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reality edited this page Jan 7, 2021 · 6 revisions

Using the server+ git etc

  1. Log in to the server using MobaXTerm
  2. Only the first time, you can type this to set up git and create a new local version of this repository (it should prompt you for your github username/password). Make sure to fill out the email/name fields in the git config commands (if you do it wrong, you can simply run the commands again):
git config --global user.email "[email protected]"
git config --global user.name "Your Name"
git clone https://github.com/reality/mimpred && cd mimpred
  1. Otherwise, you can change directory into the repository using
cd mimpred
  1. Now, we want to make sure that we have pulled the most recent changes from the server, so we're sure that we're working on the most recent version of the repository (e.g., someone else may have made some changes since you last logged in).
git pull
  1. You can start the jupyter notebook by typing:
jupyter notebook Install\ and\ Setup.ipynb

It should then open a Firefox instance with the notebook! If it doesn't work, please ensure that you have followed correctly the instructions for enabling X11 forwarding found here: https://docs.computecanada.ca/wiki/Connecting_with_MobaXTerm

  1. So, you can now edit and run things on the server. The interface might be a little slow, since it's running over the Internet, but code itself should run nice and fast. Remember that there is a focus on repeatability, so if (for example) you have to install some Python modules, include the pip install lines in the notebook. The idea is that someone can repeat the whole experiment by running the notebook!

  2. When you have finished your changes, ensure that you have saved your changes, then close firefox and return to the command line prompt. Then you have to stop the notebook by entering the key combination 'ctrl+c'. Once you have the prompt back, you can run the following two commands to save changes and upload them to the GitHub repository:

git commit -am 'description of changes'
git push

In this way, you can work on the same document together without overwriting things etc. You can go here https://github.com/reality/mimpred to ensure that your changes have been pushed to the server.

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