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+---
+jupyter:
+  jupytext:
+    text_representation:
+      extension: .md
+      format_name: markdown
+      format_version: '1.2'
+      jupytext_version: 1.3.2
+  kernelspec:
+    display_name: Python 3
+    language: python
+    name: python3
+---
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+An introduction to Git
+======================
+
+<center>
+June 28, 2021
+</center>
+
+<center>
+Department of Aerospace Engineering, IIT Bombay
+</center>
+
+<center>
+Prabhu Ramachandran
+</center>
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Agenda
+------
+
+-   Introduction to git
+-   Using github and collaborating
+-   Workflows
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Motivation
+----------
+
+<center>
+<img height="80%" src="img/phd101212s.gif" align="center" />
+</center>
+
+<br/>
+<br/>
+<br/>
+Credit: www.phdcomics.com
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+History
+-------
+
+-   VCS: Version Control Systems
+-   RCS
+-   CVS
+-   SVN
+-   Centralized repositories
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Distributed VCS
+---------------
+
+-   Peer-to-Peer system
+-   Darcs
+-   Bitkeeper
+-   Mercurial: hg
+-   Monotone
+-   Bazaar: bzr
+-   Git
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Collaboration
+-------------
+
+-   Sourceforge.net etc.
+-   github/bitbucket etc.
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Introduction to git
+-------------------
+
+- Version control
+   -   save work
+   -   review changes
+   -   do not lose history
+   -   share with others
+   -   reduce mental burden
+
+-   Distributed workflow
+-   Requirement for modern software development!
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+
+Basic model
+-----------
+
+-   A series of changesets (commits)
+-   HEAD is the last commit
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+
+Getting started
+---------------
+
+Setup your details:
+
+```bash
+    $ git config --global user.name "Guru Programmer"
+    $ git config --global user.email "your_email@youremail.com"
+```
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Create a repository
+-------------------
+
+Create a repo:
+
+```bash
+   $ cd my_project
+   $ git init
+```
+Note that a `.git` directory is present!
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Help!
+-----
+
+Find help:
+
+```bash
+    $ git help
+    $ git help status
+```
+
+<!-- #endregion -->
+
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Status
+------
+
+Helpful status of repository:
+
+```bash
+    $ git status
+```
+
+Often provides hints
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Basic commands
+--------------
+
+Add a file:
+
+```bash
+    $ vim readme.txt
+    $ git add readme.txt
+    $ git status
+    $ git commit
+```
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Changing the default editor
+---------------------------
+
+`commit` will use `$EDITOR`. Change this with:
+
+```bash
+    $ export EDITOR="emacs -q -nw"
+    $ export EDITOR=nano
+```
+
+Or :
+
+```bash
+    $ git config --global core.editor "emacs -q -nw"
+```
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+A note on commit logs
+---------------------
+Here is an example:
+
+    First line brief <= 50 chars
+
+    Detailed information below. Ideally wrapped to 72 cols as done
+    here.
+
+    - ALWAYS leave a good log message.
+    - Bullet points are fine.
+    - Multiple paras separated by blank line.
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Review history
+--------------
+
+What happened:
+
+```bash
+    $ git log
+```
+
+- Note the commit \"ID\"
+- These are unique IDs
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Notes
+-----
+
+- What happens when you commit?
+- What happens when you add?
+- The staging area
+- New files always must be added
+- Remember to `git add`!
+
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Making changes
+--------------
+
+Make changes:
+
+```bash
+    $ vim readme.txt
+    $ git status
+    $ git diff
+    $ git add readme.txt
+    $ git commit
+```
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Some useful options
+-------------------
+
+- Add all changed files and commit:
+
+```bash
+    $ git commit -a
+```
+
+Commit log on command line:
+
+```bash
+    $ git commit -m "Fix for bug #123"
+```
+
+See changes in log:
+
+```bash
+    $ git log -p
+```
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Exercise
+--------
+
+1.  Create a dummy repo.
+2.  Add some files.
+3.  Make different changes and commit them.
+4.  Review the log.
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+History
+-------
+
+- `HEAD` is the latest
+- `HEAD~1`, `HEAD~2` is one/two changes before
+- You can use the commit IDs (or a unique substring)
+
+```bash
+
+    $ git diff HEAD~1 readme.txt
+    $ git diff 737e86dd9 readme.txt
+```
+
+Differences between two points:
+
+```bash
+    $ git diff HEAD~2..HEAD~4 readme.txt
+```
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Recovering old versions
+-----------------------
+
+Get the previous version:
+
+```bash
+    $ git checkout HEAD~1 readme.txt
+```
+
+Same rules as before apply
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Ignoring files
+--------------
+
+- Add a `.gitignore`
+
+```
+    *.dat
+    *.out
+    *.pyc
+```
+
+Ignores all files with these extensions
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+
+Being Lazy: Aliases
+-------------------
+
+Convenient shorthand:
+
+```bash
+    $ git config --global alias.st status
+    $ git config --global alias.ci 'commit -v'
+    $ git config --global alias.co checkout
+```
+
+See `~/.gitconfig` for details:
+
+```bash
+    $ git st
+    $ git ci
+    $ git co
+```
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Recap
+-----
+
+- `git config`
+- `git init`
+- `git status`
+- `git add`
+- `git commit`
+- `git diff`
+- `git log`
+- `git checkout`
+- `.gitignore`: ignore files
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Deleting content
+----------------
+
+Removing a file:
+
+```bash
+    $ git rm readme.txt
+    $ git commit -m "Cleaning up"
+```
+
+-   Does the file go away?
