Version Control System: Git#
Software development is repetitions of coding, testing, and improving. A version control system (VCS) allows
parallel development of parts and re-integration
trace back to previous versions when a problem is detected
Git#
The most popular VCS today is Git, created by Linus Torvalds for developing Linux.
If git has not been installed, follow one of these to install.
Mac:
Install XCode from the App Store
or install XCode Command Line Tools by
xcode-select --installor install HomeBrew and run
brew install git
Windows:
Install Git for Windows
Detailed documentations can be found at https://git-scm.com/docs
Starting a repository#
In your working directory, you can start a new repository by git init
Here we use an example of a directory containing a python module cell.py that we created in Chapter 4.
%mkdir cell
%cd cell
mkdir: cell: File exists
/Users/doya/OIST Dropbox/kenji doya/Python/iSciComp/cell
%%file cell.py
"""Classes for cells"""
import numpy as np
import matplotlib.pyplot as plt
class Cell:
"""Class for a cell"""
def __init__(self, position = [0,0], radius=0.1, color=[1,0,0,0.5]):
"""Make a new cell"""
self.position = np.array(position)
self.radius = radius
self.color = color
def show(self):
"""Visualize as a circule"""
c = plt.Circle(self.position,self.radius,color=self.color)
plt.gca().add_patch(c)
plt.axis('equal')
if __name__ == "__main__":
c0 = Cell()
c0.show()
plt.show()
Overwriting cell.py
%pwd
'/Users/doya/OIST Dropbox/kenji doya/Python/iSciComp/cell'
Try running this code.
%run cell.py
Now we create a new repository.
!git init
Reinitialized existing Git repository in /Users/doya/OIST Dropbox/kenji doya/Python/iSciComp/cell/.git/
This creates an invisible folder .git for book keeping.
%ls -a
__pycache__/ ./ ../ .git/ cell.py gcell.py
# The contents of .git folder
%ls .git
COMMIT_EDITMSG HEAD info/ ORIG_HEAD
config hooks/ logs/ refs/
description index objects/
You can check the status of the repository by git status
!git status
On branch main
Untracked files:
(use "git add <file>..." to include in what will be committed)
__pycache__/
nothing added to commit but untracked files present (use "git add" to track)
Staging and Commiting files#
You can use git add to add files for staging.
And then git commit to register a version.
!git add cell.py
!git status
On branch main
Untracked files:
(use "git add <file>..." to include in what will be committed)
__pycache__/
nothing added to commit but untracked files present (use "git add" to track)
Register the current version by git commit with a message by -m.
!git commit -m "initial version"
!git status
On branch main
Untracked files:
(use "git add <file>..." to include in what will be committed)
__pycache__/
nothing added to commit but untracked files present (use "git add" to track)
On branch main
Untracked files:
(use "git add <file>..." to include in what will be committed)
__pycache__/
nothing added to commit but untracked files present (use "git add" to track)
Registering changes#
After editing a file, you can register a new version by git add and then git commit.
Please edit cell.py or add another file to the directory and check the status.
!git status
On branch main
Untracked files:
(use "git add <file>..." to include in what will be committed)
__pycache__/
nothing added to commit but untracked files present (use "git add" to track)
Use git add to stage updated files.
!git add cell.py
!git status
On branch main
Untracked files:
(use "git add <file>..." to include in what will be committed)
__pycache__/
nothing added to commit but untracked files present (use "git add" to track)
And the git commit the changes
!git commit -m "cell.py updated"
!git status
On branch main
Untracked files:
(use "git add <file>..." to include in what will be committed)
__pycache__/
nothing added to commit but untracked files present (use "git add" to track)
On branch main
Untracked files:
(use "git add <file>..." to include in what will be committed)
__pycache__/
nothing added to commit but untracked files present (use "git add" to track)
You can see what was changed by git show.
