Merge pull request #1133 from glotzerlab/remove-garnett

Remove Garnett as a Testing Dependency

.github/workflows/oldest-test-reqs.txt

@@ -2,7 +2,6 @@ ase==3.16.0
 cmake==3.13.0
 cython==0.29.14
 dynasor==1.1b0; platform_system != "Windows"
-garnett==0.7.1
 gsd==2.4.2
 matplotlib==3.0.0
 numpy==1.15.0

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools", "wheel", "oldest-supported-numpy", "cython>=0.29.14", "scikit-build>=0.17.3", "cmake"]
+requires = ["setuptools", "wheel", "oldest-supported-numpy", "cython>=0.29.14,<3.0.0", "scikit-build>=0.17.3", "cmake"]
 
 [tool.black]
 target-version = ['py36']

requirements/requirements-test-compatible.txt

@@ -3,9 +3,8 @@ cmake>=3.13.0
 coverage>=6.2
 cython>=0.29.14, <3.0.0
 dynasor>=1.1b0; platform_system != "Windows"
-garnett>=0.7.1
 GitPython>=3.1.24
-gsd>=2.4.2, <3.0.0
+gsd>=2.4.2
 matplotlib>=3.0.0
 numpy>=1.14.0
 pillow>=6.2.0 --only-binary=pillow

requirements/requirements-test.txt

@@ -3,9 +3,8 @@ cmake==3.27.0
 coverage==7.2.7
 cython==0.29.35
 dynasor==1.1.1; platform_system != "Windows"
-garnett==0.7.1
 GitPython==3.1.32
-gsd==2.9.0
+gsd==3.1.0
 matplotlib>=3.0.0
 numpy==1.25.2
 pillow>=8.0.0 --only-binary=pillow

setup.py

@@ -65,7 +65,6 @@
     tests_require=[
         "ase>=3.16",
         "gsd>=2.0",
-        "garnett>=0.7.1",
         "matplotlib>=3.0",
         "sympy>=1.0",
     ],

tests/integration/test_reader_integrations.py

@@ -4,12 +4,21 @@
 import os
 import sys
 
+import gsd
+import gsd.hoomd
 import numpy as np
 import numpy.testing as npt
 import pytest
 
 import freud
 
+try:
+    GSD_VERSION = gsd.__version__
+    GSD_READ_FLAG = "rb"
+except AttributeError:
+    GSD_VERSION = gsd.version.version
+    GSD_READ_FLAG = "r"
+
 
 def _relative_path(*path):
     return os.path.join(os.path.dirname(__file__), *path)
@@ -44,22 +53,7 @@ def test_mdanalysis_dcd(self):
         self.run_analyses(reader)
 
     def test_gsd_gsd(self):
-        import gsd.hoomd
-
-        with gsd.hoomd.open(LJ_GSD, "rb") as traj:
-            self.run_analyses(traj)
-
-    def test_garnett_gsd(self):
-        import garnett
-
-        with garnett.read(LJ_GSD) as traj:
-            self.run_analyses(traj)
-
-    @pytest.mark.filterwarnings("ignore:Failed to import dcdreader")
-    def test_garnett_dcd(self):
-        import garnett
-
-        with garnett.read(LJ_DCD) as traj:
+        with gsd.hoomd.open(LJ_GSD, GSD_READ_FLAG) as traj:
             self.run_analyses(traj)
 
     def test_ovito_gsd(self):

tests/validation/test_Minkowski_Structure_Metrics.py

@@ -3,13 +3,21 @@
 
 import os
 
-import garnett
+import gsd
+import gsd.hoomd
 import numpy as np
 import numpy.testing as npt
 import pytest
 
 import freud
 
+try:
+    GSD_VERSION = gsd.__version__
+    GSD_READ_FLAG = "rb"
+except AttributeError:
+    GSD_VERSION = gsd.version.version
+    GSD_READ_FLAG = "r"
+
 
 def _get_structure_data(structure, qtype):
     return np.genfromtxt(
@@ -30,15 +38,15 @@ def test_minkowski_structure_metrics(self, structure):
         expected_wl = _get_structure_data(structure, "w")
         expected_avwl = _get_structure_data(structure, "avw")
 
-        with garnett.read(
+        snap = gsd.hoomd.open(
             os.path.join(
                 os.path.dirname(__file__),
                 "files",
                 "minkowski_structure_metrics",
                 f"{structure}.gsd",
-            )
-        ) as traj:
-            snap = traj[0]
+            ),
+            mode=GSD_READ_FLAG,
+        )[0]
 
         voro = freud.locality.Voronoi()
         voro.compute(snap)