add section for command line operations

[atravitz]

signac command line operations need to be highlighted, especially signac shell

[atravitz]

@glotzerlab/signac-committers - thoughts on if CLI documentation should be under "Getting Started" or "User Guide"? I think it should be its own section

[klywang]

Once the CLI section is created, we should make sure to link it to the Tutorial section (and anywhere else it may be relevant).

[vyasr]

@atravitz I think as per our discussion yesterday I agree with the sectioning suggested in #85 (a separate command line section that falls under the User Guides, whether or not we keep that User Guides header). However, I also think it would be worth updating the tutorial to have more (and more clearly delineated) examples of command line usage. Right now I see only three mentions of the command line interface in the signac (not flow) part of the tutorial, and only two actually show code (for signac find and signac schema).

My suggestion would be to change all the existing lines in the tutorial into pure Python interface (except the creation of the project folder), but then add little info bubbles next to some subset of the Python snippets in the tutorial showing how you'd achieve the equivalent on the command line. For example, next to where we currently have signac.init_project(PROJECT_NAME), we could have a little bubble showing $ signac init PROJECT_NAME. For schema detection, you would change the existing snippet to project.detect_schema(), but then show that that's equivalent to $ signac schema, and so on. Thoughts?

[klywang]

@vyasr I think this is a good idea. We just need to be careful that the info bubbles don't overwhelm the rest of the tutorial.

[cbkerr]

For reference, here is how this was done in the signac project.

I found a package (on conda) that enables embedding the output of any command line command. I tried it on the signac help commands and it works as expected.

After adding it to extensions, we invoke it with:

.. program-output:: signac project -h

We can use this method to insert relevant command line commands into the documentation?