Git Stash

Before you can git pull, you need to have committed any changes you have made. If you find you want to pull, but you’re not ready to commit, you have to temporarily “put aside” your uncommitted changes. For this, you can use the git stash command, like in the following example:

import os

top_dir = os.getcwd()
git_dir = os.path.join(top_dir, "learning_git")
working_dir = os.path.join(git_dir, "git_example")
os.chdir(working_dir)

Remind ourselves which branch we are using:

%%bash
git branch -vv
* experiment 497c32c Add Cadair Idris
  main       71cdbbe [origin/main] Merge branch 'main' of github.com:alan-turing-institute/github-example
%%writefile Wales.md
Mountains In Wales
==================

* Pen y Fan
* Tryfan
* Snowdon
* Glyder Fawr
* Fan y Big
* Cadair Idris
* Penygader
Overwriting Wales.md
%%bash
git stash
Saved working directory and index state WIP on experiment: 497c32c Add Cadair Idris
%%bash
git pull
There is no tracking information for the current branch.
Please specify which branch you want to merge with.
See git-pull(1) for details.

    git pull <remote> <branch>

If you wish to set tracking information for this branch you can do so with:

    git branch --set-upstream-to=origin/<branch> experiment

---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
Input In [5], in <cell line: 1>()
----> 1 get_ipython().run_cell_magic('bash', '', 'git pull\n')

File /opt/hostedtoolcache/Python/3.8.13/x64/lib/python3.8/site-packages/IPython/core/interactiveshell.py:2358, in InteractiveShell.run_cell_magic(self, magic_name, line, cell)
   2356 with self.builtin_trap:
   2357     args = (magic_arg_s, cell)
-> 2358     result = fn(*args, **kwargs)
   2359 return result

File /opt/hostedtoolcache/Python/3.8.13/x64/lib/python3.8/site-packages/IPython/core/magics/script.py:153, in ScriptMagics._make_script_magic.<locals>.named_script_magic(line, cell)
    151 else:
    152     line = script
--> 153 return self.shebang(line, cell)

File /opt/hostedtoolcache/Python/3.8.13/x64/lib/python3.8/site-packages/IPython/core/magics/script.py:305, in ScriptMagics.shebang(self, line, cell)
    300 if args.raise_error and p.returncode != 0:
    301     # If we get here and p.returncode is still None, we must have
    302     # killed it but not yet seen its return code. We don't wait for it,
    303     # in case it's stuck in uninterruptible sleep. -9 = SIGKILL
    304     rc = p.returncode or -9
--> 305     raise CalledProcessError(rc, cell)

CalledProcessError: Command 'b'git pull\n'' returned non-zero exit status 1.

By stashing your work first, your repository becomes clean, allowing you to pull. To restore your changes, use git stash apply.

%%bash
git stash apply
On branch main
Your branch is up to date with 'origin/main'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
	modified:   Wales.md

Untracked files:
  (use "git add <file>..." to include in what will be committed)
	__pycache__/
	wsd.py

no changes added to commit (use "git add" and/or "git commit -a")

The “Stash” is a way of temporarily saving your working area, and can help out in a pinch.

Tagging

Tags are easy to read labels for revisions, and can be used anywhere we would name a commit.

Produce real results only with tagged revisions.

NB: we delete previous tags with the same name remotely and locally first, to avoid duplicates.

git tag -a v1.0 -m "Release 1.0"
git push --tags

You can also use tag names in the place of commmit hashes, such as to list the history between particular commits:

git log v1.0.. --graph --oneline

If .. is used without a following commit name, HEAD is assumed.

Working with generated files: gitignore

We often end up with files that are generated by our program. It is bad practice to keep these in Git; just keep the sources.

Examples include .o and .x files for compiled languages, .pyc files in Python.

In our example, we might want to make our .md files into a PDF with pandoc:

%%writefile Makefile

MDS=$(wildcard *.md)
PDFS=$(MDS:.md=.pdf)

default: $(PDFS)

%.pdf: %.md
	pandoc $< -o $@
Writing Makefile
%%bash
make
pandoc Scotland.md -o Scotland.pdf
pandoc Wales.md -o Wales.pdf
pandoc lakeland.md -o lakeland.pdf
pandoc test.md -o test.pdf

We now have a bunch of output .pdf files corresponding to each Markdown file.

