    - item 1
+    %    - item 2
 
-  % The code goes below
+    % The code goes below
 
 end
diff --git a/src/templates/templateFunctionExample.m b/src/templates/templateFunctionExample.m
index 3c247b2a..99670d10 100644
--- a/src/templates/templateFunctionExample.m
+++ b/src/templates/templateFunctionExample.m
@@ -1,42 +1,42 @@
-% (C) Copyright 2020 CPP_PTB developpers
+% (C) Copyright 2020 CPP_PTB developers
 
 function templateFunctionExample()
-  % This function illustrates a documentation test defined for MOdox.
-  % Other than that it does absolutely nothinghort description of what
-  % the function does goes here.
-  %
-  % Examples:
-  %   a=2;
-  %   disp(a)
-  %   % Expected output is prefixed by '%||' as in the following line:
-  %   %|| 2
-  %   %
-  %   % The test continues because no interruption through whitespace,
-  %   % as the previous line used a '%' comment character;
-  %   % thus the 'a' variable is still in the namespace and can be
-  %   % accessed.
-  %   b=3+a;
-  %   disp(a+[3 4])
-  %   %|| [5 6]
-  %
-  %   % A new test starts here because the previous line was white-space
-  %   % only. Thus the 'a' and 'b' variables are not present here anymore.
-  %   % The following expression raises an error because the 'b' variable
-  %   % is not defined (and does not carry over from the previous test).
-  %   % Because the expected output indicates an error as well,
-  %   % the test passes
-  %   disp(b)
-  %   %|| error('Some error')
-  %
-  %   % A set of expressions is ignored if there is no expected output
-  %   % (that is, no lines starting with '%||').
-  %   % Thus, the following expression is not part of any test,
-  %   % and therefore does not raise an error.
-  %   error('this is never executed)
-  %
-  %
-  % % tests end here because test indentation has ended
+    % This function illustrates a documentation test defined for MOdox.
+    % Other than that it does absolutely nothinghort description of what
+    % the function does goes here.
+    %
+    % Examples:
+    %   a=2;
+    %   disp(a)
+    %   % Expected output is prefixed by '%||' as in the following line:
+    %   %|| 2
+    %   %
+    %   % The test continues because no interruption through whitespace,
+    %   % as the previous line used a '%' comment character;
+    %   % thus the 'a' variable is still in the namespace and can be
+    %   % accessed.
+    %   b=3+a;
+    %   disp(a+[3 4])
+    %   %|| [5 6]
+    %
+    %   % A new test starts here because the previous line was white-space
+    %   % only. Thus the 'a' and 'b' variables are not present here anymore.
+    %   % The following expression raises an error because the 'b' variable
+    %   % is not defined (and does not carry over from the previous test).
+    %   % Because the expected output indicates an error as well,
+    %   % the test passes
+    %   disp(b)
+    %   %|| error('Some error')
+    %
+    %   % A set of expressions is ignored if there is no expected output
+    %   % (that is, no lines starting with '%||').
+    %   % Thus, the following expression is not part of any test,
+    %   % and therefore does not raise an error.
+    %   error('this is never executed)
+    %
+    %
+    % % tests end here because test indentation has ended
 
-  % The code goes below
+    % The code goes below
 
 end
diff --git a/src/templates/templateFunctionNumpy.m b/src/templates/templateFunctionNumpy.m
index 4ae9a956..a5974bf0 100644
--- a/src/templates/templateFunctionNumpy.m
+++ b/src/templates/templateFunctionNumpy.m
@@ -1,21 +1,21 @@
-% (C) Copyright 2020 CPP_PTB developpers
+% (C) Copyright 2020 CPP_PTB developers
 
 function [argout] = templateFunctionNumpy(argin1, argin2, argin3)
-  %
-  % Short description of what the function does goes here.
-  %
-  %  y = templateFunction(argin1, argin2, argin3)
-  %
-  % Parameters:
-  %    argin1: The first input value
-  %
-  %    argin2: The second input value
-  %
-  %    argin3: The third input value
-  %
-  % Returns:
-  %    The input value multiplied by two
+    %
+    % Short description of what the function does goes here.
+    %
+    %  y = templateFunction(argin1, argin2, argin3)
+    %
+    % Parameters:
+    %    argin1: The first input value
+    %
+    %    argin2: The second input value
+    %
+    %    argin3: The third input value
+    %
+    % Returns:
+    %    The input value multiplied by two
 
