Support GSD >= 2.9 (#1131)

* pin gsd>=2.9; update gsd.hoomd.Snapshot to gsd.hoomd.Frame

* remove outdated unit test

* fix numpy to 1.24.2 to fix unyt comparison bug

---------

Co-authored-by: CalCraven <nicholas.c.craven@vanderbilt.edu>

environment-dev-win.yml

@@ -9,12 +9,12 @@ dependencies:
   - gmso>=0.9.0
   - foyer>=0.11.0
   - garnett>=0.7.1
-  - gsd>=1.2
+  - gsd>=2.9
   - intermol
   - mdtraj
   - networkx
   - nglview>=2.7
-  - numpy
+  - numpy=1.24.2
   - openbabel>=3.0.0
   - packmol=1!18.013
   - parmed>=3.4.3

environment-dev.yml

@@ -9,13 +9,13 @@ dependencies:
   - foyer>=0.11.0
   - freud>=2.0.0
   - garnett>=0.7.1
-  - gsd>=2
+  - gsd>=2.9
   - hoomd>=3
   - intermol
   - mdtraj
   - networkx
   - nglview>=3
-  - numpy
+  - numpy=1.24.2
   - openbabel>=3
   - packmol>=20
   - parmed>=3.4.3

environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - ele
-  - numpy
+  - numpy=1.24.2
   - packmol>=18
   - gmso>=0.9.0
   - parmed>=3.4.3

mbuild/formats/gsdwriter.py

@@ -60,7 +60,7 @@ def write_gsd(
     if shift_coords:
         xyz = coord_shift(xyz, structure.box[:3])
 
-    gsd_snapshot = gsd.hoomd.Snapshot()
+    gsd_snapshot = gsd.hoomd.Frame()
 
     gsd_snapshot.configuration.step = 0
     gsd_snapshot.configuration.dimensions = 3
@@ -101,7 +101,7 @@ def write_gsd(
     if structure.rb_torsions:
         _write_dihedral_information(gsd_snapshot, structure)
 
-    with gsd.hoomd.open(filename, mode="wb") as gsd_file:
+    with gsd.hoomd.open(filename, mode="w") as gsd_file:
         gsd_file.append(gsd_snapshot)
 
 

mbuild/formats/hoomd_snapshot.py

@@ -27,11 +27,11 @@ def _get_hoomd_version():
 def from_snapshot(snapshot, scale=1.0):
     """Convert a Snapshot to a Compound.
 
-    Snapshot can be a hoomd.Snapshot or a gsd.hoomd.Snapshot.
+    Snapshot can be a hoomd.Snapshot or a gsd.hoomd.Frame.
 
     Parameters
     ----------
-    snapshot : hoomd.Snapshot or gsd.hoomd.Snapshot
+    snapshot : hoomd.Snapshot or gsd.hoomd.Frame
         Snapshot from which to build the mbuild Compound.
     scale : float, optional, default 1.0
         Value by which to scale the length values

mbuild/tests/test_compound.py

@@ -2360,15 +2360,6 @@ def test_from_rdkit_smiles(self, test_smiles):
             np.diff(np.vstack(pos).reshape(len(pos), -1), axis=0) == 0
         ).all()
 
-    @pytest.mark.parametrize("bad_smiles", ["F[P-](F)(F)(F)(F)F"])
-    @pytest.mark.skipif(not has_rdkit, reason="RDKit is not installed")
-    def test_incorrect_rdkit_smiles(self, bad_smiles):
-        with pytest.raises(
-            MBuildError,
-            match=r"RDKit was unable to generate " r"3D coordinates",
-        ):
-            mb.load(bad_smiles, smiles=True, backend="rdkit", seed=29)
-
     @pytest.mark.skipif(not has_openbabel, reason="Pybel is not installed")
     def test_get_smiles(self):
         test_strings = ["CCO", "CCCCCCCC", "c1ccccc1", "CC(=O)Oc1ccccc1C(=O)O"]

mbuild/tests/test_gsd.py

@@ -43,7 +43,7 @@ def test_particles(self, ethane):
         from mbuild.utils.sorting import natural_sort
 
         ethane.save(filename="ethane.gsd", forcefield_name="oplsaa")
-        with gsd.hoomd.open("ethane.gsd", mode="rb") as f:
+        with gsd.hoomd.open("ethane.gsd", mode="r") as f:
             frame = f[0]
 
