fix write modes

cmeutils/dynamics.py

@@ -30,7 +30,7 @@ def msd_from_gsd(
         Choose from "window" or "direct". See Freud for the differences
         https://freud.readthedocs.io/en/latest/modules/msd.html#freud.msd.MSD
     """
-    with gsd.hoomd.open(gsdfile, "rb") as trajectory:
+    with gsd.hoomd.open(gsdfile, "r") as trajectory:
         init_box = trajectory[start].configuration.box
         final_box = trajectory[stop].configuration.box
         assert all(

cmeutils/gsd_utils.py

@@ -125,7 +125,7 @@ def _validate_inputs(gsd_file, snap, gsd_frame):
     if gsd_file:
         assert isinstance(gsd_frame, int)
         try:
-            with gsd.hoomd.open(name=gsd_file, mode="rb") as f:
+            with gsd.hoomd.open(name=gsd_file, mode="r") as f:
                 snap = f[gsd_frame]
         except Exception as e:
             print("Unable to open the gsd_file")
@@ -307,7 +307,7 @@ def ellipsoid_gsd(gsd_file, new_file, lpar, lperp):
         Value of lperp of the ellipsoids
 
     """
-    with gsd.hoomd.open(new_file, "wb") as new_t:
+    with gsd.hoomd.open(new_file, "w") as new_t:
         with gsd.hoomd.open(gsd_file) as old_t:
             for snap in old_t:
                 snap.particles.type_shapes = [
@@ -352,7 +352,7 @@ def xml_to_gsd(xmlfile, gsdfile):
             overwrite=True,
         )
         hoomd.util.unquiet_status()
-        with gsd.hoomd.open(f.name) as t, gsd.hoomd.open(gsdfile, "wb") as newt:
+        with gsd.hoomd.open(f.name) as t, gsd.hoomd.open(gsdfile, "w") as newt:
             snap = t[0]
             bonds = snap.bonds.group
             bonds = bonds[np.lexsort((bonds[:, 1], bonds[:, 0]))]

cmeutils/structure.py

@@ -78,7 +78,7 @@ def angle_distribution(
     elif degrees and theta_max is None:
         theta_max = 180
 
-    trajectory = gsd.hoomd.open(gsd_file, mode="rb")
+    trajectory = gsd.hoomd.open(gsd_file, mode="r")
     name = "-".join([A_name, B_name, C_name])
     name_rev = "-".join([C_name, B_name, A_name])
 
@@ -179,7 +179,7 @@ def bond_distribution(
         If histogram is True, returns a 2D array of bin centers and bin heights.
 
     """
-    trajectory = gsd.hoomd.open(gsd_file, mode="rb")
+    trajectory = gsd.hoomd.open(gsd_file, mode="r")
     name = "-".join([A_name, B_name])
     name_rev = "-".join([B_name, A_name])
 
@@ -273,7 +273,7 @@ def dihedral_distribution(
         If histogram is True, returns a 2D array of bin centers and bin heights.
 
     """
-    trajectory = gsd.hoomd.open(gsd_file, mode="rb")
+    trajectory = gsd.hoomd.open(gsd_file, mode="r")
     name = "-".join([A_name, B_name, C_name, D_name])
     name_rev = "-".join([D_name, C_name, B_name, A_name])
 
@@ -413,7 +413,7 @@ def gsd_rdf(
     -------
     (freud.density.RDF, float)
     """
-    with gsd.hoomd.open(gsdfile, mode="rb") as trajectory:
+    with gsd.hoomd.open(gsdfile, mode="r") as trajectory:
         snap = trajectory[0]
 
         if r_max is None:
@@ -482,8 +482,8 @@ def get_centers(gsdfile, new_gsdfile):
     new_gsdfile : str
         Filename of new GSD for centers.
     """
-    with gsd.hoomd.open(new_gsdfile, "wb") as new_traj, gsd.hoomd.open(
-        gsdfile, "rb"
+    with gsd.hoomd.open(new_gsdfile, "w") as new_traj, gsd.hoomd.open(
+        gsdfile, "r"
     ) as traj:
         snap = traj[0]
         cluster_idx = gsd_utils.get_molecule_cluster(snap=snap)
@@ -640,7 +640,7 @@ def all_atom_rdf(
     -------
     freud.density.RDF
     """
-    with gsd.hoomd.open(gsdfile, mode="rb") as trajectory:
+    with gsd.hoomd.open(gsdfile, mode="r") as trajectory:
         snap = trajectory[start]
         if r_max is None:
             # Use a value just less than half the maximum box length.

cmeutils/tests/base_test.py

@@ -31,13 +31,13 @@ def gsdfile_images(self, tmp_path):
 
     @pytest.fixture
     def snap(self, gsdfile):
-        with gsd.hoomd.open(name=gsdfile, mode="rb") as f:
+        with gsd.hoomd.open(name=gsdfile, mode="r") as f:
             snap = f[-1]
         return snap
 
     @pytest.fixture
     def snap_bond(self, gsdfile_bond):
-        with gsd.hoomd.open(name=gsdfile_bond, mode="rb") as f:
+        with gsd.hoomd.open(name=gsdfile_bond, mode="r") as f:
             snap = f[-1]
         return snap
 
@@ -93,7 +93,7 @@ def create_frame(i, add_bonds, images, seed=42):
 
 
 def create_gsd(filename, add_bonds=False, images=False):
-    with gsd.hoomd.open(name=filename, mode="wb") as f:
+    with gsd.hoomd.open(name=filename, mode="w") as f:
         f.extend(
             [
                 create_frame(i, add_bonds=add_bonds, images=images)

cmeutils/tests/test_gsd.py

@@ -33,7 +33,7 @@
 class TestGSD(BaseTest):
     def test_ellipsoid_gsd(self, butane_gsd):
         ellipsoid_gsd(butane_gsd, "ellipsoid.gsd", 0.5, 1.0)
-        with gsd.hoomd.open(name="ellipsoid.gsd", mode="rb") as f:
+        with gsd.hoomd.open(name="ellipsoid.gsd", mode="r") as f:
             snap = f[-1]
         assert snap.particles.type_shapes[0]["type"] == "Ellipsoid"