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Practice and theory of brain imaging

Week 5 session 1: Github walkthrough; modules and testing

Recording

Week5 session 1 recording

Schedule and plan

Github walkthrough

Diagram of the workflow:

Team leader:

  1. Before you start, agree a team name with your team, and get your team members’ Github usernames — e.g. matthew-brett.
  2. Go to https://github.com/nipraxis/diagnostics-template
  3. Open the Issues tab. You can get there directly by appending issues to the URL, like this: https://github.com/nipraxis/diagnostics-template/issues
  4. Make a “New Issue”.
  5. In the issue, ask for a new diagnostics repository for your team. Specify a name for your team.
  6. Wait for our response, on that issue.
  7. You will see URL to your new repository named nipraxis-summer-2023/diagnostics-<teamname> where <teamname> is the name you specified in your issue. You may also get an email telling you about the repository.
  8. Go to the link for your repository. It will be of form https://github.com/nipraxis-summer-2023/diagnostics-<teamname>.
  9. Make sure you know the Github usernames of your team members.
  10. Go to the Settings tab.
  11. Click on “Collaborators and Teams” on the left.
  12. Click on “Add people”. Add the team members with whatever permissions you agree. Maybe “maintain” is a good default.
  13. Wait for your team members to accept their invitations.

Everyone (including the team leader):

  1. You should get an invitation to your team repository.
  2. Click on the link, that should be of form https://github.com/nipraxis-summer-2023/diagnostics-<teamname>, where <teamname> is your agreed team name.
  3. Click on the “Fork” button near the top right of the screen.
  4. Accept the defaults, click “Create Fork”.
  5. Now you should be at a new page, with URL of form: https://github.com/<your-gh-user>/diagnostics-<teamname> where <your-gh-user> is your Github username.
  6. Click on the green “Code” button, select the “HTTPS” tab. Copy the link there, which will be of form: https://github.com/<your-gh-user>/diagnostics-<teamname>. If you have got SSH keys set up, you might instead consider using the “SSH” tab, and link.
  7. Open a terminal on your computer. Change to a suitable directory to store your code. Consider cd $HOME/Documents/nipraxis-work if you don’t have a strong alternative preference.
  8. Type a suitably modified version of this command: git clone https://github.com/<your-gh-user>/diagnostics-<teamname>, replacing the relevant parts with your username and your team name. (If you used SSH above, modify the clone command to something of form git clone git@github.com:<your-gh-user>/diagnostics-<teamname>
  9. You should now have a local clone of your fork.
  10. Change directory to the new cloned repository, with command of form cd diagnostics-<teamname>.
  11. Add a new remote that points to the main “upstream” version of your team code, using a command of form: git remote add upstream https://github.com/nipraxis-summer-2023/diagnostics-<teamname>.
  12. Check your remote worked with the command git fetch upstream.
  13. Make a new feature branch editing-readme, with the command git branch editing-readme.
  14. Checkout this branch with git checkout editing-readme.
  15. Make sure you are up to date with the latest code from upstream with git merge upstream/main. This may do nothing, if there are no new changes in the upstream main branch.
  16. Use your text editor to make a change to the README.md file.
  17. Confirm Git agrees that you have changed the file with git status
  18. Add the file to the staging area with git add README.md
  19. Confirm Git agrees that you have added the file with git status
  20. git commit (if you have your text editor set up correctly to work with Git) or git commit -m 'Edit to README' (if you do not).
  21. Push up your changes to your fork with git push origin editing-readme --set-upstream.
  22. Next make a pull request from this branch on Github. Either use the URL that Github displays in your terminal from the command above, of form https://github.com/<your-gh-user>/diagnostics-<teamname}/pull/new/editing-readme, OR go to your fork URL (of https://github.com/<your-gh-user>/diagnostics-<teamname>, and use the new green “Compare and pull request” button for your editing-readme branch. Click on that
  23. Fill in the pull request description and submit the pull request.

The team leader should:

  1. Go to the main repository page — of form https://github.com/nipraxis-summer-2023/diagnostics-<teamname>.
  2. Click on one or more of the Pull Request pages available there, and click on the green Merge button to merge it / them. (In fact, there are several options available via that green button, we are taking the default route by clicking on the green button. See the Github merge page for more details.

Techniques

  • @ mentions on Github.

Modules and testing

Reading and homework for next week

You should (by Thursday) receive a pull request into your upstream repository. Please check there for the homework.

If you do not see a pull request, please email Matthew.

The pull request has instructions, and some more pages to read.

Your task:

  • Merge the pull request.
  • Go to your local clone of your fork.
  • git fetch upstream
  • git branch fix-validation upstream/main
  • git checkout fix-validation

For instructions, first, look in the Get the data section of the README.md file, and follow the instructions there.

Then look at the files:

  • scripts/validate_data.py

Next work on the code to run the given commands and fix the errors. See the instructions in the PR.

Now push, and make a pull request. Work together to find the best solution, review the pull request, and merge it.