First refactor effort on march to first release version 0.1

[gwaybio]

This PR mostly touches the preprocessing module. The PR also introduces minor changes in two files in the generate profiles module: 1.generate-profiles/profiling_config.yaml and 1.generate-profiles/0.merge-single-cells.py

Changelog

• Abstracting command arguments (loading config file and --force flag) to new function parse_command_args()
• Updating "force" logic. There are now two ways to toggle overwriting (perhaps more decisions need to be made here, see #24)
  • This logic is encapsulated in a new function check_if_write().
• Updating language from master to main config.
• [BUG FIX] in 2.process-cells.py we were renaming columns and assigning a site column without actually saving it to the dataframe (here)
• [BUG FIX] closes #32
• close #26
• [BUG FIX] closes #12
• Update script order

[gwaybio]

Thanks for the review - sorry it took me so long to revisit

Readme formatting

See my clarification above.

Do we include both command line and config force_overwrite? (Discussed here)

Yep, we do. See https://github.com/broadinstitute/pooled-cell-painting-profiling-recipe/pull/34/files#diff-6cb5ff5c1a4737e846595bbb4e05719fR11. We can revisit this decision too, once we get some time to play with the welding

You said this PR only touches preprocessing module, but there are commits that touch 1.generate-profiles/profiling_config.yaml and 1.generate-profiles/0.merge-single-cells.py. Do you want to revert them and move them to a different PR?

Nice catch. Can't sneak anything by! Since it is not doing any harm, how about I edit the note in the initial description, and then we can go ahead and merge?

[ErinWeisbart]

LGTM!