====== Git ======
''[[https://git-scm.com/|git]]'' is a "distributed version control system" (dVCS) or "source control management" (SCM) tool used to track changes, primarily for source code in text files. git has command line and graphical interfaces. 

Alternative SCM tools include ''[[https://fossil-scm.org/|fossil]]'', ''[[https://www.mercurial-scm.org/|hg]]'', ''[[https://pijul.org/|pijul]]''. For version controlling (large binary/non-text neuroimaging) data, see [[https://handbook.datalad.org/|datalad]] or [[https://dvc.org/|dvc]]

''git'' is not github. [[https://github.com|Github]] is a Microsoft-owned source forge adding a social network, identity services, and other features not included in the git system (issue tracking, patch/fork management). Other forges include [[https://gitlab.com|gitlab]], [[https://sr.ht/|sr.ht]], [[https://codeberg.org/|codeberg]]. 

See [[:tools:github]] for integrating local repos with github remote.


For more see
  * https://happygitwithr.com/
  * http://neuroimaging-data-science.org/content/002-datasci-toolbox/002-git.html
  * https://git-scm.com/doc

===== Track Changes =====

{{:tools:pasted:20250918-141941.png?300}}

On the command line in terminal/with shell, using git follows the ''add'',''commit'',''push'' pattern. 
Need a mnemonic? Think of the ''**A**dorable **C**omputer **P**enguins'' on the [[:tools:mobaxterm]] screensaver.

<code>
git add $file   # move changes in $file to "staging"
git commit      # annotate staged files, commit to history
git push        # send changes to a server (e.g. github)
</code>

<WRAP alert round>
 **Don't give file paths to ''commit'' or ''push''**.

Only the ''git add'' (or friends like ''git mv'' and ''git rm'') command takes file paths as arguments.

''git commit'' and ''push'' work on the cumulative ''add''s to create a single snapshot, not individual files.
</WRAP>

By default, ''git commit'' will open [[:tools:vim]] to use to write the commit message. 

  - Push ''i'' to put vim in insert mode. 
  - write your message. 
  - push ''Esc'' to go back to command mode 
  - '':wq'' to write and quit.

==== Commit messages ====

Each commit in git includes a human-annotated short description in prose. While it's tempting and easy use `"update"` as the entire commit message, future you and colleges will appreciate a more detailed history. There are competing specifications to help guide better commit messages:
  * https://www.conventionalcommits.org/
  * https://gitmoji.dev/specification

=== Examples ===
Two commit messages in ''conventional commits'' vs ''gitmoji''
<code>
feat: age model with GAM instead of LM
fix: outlier detection applied to all EEG columns
</code>

<code>
✨️ model.py: age GAM instead of LM
🐛 plot.R: apply outlier detection ∀ EEG cols
</code>

===== See Changes =====

A huge benefit of version control is to see the what's changed. This can be done with web, graphical, and command line interfaces.


The command line/terminal commands for viewing what's changed include
<code>
git log         # history of all changes
git status      # what's been git add-ed/git rm-ed, modified, and untracked
git diff        # what's changed in tracked files
git blame $file # show what commit/author is responsible for each line
</code>

If the output is more than a screenful, these commands will launched put the output in the pager ''less''. 
  * arrow keys navigate
  * push ''/'' to start a search
  * push ''q'' to quit

===== Advanced =====
  * [[https://git-scm.com/docs/git-worktree|working trees]] for working on more than one branch at a time
  * ''git add $file; git commit --amend --noedit; git push --force''
  * rebase, esp with [[https://magit.vc/manual/magit/Rebasing.html|emacs+magit's rebase UI]] 
  * [[https://jvns.ca/blog/2023/11/01/confusing-git-terminology/|confusing terms]]
  * [[https://jvns.ca/blog/2024/02/16/popular-git-config-options/|popular git config options]]