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
COMMIT_EDITMSG config index objects/
HEAD description info/ refs/
ORIG_HEAD hooks/ logs/
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 ada6e011b864c93c202a176b18ab3b01db8f4801 (HEAD -> main, myBranch)
Author: Kenji Doya <doya@oist.jp>
Date: Mon Dec 16 14:54:00 2024 +0900
added gcell.py
diff --git a/gcell.py b/gcell.py
new file mode 100644
index 0000000..cd7b2a5
--- /dev/null
+++ b/gcell.py
@@ -0,0 +1,25 @@
+"""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()
You can check the revision history by git log
!git log
commit ada6e011b864c93c202a176b18ab3b01db8f4801 (HEAD -> main, myBranch)
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 ada6e011b864c93c202a176b18ab3b01db8f4801 (HEAD -> myBranch, main)
Author: Kenji Doya <doya@oist.jp>
Date: Mon Dec 16 14:54:00 2024 +0900
added gcell.py
diff --git a/gcell.py b/gcell.py
new file mode 100644
index 0000000..cd7b2a5
--- /dev/null
+++ b/gcell.py
@@ -0,0 +1,25 @@
+"""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()
!git log --all --graph
* commit ada6e011b864c93c202a176b18ab3b01db8f4801 (HEAD -> myBranch, main)
| 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 ada6e011b864c93c202a176b18ab3b01db8f4801 (HEAD -> main, myBranch)
| 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 ada6e011b864c93c202a176b18ab3b01db8f4801 (HEAD -> main, myBranch)
| 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