diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
index b7ab6ff..339fc94 100644
--- a/.github/workflows/codespell.yml
+++ b/.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
diff --git a/.github/workflows/miss_hit_quality.yml b/.github/workflows/miss_hit_quality.yml
index 7fab7fd..2bfbc74 100644
--- a/.github/workflows/miss_hit_quality.yml
+++ b/.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
 
diff --git a/.github/workflows/miss_hit_style.yml b/.github/workflows/miss_hit_style.yml
index 9a4ae4a..594b3c5 100644
--- a/.github/workflows/miss_hit_style.yml
+++ b/.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
 
diff --git a/.github/workflows/moxunit.yml b/.github/workflows/moxunit.yml
index 81e395b..81fc93a 100644
--- a/.github/workflows/moxunit.yml
+++ b/.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
diff --git a/.github/workflows/update_submodules.yml b/.github/workflows/update_submodules.yml
deleted file mode 100644
index 3c6ea53..0000000
--- a/.github/workflows/update_submodules.yml
+++ /dev/null
@@ -1,100 +0,0 @@
-name: update submodules
-
-# requires sudmodules URL to be "https..." (no ssh)
-#
-# requires submodule to be specified to follow a specific branch (stored in .gitmodules)
-#
-# clone them with:
-#
-#   git submodule add -b branch_to_follow https://github.com/... submodule_path
-#
-# or specify it with:
-#
-#   git config -f .gitmodules submodule.submodule_path.branch branch_to_follow
-#
-
-  # Uses the cron schedule for github actions
-  #
-  # https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
-  #
-  #          ┌───────────── minute (0 - 59)
-  #          │ ┌───────────── hour (0 - 23)
-  #          │ │ ┌───────────── day of the month (1 - 31)
-  #          │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
-  #          │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
-  #          │ │ │ │ │
-  #          │ │ │ │ │
-  #          │ │ │ │ │
-  #          * * * * *
-
-on:
-  push:
-    branches:
-      - main
-      - master
-      - dev
-  schedule:
-    - cron: "0 0 1 * *"
-
-  # to trigger update manually from the Action tab in github
-  workflow_dispatch:
-    inputs:
-      log:
-        description: "Log"
-        required: false
-
-env:
-  # to update all submodules
-  SUBMOD_TO_UPDATE: "*"
-  # otherwise use a space separated list of the relative paths of each submodule to update
-  # SUBMOD_TO_UPDATE: "lib/sub_3 lib/sub_1"
-
-defaults:
-  run:
-    shell: bash
-
-jobs:
-  update_submodules:
-    # only trigger update on upstream repo
-    if: github.repository_owner == 'cpp-lln-lab'
-
-    runs-on: ubuntu-latest
-
-    steps:
-
-      - name: Clone repo
-        uses: actions/checkout@v3
-        with:
-          submodules: true
-
-      # check out the correct branch for each submodule and pull them all
-      # https://stackoverflow.com/questions/5828324/update-git-submodule-to-latest-commit-on-origin
-      - name: Update submodules
-        run: |
-              start_dir=$PWD
-              if [ "${SUBMOD_TO_UPDATE}" = "*" ]; then
-                  submodules=$(git submodule | awk '{print $2}')
-              else
-                  submodules=$(echo -e ${SUBMOD_TO_UPDATE} | sed "s/ /\n/g")
-              fi
-              nb_submod=$(echo "${submodules}" | wc -l)
-              echo -e "\nUPDATING ${nb_submod} SUBMODULES"
-              echo -e "${submodules}"
-              for i in $(seq 1 ${nb_submod}); do
-                  path=$(echo -e ${submodules} | awk -v i=${i} '{print $i}')
-                  branch=$(git config --get --file .gitmodules submodule.${path}.branch)
-                  echo -e "\nswitching submodule ${path} to ${branch}"
-                  cd "${path}" || exit
-                  git checkout ${branch}
-                  cd "${start_dir}"
-              done
-              git submodule update --remote --merge
-
-      # if there have been changes,
-      # a PR is created using the checkout branch for this workflow
-      # https://github.com/peter-evans/create-pull-request
-      - name: Create Pull-Request
-        uses: peter-evans/create-pull-request@v4
-        with:
-          commit-message: Update submodules
-          delete-branch: true
diff --git a/README.md b/README.md
index 598d19b..30de111 100644
--- a/README.md
+++ b/README.md
@@ -1,30 +1,17 @@
 [![](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
@@ -32,39 +19,25 @@
 ├── 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
 ```
@@ -72,6 +45,7 @@ git clone --recurse-submodules https://github.com/your_github_account/the_name_o
 Set parameters in `setParameters.m`
 
 Run
+
 ```
 mainScript
 ```
diff --git a/initEnv.m b/initEnv.m
index febf28a..10efd18 100644
--- a/initEnv.m
+++ b/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
diff --git a/lib/CPP_BIDS b/lib/CPP_BIDS
index f814264..8536d1c 160000
--- a/lib/CPP_BIDS
+++ b/lib/CPP_BIDS
@@ -1 +1 @@
-Subproject commit f814264af94fbfd5a4ef6644abd68f30f90883f2
+Subproject commit 8536d1cf4c6ca379a2b77feff5b35a94ed9dc317
diff --git a/lib/CPP_PTB b/lib/CPP_PTB
index 0738579..b5dcdff 160000
--- a/lib/CPP_PTB
+++ b/lib/CPP_PTB
@@ -1 +1 @@
-Subproject commit 073857927bd9c9ebb35a0d0d9675239b135960b3
+Subproject commit b5dcdff754cfc77706f36f9f6416be09ef43f463
diff --git a/mainScript.m b/mainScript.m
index 2f3fa11..6ab993a 100644
--- a/mainScript.m
+++ b/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();
diff --git a/notebooks/README.md b/notebooks/README.md
deleted file mode 100644
index 1237a6d..0000000
--- a/notebooks/README.md
+++ /dev/null
@@ -1 +0,0 @@
-# Jupyter notebooks