-  % The code goes below
+    % The code goes below
 
 end
diff --git a/src/waitForTrigger.m b/src/waitForTrigger.m
index 147fe895..6f603290 100644
--- a/src/waitForTrigger.m
+++ b/src/waitForTrigger.m
@@ -5,7 +5,10 @@
     %
     % USAGE:
     %
-    %   [lastTriggerTimeStamp] = waitForTrigger([cfg,] [deviceNumber,] [quietMode,] [nbTriggersToWait])
+    %   [lastTriggerTimeStamp] = waitForTrigger([cfg,] ...
+    %                                           [deviceNumber,] ...
+    %                                           [quietMode,] ...
+    %                                           [nbTriggersToWait])
     %
     % :param cfg:
     % :type cfg: struct
@@ -16,7 +19,10 @@
     % :param nbTriggersToWait: number of triggers to wait
     % :type nbTriggersToWait: integer
     %
-    % :returns: - :lastTriggerTimeStamp: (optional) it can be used as experimentStart timestamp (``cfg.experimentStart``)
+    % :returns:
+    %
+    % - :lastTriggerTimeStamp: (optional) it can be used as experimentStart
+    %                          timestamp (``cfg.experimentStart``)
     %
     % If you are not using the quietMode, it flips and waits for half a TR before starting to
     % check for the next trigger (unless this was the last trigger to wait for and in

From 4400ab9b6be2a97c36c42a0d5bcfe6e0b32f9eb2 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 1 Nov 2020 06:24:15 +0100
Subject: [PATCH 14/15] add headings to function description doc

---
 docs/source/function_description.rst | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/docs/source/function_description.rst b/docs/source/function_description.rst
index 5a897f5f..0fe8f7e8 100644
--- a/docs/source/function_description.rst
+++ b/docs/source/function_description.rst
@@ -1,5 +1,5 @@
 Function description
-====================
+********************
 
 The functions of our pipeline
 
@@ -21,6 +21,9 @@ List of functions in the ``src`` folder.
 
 ----
 
+Aperture
+========
+
 List of functions in the ``src/aperture`` folder.
 
 (to add saveAperture)
@@ -36,6 +39,9 @@ List of functions in the ``src/aperture`` folder.
 
 ----
 
+Dot
+===
+
 List of functions in the ``src/dot`` folder.
 
 .. module:: src.dot
@@ -54,6 +60,9 @@ List of functions in the ``src/dot`` folder.
 
 ----
 
+Errors
+======
+
 List of functions in the ``src/errors`` folder.
 
 .. module:: src.errors
@@ -65,6 +74,9 @@ List of functions in the ``src/errors`` folder.
 
 ----
 
+Fixation
+========
+
 List of functions in the ``src/fixation`` folder.
 
 .. module:: src.fixation
@@ -74,6 +86,9 @@ List of functions in the ``src/fixation`` folder.
 
 ----
 
+Keyboard
+========
+
 List of functions in the ``src/keyboard`` folder.
 
 .. module:: src.keyboard
@@ -87,6 +102,9 @@ List of functions in the ``src/keyboard`` folder.
 
 ----
 
+Randomization
+=============
+
 List of functions in the ``src/randomization`` folder.
 
 .. module:: src.randomization
@@ -97,6 +115,9 @@ List of functions in the ``src/randomization`` folder.
 
 ----
 
+Screen
+======
+
 List of functions in the ``src/screen`` folder.
 
 .. module:: src.screen
@@ -106,6 +127,9 @@ List of functions in the ``src/screen`` folder.
 
 ----
 
+Utilities
+=========
+
 List of functions in the ``src/utils`` folder.
 