         assert frame.configuration.step == 0
@@ -88,7 +88,7 @@ def test_box(self, ethane):
         ethane.box = Box(lengths=[2.0, 3.0, 4.0])
 
         ethane.save(filename="ethane.gsd", forcefield_name="oplsaa")
-        with gsd.hoomd.open("ethane.gsd", mode="rb") as f:
+        with gsd.hoomd.open("ethane.gsd", mode="r") as f:
             frame = f[0]
 
         box_from_gsd = frame.configuration.box.astype(float)
@@ -101,7 +101,7 @@ def test_box(self, ethane):
 
         ethane.periodicity = (True, True, True)
         ethane.save(filename="ethane-periodicity.gsd", forcefield_name="oplsaa")
-        with gsd.hoomd.open("ethane-periodicity.gsd", mode="rb") as f:
+        with gsd.hoomd.open("ethane-periodicity.gsd", mode="r") as f:
             frame = f[0]
         box_from_gsd_periodic = frame.configuration.box.astype(float)
         assert np.array_equal(box_from_gsd, box_from_gsd_periodic)
@@ -111,7 +111,7 @@ def test_box(self, ethane):
         ethane.save(
             filename="triclinic-box.gsd", forcefield_name="oplsaa", box=box
         )
-        with gsd.hoomd.open("triclinic-box.gsd", mode="rb") as f:
+        with gsd.hoomd.open("triclinic-box.gsd", mode="r") as f:
             frame = f[0]
         lx, ly, lz, xy, xz, yz = frame.configuration.box
 
@@ -131,7 +131,7 @@ def test_rigid(self, benzene):
 
         benzene.label_rigid_bodies(rigid_particles="C")
         benzene.save(filename="benzene.gsd", forcefield_name="oplsaa")
-        with gsd.hoomd.open("benzene.gsd", mode="rb") as f:
+        with gsd.hoomd.open("benzene.gsd", mode="r") as f:
             frame = f[0]
 
         rigid_bodies = frame.particles.body
@@ -150,7 +150,7 @@ def test_bonded(self, ethane):
         from foyer import Forcefield
 
         ethane.save(filename="ethane.gsd", forcefield_name="oplsaa")
-        with gsd.hoomd.open("ethane.gsd", mode="rb") as f:
+        with gsd.hoomd.open("ethane.gsd", mode="r") as f:
             frame = f[0]
 
         structure = ethane.to_parmed()
@@ -244,7 +244,7 @@ def test_pairs(self, benzene):
         from foyer import Forcefield
 
         benzene.save(filename="benzene.gsd", forcefield_name="oplsaa")
-        with gsd.hoomd.open("benzene.gsd", mode="rb") as f:
+        with gsd.hoomd.open("benzene.gsd", mode="r") as f:
             frame = f[0]
 
         structure = benzene.to_parmed()
@@ -273,7 +273,7 @@ def test_units(self, ethane):
             ref_mass=ref_mass,
             box=box,
         )
-        with gsd.hoomd.open("ethane.gsd", mode="rb") as f:
+        with gsd.hoomd.open("ethane.gsd", mode="r") as f:
             frame = f[0]
 
         box_from_gsd = frame.configuration.box.astype(float)
@@ -312,7 +312,7 @@ def test_box_dimensions(self, benzene):
             benzene, n_compounds=n_benzenes, box=[0, 0, 0, 4, 4, 4]
         )
         filled.save(filename="benzene.gsd")
-        with gsd.hoomd.open("benzene.gsd", mode="rb") as f:
+        with gsd.hoomd.open("benzene.gsd", mode="r") as f:
             frame = f[0]
         positions = frame.particles.position.astype(float)
         for coords in positions:

mbuild/tests/test_hoomd.py

@@ -74,7 +74,7 @@ def test_compound_from_gsdsnapshot(self, ethane):
         snap, _ = to_hoomdsnapshot(filled)
 
         # copy attributes from the snapshot to a gsd snapshot
-        gsd_snap = gsd.hoomd.Snapshot()
+        gsd_snap = gsd.hoomd.Frame()
         gsd_snap.particles.N = snap.particles.N
         gsd_snap.particles.types = snap.particles.types
         gsd_snap.particles.typeid = snap.particles.typeid