diff --git a/index.qmd b/index.qmd index 04ae48e540d46b639208abbd75406a9d694456e4..f39f52cadd378a953aa6ae29f62a16be3354d211 100755 --- a/index.qmd +++ b/index.qmd @@ -140,9 +140,15 @@ There are several tools available but we will use **Rstudio** (perhaps not the b ### Install tools - - git : https://git-scm.com/book/en/v2/Getting-Started-Installing-Git + - **git** : https://git-scm.com/book/en/v2/Getting-Started-Installing-Git + + - (Windows users: For Windows operating systems, we recommend that you select the Git Bash and Git Gui components in step 3) + + <img src="https://gitlab.cirad.fr/cirad/documentation/-/wikis/uploads/dbdc699677639995106fb84b45d07255/git-rstudio-1.png" alt="" width="400"/> + + For more details for Windows users: https://gitlab.cirad.fr/cirad/documentation/-/wikis/Installation-de-Git-sur-Windows) - - rstudio : https://posit.co/download/rstudio-desktop/ + - **rstudio** : https://posit.co/download/rstudio-desktop/ ### Create an account on [ENS's Gitlab].(https://gitbio.ens-lyon.fr/): <https://gitbio.ens-lyon.fr/> @@ -312,7 +318,7 @@ By default, when creating the Rstudio project, a .gitignore file is added contai This means that the Rstudio project configuration files are not tracked. -For TP and in general, we don't want to track changes to raw data or results. +In general, we don't want to track changes to raw data or results, maybe for small metadata files **but NEVER for big raw data files !!**. 1. Add the following lines to the *.gitignore* file: @@ -331,6 +337,14 @@ results/ 5. View changes on gitlab +::: callout-important +# Never commit data into version control repositories +Why you should never commit data to Git: + +Data should never be committed into your Git repositories. This is because git was designed to version small files of source code; committing data, a different category of things from source code, into your repositories will first and foremost lead to repository size bloat. Also, committing data into repositories means the data get shipped alongside the source code to anybody who has access to the source code. This might not necessarily be in-line with organizational practices. +::: + + ## Organizing your working directory It's a good idea to put all your project-related files in the same folder: @@ -390,15 +404,28 @@ At the end of the course, the quality of your README.md will be particularly imp 4. Index, commit, push ... + + +::: callout-important +# Never commit data into version control repositories +Why you should never commit data to Git: + +Data should never be committed into your Git repositories. This is because git was designed to version small files of source code; committing data, a different category of things from source code, into your repositories will first and foremost lead to repository size bloat. Also, committing data into repositories means the data get shipped alongside the source code to anybody who has access to the source code. This might not necessarily be in-line with organizational practices. +::: + # Time to work on your data Import scripts of your own project on gitlab. - # Resolve conflicts +Some resources to resolve conflicts: + + - https://docs.gitlab.com/ee/user/project/merge_requests/conflicts.html + - https://www.simplilearn.com/tutorials/git-tutorial/merge-conflicts-in-git + If you cannot resolve the conflicts : @@ -412,6 +439,12 @@ If you cannot resolve the conflicts : <img src="figures/git_clone_again.jpg" alt="" width="600"/> +# Collaboration with multiple people on the same project : the use of multiple branches + +See: + + - https://git-scm.com/book/en/v2/Git-Branching-Branches-in-a-Nutshell + - https://cupofcode.blog/intro-to-git/ ------------------------------------------------------------------------