Bugfixes (Python version and Python tests)

.github/workflows/build.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11']
     steps:
     - name: Cancel previous
       uses: styfle/cancel-workflow-action@0.11.0

.readthedocs.yml

@@ -15,6 +15,6 @@ formats:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.8
+  version: 3.10
   install:
     - requirements: docs/requirements.txt

setup.py

@@ -54,10 +54,11 @@
     long_description=long_description,
     long_description_content_type='text/markdown',
     description='Differentiable, Hardware Accelerated, Molecular Dynamics',
-    python_requires='>=2.7',
+    python_requires='>=3.9',
     classifiers=[
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
         'License :: OSI Approved :: Apache Software License',
         'Operating System :: MacOS',
         'Operating System :: POSIX :: Linux',

tests/elasticity_test.py

@@ -35,14 +35,13 @@
 from jax_md.util import *
 
 jax_config.parse_flags_with_absl()
-FLAGS = jax_config.FLAGS
 
 PARTICLE_COUNT = 64
 NUM_SAMPLES = 2
 SPATIAL_DIMENSION = [2, 3]
 LOWPRESSURE = [True, False]
 
-if FLAGS.jax_enable_x64:
+if jax_config.jax_enable_x64:
   DTYPE = [f32, f64]
 else:
   DTYPE = [f32]

tests/energy_test.py

@@ -37,7 +37,6 @@
 from jax_md.interpolate import spline
 
 config.parse_flags_with_absl()
-FLAGS = config.FLAGS
 
 # TODO: Replace np by jnp everywhere.
 jnp = np

tests/minimize_test.py

@@ -32,14 +32,13 @@
 from jax_md import test_util
 
 jax_config.parse_flags_with_absl()
-FLAGS = jax_config.FLAGS
 
 PARTICLE_COUNT = 10
 OPTIMIZATION_STEPS = 10
 STOCHASTIC_SAMPLES = 10
 SPATIAL_DIMENSION = [2, 3]
 
-if FLAGS.jax_enable_x64:
+if jax_config.jax_enable_x64:
   DTYPE = [f32, f64]
 else:
   DTYPE = [f32]

tests/nn_test.py

@@ -31,9 +31,8 @@
 from jax_md import test_util
 
 jax_config.parse_flags_with_absl()
-FLAGS = jax_config.FLAGS
 
-if FLAGS.jax_enable_x64:
+if jax_config.jax_enable_x64:
   DTYPES = [f32, f64]
 else:
   DTYPES = [f32]
@@ -106,7 +105,7 @@ def test_radial_symmetry_functions_neighbor_list(self,
     gr_exact = gr(R)
     gr_nbrs = gr_neigh(R, neighbor=nbrs)
 
-    tol = 1e-13 if FLAGS.jax_enable_x64 else 1e-6
+    tol = 1e-13 if jax_config.jax_enable_x64 else 1e-6
     self.assertAllClose(gr_exact, gr_nbrs, atol=tol, rtol=tol)
 
   @parameterized.named_parameters(test_util.cases_from_list(
@@ -160,7 +159,7 @@ def test_angular_symmetry_functions_neighbor_list(self,
     gr_exact = gr(R)
     gr_nbrs = gr_neigh(R, neighbor=nbrs)
 
-    tol = 1e-13 if FLAGS.jax_enable_x64 else 1e-6
+    tol = 1e-13 if jax_config.jax_enable_x64 else 1e-6
     self.assertAllClose(gr_exact, gr_nbrs, atol=tol, rtol=tol)
 
   @parameterized.named_parameters(test_util.cases_from_list(

tests/partition_test.py

@@ -36,14 +36,12 @@
 
 jax_config.parse_flags_with_absl()
 
-FLAGS = jax_config.FLAGS
-
 
 PARTICLE_COUNT = 1000
 STOCHASTIC_SAMPLES = 10
 SPATIAL_DIMENSION = [2, 3]
 
-if FLAGS.jax_enable_x64:
+if jax_config.jax_enable_x64:
   POSITION_DTYPE = [f32, f64]
 else:
   POSITION_DTYPE = [f32]

tests/quantity_test.py

@@ -32,7 +32,6 @@
 
 
 jax_config.parse_flags_with_absl()
-FLAGS = jax_config.FLAGS
 
 PARTICLE_COUNT = 10
 STOCHASTIC_SAMPLES = 10
@@ -42,7 +41,7 @@
                         partition.Sparse,
                         partition.OrderedSparse]
 
-DTYPES = [f32, f64] if FLAGS.jax_enable_x64 else [f32]
+DTYPES = [f32, f64] if jax_config.jax_enable_x64 else [f32]
 COORDS = ['fractional', 'real']
 
 
@@ -603,7 +602,7 @@ def test_phop(self, spatial_dim, dtype, window):
 
 
   def test_maybe_downcast(self):
-    if not FLAGS.jax_enable_x64:
+    if not jax_config.jax_enable_x64:
       self.skipTest('Maybe downcast only works for float32 mode.')
 
     x = np.array([1, 2, 3], np.float64)

tests/rigid_body_test.py

@@ -45,7 +45,6 @@
 
 jax_config.parse_flags_with_absl()
 
-FLAGS = jax_config.FLAGS
 
 
 f32 = util.f32
@@ -64,7 +63,7 @@
 BROWNIAN_DYNAMICS_STEPS = 8000
 
 DTYPE = [f32]
-if FLAGS.jax_enable_x64:
+if jax_config.jax_enable_x64:
   DTYPE += [f64]
 
 

tests/simulate_test.py

@@ -41,7 +41,6 @@
 from functools import partial
 
 jax_config.parse_flags_with_absl()
-FLAGS = jax_config.FLAGS
 
 
 PARTICLE_COUNT = 1000
@@ -58,7 +57,7 @@
 BROWNIAN_DYNAMICS_STEPS = 8000
 
 DTYPE = [f32]
-if FLAGS.jax_enable_x64:
+if jax_config.jax_enable_x64:
   DTYPE += [f64]
 
 

tests/smap_test.py

@@ -31,7 +31,6 @@
 from jax_md import test_util
 
 jax_config.parse_flags_with_absl()
-FLAGS = jax_config.FLAGS
 
 test_util.update_test_tolerance(f32_tol=5e-6, f64_tol=1e-14)
 
@@ -44,7 +43,7 @@
 
 NEIGHBOR_LIST_PARTICLE_COUNT = 100
 
-if FLAGS.jax_enable_x64:
+if jax_config.jax_enable_x64:
   POSITION_DTYPE = [f32, f64]
 else:
   POSITION_DTYPE = [f32]

tests/space_test.py

@@ -32,15 +32,14 @@
 test_util.update_test_tolerance(5e-5, 5e-13)
 
 jax_config.parse_flags_with_absl()
-FLAGS = jax_config.FLAGS
 
 PARTICLE_COUNT = 10
 STOCHASTIC_SAMPLES = 10
 SHIFT_STEPS = 10
 SPATIAL_DIMENSION = [2, 3]
 BOX_FORMATS = ['scalar', 'vector', 'matrix']
 
-if FLAGS.jax_enable_x64:
+if jax_config.jax_enable_x64:
   POSITION_DTYPE = [f32, f64]
 else:
   POSITION_DTYPE = [f32]

tests/tpu_test.py

@@ -40,8 +40,6 @@
 
 update_test_tolerance(5e-5, 1e-7)
 
-FLAGS = jax_config.FLAGS
-
 
 def get_test_grid(rng_key, topology=None, num_dims=2, add_aux=False, ):
   # magic numbers to make the gird fold evenly, after splitting