Elemental Microscopy Quickstart

This repository contains minimal configuration files to get started for an Elemental Microscopy article.

People

This quickstart guide was developed by Colin Ophus and Georgios Varnavides.

Installation Instructions

Edit locally and push changes

Warning

First, ask one of the organization members to give you write access to the forked repo.

Warning

In what follows and the configuration files, you will see references to change-to-repo-name, which you should replace with the repo name. E.g. this article would be em-quickstart.

Steps to edit locally:

• git clone repo (git clone [email protected]:msa-em/change-to-repo-name.git)
• switch to dev branch (git checkout dev)
• edit environment.yml to
  • change the environment name to the repo name
  • add your package dependencies, pinning versions as necessary
• create virtual environment (conda env create -f environment.yml)
  • you might need to remove the environment if it already exists (conda remove -n change-to-repo-name --all)
• activate virtual environment in two terminal windows (conda activate change-to-repo-name)
• 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
  • this will enable live previews and checks (see below)
  • when you're ready, merge pull request into main. Note this need to be "final" -- it's best practice to merge thematic content changes together

Note

If you don't plan on editing the notebooks, you can skip the myst.yml and jupyter lab steps above

Preview draft deployed site

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.