last changes before workshop

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/
 
 
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