4.8 Advanced git concepts#

Estimated time to complete this notebook: 15 minutes

Stashing changes#

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 af61879 Add Cadair Idris

  main       b14af2b [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: af61879 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)
Cell In[5], line 1
----> 1 get_ipython().run_cell_magic('bash', '', 'git pull\n')

File /opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/IPython/core/interactiveshell.py:2478, in InteractiveShell.run_cell_magic(self, magic_name, line, cell)
   2476 with self.builtin_trap:
   2477     args = (magic_arg_s, cell)
-> 2478     result = fn(*args, **kwargs)
   2480 # The code below prevents the output from being displayed
   2481 # when using magics with decodator @output_can_be_silenced
   2482 # when the last Python token in the expression is a ';'.
   2483 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):

File /opt/hostedtoolcache/Python/3.8.18/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/3.8.18/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.

Ignoring files#

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 rinohtype:

%%writefile Makefile

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

default: $(PDFS)

%.pdf: %.md
	rinoh $< 2> /dev/null
	rm $(basename $@).rtc $(basename $@).stylelog

Writing Makefile

%%bash
make

rinoh Scotland.md 2> /dev/null
Using the CommonMark frontend [built-in]
rinohtype 0.5.4 (2022-06-17)  Copyright (c) Brecht Machiels and contributors
This program comes with ABSOLUTELY NO WARRANTY. Its use is subject
to the terms of the GNU Affero General Public License version 3.
100% [========================================] ETA 00:00 (00:00) page 3
Not yet converged, rendering again...
100% [========================================] ETA 00:00 (00:00) page 3
Writing output: Scotland.pdf
rm Scotland.rtc Scotland.stylelog
rinoh Wales.md 2> /dev/null
Using the CommonMark frontend [built-in]
rinohtype 0.5.4 (2022-06-17)  Copyright (c) Brecht Machiels and contributors
This program comes with ABSOLUTELY NO WARRANTY. Its use is subject
to the terms of the GNU Affero General Public License version 3.
100% [========================================] ETA 00:00 (00:00) page 3
Not yet converged, rendering again...
100% [========================================] ETA 00:00 (00:00) page 3
Writing output: Wales.pdf
rm Wales.rtc Wales.stylelog
rinoh lakeland.md 2> /dev/null
Using the CommonMark frontend [built-in]
rinohtype 0.5.4 (2022-06-17)  Copyright (c) Brecht Machiels and contributors
This program comes with ABSOLUTELY NO WARRANTY. Its use is subject
to the terms of the GNU Affero General Public License version 3.
100% [========================================] ETA 00:00 (00:00) page 3
Not yet converged, rendering again...
100% [========================================] ETA 00:00 (00:00) page 3
Writing output: lakeland.pdf
rm lakeland.rtc lakeland.stylelog
rinoh test.md 2> /dev/null
Using the CommonMark frontend [built-in]
rinohtype 0.5.4 (2022-06-17)  Copyright (c) Brecht Machiels and contributors
This program comes with ABSOLUTELY NO WARRANTY. Its use is subject
to the terms of the GNU Affero General Public License version 3.
100% [========================================] ETA 00:00 (00:00) page 3
Not yet converged, rendering again...
100% [========================================] ETA 00:00 (00:00) page 3
Writing output: test.pdf
rm test.rtc test.stylelog

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

Cleaning your directory#

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 remove .gitignored files
with -X: Only remove .gitignored 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,?]?

Research Software Engineering with Python

4.8 Advanced git concepts

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