This repository contains the article template for an Elemental Microscopy article. It also contains several examples of interactive figures:

This template was developed by Colin Ophus and Georgios Varnavides.

Steps to edit locally:

• git clone repo (git clone [email protected]:msa-em/em-template.git)
• switch to dev branch (git checkout dev)
• create virtual environment (conda env create -f environment.yml)
  • you might need to remove the environment if it already exists (conda remove -n em-template --all)
• activate virtual environment in two terminal windows (conda activate em-template)
• edit myst.yml file by:
  • commenting these lines out

    jupyter: true

  • uncommenting these lines

  #  jupyter:
    #    server:
    #      url: 'http://localhost:8888'
    #      token: '512ac78f14e1141db1fac17e8b4099c1e5bc7d589518b38c'

• start the jupyter server in one of the terminal windows (jupyter lab --IdentityProvider.token=512ac78f14e1141db1fac17e8b4099c1e5bc7d589518b38c --ServerApp.allow_origin='http://localhost:3000' --port=8888)
• start MyST in the other terminal window (myst start)
• edit, commit, and push to dev as per usual
  • make sure NOT to commit your must.yml changes!
• open a draft pull request into main (if one doesn't already exist) and keep pushing your changes to dev

The repo has two github actions to automatically deploy computational sites, for the following two case:

• Commits to main directly
• Pull requests into main

If you followed the instructions above (i.e. working off of dev and have an open pull request into main), then you should see a github-actions bot at the top of your pull request which will keep getting edited. Simply click on the Inspect link to see the curvenote staging site, and press preview to see the deployed site based on your latest commit.