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MPHY0021: Research Software Engineering With Python

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Solo work with Git

So, we're in our git working directory:

In [1]:
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)
working_dir
Out[1]:
'/home/runner/work/rsd-engineeringcourse/rsd-engineeringcourse/ch02git/learning_git/git_example'

A first example file

So let's create an example file, and see how to start to manage a history of changes to it.

<my editor> index.md # Type some content into the file.
In [2]:
%%writefile index.md
Mountains in the UK   
===================   
England is not very mountainous.   
But has some tall hills, and maybe a mountain or two depending on your definition.
Writing index.md
In [3]:
cat index.md
Mountains in the UK   
===================   
England is not very mountainous.   
But has some tall hills, and maybe a mountain or two depending on your definition.

Telling Git about the File

So, let's tell Git that index.md is a file which is important, and we would like to keep track of its history:

In [4]:
%%bash
git add index.md

Don't forget: Any files in repositories which you want to "track" need to be added with git add after you create them.

Our first commit

Now, we need to tell Git to record the first version of this file in the history of changes:

In [5]:
%%bash
git commit -m "First commit of discourse on UK topography"
[master (root-commit) c26b924] First commit of discourse on UK topography
 1 file changed, 4 insertions(+)
 create mode 100644 index.md

And note the confirmation from Git.

There's a lot of output there you can ignore for now.

Configuring Git with your editor

If you don't type in the log message directly with -m "Some message", then an editor will pop up, to allow you to edit your message on the fly.

For this to work, you have to tell git where to find your editor.

In [6]:
%%bash
git config --global core.editor vim

You can find out what you currently have with:

In [7]:
%%bash
git config --get core.editor
vim

To configure Notepad++ on windows you'll need something like the below, ask a demonstrator to help for your machine.

$ git config --global core.editor "code --wait"

I'm going to be using vim as my editor, but you can use whatever editor you prefer. Find how to setup your favourite editor in the setup chapter of Software Carpentry's Git lesson.

Git log

Git now has one change in its history:

In [8]:
%%bash
git log
commit c26b924d0c7246041b8a694bc807005d267eefa1
Author: Lancelot the Brave <l.brave@spamalot.uk>
Date:   Tue Dec 7 14:36:06 2021 +0000

    First commit of discourse on UK topography

You can see the commit message, author, and date...

Hash Codes

The commit "hash code", e.g.

c438f1716b2515563e03e82231acbae7dd4f4656

is a unique identifier of that particular revision.

(This is a really long code, but whenever you need to use it, you can just use the first few characters, however many characters is long enough to make it unique, c438 for example. )

Nothing to see here

Note that git will now tell us that our "working directory" is up-to-date with the repository: there are no changes to the files that aren't recorded in the repository history:

In [9]:
%%bash
git status
On branch master
nothing to commit, working tree clean

Let's edit the file again:

vim index.md
In [10]:
%%writefile index.md
Mountains in the UK   
===================   
England is not very mountainous.   
But has some tall hills, and maybe a mountain or two depending on your definition.

Mount Fictional, in Barsetshire, U.K. is the tallest mountain in the world.
Overwriting index.md
In [11]:
cat index.md
Mountains in the UK   
===================   
England is not very mountainous.   
But has some tall hills, and maybe a mountain or two depending on your definition.

Mount Fictional, in Barsetshire, U.K. is the tallest mountain in the world.

Unstaged changes

In [12]:
%%bash
git status
On branch master
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:   index.md

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

We can now see that there is a change to "index.md" which is currently "not staged for commit". What does this mean?

If we do a git commit now nothing will happen.

Git will only commit changes to files that you choose to include in each commit.

This is a difference from other version control systems, where committing will affect all changed files.

We can see the differences in the file with:

In [13]:
%%bash
git diff
diff --git a/index.md b/index.md
index a1f85df..3a2f7b0 100644
--- a/index.md
+++ b/index.md
@@ -2,3 +2,5 @@ Mountains in the UK
 ===================   
 England is not very mountainous.   
 But has some tall hills, and maybe a mountain or two depending on your definition.
+
+Mount Fictional, in Barsetshire, U.K. is the tallest mountain in the world.

Deleted lines are prefixed with a minus, added lines prefixed with a plus.

Staging a file to be included in the next commit

To include the file in the next commit, we have a few choices. This is one of the things to be careful of with git: there are lots of ways to do similar things, and it can be hard to keep track of them all.

In [14]:
%%bash
git add --update

This says "include in the next commit, all files which have ever been included before".

Note that git add is the command we use to introduce git to a new file, but also the command we use to "stage" a file to be included in the next commit.

The staging area

The "staging area" or "index" is the git jargon for the place which contains the list of changes which will be included in the next commit.

You can include specific changes to specific files with git add, commit them, add some more files, and commit them. (You can even add specific changes within a file to be included in the index.)

