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tools:git [2023/10/21 11:14] – datalad, dvd willtools:git [2026/06/17 14:17] (current) – [Git] will
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 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]] 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]].+''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]], [[https://radicle.dev/|radicle]].  
 + 
 +See [[:tools:github]] for integrating local repos with github remote.
  
  
 For more see For more see
   * https://happygitwithr.com/   * https://happygitwithr.com/
 +  * http://neuroimaging-data-science.org/content/002-datasci-toolbox/002-git.html
   * https://git-scm.com/doc   * https://git-scm.com/doc
  
-===== Using ===== +===== Track Changes ===== 
-On the command line in terminal/with shell, using git follows the ''add'',''commit'',''push'' pattern: + 
 +{{: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> <code>
 git add $file   # move changes in $file to "staging" git add $file   # move changes in $file to "staging"
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 git push        # send changes to a server (e.g. github) git push        # send changes to a server (e.g. github)
 </code> </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.  By default, ''git commit'' will open [[:tools:vim]] to use to write the commit message. 
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   - '':wq'' to write and quit.   - '':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
  
-==== Github https push ==== +===== Advanced ===== 
-To push to ''https'' (vs ssh like ''git@'') repos, you'll need to use a personal authentication token when prompted for a password. See [[https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens|github's documentation]] +  * [[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'' 
-==== ssh push ==== +  * rebase, esp with [[https://magit.vc/manual/magit/Rebasing.html|emacs+magit's rebase UI]]  
-''git push'' can use ssh authentication. You need a key likey in ''~/.ssh/id_rsa.pub''. If that doesn't exist, ''ssh-keygen'' can make it (use empty password for convience. hit enter at password prompt to leave blank). See more [[https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent|documentaiton on github]]+  * [[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]] 
 +