Improve `Add as a submodule` section

[marcobarilari]

from #92

Example for submodule usage

So say you want to clone a repo that has some nested submodules, then you would type this to get the content of all the submodules at once (here with my experiment repo):

git clone --recurse-submodules https://github.com/user_name/yourExperiment.git

This would be the way to do it "by hand"

# clone the repo
git clone https://github.com/user_name/yourExperiment.git

# go into the directory
cd yourExperiment

# initialize and get the content of the first level of submodules  (CPP_PTB and CPP_BIDS)
git submodule init
git submodule update

# get the nested submodules JSONio and BIDS-matlab for CPP_BIDS
git submodule foreach --recursive 'git submodule init'
git submodule foreach --recursive 'git submodule update'

@marcobarilari marcobarilari 8 days ago Member in 3.2.1 you are describing how to clone a repo with the submodules and not how to use the submodules (and why?) in the repo of a new experiment (e.g. experiment/lib/submodule1 and add the folder to the path in the exp script)

As it is here might be a bit confusing. This example might be more helpful in the repo of an experiment with submodules (e.g. the localizers) to explain how to clone them

[CerenB]

I do not know where is 3.2.1 but it might be me who did that example. It was the time I was trying to understand submodule etc.. Feel free to delete/change it.

[Remi-Gau]

I think that generally the install section can be improved so I would keep that issue opened as a reminder.

Also I remove the numbering of the TOC in one of my last commits: would you prefer to have it back ?

[Remi-Gau]

• [x] mention that the best way to use it is actually to clone the template_PTB repo : https://github.com/cpp-lln-lab/PTB_experiment

[Remi-Gau]

Maybe those having a common install section in the .github repo of the orga might make more sense (since this is a common thing to CPP_BIDS, CPP_PTB and CPP_SPM), we would have only one doc to curate

[Remi-Gau]

this is included on the doc on RTD