But we don’t want those to show up in git:

%%bash
git status
On branch main
Your branch is up to date with 'origin/main'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
	modified:   Wales.md

Untracked files:
  (use "git add <file>..." to include in what will be committed)
	Makefile
	Scotland.pdf
	Wales.pdf
	__pycache__/
	lakeland.pdf
	test.pdf
	wsd.py

no changes added to commit (use "git add" and/or "git commit -a")

Use .gitignore files to tell Git not to pay attention to files with certain paths:

%%writefile .gitignore
*.pdf
Writing .gitignore
%%bash
git status
On branch main
Your branch is up to date with 'origin/main'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
	modified:   Wales.md

Untracked files:
  (use "git add <file>..." to include in what will be committed)
	.gitignore
	Makefile
	__pycache__/
	wsd.py

no changes added to commit (use "git add" and/or "git commit -a")
%%bash
git add Makefile
git add .gitignore
git commit -am "Add a makefile and ignore generated files"
git push
[main c8ba483] Add a makefile and ignore generated files
 3 files changed, 12 insertions(+), 1 deletion(-)
 create mode 100644 .gitignore
 create mode 100644 Makefile
To github.com:alan-turing-institute/github-example.git
   537950c..c8ba483  main -> main

Git clean

Sometimes you end up creating various files that you do not want to include in version control. An easy way of deleting them (if that is what you want) is the git clean command, which will remove the files that git is not tracking.

%%bash
git clean -fX
Removing Scotland.pdf
Removing Wales.pdf
Removing lakeland.pdf
Removing test.pdf
%%bash
ls
Makefile
Scotland.md
Wales.md
__pycache__
lakeland.md
test.md
wsd.py
  • With -f: don’t prompt

  • with -d: remove directories

  • with -x: Also remote .gitignored files

  • with -X: Only remove .gitignore files

Hunks

Git Hunks

A “Hunk” is one git change. This changeset has three hunks:

+import matplotlib
+import numpy as np

 from matplotlib import pylab
 from matplotlib.backends.backend_pdf import PdfPages

+def increment_or_add(key,hash,weight=1):
+       if key not in hash:
+               hash[key]=0
+       hash[key]+=weight
+
 data_path=os.path.join(os.path.dirname(
                        os.path.abspath(__file__)),
-regenerate=False
+regenerate=True

Interactive add

git add and git reset can be used to stage/unstage a whole file, but you can use interactive mode to stage by hunk, choosing yes or no for each hunk.

git add -p myfile.py
+import matplotlib
+import numpy as np
#Stage this hunk [y,n,a,d,/,j,J,g,e,?]?

GitHub pages

Yaml Frontmatter

GitHub will publish repositories containing markdown as web pages, automatically.

You’ll need to add this content:

   ---
   ---

A pair of lines with three dashes, to the top of each markdown file. This is how GitHub knows which markdown files to make into web pages. Here’s why for the curious.

%%writefile test.md
---
title: Github Pages Example
---
Mountains and Lakes in the UK
===================

Engerland is not very mountainous.
But has some tall hills, and maybe a mountain or two depending on your definition.
Overwriting test.md
%%bash
git commit -am "Add github pages YAML frontmatter"
[main 12ee6ad] Add github pages YAML frontmatter
 1 file changed, 7 insertions(+), 4 deletions(-)

The gh-pages branch

GitHub creates github pages when you use a special named branch. By default this is gh-pages although you can change it to something else if you prefer. This is best used to create documentation for a program you write, but you can use it for anything.

os.chdir(working_dir)
%%bash

git checkout -b gh-pages
git push -uf origin gh-pages
Branch 'gh-pages' set up to track remote branch 'gh-pages' from 'origin'.
Switched to a new branch 'gh-pages'
remote: 
remote: Create a pull request for 'gh-pages' on GitHub by visiting:        
remote:      https://github.com/alan-turing-institute/github-example/pull/new/gh-pages        
remote: 
To github.com:alan-turing-institute/github-example.git
 * [new branch]      gh-pages -> gh-pages

The first time you do this, GitHub takes a few minutes to generate your pages.

The website will appear at http://username.github.io/repositoryname, for example:

http://alan-turing-institute.github.io/github-example/

Layout for GitHub pages

You can use GitHub pages to make HTML layouts, here’s an example of how to do it, and how it looks. We won’t go into the detail of this now, but after the class, you might want to try this.

%%bash
# Cleanup by removing the gh-pages branch 
git checkout main
git push
git branch -d gh-pages
git push --delete origin gh-pages 
git branch --remote
Your branch is ahead of 'origin/main' by 1 commit.
  (use "git push" to publish your local commits)
Deleted branch gh-pages (was 12ee6ad).
  origin/main
Switched to branch 'main'
To github.com:alan-turing-institute/github-example.git
   c8ba483..12ee6ad  main -> main
To github.com:alan-turing-institute/github-example.git
 - [deleted]         gh-pages