!git show
commit 96cb22c81db0feca54ab556f3072ef3311260ebb (HEAD -> main)
Merge: 8ad5cf6 49dea46
Author: Kenji Doya <doya@starfishM4-4.local>
Date: Wed Oct 14 16:46:59 2026 +0900
initial version
You can check the revision history by git log
!git log
commit 96cb22c81db0feca54ab556f3072ef3311260ebb (HEAD -> main)
Merge: 8ad5cf6 49dea46
Author: Kenji Doya <doya@starfishM4-4.local>
Date: Wed Oct 14 16:46:59 2026 +0900
initial version
commit 49dea466a8005e5df185832e52913f4230e475c8 (myBranch)
Author: Kenji Doya <doya@starfishM4-4.local>
Date: Wed May 6 19:09:20 2026 +0900
added gcell.py
commit 8ad5cf6b1faf65d78b248c78171ac979e17106b6
Author: Kenji Doya <doya@starfishM4-4.local>
Date: Wed May 6 19:09:18 2026 +0900
initial version
commit ff72690d9950381e4171528c547c364659c70875
Merge: 6dc49e0 86d9170
Author: Kenji Doya <doya@starfishM4.local>
Date: Sat Mar 29 07:18:35 2025 +0900
initial version
commit 86d9170fe5cf379ddec96cb0484854b3f047797f
Author: Kenji Doya <doya@starfishM4.local>
Date: Sat Mar 29 03:20:18 2025 +0900
added gcell.py
commit 6dc49e077609837209c57b8b52a58b36340f8250
Author: Kenji Doya <doya@starfishM4.local>
Date: Sat Mar 29 03:20:16 2025 +0900
initial version
commit ada6e011b864c93c202a176b18ab3b01db8f4801
Author: Kenji Doya <doya@oist.jp>
Date: Mon Dec 16 14:54:00 2024 +0900
added gcell.py
commit fba656aec31be16236f9de2b429e91fac5ef7b2a
Author: Kenji Doya <doya@oist.jp>
Date: Mon Dec 16 14:53:57 2024 +0900
initial version
!pwd
/Users/doya/OIST Dropbox/kenji doya/Python/iSciComp/cell
Branch#
You can create a new branch to update the codes while keeping the current version untouched.
After creating a branch, switch to that branch by git checkout.
!git branch myBranch
!git checkout myBranch
fatal: a branch named 'myBranch' already exists
Switched to branch 'myBranch'
Now let us add a new module gCell.
!git status
On branch myBranch
Untracked files:
(use "git add <file>..." to include in what will be committed)
__pycache__/
nothing added to commit but untracked files present (use "git add" to track)
%%file gcell.py
"""Classes for cells"""
import numpy as np
import matplotlib.pyplot as plt
import cell
class gCell(cell.Cell):
"""Class of growing cell based on Cell class"""
def grow(self, scale=2):
"""Grow the area of the cell"""
self.radius *= np.sqrt(scale)
def duplicate(self):
"""Make a copy with a random shift"""
c = gCell(self.position+np.random.randn(2)*self.radius, self.radius, self.color)
return c
if __name__ == "__main__":
c0 = gCell()
c0.show()
c1 = c0.duplicate()
c1.grow()
c1.show()
plt.show()
Overwriting gcell.py
!ls
__pycache__ cell.py gcell.py
%run gcell.py
Then git add and git commit.
!git add gcell.py
!git commit -m "added gcell.py"
!git status
On branch myBranch
Untracked files:
(use "git add <file>..." to include in what will be committed)
__pycache__/
nothing added to commit but untracked files present (use "git add" to track)
On branch myBranch
Untracked files:
(use "git add <file>..." to include in what will be committed)
__pycache__/
nothing added to commit but untracked files present (use "git add" to track)
!git show
commit 49dea466a8005e5df185832e52913f4230e475c8 (HEAD -> myBranch)
Author: Kenji Doya <doya@starfishM4-4.local>
Date: Wed May 6 19:09:20 2026 +0900
added gcell.py
diff --git a/gcell.py b/gcell.py
index db1f7b9..cd7b2a5 100644
--- a/gcell.py
+++ b/gcell.py
@@ -6,11 +6,11 @@ import cell
class gCell(cell.Cell):
"""Class of growing cell based on Cell class"""
-
+
def grow(self, scale=2):
"""Grow the area of the cell"""
self.radius *= np.sqrt(scale)
-
+
def duplicate(self):
"""Make a copy with a random shift"""
c = gCell(self.position+np.random.randn(2)*self.radius, self.radius, self.color)
!git log --all --graph
* commit 96cb22c81db0feca54ab556f3072ef3311260ebb (main)
|\ Merge: 8ad5cf6 49dea46
| | Author: Kenji Doya <doya@starfishM4-4.local>
| | Date: Wed Oct 14 16:46:59 2026 +0900
| |
| | initial version
| |
| * commit 49dea466a8005e5df185832e52913f4230e475c8 (HEAD -> myBranch)
| | Author: Kenji Doya <doya@starfishM4-4.local>
| | Date: Wed May 6 19:09:20 2026 +0900
| |
| | added gcell.py
| |
* | commit 8ad5cf6b1faf65d78b248c78171ac979e17106b6
| | Author: Kenji Doya <doya@starfishM4-4.local>
| | Date: Wed May 6 19:09:18 2026 +0900
| |
| | initial version
| |
* | commit ff72690d9950381e4171528c547c364659c70875
|\| Merge: 6dc49e0 86d9170
| | Author: Kenji Doya <doya@starfishM4.local>
| | Date: Sat Mar 29 07:18:35 2025 +0900
| |
| | initial version
| |
| * commit 86d9170fe5cf379ddec96cb0484854b3f047797f
| | Author: Kenji Doya <doya@starfishM4.local>
| | Date: Sat Mar 29 03:20:18 2025 +0900
| |
| | added gcell.py
| |
* | commit 6dc49e077609837209c57b8b52a58b36340f8250
|/ Author: Kenji Doya <doya@starfishM4.local>
| Date: Sat Mar 29 03:20:16 2025 +0900
|
| initial version
|
* commit ada6e011b864c93c202a176b18ab3b01db8f4801
| Author: Kenji Doya <doya@oist.jp>
| Date: Mon Dec 16 14:54:00 2024 +0900
|
| added gcell.py
|
* commit fba656aec31be16236f9de2b429e91fac5ef7b2a
Author: Kenji Doya <doya@oist.jp>
Date: Mon Dec 16 14:53:57 2024 +0900
initial version
You can go back to a previous branch by checkout.
