10. Software Management: Exercise#
Name:
GitHub#
Let us try collaborative software development by OIST GitHub oist
For account setup, see https://groups.oist.jp/it/github-oist
Create your GitHub account if you haven’t
Submit the request form: https://oist.service-now.com/sp?id=sc_cat_item&sys_id=2899d8dcdbad2f40d7c7e5951b961985&sysparm_category=332e888edb47df004a187b088c9619be
Our course repository is oist/ComputationalMethods2022
SSH key#
For using a private repository, you need to setup a SSH key for secure connection.
If you have not set up a SSH key on your computer, make a new one by
mkdir ~/.ssh
cd ~/.ssh
ssh-keygen -t rsa
You shuld set a passphrase, which you will be asked when using the key.
On GitHub, from your account menu on the top right corner, select Settings and then SSH and CPG keys on the left side bar.
Press New SSH Key, paste the content of .ssh/rsa.pub, and press Add SSH.
You may also need to press Configure SSO to link it with your OIST login.
If SSH doesn’t work, an alternative way is to use https after generating a personal access token from Settings/Developer settings.
Cloning a repository#
If you just use a copy of a stable software, and not going to contribute your changes, just downloading a zip file is fine.
But if you would congribute to joint development, or catch up with updates, git clone is the better way.
Cloning ComputationalMethods repository#
To download a copy of the repository, run
git clone git@github.com:oist/ComputationalMethods2022.git
You are asked to input the passphrase you set in creating your SSH Key.
This should create a folder ComputationalMethods2022.
%pwd
'/Users/doya/OIST Dropbox/kenji doya/Python/iSciComp'
!git clone git@github.com:oist/ComputationalMethods2022.git
Cloning into 'ComputationalMethods2022'...
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%ls
01_Introduction.ipynb 08_Optimization_Sol.ipynb
01_Introduction_Ex.ipynb 09_Stochastic.ipynb
01_Introduction_Sol.ipynb 09_Stochastic_Ex.ipynb
02_Visualization.ipynb 09_Stochastic_Sol.ipynb
02_Visualization_3D.ipynb 10_Management.ipynb
02_Visualization_Animation.ipynb 10_Management_Ex.ipynb
02_Visualization_Ex.ipynb ComputationalMethods2022/
02_Visualization_Sol.ipynb LICENSE
03_Matrix.ipynb README.md
03_Matrix_Ex.ipynb References.ipynb
03_Matrix_Sol.ipynb SC_logo.png
04_Function.ipynb Solutions.ipynb
04_Function_Ex.ipynb __pycache__/
04_Function_Sol.ipynb _build/
05_Iteration.ipynb _config.yml
05_Iteration_Ex.ipynb _toc.yml
05_Iteration_Sol.ipynb data/
06_ODE.ipynb figures/
06_ODE_Ex.ipynb haisai.py
06_ODE_Sol.ipynb iSciComp.bib
07_PDE.ipynb iSciComp.ipynb
07_PDE_Ex.ipynb index.html
07_PDE_Sol.ipynb lp.py
08_Optimization.ipynb odesim/
08_Optimization_Ex.ipynb pend.gif
Move into the folder and test odesim.py program.
%cd ComputationalMethods2022
/Users/doya/OIST Dropbox/kenji doya/Python/iSciComp/ComputationalMethods2022
%ls
README.md odesim.py second.py test.py
first.py outputs/ simple_growth.py
lorenz.py pendulum.py tatsuo.py
From the console you can run interactively after reading the module as:
python -i odesim.py
sim = odesim('first')
sim.run()
from odesim import *
sim = odesim('first')
Importing ODE: first
sim.run()
t= 10.0 ; state= [0.36787947]
Your branch#
Now make your own branch, check it out, and add your own ODE module.
!git branch myname
!git checkout myname
Switched to branch 'myname'
Make a copy of a dynamics file first.py or second.py, implement your own ODE, and save with a new name, e.g. vdp.py.
Run odesim and confirm that your ODE runs appropriately.
Then you can add and commit your change.