+-   Can you get back the file?
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Exercise
+--------
+
+1.  Add a file with a few additional changes.
+2.  Remove it.
+3.  Make other changes to other files.
+4.  Revive the deleted file.
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Undoing
+-------
+
+Deleted too quick:
+
+```bash
+    $ git rm readme.txt
+    # Oops made a mistake.
+    $ git checkout -- readme.txt
+```
+
+Phew! Saved!
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Moving content
+--------------
+
+Moving stuff:
+
+```bash
+    $ git mv readme.txt README.txt
+    $ git commit -m "Renaming readme."
+```
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Some internals
+--------------
+
+- A series of changesets (commits)
+- Blobs: a bunch of bytes
+- Tree:
+   - Collection of blobs
+   - Other trees
+
+- Commits:
+   - Information on who committed it
+   - Points to a tree
+   - Parent to this commit.
+
+- Tag:
+   - A reference to a specific commit
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Branches
+--------
+
+- Why branches?
+
+   - Cheap, super-convenient
+   - Allow experimentation
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Simple repository
+-----------------
+
+This is what we had so far
+
+![image](img/git_branch_basic.png)
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Branches
+--------
+
+![image](img/git_branch.png)
+
+-   Can commit on either branch
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Branch basics
+-------------
+
+- `master` is the default branch
+- Create:
+```bash
+  $ git checkout -b new_branch
+```
+- List branches:
+```bash
+  $ git branch
+```
+- Note `branch` branches from current branch
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+More branch commands
+--------------------
+
+- Switch:
+
+```bash
+      $ git checkout master
+      $ git checkout new_branch
+```
+- Delete:
+
+```bash
+      $ git branch -d new_branch
+```
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Merging branches
+----------------
+
+- Merge changes from `new_branch` to `master`:
+
+```bash
+      [new_branch] $ git checkout master
+      [master] $ git merge new_branch
+```
+- Always merges to current branch
+- Adds the changes from that branch to current one
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+What just happened?
+-------------------
+
+![image](img/git_branch_merge.png)
+
+Let us take a look at `gitk` quickly
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Exercise
+--------
+
+1.  Create a new branch.
+2.  Add some commits there (add files, edit files \...)
+3.  Check the logs on new branch and master
+4.  Merge the branch to master.
+5.  Delete the new branch.
+6.  Check logs again.
+
+HW: Try to delete an unmerged branch.
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+What if there are conflicts?
+----------------------------
+
+-   Merges can lead to conflicts:
+
+```bash
+        [master] $ git merge foo
+        Auto-merging readme.txt
+        CONFLICT (content): Merge conflict in readme.txt
+```
+-   Edit `readme.txt` and resolve conflicts
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Resolving conflicts
+-------------------
+
+-   Look for lines like so:
+
+        <<<<<<< HEAD
+        Line in master
+        =======
+        Same line in my_branch
+        >>>>>>> my_branch
+
+-   Edit and remove the markers and:
+
+```bash
+    $ git add readme.txt
+    $ git ci
+```
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Recap
+-----
+
+-   new branch: `git checkout -b new_branch`
+-   switch: `git checkout master`
+-   list: `git branch`
+-   merge: `git merge new_branch`
+-   delete: `git branch -d new_branch`
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Recap
+-----
+
+- Conflicts:
+   - Manually fix files
+   - Remove markers
+   - Add and commit
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Collaborating
+-------------
+
+- github.com
+- gitlab.com
+- bitbucket.org
+- etc.
+- Provide hosting for a git repository
+- Plus other powerful features
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Collaboration Overview
+----------------------
+
+<center>
+<img src="img/git_server.png" align="center"/>
+</center>
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Basic ideas
+-----------
+
+- `clone` the entire repository
+- `pull` changes from server
+- `push` changes to server
+- Share content with other users
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Local demo
+----------
+
+- The principles can be demonstrated without a server!
+- Consider two users:
+   1.  Alice
+   2.  Bob
+
+- Make a server-like repository:
+```bash
+    $ mkdir -p server/project
+    $ git init --bare
+    $ cd ../../
+```
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Quick demo: Bob
+---------------
+
+Bob:
+```bash
+    $ mkdir bob
+    $ git clone ../../server/project
+```
+Goes to sleep
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Quick demo: Alice
+-----------------
+
+Alice:
+```bash
+    $ mkdir alice
+    $ git clone ../../server/project
+    $ touch readme.txt
+    $ git add readme.txt
+    $ git ci -a -m "Initial commit"
+    $ git push origin master
+```
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Bob next morning
+----------------
+
+Bob (yawn):
+
+```bash
+    $ git pull
+    $ git pull origin master
+    $ add/commit whatever.
