Bump actions/checkout from 4 to 6

.github/workflows/codespell.yml

@@ -15,5 +15,5 @@ jobs:
   codespell:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
       - uses: codespell-project/actions-codespell@master

.github/workflows/miss_hit_quality.yml

@@ -10,13 +10,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
         with:
           submodules: true
           fetch-depth: 1
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 

.github/workflows/miss_hit_style.yml

@@ -10,13 +10,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
         with:
           submodules: true
           fetch-depth: 1
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 

.github/workflows/moxunit.yml

@@ -14,7 +14,7 @@ jobs:
 
     steps:
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v6
       with:
         submodules: true
         fetch-depth: 1
@@ -28,7 +28,7 @@ jobs:
         cover_xml_file: coverage.xml
 
     - name: Code coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v5
       with:
        token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
        file:  coverage.xml # optional

README.md

@@ -1,77 +1,51 @@
 [![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/template_PTB_experiment/actions)
 ![](https://github.com/Remi-gau/template_matlab_analysis/workflows/CI/badge.svg)
 [![codecov](https://codecov.io/gh/Remi-gau/template_matlab_analysis/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/template_PTB_experiment)
-[![Build Status](https://travis-ci.com/Remi-gau/template_matlab_analysis.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/template_PTB_experiment)
 
-# Template repository for matlab analysis project
+# Template repository for psycthoolbox experiment
 
 ## Content
 
 ```bash
 ├── .git
-│   ├── COMMIT_EDITMSG
-│   ├── FETCH_HEAD
-│   ├── HEAD
-│   ├── ORIG_HEAD
-│   ├── branches
-│   ├── config
-│   ├── description
-│   ├── hooks
-│   │   ├── pre-commit.sample
-│   │   └── pre-push.sample
-│   ├── ...
-│   └── ...
 ├── .github  # where you put anything github related
 │   └── workflows # where you define your github actions
 │       └── moxunit.yml # a yaml file that defines a github action
-├── lib # where you put the code from external libraries (mathworks website or other github repositories)
+├── lib # external libraries (mathworks website or other github repositories)
 │   └── README.md
 ├── src # where you put your code
 │   ├── README.md
 │   └── miss_hit.cfg
 ├── tests # where you put your unit tests
 |   ├── README.md
 |   └── miss_hit.cfg
-├── .travis.yml # where you define the continuous integration done by Travis
 ├── LICENSE
 ├── README.md
-├── requirements.txt # list of python packages used in this repo: to install `pip install -r requirements.txt`
+├── requirements.txt # python packages used: to install `pip install -r requirements.txt`
 ├── miss_hit.cfg # configuration file for the matlab miss hit linter
 └── initEnv.m # a .m file to set up your project (adds the right folder to the path)
 ```
 
-## Keeping your code stylish: miss hit linter
-
-## Python environment
-
-More on this
-[here](https://the-turing-way.netlify.app/reproducible-research/renv/renv-package.html)
-
-[Conda cheat sheet](https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf)
-
-## Testing your code
-
-## Continuous integration
-
 ## How to install and use this template
 
 By using the
 [template PTB experiment repository](https://github.com/cpp-lln-lab/template_PTB_experiment):
-you can create 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.
-
+you can create 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.
 
 ## How to install and run
 
 Install
+
 ```
 git clone --recurse-submodules https://github.com/your_github_account/the_name_of_your_new_experiment.git
 ```
 
 Set parameters in `setParameters.m`
 
 Run
+
 ```
 mainScript
 ```

initEnv.m

@@ -1,18 +1,45 @@
-%
-% 1 - Check if version requirements
-% are satisfied and the packages are
-% are installed/loaded:
-%   Octave > 4
-%       - image
-%       - optim
-%       - struct
-%       - statistics
-%
-%   MATLAB >= R2015b
-%
-% 2 - Add project to the O/M path
-
-function initEnv
+function initEnv(varargin)
+    %
+    % 1 - Check if version requirements are satisfied and the packages are are installed/loaded:
+    %   Octave > 4
+    %       - image
+    %       - optim
+    %       - struct
+    %       - statistics
+    %
+    %   MATLAB >= R2015b
+    %
+    % 2 - Add project to the O/M path
+    %
+    % USAGE::
+    %
+    %   initEnv
+    %   initEnv('init')
+    %   initEnv('uninit')
+    %
+    % :param action:
+    % :type action: string
+    %
+    % :returns: - :action: (type) (dimension)
+    %
+    % Example::
+    %
+
+    % (C) Copyright 2022 CPP_BIDS developers
+
+    p = inputParser;
+
+    defaultAction = 'init';
+
+    addOptional(p, 'action', defaultAction, @ischar);
+    % addParameter(p, 'verbose', true);
+
+    parse(p, varargin{:});
+
+    action = p.Results.action;
+    % verbose = p.Results.verbose;
+
+    % Check Matlab and Octave version
 
     octaveVersion = '4.0.3';
     matlabVersion = '8.6.0';
@@ -59,7 +86,7 @@
                'Try this in your terminal:', ...
                ' git submodule update --recursive ']);
     else
-        addDependencies();
+        addDependencies(action);
     end
 
     disp('Correct matlab/octave versions and added to the path!');
@@ -96,13 +123,24 @@ function tryInstallFromForge(packageName)
 
 end
 
-function addDependencies()
+function addDependencies(action)
 
     pth = fileparts(mfilename('fullpath'));
-    addpath(fullfile(pth, 'lib', 'CPP_BIDS'));
-    addpath(genpath(fullfile(pth, 'lib', 'CPP_PTB', 'src')));
-    addpath(fullfile(pth, 'subfun'));
 
-    checkCppBidsDependencies();
+    switch lower(action)
+
+        case 'init'
+
+            run(fullfile(pth, 'lib', 'CPP_PTB', 'cpp_ptb'));
+            run(fullfile(pth, 'lib', 'CPP_BIDS', 'cpp_bids'));
+            addpath(genpath(fullfile(pth, 'src')));
+
+        case 'uninit'
+
+            cpp_ptb('uninit');
+            cpp_bids('uninit');
+            rmpath(genpath(fullfile(pth, 'src')));
+
+    end
 
 end

mainScript.m

@@ -11,7 +11,7 @@
 end
 
 % make sure we got access to all the required functions and inputs
-initEnv();
+initEnv('init');
 
 % set and load all the parameters to run the experiment
 cfg = setParameters;
@@ -125,6 +125,8 @@
 
     cleanUp();
 
+    initEnv('uninit');
+
 catch
 
     cleanUp();