!git status
On branch myname
nothing to commit, working tree clean
!git add vdp.py
fatal: pathspec 'vdp.py' did not match any files
!git commit -m "adding my model vdp.py"
On branch myname
nothing to commit, working tree clean
!git log --graph --oneline --all
* c7c6fe1 (HEAD -> myname, origin/myname, origin/main, origin/HEAD, main) Merge pull request #5 from oist/Sougato
|\
| * 3784ba9 (origin/Sougato) Adding pendulum.py after fixing errors
| * 5d6b385 Adding a pendulum ODE module
* | cdce9fb Merge pull request #4 from oist/Amy
|\ \
| * | 79900ea (origin/Amy) changed into a cubic nonlinearity
| * | 4c16aca edited test.py
| * | 831f82f adding my model test.py
| * | 0ef7d6a adding my model test.py
* | | 86c34e3 Merge pull request #6 from oist/lily
|\ \ \
| * | | dc9432c (origin/lily) Create simple_growth.py
|/ / /
* | | 84f49b7 Merge pull request #2 from oist/rui_fukushima
|\ \ \
| * | | e6b32f9 (origin/rui_fukushima) fix parameter part according prof. comments
| * | | f73f9c2 remove vdp module
| * | | 56110fe remove project notebook
| * | | 7b64069 add lorenz module
| * | | 0e84f70 adding personal project notebook
| * | | 28d072a adding my model vdp.py
| | |/
| |/|
* | | d546ed1 Merge pull request #3 from oist/tatsuo
|\ \ \
| |_|/
|/| |
| * | 919412b (origin/tatsuo) adding my model tatsuo.py
| * | 7109914 adding my model ti.py
| * | ad683ef adding my model tatsuo.py
| |/
| | * c6538a0 (origin/fhn) added pplot method to odesim.py
| | * 0fb56f7 fhn.py module and run_fhn.py for testing it in scripts folder
| | * 37e5425 (origin/kazuma-class2022AY1) Feat: add henonmap and cleanup fhn model
| | * 409d7b5 Feat: add FHN model in odesim.py
| | * d510ba8 Fix: move all images to outputs dir
| | * ed3afff Merge branch 'main' into kazuma-class2022AY1
| | |\
| |_|/
|/| |
* | | 576a0aa added outputs folder
|/ /
| * 16b8943 Feat: add phase plot and bifuraction diagram
| * 4ef681d Feat: add simple fhn plot
| * 5d2b871 Feat: add FHN model script
| * 64e1fbc Feat: add cell executer comment
| * a93c0e4 Feat: create a new script
|/
| * 2ffd690 (origin/kenji) adding my model vdp.py
|/
* 19a1a40 (origin/initial) added .gitignore
* eab5bf5 initial form
* 96d27bf (origin/clean) Delete old folders
* 680c44b Delete old folders
* d9e432e Delete old folders
* a630596 Created for 2022
* 1dc906b first three dynamics functions
* ef02eb6 original dynamics viewer
* 9251e5d Cleanup
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* 7aa7977 Delete Masato-first.py
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* 12c9d16 Dynamics viewer
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* b32f02a sample dynamics files
* eae595e Uploaded the same code as 2018
* 523a383 Create Readme.md
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* 9e9ed1b 2017 files
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* | | | | | | | | 2b2726b Create Readme.md
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* | 5bf9e0f Update Readme.md
* | dc803f7 Some notes on the exercise
* | 8e2b144 Merge pull request #9 from otistwo/master
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* / c456b82 i updated first_Tabbal
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* 69e0154 Create hsiaochiao
* fd4d5c5 DynaView.py and two dynamics modules
* 3d5b491 Create Readme.md
* baf2bb6 First version for "Software Management"
* 50cabde Initialized Readme.md
* b8dc4bb Initial commit
Now push your branch to GitHub repository by, e.g.
git push origin myname
!git push origin myname
Everything up-to-date
Check the status on GitHub: oist/ComputationalMethods2022
and make a pull request for the repository administrator to check your updates.
The administrator may reply back with a comment for revision or merge your change to the main branch.
Pulling updates#
While you are working on your local code, the codes on the origial repository may be updated. You may also want to check the branches other people have created.
You can use git pull to reflect the changes in the GitHub to your local repository.
You can use git branch to see what branches are there and git checkout to try with the codes in other branches.
!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> myname
!git branch
main
* myname
Optional) In addition to adding a new module, you are welcome to improve the main program odesim.py itself. For example,
add other visualization like a phese plot.
fix any bugs or improve error handling.
add documentation.
…