 (to add makeGif)

From 7dd40a0b2ddaa4ee863242df44ea0b5164ebfb9b Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 1 Nov 2020 06:40:33 +0100
Subject: [PATCH 15/15] fix mh and sphinx

---
 src/keyboard/getResponse.m | 45 ++++++++++++++++++++++++--------------
 src/readAndFilterLogfile.m |  4 ++--
 2 files changed, 30 insertions(+), 19 deletions(-)

diff --git a/src/keyboard/getResponse.m b/src/keyboard/getResponse.m
index 93805a77..7e482e2d 100644
--- a/src/keyboard/getResponse.m
+++ b/src/keyboard/getResponse.m
@@ -2,12 +2,13 @@
 
 function responseEvents = getResponse(action, deviceNumber, cfg, getOnlyPress)
     %
-    % Wrapper function to use KbQueue. The queue will be listening to key presses on a keyboard device:
-    % ``cfg.keyboard.responseBox`` or ``cfg.keyboard.keyboard`` are 2 main examples. When no deviceNumber
-    % is set then it will listen to the default device. Check the ``CPP_getResponseDemo`` for a quick
-    % script on how to use it.
+    % Wrapper function to use KbQueue. The queue will be listening to key presses
+    % on a keyboard device:
+    % ``cfg.keyboard.responseBox`` or ``cfg.keyboard.keyboard`` are 2 main examples.
+    % When no ``deviceNumber`` is set then it will listen to the default device.
+    % Check the ``CPP_getResponseDemo`` for a quick script on how to use it.
     %
-    % USAGE:
+    % USAGE::
     %
     %   responseEvents = getResponse(action, deviceNumber, cfg, getOnlyPress)
     %
@@ -19,20 +20,25 @@
     %                      return when the keys were released (default=true). See the section on
     %                      `Returns` below for more info
     %
-    % :returns: - :responseEvents: returns all the keypresses and return them as a structure with field names that make it easier to save the output of in a BIDS format
+    % :returns:
     %
-    % - ``responseEvents.onset`` this is an absolute value and you should substract the "experiment start time" to get a value relative to when the experiment was started.
+    % - :responseEvents: returns all the keypresses and return them
+    %                    as a structure with field names that make it easier
+    %                    to save the output of in a BIDS format
     %
-    % - ``responseEvents.trial_type = response``
+    %   - ``responseEvents.onset`` this is an absolute value and you should substract
+    %     the "experiment start time" to get a value relative to when the experiment was started.
     %
-    % - ``responseEvents.duration = 0``
+    %   - ``responseEvents.trial_type = response``
     %
-    % - ``responseEvents.keyName`` the name of the key pressed
+    %   - ``responseEvents.duration = 0``
     %
-    % - ``responseEvents(iEvent,1).pressed`` if
+    %   - ``responseEvents.keyName`` the name of the key pressed
     %
-    %  - pressed == 1  --> the key was pressed
-    %  - pressed == 0  --> the key was released
+    %   - ``responseEvents(iEvent,1).pressed`` if
+    %
+    %      - ``pressed == 1``  --> the key was pressed
+    %      - ``pressed == 0``  --> the key was released
     %
     % ---
     %
@@ -42,11 +48,16 @@
     %
     % - ``start`` to start listening to keypresses
     %
-    % - ``check`` checks all the key presses events since 'start', or since last 'check' or 'flush' (whichever was the most recent)
+    % - ``check`` checks all the key presses events since 'start', or since last 'check'
+    %   or 'flush' (whichever was the most recent)
+    %
+    %   - can check for demand to abort if the ``escapeKey`` is listed in the Keys of interest
+    %
+    %   - can only check for demands to abort when ``getResponse('check')`` is called
+    %     so there will be a delay between the key press and the experiment stopping
     %
-    %  - can check for demand to abort if the ``escapeKey`` is listed in the Keys of interest
-    %  - can only check for demands to abort when ``getResponse('check')`` is called so there will be a delay between the key press and the experiment stopping
-    %  - abort errors send specific signals that allow the catch to get them and allows us to "close" nicely
+    %   - abort errors send specific signals that allow the catch to get them and allows us
+    %     to "close" nicely
     %
     % - ``flush`` empties the queue of events in case you want to restart from a clean queue
     %
diff --git a/src/readAndFilterLogfile.m b/src/readAndFilterLogfile.m
index a1735b12..00b54ad7 100644
--- a/src/readAndFilterLogfile.m
+++ b/src/readAndFilterLogfile.m
@@ -19,9 +19,9 @@
     % :type filterBy: string
     % :param varargin: either ``cfg`` (to display the last run output) or the file path as string
     %
-    % :returns: 
+    % :returns:
     %
-    % - :outputFiltered: dataset with only the specified content to see it in the 
+    % - :outputFiltered: dataset with only the specified content to see it in the
     %                    command window use display(outputFiltered)
     %
     %