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Aug 2, 2020
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update readme #64

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99 changes: 63 additions & 36 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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.
Expand Down