Message Sequence Charts

In order to illustrate the behaviour of Git, it will be useful to be able to generate figures in Python of a "message sequence chart" flavour.

There's a nice online tool to do this, called "Web Sequence diagrams".

Instead of just showing you these diagrams, I'm showing you in this notebook how I make them. This is part of our "reproducible computing" approach; always generating all our figures from code.

Here's some quick code in the Notebook to download and display an MSC illustration, using the Web Sequence Diagrams API:

In [15]:
%%writefile wsd.py
import requests
import re
import IPython

def wsd(code):
    response = requests.post("http://www.websequencediagrams.com/index.php", data={
            'message': code,
            'apiVersion': 1,
        })
    expr = re.compile("(\?(img|pdf|png|svg)=[a-zA-Z0-9]+)")
    m = expr.search(response.text)
    if m == None:
        print("Invalid response from server.")
        return False
                            
    image=requests.get("http://www.websequencediagrams.com/" + m.group(0))
    return IPython.core.display.Image(image.content)
Writing wsd.py
In [16]:
from wsd import wsd
%matplotlib inline
wsd("Sender->Recipient: Hello\n Recipient->Sender: Message received OK")
Out[16]:

The Levels of Git

Let's make ourselves a sequence chart to show the different aspects of Git we've seen so far:

In [17]:
message="""
Working Directory -> Staging Area : git add
Staging Area -> Local Repository : git commit
Working Directory -> Local Repository : git commit -a
"""
wsd(message)
Out[17]:

Review of status

In [18]:
%%bash
git status
On branch master
Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
	modified:   index.md

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

In [19]:
%%bash
git commit -m "Add a lie about a mountain"
[master d94bbd3] Add a lie about a mountain
 1 file changed, 2 insertions(+)
In [20]:
%%bash
git log
commit d94bbd3d5b73d69ca4ff5333f0bdbb069065fa3f
Author: Lancelot the Brave <l.brave@spamalot.uk>
Date:   Tue Dec 7 14:36:08 2021 +0000

    Add a lie about a mountain

commit c26b924d0c7246041b8a694bc807005d267eefa1
Author: Lancelot the Brave <l.brave@spamalot.uk>
Date:   Tue Dec 7 14:36:06 2021 +0000

    First commit of discourse on UK topography

Great, we now have a file which contains a mistake.

Carry on regardless

In a while, we'll use Git to roll back to the last correct version: this is one of the main reasons we wanted to use version control, after all! But for now, let's do just as we would if we were writing code, not notice our mistake and keep working...

vim index.md
In [21]:
%%writefile index.md
Mountains and Hills in the UK   
===================   
England is not very mountainous.   
But has some tall hills, and maybe a mountain or two depending on your definition.

Mount Fictional, in Barsetshire, U.K. is the tallest mountain in the world.
Overwriting index.md
In [22]:
cat index.md
Mountains and Hills in the UK   
===================   
England is not very mountainous.   
But has some tall hills, and maybe a mountain or two depending on your definition.

Mount Fictional, in Barsetshire, U.K. is the tallest mountain in the world.

Commit with a built-in-add

In [23]:
%%bash
git commit -am "Change title"
[master c730d31] Change title
 1 file changed, 1 insertion(+), 1 deletion(-)

This last command, git commit -a automatically adds changes to all tracked files to the staging area, as part of the commit command. So, if you never want to just add changes to some tracked files but not others, you can just use this and forget about the staging area!

Review of changes

In [24]:
%%bash
git log | head
commit c730d310cd5cc5f4dfb82b503b3ec18a45503194
Author: Lancelot the Brave <l.brave@spamalot.uk>
Date:   Tue Dec 7 14:36:08 2021 +0000

    Change title

commit d94bbd3d5b73d69ca4ff5333f0bdbb069065fa3f
Author: Lancelot the Brave <l.brave@spamalot.uk>
Date:   Tue Dec 7 14:36:08 2021 +0000

We now have three changes in the history:

In [25]:
%%bash
git log --oneline
c730d31 Change title
d94bbd3 Add a lie about a mountain
c26b924 First commit of discourse on UK topography

Git Solo Workflow

We can make a diagram that summarises the above story:

In [26]:
message="""
participant "Cleese's repo" as R
participant "Cleese's index" as I
participant Cleese as C

note right of C: vim index.md

note right of C: git init
C->R: create

note right of C: git add index.md

C->I: Add content of index.md

note right of C: git commit
I->R: Commit content of index.md

note right of C:  vim index.md

note right of C: git add --update
C->I: Add content of index.md
note right of C: git commit -m "Add a lie"
I->R: Commit change to index.md

note right of C:  vim index.md
note right of C: git commit -am "Change title"
C->R: Add and commit change to index.md (and all tracked files)
"""
wsd(message)
Out[26]: