Minor fixes; pyproject.toml file

[matsen]

• Various fixes concerning tensor and GPU handling
• Adding a pyproject.toml file
• Adding an orig_pcp_idx column to the pcp_dfs
• refactoring so we can get dnsm and mut rate estimation separately

[matsen]

The pyproject.toml file is to avoid this warning:

DEPRECATION: Legacy editable install of netam==0.1.0 from file:///home/matsen/tmp/sabdab/netam (setup.py develop) is deprecated. pip 25.0 will enforce this behaviour change. A possible replacement is to add a pyproject.toml or enable --use-pep517, and use setuptools >= 64. If the resulting installation is not behaving as expected, try using --config-settings editable_mode=compat. Please consult the setuptools documentation for more information. Discussion can be found at pypa/pip#11457