From 4dfd9cf02dae4d953d80991852ed6ae139d4a5f2 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Fri, 6 Oct 2023 10:33:49 -0500
Subject: [PATCH 1/2] Do not use 'old' OpenFF Toolkit API

---
 .github/workflows/CI.yaml |  4 +--
 environment-dev.yml       |  1 +
 foyer/topology_graph.py   | 56 +++++++++++----------------------------
 3 files changed, 19 insertions(+), 42 deletions(-)

diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index 269fd7dd..56291faa 100644
--- a/.github/workflows/CI.yaml
+++ b/.github/workflows/CI.yaml
@@ -50,7 +50,7 @@ jobs:
         run: python -m pip install -e .
 
       - name: Test (OS -> ${{ matrix.os }} / Python -> ${{ matrix.python-version }})
-        run: python -m pytest -v --cov=foyer --cov-report=xml --cov-append --cov-config=setup.cfg --color yes --pyargs foyer
+        run: python -m pytest -v -nauto --cov=foyer --cov-report=xml --cov-append --cov-config=setup.cfg --color yes --pyargs foyer
 
       - name: Upload Coverage Report
         uses: codecov/codecov-action@v2
@@ -95,7 +95,7 @@ jobs:
 
       - name: Run Bleeding Edge Tests
         run: |
-          python -m pytest -v --color yes --pyargs foyer
+          python -m pytest -v -nauto --color yes --pyargs foyer
 
   docker:
     runs-on: ubuntu-latest
diff --git a/environment-dev.yml b/environment-dev.yml
index e6f42b5b..f565e5e2 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -21,6 +21,7 @@ dependencies:
   - pytest-azurepipelines
   - pytest-cov
   - pytest-timeout
+  - pytest-xdist
   - python>=3.8
   - requests
   - requests-mock
diff --git a/foyer/topology_graph.py b/foyer/topology_graph.py
index e187e774..2fef4776 100644
--- a/foyer/topology_graph.py
+++ b/foyer/topology_graph.py
@@ -190,51 +190,27 @@ def from_openff_topology(cls, openff_topology: "OpenFFTopology"):
                 f"Got {type(openff_topology).__name__} instead"
             )
 
-        uses_old_api = hasattr(Topology(), "_topology_molecules")
-
         top_graph = cls()
 
-        if uses_old_api:
-            from parmed import periodic_table as pt
-
-            for top_atom in openff_topology.atoms:
-                atom = top_atom.atom
-                element_symbol = pt.Element[atom.atomic_number]
-                top_graph.add_atom(
-                    name=atom.name,
-                    index=top_atom.topology_atom_index,
-                    atomic_number=atom.atomic_number,
-                    symbol=element_symbol,
-                )
+        from openff.units.elements import SYMBOLS
 
-            for top_bond in openff_topology.topology_bonds:
-                atoms_indices = [
-                    atom.topology_atom_index for atom in top_bond.atoms
-                ]
-                top_graph.add_bond(atoms_indices[0], atoms_indices[1])
+        for atom in openff_topology.atoms:
+            atom_index = openff_topology.atom_index(atom)
+            element_symbol = SYMBOLS[atom.atomic_number]
+            top_graph.add_atom(
+                name=atom.name,
+                index=atom_index,
+                atomic_number=atom.atomic_number,
+                symbol=element_symbol,
+            )
 
-            return top_graph
+        for bond in openff_topology.bonds:
+            atoms_indices = [
+                openff_topology.atom_index(atom) for atom in bond.atoms
+            ]
+            top_graph.add_bond(*atoms_indices)
 
-        else:
-            from openff.units.elements import SYMBOLS
-
-            for atom in openff_topology.atoms:
-                atom_index = openff_topology.atom_index(atom)
-                element_symbol = SYMBOLS[atom.atomic_number]
-                top_graph.add_atom(
-                    name=atom.name,
-                    index=atom_index,
-                    atomic_number=atom.atomic_number,
-                    symbol=element_symbol,
-                )
-
-            for bond in openff_topology.bonds:
-                atoms_indices = [
-                    openff_topology.atom_index(atom) for atom in bond.atoms
-                ]
-                top_graph.add_bond(*atoms_indices)
-
-            return top_graph
+        return top_graph
 
     @classmethod
     def from_gmso_topology(cls, gmso_topology: "gmso.Topology"):

From 81085c5e591f1db9be7a5058415655ee93391741 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Fri, 6 Oct 2023 10:45:34 -0500
Subject: [PATCH 2/2] Update environments

---
 environment-dev-win.yml | 1 +
 environment-win.yml     | 1 +
 2 files changed, 2 insertions(+)

diff --git a/environment-dev-win.yml b/environment-dev-win.yml
index 6304798b..a5143168 100644
--- a/environment-dev-win.yml
+++ b/environment-dev-win.yml
@@ -18,6 +18,7 @@ dependencies:
   - pytest-azurepipelines
   - pytest-cov
   - pytest-timeout
+  - pytest-xdist
   - python>=3.8
   - requests
   - requests-mock
diff --git a/environment-win.yml b/environment-win.yml
index d47d9136..f7ba8545 100644
--- a/environment-win.yml
+++ b/environment-win.yml
@@ -15,4 +15,5 @@ dependencies:
   - pytest-azurepipelines
   - pytest-cov
   - pytest-timeout
+  - pytest-xdist
   - python<=3.8