+    $ git push origin master
+```
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Working together
+----------------
+
+- Lets say both Bob and Alice make changes but Alice pushes first
+- Git will refuse to allow Bob to `push` his changes
+- So Bob will first pull:
+
+```bash
+      [bob] $ git pull origin master
+```
+- Resolves any conflicts
+- Then Bob can push his changes
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+# Recap
+-----
+
+<center>
+<img src="img/git_server.png" align="center"/>
+</center>
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Working with remote repos
+-------------------------
+
+Clone a repo:
+
+```bash
+    $ git clone https://github.com/FOSSEE/sees.git
+```
+
+Pulling changes (merges into current branch):
+
+```bash
+    $ git pull
+    $ git pull origin master
+```
+
+Fetch only gets changes, it doesn\'t merge it:
+
+```bash
+    $ git fetch
+```
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Remotes
+-------
+
+- The name `origin` is called a **remote**
+- A shorthand to refer to a repo
+- One can add additional remotes
+
+  - remote is a name for another fork/repo
+  - You could pull/push to these remotes
+
+- See `.git/config`
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Sharing
+-------
+
+- Share your changes by pushing:
+```bash
+   $ git push origin master
+```
+
+- To push a branch you have made:
+```bash
+   $ git push origin my_branch
+```
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Permissions
+-----------
+
+- You cannot write to every repository!
+- So how do you contribute?
+- "FORK" the repository
+   - This makes a clone of repo on github
+   - You have write access to your fork
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Forking
+-------
+
+<center>
+<img src="img/git_fork.png" align="center"/>
+</center>
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Pull-requests
+-------------
+
+<center>
+<img src="img/git_pull_request.png" align="center"/>
+</center>
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Contributing to another project
+-------------------------------
+
+- You cannot write to every repository!
+- **Fork** their repository:
+   - Makes a copy of their repo on github
+   - This is your repo so you can share it
+
+- Push to your fork
+- Pull master of upstream
+- Send a pull-request to upstream
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Pull-requests (PR)
+------------------
+
+- Fantastic for sharing code
+- Easy to review/get feedback/change
+- Process:
+   - Make a branch locally
+   - Push to your fork (typically)
+   - Select branch on bitbucket
+   - "Create pull request"
+   - target PR to reponame/master
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Managing remotes
+----------------
+
+Add new remotes:
+
+```bash
+    $ git remote add <name> <server>
+```
+for example:
+
+```bash
+    $ git remote add fossee git@github.com:FOSSEE/sees.git
+    $ git pull fossee some_branch
+```
+See remotes already defined:
+
+```bash
+    $ git remote -v
+```
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Managing remotes
+----------------
+
+Renaming:
+
+```bash
+    $ git remote rename origin upstream
+```
+
+Delete a remote branch:
+
+```bash
+    $ git br -d branch_to_delete # deletes it locally
+
+    # This deletes the branch on the server.
+    $ git push origin :branch_to_delete
+```
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Example: simple workflow
+------------------------
+
+- Single developer with repo on github:
+
+```bash
+      $ git add readme.txt
+      $ git commit
+      $ git push origin master
+      ...
+```
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Example: two developers
+-----------------------
+
+- Two developers collaborating on github
+- Same as Alice and Bob:
+
+```bash
+      [alice] $ git pull origin master
+      [alice] $ git add readme.txt
+      [alice] $ git commit
+      [alice] $ git push origin master
+      ...
+      [bob] $ git pull origin master
+      [bob] $ vim readme.txt
+      [bob] $ git commit -a -m "Update readme"
+      [bob] $ git push origin master
+```
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Example: contribute to project
+------------------------------
+
+1.  Fork their repo on github
+2.  Clone *your* fork (origin)
+3.  `git remote add https://.../sees upstream`
+4.  Make branch locally
+5.  Add changes to branch
+6.  Push branch to origin
+7.  Send PR to upstream
+
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Odds and ends: `add -p`
+----------------------
+
+Adding only parts of changes "hunks"
+
+```bash
+    $ git add -p
+    $ git commit
+```
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+Odds and ends: `stash`
+----------------------
+
+Stashing lets you stow your changes away without commiting:
+
+```bash
+    $ git stash list
+    $ git stash
+    $ git stash pop
+```
+<!-- #endregion -->
+
+<!-- #region slideshow={"slide_type": "slide"} -->
+More git resources
+------------------
+
+- Software carpentry lessons http://software-carpentry.org/v5/novice/git/index.html
+
+- Bitbucket tutorials:
+
+   - https://www.atlassian.com/git/
+   - https://www.atlassian.com/git/tutorial
+
+- Newbie/Github:
+
+   - http://readwrite.com/2013/09/30/understanding-github-a-journey-for-beginners-part-1
+
+   - http://readwrite.com/2013/10/02/github-for-beginners-part-2
+   - https://help.github.com/
+
+- Quick: http://rogerdudler.github.io/git-guide/
+
+<!-- #endregion -->