Git authors
Introduction
We need your help to contribute to this project!
If you are interested in moving your script in to the repository, please read through these options.
Github user setup
Create a free account at github
https://github.com/plans
Then go to
https://github.com/Pymol-Scripts/Pymol-script-repo
Near the top right corner, click: Fork
In the top left corner, it should now say: YOUR_NAME / Pymol-script-repo. This is your own repository.
Click HTTP in the middle. We will use this, and it should be like.
https://GIT_USER_NAME@github.com/GIT_USER_NAME/Pymol-script-repo.git
You also have to find your Github API-token for the acces.
Locate token at: Account settings -> Account admin -> API Token Configure git
0123456789yourf0123456789token
Online - make changes to a file
You can change a file online, by clicking it, and then at the right side, click Edit this file.
Make changes, write a "commit message", and in the lower right, click Commit changes.
If you want to your changes to be part of the official repository, click Pull Request, and write a message.
This will notify the group of admins to review your changes.
If the changes reasonable and not malicious for the computer, your Pull Request will quickly be in the official repository.
Note, that you can not add files online.
Git setup - Add scripts to the project
The next setup can be followed for both linux and windows users, if windows users use the Bash terminal.
You can paste from the wiki into the Bash window by using the console's window icon (topleft) and choosing Edit -> Paste
- Navigate to C:/Users/YOURNAME/Documents/Pymol-script-repo OR /home/YOURNAME/Software/pymol/Pymol-script-repo
- Win users: Right click in folder -> Select: Git Bash
- Write in terminal
git config --global user.name "Your Name" git config --global user.email you@example.com git config --global github.user GIT_USER_NAME git config --global github.token 0123456789yourf0123456789token git remote set-url origin https://GIT_USER_NAME@github.com/GIT_USER_NAME/Pymol-script-repo.git
See your information
cat ~/.gitconfig git branch git remote show origin
Daily workflow
We now imagine that you would like to make a script called testscript.py. Remember that the filename should be with small letters, and without minus "-" in the name.
You will like to work on this script, and try it out, until its ready for sharing and make it public at the PyMOL wiki.
To follow the following guidelines, you can consider reading some other introduction pages to git.
Git commands, fork-a-repo, send-pull-requests
First we make branch where we will work with the script testscript.py. We will create the branch testscript, by making a copy of the master branch.
git branch # See what branches exist git checkout -b testscript master # Make branch "testscript" from branch "master", and change into the branch "testscript" git branch # The star mark you are in the "testscript" branch git ls-tree --name-only testscript # See which files are tracked
Then we create a first initial version of the file
(echo 'from pymol import cmd' && echo 'def testme():' && echo ' print("Hello world")' && echo 'cmd.extend("testme",testme)') > testscript.py
Then we want git to track the file, so we have to add the file. And we then commit it.
git status # testscript.py is untracked git add testscript.py # To start tracking the file git status # testscript.py is added and staged. git commit -m "I added testscript" # So, now you are done with the first thing.
Then start PyMOL, import the script and initiate the function testme
import testscript # To import the functions in the script help(testscript) # To see the defined functions testme # To activate the function. Is write "Hello world"
You then make some changes to your script.
After you have made some changes, you put your changes to the stage area, before you commit.
(echo 'from pymol import cmd' && echo 'def testme():' && echo ' print("Hello world")' && echo ' print("Hello changes")' && echo 'cmd.extend("testme",testme)') > testscript.py git status # To see that there has been a change git stage testscript.py # To add to stage area git status # See info again git commit -m "Updated print command" # Change is now committed git status # Nothing to report
Every time you do a change to your script, you stage and commit. Repeatedly through the progress.
git stage testscript.py git commit -m "Changed x,y,z"
Once you have work isolated in a branch, you will eventually want to incorporate it into your main branch. You can merge any branch into your current branch with the git merge command.
git checkout master # First go into the branch, in which you like to merge the changes to. git branch # See branches git ls-tree --name-only master # See which files branch "master" is taking care of git merge testscript # To merge into branch "master" from "testscript". git ls-tree --name-only master # Now branch "master" is also taking care of testscript.py git status # Nothing to report git branch -d testscript # We are done with the branch and delete it.
Now you want to push your changes to the remote repository at github.
git remote # List your aliases for remote repositories git remote show origin # List detailed information of the alias "origin". git push origin master # Push changes to your remote repository with alias "origin" from your branch "master"
You now want to make you new script part of the official repository by making a Pull request at the github page.
Make Pull request
Go to https://github.com/ and click "Dashboard" at the top.
Click your repository to the right. Click in the near top right "Pull request", and write a message what you have done.
This will notify the group of admins to review your changes.
If the changes reasonable and not malicious for the computer, your Pull Request will quickly be in the official repository.
You now have to make description at the PyMOL wiki page.
Please read these guidelines, when you create a script PyMOL wiki page.