Easier alternative to `mpm` to manage this repo inside other projects

[marcobarilari]

A not exhaustive list of alternatives (literally everything is coming up to my mind), please provide any comment and solutions. I would be also happy to suggest all of them in the read-me with user-case examples.

• MatlabPackageManager
  pros: 'easy' to get and then forget about it,
  cons: does it work in octave? Would be better to download a specific version/commit, it can only be used with one specific version of the package (right?)

• 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.

• 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?)

[Remi-Gau]

I would say that option 1 is out until it becomes easier to use and octave compatible.

I would make option 2 the default.

Option 3 has the advantage that it is not mutually exclusive with option 2 and can be used to over ride it.

[CerenB]

The 3rd option is not under version control, right?
What I did for my current exp, I have CPP repos (BIDS and PTB) in separate folders. But I've inserted the "copy" of these repos inside my exp scripts. Every time there's a major update on CPP repos, I copy paste manually into my exp script folder.
Is 3rd option like the one I explained above?

[Remi-Gau]

From my understanding, yes the 3rd option describes what you have been doing. :-) Sent from my Samsung Galaxy smartphone.

…

-------- Original message -------- From: CerenB <notifications@github.com> Date: 14/07/2020 10:28 (GMT+01:00) To: cpp-lln-lab/CPP_PTB <CPP_PTB@noreply.github.com> Cc: Remi Gau <remi_gau@hotmail.com>, Assign <assign@noreply.github.com> Subject: Re: [cpp-lln-lab/CPP_PTB] Easier alternative to `mpm` to manage this repo inside other projects (#21) The 3rd option is not under version control, right? What I did for my current exp, I have CPP repos (BIDS and PTB) in separate folders. But I've inserted the "copy" of these repos inside my exp scripts. Every time there's a major update on CPP repos, I copy paste manually into my exp script folder. Is 3rd option like the one I explained above? — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub<#21 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABVDQIKQWXVPI7QEMNJESXTR3QJKLANCNFSM4OYUSN4A>.

[Remi-Gau]

OK so I played around with submodules this morning on a dummy example and I did this.

Have a look and let me know if this makes sense and works for you.

https://github.com/Remi-Gau/repo_with_submod

[Remi-Gau]

@marcobarilari @CerenB

I added some sections to the READMEs.

Let me know what you think.

https://github.com/cpp-lln-lab/CPP_PTB#how-to-install
https://github.com/cpp-lln-lab/CPP_BIDS#how-to-install

[CerenB]

I'm new to submodules, sorry for my naive question below.

PTB//BIDS also have their own submodules to get, right? (I think BIDS repo has submodules) In order to get those when I install the BIDS repo, I'll also do the following in the README file? Or that would be with:
Option1 :
git submodule foreach --recursive 'git submodule init'

Option2:
Add it as a submodule in the repo you are working on.

cd fullpath_to_directory_where_to_install
# use git to download the code
git submodule add https://github.com/cpp-lln-lab/CPP_PTB.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))"

To get the latest commit you then need to update the submodule with the information on its remote repository and then merge those locally.

git submodule update --remote --merge

[CerenB]

Another question is with this submodule installing as you explained in README, is good for using CPP_PTB as a submodule within my experiment folder. I'm preparing my scripts in one repo and I'll add PTB repo within this as a submodule. Right?
Then somewhere it should "save" the version so I can keep track of it?

[Remi-Gau]

Yeah I am figuring out submodule as I go too.

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 retinotopy repo):

git clone --recurse-submodules https://github.com/Remi-Gau/retinotopy_experiment_fMRI.git

And apparently this would be the way to do it "by hand"

# clone the repo
git clone https://github.com/Remi-Gau/retinotopy_experiment_fMRI.git

# go into the directory
cd retinotopy_experiment_fMRI

# 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'

Does that help?

[Remi-Gau]

Then somewhere it should "save" the version so I can keep track of it?

Actually this part is simpler than I thought as a submodule is directly "linked" to a specific commit in the history of the repo.

For example, in CPP_BIDS the submodule have an @somethingSomethingSomething. This somethingSomethingSomething is the "shasum" of the commit (its codename) it is "tracking".

https://github.com/cpp-lln-lab/CPP_BIDS/tree/master/lib

So that is effectively tracking which version of the dependency you are using.

Does that make sense?