* Optimizations to _findNearestDistance()

* Minor changes based on review comments

Also remove trailing whitespace.

As to PDB 3TDZ, MK8 is 2-METHYL-L-NORLEUCINE, which is an isomer of LEU.

https://www.rcsb.org/ligand/5OW is based on LYS and appears in PDB 5EIG.

Resolves openmm/pdbfixer#233.

* Fix typos discovered by codespell

* Revert changes to CI

* Revamp PDBFixer testing

* Use GitHub Actions to run a suite of tests
* Switch from nose to pytest (nose has not been supported in years)
* Download a PDB file and track it instead of fetching it during CI
  (RCSB has blocked testing frameworks in the past).

* Add missing environment.yaml file

* Try the workflow on my branch

* Try to fix the pipeline

* Stop building on jms-updates

Updated version in setup.py

Support all lipid types from OpenMM 7.5

Fixed 'See our manual' link

Fixed box vectors for truncated octahedron

Added option to save files in PDBx/mmCIF format

maintain insertion codes

Fixed exception loading PDBx/mmCIF files with missing blocks

Updated version number to 1.6

Improved handling of insertion codes

Fixed error when calling _matchResidue(). OpenMM now uses compiled functions

Added a seed parameter to addMissingAtoms to allow reproducible results

Update usage as "prog filename [options]"