Prep v0.1.0 by creating entrypoints and conda environments

[alexanian]

What type of PR is this? (check all applicable)

• Refactor
• Feature
• Bug Fix
• Optimization
• Documentation Update

What does this implement/fix? Explain your changes.

This is a major reorganization of the code to allow it to be packaged as a conda package called commec which includes three commands:

screen  Run Common Mechanism screening on an input FASTA.
flag    Parse all .screen files in a directory and create two CSVs file of flags raised
split   Split a multi-record FASTA file into individual files, one for each record

This involved rewriting some scripts (including a full Python rewrite of run_pipeline.sh, introducing a pyproject.toml and environment.yml and drafting a meta.yaml (which will eventually end up in https://github.com/bioconda/bioconda-recipes).

A few other, smaller changes:

• Add standard header to files
• Deleted unused files
• Delete commented-out lines

[nwheeler443]

Happy to approve this