Drop support/testing for py3.8 (mosdef-hub#781)

* drop testing for python 3.8

* convert residue number instead of residue idx when going to and from parmed

.github/workflows/CI.yaml

@@ -19,7 +19,7 @@ jobs:
  fail-fast: false
  matrix:
  os: [macOS-latest, ubuntu-latest]
- python-version: ["3.8", "3.9", "3.10", "3.11"]
+ python-version: ["3.9", "3.10", "3.11"]
  pydantic-version: ["2"]
 
  defaults:

gmso/external/convert_parmed.py

@@ -72,10 +72,10 @@ def from_parmed(structure, refer_type=True):
  charge=atom.charge * u.elementary_charge,
  position=[atom.xx, atom.xy, atom.xz] * u.angstrom,
  atom_type=None,
- residue=(residue.name, residue.idx + 1),
+ residue=(residue.name, residue.number),
  element=element,
  )
- site.molecule = (residue.name, residue.idx + 1) if ind_res else None
+ site.molecule = (residue.name, residue.number) if ind_res else None
  site.atom_type = (
  copy.deepcopy(pmd_top_atomtypes[atom.atom_type])
  if refer_type and isinstance(atom.atom_type, pmd.AtomType)
@@ -474,7 +474,7 @@ def to_parmed(top, refer_type=True):
  structure.add_atom(
  pmd_atom,
  resname=site.residue.name,
- resnum=site.residue.number - 1,
+ resnum=site.residue.number,
  )
  else:
  structure.add_atom(pmd_atom, resname="RES", resnum=-1)