2. Revision of Python and best practices. Coding Molecular Dynamics
Overview
Teaching: min
Exercises: minQuestions
Objectives
Table of Content
- Brief Python overview
- Best practices
- Working on collaborative projects with Git and GitHub
- Constructing MD integrators
1. Python introduction
My best referece is this site
Copy the example from
Instructors_material/Python/Python_overview.ipynb
or from:
https://github.com/compchem-cybertraining/Tutorials_Python
2. Best practices
- PEP standards, readability and modularity of the codes
- testing (covered above)
- GitHub (this section)
This section can also be found here
I also recommend this reference
And a more complete documentation
Below I will summarize the list of most important Git commands. Note that the names in the UPPER CASE have to be substituted with the actual names specific to your work.
2.1. Working locally (development and info)
2.1.1. Initializing an empty repo
To create a brand-new Git repo with nothig else
git init
2.1.2. The status of your repo
To shows the current state of your project. This will show which files/directories are in unstaged/staged/commited/uncommited as well as the branch on which you are currently on
git status
2.1.3. The history of commits
To show the history of all commits and the development tree, highlights the sections
git log
A better version of this
git log --graph --pretty=format:'%C(magenta)%h%C(blue)%d%Creset %s %C(blue bold)- %an, %ar%Creset'
or
git log --decorate
2.1.4. Diff
To show the changes of the present state made w.r.t. the latest commit
git diff
2.1.5. Adding files and directories in the repo
To add the FILES-OR-DIRECTORIES to a so-called “staging” area (think of concert) - something you are working with at the moment. The FILES-OR-DIRECTORIES are the names of the files or directories to add. You can use an asterisk to match multiple files
git add FILES-OR-DIRECTORIES
2.1.6. Commiting
This will commit the files in the current “staging” area to the development history of the code - this way you save the most valuable and recent state of the project. You can also think of this as making a snapshot of the history of your code. The message should be informative and must describe clearly what changes have you made in the present version w.r.t. the older state of the code.
git commit -m "Some-message"
2.2. Working with branches
2.2.1. Find out the current branch
To show the list of available branches and highlight the active branch
git branch
or slightly more verbose
git branch -rv
2.2.2. Creating a new branch
To create a new branch called BRANCH-NAME. The present repository in its present state will be copied into the new branch.
git branch BRANCH-NAME
2.2.3. Deleting a branch
To delete a branch called BRANCH-NAME.
git branch -d BRANCH-NAME
2.2.4. Switching into a new branch
To switch into the existing BRANCH-NAME branch. This will bring up all the files at the stage of the last commit on that branch. Be careful - this may override your existing files, so you’d need to commit all the changes you have made to those files, otherwise all those changes will be lost. Also - this is a way to “recover” accidentally deleted files or “roll back” to the latest commited stage.
git checkout BRANCH-NAME
2.2.5. Merging
To merge the branch called BRANCH-NAME into your currently active branch
git merge BRANCH-NAME
2.2. Working with remotes
2.2.1. cloning
To clone another repository located at the REPOSITORY_URL (remote = e.g. GitHub repo) to your current repository (local computer)
git clone REPOSITORY_URL.git
2.2.2. Info on the remotes
To show the list of available remotes
git remote -v
2.2.3. Adding a remote
Add a “remote” you can pull from and push to. The REMOTE-NAME will be a short name of the remote, whereas REMOTE-URL is the actual link to the remote repository (ending with .git).
There are couple standard names of the remotes:
-
origin
- this is your own GitHub repository which mirrors your local repo -
upstream
- this is the GitHub repository which you may not have rights to, but the one where you are planning to contribute togit remote add REMOTE-NAME REMOTE-URL
2.2.4. Renaming a remote
To rename the name of the already existing remote
git remote rename OLD-REMOTE-NAME NEW-REMOTE-NAME
2.2.5. Removing a remote
To remove the remote (a link to the remote repository, known to your git package) named REMOTE-NAME. This will remote the name of the remote from your list of available remotes. This doesn’t change the remote repository, of course
git remote rm REMOTE-NAME
2.2.6. Pulling
To get the latest version of the REMOTE-BRANCH branch on the remote repository REMOTE-NAME and merge it into you presently chosen branch.
git pull REMOTE-NAME REMOTE-BRANCH
2.2.7. Pushing
To update the branch REMOTE-BRANCH of a remote reporisotry you have (write) access to called REMOTE-NAME with the latests updates (commits) on the branch of a local repository you are currently in
git push REMOTE-NAME REMOTE-BRANCH
2.3. Using GIT - practical exercies
git clone https://github.com/<your-account>/Cyber_Training_Workshop_2021.git
git remote add origin https://github.com/<your-account>/Cyber_Training_Workshop_2021.git
cd course_work
mkdir my_name
git add my_name
git commit -m "Added my stuff"
git push origin main
A typical session is:
git init
git status
git add my_code.py
git status
git commit -m "Added my new code"
git status
git push origin master
A session with branching and external repo
git clone https://github.com/Quantum-Dynamics-Hub/libra-code.git
git branch my_new_feature
git branch
git add my_code.py
git commit -m "fixed a bug"
git remote add origin https://github.com/alexvakimov/libra-code.git
git push origin my_new_feature
A session with merging and upstream update
git remote add origin https://github.com/alexvakimov/libra-code.git
git remote add upstream https://github.com/Quantum-Dynamics-Hub/libra-code.git
git pull upstream master
git branch my_new_feature
git branch
git add my_code.py
git commit -m "fixed a bug"
git status
git checkout master
git merge my_new_feature
git push origin master
3. Working on collaborative projects with Git and GitHub
4. Molecular Dynamics
Presentation
Key Points