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
./ ../ .git/ __pycache__/ cell.py gcell.py
# The contents of .git folder
%ls .git
AUTO_MERGE MERGE_HEAD ORIG_HEAD hooks/ logs/
COMMIT_EDITMSG MERGE_MODE config index objects/
HEAD MERGE_MSG description info/ refs/
You can check the status of the repository by git status
!git status
On branch main
All conflicts fixed but you are still merging.
(use "git commit" to conclude merge)
Changes to be committed:
modified: gcell.py
Untracked files:
(use "git add <file>..." to include in what will be committed)
__pycache__/
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
All conflicts fixed but you are still merging.
(use "git commit" to conclude merge)
Changes to be committed:
modified: gcell.py
Untracked files:
(use "git add <file>..." to include in what will be committed)
__pycache__/
Register the current version by git commit with a message by -m.
!git commit -m "initial version"
!git status
[main ff72690] initial version
Committer: Kenji Doya <doya@starfishM4.local>
Your name and email address were configured automatically based
on your username and hostname. Please check that they are accurate.
You can suppress this message by setting them explicitly. Run the
following command and follow the instructions in your editor to edit
your configuration file:
git config --global --edit
After doing this, you may fix the identity used for this commit with:
git commit --amend --reset-author
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 ff72690d9950381e4171528c547c364659c70875 (HEAD -> main)
Merge: 6dc49e0 86d9170
Author: Kenji Doya <doya@starfishM4.local>
Date: Sat Mar 29 07:18:35 2025 +0900
initial version
You can check the revision history by git log
!git log
commit ff72690d9950381e4171528c547c364659c70875 (HEAD -> main)
Merge: 6dc49e0 86d9170
Author: Kenji Doya <doya@starfishM4.local>
Date: Sat Mar 29 07:18:35 2025 +0900
initial version
commit 86d9170fe5cf379ddec96cb0484854b3f047797f (myBranch)
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 86d9170fe5cf379ddec96cb0484854b3f047797f (HEAD -> myBranch)
Author: Kenji Doya <doya@starfishM4.local>
Date: Sat Mar 29 03:20:18 2025 +0900
added gcell.py
diff --git a/gcell.py b/gcell.py
index cd7b2a5..db1f7b9 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 ff72690d9950381e4171528c547c364659c70875 (main)
|\ Merge: 6dc49e0 86d9170
| | Author: Kenji Doya <doya@starfishM4.local>
| | Date: Sat Mar 29 07:18:35 2025 +0900
| |
| | initial version
| |
| * commit 86d9170fe5cf379ddec96cb0484854b3f047797f (HEAD -> myBranch)
| | 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 ff72690d9950381e4171528c547c364659c70875 (HEAD -> main)
|\ Merge: 6dc49e0 86d9170
| | Author: Kenji Doya <doya@starfishM4.local>
| | Date: Sat Mar 29 07:18:35 2025 +0900
| |
| | initial version
| |
| * commit 86d9170fe5cf379ddec96cb0484854b3f047797f (myBranch)
| | 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 ff72690d9950381e4171528c547c364659c70875 (HEAD -> main)
|\ Merge: 6dc49e0 86d9170
| | Author: Kenji Doya <doya@starfishM4.local>
| | Date: Sat Mar 29 07:18:35 2025 +0900
| |
| | initial version
| |
| * commit 86d9170fe5cf379ddec96cb0484854b3f047797f (myBranch)
| | 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