Clean up tools and tests dirs

[EvanKirshenbaum]

Working on #22, it became clear just how much of a mess the tools and tests dirs are. There is a lot of code that nobody needs, especially in the tests dir, but every time something changes, we need to make sure that everything still runs (at least in tools) or the mypy checks fail.

What I'm proposing is

1. Get rid of all code in tools and tests that nobody needs.
2. Make sure that nothing in tests actually belongs somewhere else.
3. Split tools into
   • tools: Scripts that we expect users to use
   • tools/deprecated: Old scripts that I'd rather people stop using.
   • dev-tools: Scripts needed for building code. This includes
     • Code for generating dimensions.py (dim_generator.py, gen_dims.py)
     • Code for finding mixing and dilution sequences.

       Migrated from internal repository. Originally created by @EvanKirshenbaum on Feb 21, 2023 at 10:29 AM PST. Closed on Feb 21, 2023 at 1:37 PM PST.

[EvanKirshenbaum]

This issue was referenced by the following commit before migration:

• 625c8aec3ac7e4e0473f5ffe34e0ab5a49b05451 by @EvanKirshenbaum on Feb 21, 2023 at 11:51 AM PST

[EvanKirshenbaum]

My apologies for all the commit messages above with failing checks. The reorganization broke the MyPy checks on the server in ways that were difficult to track down, since the code was passing on my machine. I think it's better now.

Anyway, I removed most of the contents of tests, leaving just scratch.py and a few others that might be useful in the future. I split tools into

• tools: Just the scripts that we expect users to run.
  • Currently interactive.py and cs.py.
• tools/support: Modules that are needed by other tools.
  • Currently just pcr.py, which had its Exerciser removed, so it can't be run directly.
• tools/deprecated: Tools that we don't want users to run anymore.
  • wombat.py, joey.py, opendrop.py and bilby.py. They should use interactive.py.
  • joey_pcr.py (the Exerciser from the old pcr.py) and bilby_pcr.py. They should use cs.py for the combinatorial synthesis and add new scripts modeled on it for the others.
• dev-tools: Scripts and support modules to be used by developers rather than users.
  • Generating dimensions.py: dim_generator.py,gen_dims.py`
  • Generating documentation: build_doc.py
  • Finding new mixing and dilution sequences: mix_ga_placed.py, dilution_ga_placed.py, dilution_ga.py. (The last may not be needed.)

When doing this, I realized that I had never checked in quantities/scalar.py (#22), so I did so.

Also, since I made the call to say that Python version 10 is the baseline supported version (https://github.com/HPInc/HP-Digital-Microfluidics/issues/237#issue-1222592), I removed the 3.9 MyPy checking from the GitHub workflow.

Migrated from internal repository. Originally created by @EvanKirshenbaum on Feb 21, 2023 at 1:24 PM PST.