!git checkout main
!git log --all --graph
Switched to branch 'main'
* commit 96cb22c81db0feca54ab556f3072ef3311260ebb (HEAD -> main)
|\ Merge: 8ad5cf6 49dea46
| | Author: Kenji Doya <doya@starfishM4-4.local>
| | Date: Wed Oct 14 16:46:59 2026 +0900
| |
| | initial version
| |
| * commit 49dea466a8005e5df185832e52913f4230e475c8 (myBranch)
| | Author: Kenji Doya <doya@starfishM4-4.local>
| | Date: Wed May 6 19:09:20 2026 +0900
| |
| | added gcell.py
| |
* | commit 8ad5cf6b1faf65d78b248c78171ac979e17106b6
| | Author: Kenji Doya <doya@starfishM4-4.local>
| | Date: Wed May 6 19:09:18 2026 +0900
| |
| | initial version
| |
* | commit ff72690d9950381e4171528c547c364659c70875
|\| Merge: 6dc49e0 86d9170
| | Author: Kenji Doya <doya@starfishM4.local>
| | Date: Sat Mar 29 07:18:35 2025 +0900
| |
| | initial version
| |
| * commit 86d9170fe5cf379ddec96cb0484854b3f047797f
| | Author: Kenji Doya <doya@starfishM4.local>
| | Date: Sat Mar 29 03:20:18 2025 +0900
| |
| | added gcell.py
| |
* | commit 6dc49e077609837209c57b8b52a58b36340f8250
|/ Author: Kenji Doya <doya@starfishM4.local>
| Date: Sat Mar 29 03:20:16 2025 +0900
|
| initial version
|
* commit ada6e011b864c93c202a176b18ab3b01db8f4801
| Author: Kenji Doya <doya@oist.jp>
| Date: Mon Dec 16 14:54:00 2024 +0900
|
| added gcell.py
|
* commit fba656aec31be16236f9de2b429e91fac5ef7b2a
Author: Kenji Doya <doya@oist.jp>
Date: Mon Dec 16 14:53:57 2024 +0900
initial version
%ls
__pycache__/ cell.py gcell.py
!git branch
* main
myBranch
You can merge another branche to the current branch by git merge
!git merge myBranch
!git log --all --graph
Already up to date.
* commit 96cb22c81db0feca54ab556f3072ef3311260ebb (HEAD -> main)
|\ Merge: 8ad5cf6 49dea46
| | Author: Kenji Doya <doya@starfishM4-4.local>
| | Date: Wed Oct 14 16:46:59 2026 +0900
| |
| | initial version
| |
| * commit 49dea466a8005e5df185832e52913f4230e475c8 (myBranch)
| | Author: Kenji Doya <doya@starfishM4-4.local>
| | Date: Wed May 6 19:09:20 2026 +0900
| |
| | added gcell.py
| |
* | commit 8ad5cf6b1faf65d78b248c78171ac979e17106b6
| | Author: Kenji Doya <doya@starfishM4-4.local>
| | Date: Wed May 6 19:09:18 2026 +0900
| |
| | initial version
| |
* | commit ff72690d9950381e4171528c547c364659c70875
|\| Merge: 6dc49e0 86d9170
| | Author: Kenji Doya <doya@starfishM4.local>
| | Date: Sat Mar 29 07:18:35 2025 +0900
| |
| | initial version
| |
| * commit 86d9170fe5cf379ddec96cb0484854b3f047797f
| | Author: Kenji Doya <doya@starfishM4.local>
| | Date: Sat Mar 29 03:20:18 2025 +0900
| |
| | added gcell.py
| |
* | commit 6dc49e077609837209c57b8b52a58b36340f8250
|/ Author: Kenji Doya <doya@starfishM4.local>
| Date: Sat Mar 29 03:20:16 2025 +0900
|
| initial version
|
* commit ada6e011b864c93c202a176b18ab3b01db8f4801
| Author: Kenji Doya <doya@oist.jp>
| Date: Mon Dec 16 14:54:00 2024 +0900
|
| added gcell.py
|
* commit fba656aec31be16236f9de2b429e91fac5ef7b2a
Author: Kenji Doya <doya@oist.jp>
Date: Mon Dec 16 14:53:57 2024 +0900
initial version