update readme

Author: Remi-Gau

README.md

@@ -16,7 +16,9 @@
     - [checkCFG](#checkcfg)
   - [CFG content](#cfg-content)
   - [How to install](#how-to-install)
-    - [Use the matlab package manager](#use-the-matlab-package-manager)
+    - [Download with git](#download-with-git)
+    - [Add as a submodule](#add-as-a-submodule)
+    - [Direct download](#direct-download)
   - [Contributing](#contributing)
     - [Guidestyle](#guidestyle)
     - [BIDS naming convention](#bids-naming-convention)
@@ -281,49 +283,74 @@ cfg.fileName.datasetDescription
 
 ## How to install
 
-### Use the matlab package manager
+### Download with git
 
-This repository can be added as a dependencies by listing it in a
-[mpm-requirements.txt file](.mpm-requirements.txt) as follows:
+``` bash
+cd fullpath_to_directory_where_to_install
+# use git to download the code
+git clone https://github.com/cpp-lln-lab/CPP_BIDS.git
+# move into the folder you have just created
+cd CPP_PTB
+# add the src folder to the matlab path and save the path
+matlab -nojvm -nosplash -r "addpath(fullfile(pwd, 'src')); savepath ();"
+```
 
+Then get the latest commit:
+```bash
+# from the directory where you downloaded the code
+git pull origin master
 ```
-CPP_BIDS -u https://github.com/cpp-lln-lab/CPP_BIDS.git
+
+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 v0.0.1
+git checkout -b version1 v0.0.1
 ```
 
-You can then use the [matlab package manager](https://github.com/mobeets/mpm), to simply download
-the appropriate version of those dependencies and add them to your path by running a
-`getDependencies` function like the one below where you just need to replace
-`YOUR_EXPERIMENT_NAME` by the name of your experiment.
+### Add as a submodule
 
-```matlab
-function getDependencies(action)
-% Will install on your computer the matlab dependencies specified in the mpm-requirements.txt
-%  and add them to the matlab path. The path is never saved so you need to run getDependencies() when
-%  you start matlab.
-%
-% getDependencies('update') will force the update and overwrite previous version of the dependencies.
-%
-% getDependencies() If you only already have the appropriate version but just want to add them to the matlab path.
-
-experimentName = YOUR_EXPERIMENT_NAME;
-
-if nargin<1
-    action = '';
-end
-
-switch action
-    case 'update'
-        % install dependencies
-        mpm install -i mpm-requirements.txt -f -c YOUR_EXPERIMENT_NAME
-end
-
-% adds them to the path
-mpm_folder = fileparts(which('mpm'));
-addpath(genpath(fullfile(mpm_folder, 'mpm-packages', 'mpm-collections', experimentName)));
-
-end
+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_BIDS.git
+# move into the folder you have just created
+cd CPP_PTB
+# add the src folder to the matlab path and save the path
+matlab -nojvm -nosplash -r "addpath(fullfile(pwd, 'src'))"
 ```
 
+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 commited as well. 
+
+**TO DO**
+<!-- Submodules
+pros: in principle, downloading the experiment you have the whole package plus the benefit to stay updated and use version control of this dependency. Can probably handle a use case in which one uses different version on different projects (e.g. older and newer projects).
+cons: for pro users and not super clear how to use it at the moment. -->
+
+### Direct download
+
+Download the code. Unzip. And add to the matlab path.
+
+Pick a specific version:
+
+https://github.com/cpp-lln-lab/CPP_BIDS/releases
+
+Or take the latest commit (NOT RECOMMENDED):
+
+https://github.com/cpp-lln-lab/CPP_BIDS/archive/master.zip
+
+**TO DO**
+<!-- Download a specific version and c/p it in a subfun folder
+pros: the easiest solution to share the code and 'installing' it on the stimulation computer (usually not the one used to develop the code).
+cons: extreme solution useful only at the very latest stage (i.e. one minute before acquiring your data); prone to be customized/modified (is it what we want?) -->
+
 ## Contributing
 
 Feel free to open issues to report a bug and ask for improvements.