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Additional Guidelines and Suggestions

When you've made significant changes to a method, you might need to find all its instances in Simmate. You can use Spyder's Find window for this. Here's how to set it up:

  1. In Spyder, go to the View tab (at the top of the window) > Panes > select Find.
  2. The Find option should now appear in the top-right window of Spyder, alongside your Help window and Variable Explorer.
  3. In the Find window, set Exclude to the following to prevent these files from being searched:
    *.csv, *.dat, *.log, *.tmp, *.bak, *.orig, *.egg-info, *.svg, *.xml, OUTCAR, *.js, *.html
  4. Set Search in to the src/simmate directory to limit the search to source code.

Command-Line Git

While we suggest using GitKraken, there might be times when you need to use the git command-line. Github offers detailed guides for this, but we've summarized the essentials here.

To set up 2-factor-auth, follow these steps (according to these instructions):

1. Go to Profile >> Settings >> Account Security
2. Click on "Enable two-factor" authentication
3. Follow the prompts to finish setup (I used SMS and saved my codes to BitWarden)

To create your API token, follow these steps (according to these instructions):

1. Go to Profile >> Settings >> Developer Settings >> Personal Access tokens
2. Generate a new token for 90 days with the "repo" scope and "read:org"
3. Use this token as your password when running git commands

To set up permissions with git on the command-line, follow these steps (using this guide):

1. Make sure the GitHub CLI is installed (`conda install -c conda-forge gh`)
2. Run `gh auth login` and follow the prompts to enter your personal token from above

Here are some frequently used commands...

# To clone a remote directory to your local disk
git clone <GITHUB-URL>

# To pull a specific branch (main here) while in a git directory
git pull origin main

# To discard all changes and reset your branch
git restore .