chore(deps): cleanup dev deps (#209)

* chore(deps): cleanup dev deps

* fix(ci): run clippy on stable toolchain

* fix(tests): update

* fix(tests): atol on macOS

* chore(deps): relax constraint on Equinox (and JAX)

.github/workflows/lint.yml

@@ -50,10 +50,15 @@ jobs:
       with:
         enable-cache: true
 
+    - name: Install Rust stable
+      uses: dtolnay/rust-toolchain@stable
+      with:
+        components: clippy
+
     - name: Install Rust nightly
       uses: dtolnay/rust-toolchain@nightly
       with:
-        components: clippy,rustfmt
+        components: rustfmt
 
     - name: Install dependencies
       run: uv sync

differt-core/src/geometry/triangle_mesh.rs

@@ -365,7 +365,7 @@ impl TriangleMesh {
                             }),
                     );
                 },
-                name => log::info!("Unexpeced element: {name}, skipping."),
+                name => log::info!("Unexpected element: {name}, skipping."),
             }
         }
 

differt/src/differt/em/_antenna.py

@@ -529,8 +529,8 @@ def directivity(
 
             :meth:`directive_gain`
         """
-        u, du = jnp.linspace(0, 2 * jnp.pi, num_points * 2, retstep=True)
-        v, dv = jnp.linspace(0, jnp.pi, num_points, retstep=True)
+        u, _du = jnp.linspace(0, 2 * jnp.pi, num_points * 2, retstep=True)
+        v, _dv = jnp.linspace(0, jnp.pi, num_points, retstep=True)
         x = jnp.outer(jnp.cos(u), jnp.sin(v))
         y = jnp.outer(jnp.sin(u), jnp.sin(v))
         z = jnp.outer(jnp.ones_like(u), jnp.cos(v))
@@ -637,11 +637,11 @@ def polarization_vectors(
         cos_theta = dot(r_hat, self.direction)
         sin_theta = jnp.sqrt(1 - cos_theta**2)
 
-        d = 1.640922376984585  # Directive gain: 4 / Cin(2*pi)
+        _d = 1.640922376984585  # Directive gain: 4 / Cin(2*pi)
 
         cos_theta = dot()  # type: ignore
         sin_theta = jnp.sin()  # type: ignore
-        d = safe_divide(jnp.cos(0.5 * jnp.pi * cos_theta), sin_theta)
+        _d = safe_divide(jnp.cos(0.5 * jnp.pi * cos_theta), sin_theta)
 
 
 class ShortDipolePattern(RadiationPattern):

differt/src/differt/geometry/_paths.py

@@ -370,23 +370,23 @@ def group_by_objects(self) -> Int[Array, " *batch"]:
             >>> vertices = jax.random.uniform(key_v, (*batch, path_length, 3))
             >>> objects = jax.random.randint(key_o, (*batch, path_length), 0, 2)
             >>> objects
-            Array([[[1, 0, 0],
-                    [1, 0, 0],
-                    [0, 1, 1],
+            Array([[[1, 1, 0],
+                    [0, 0, 1],
                     [1, 0, 1],
-                    [0, 1, 0],
-                    [0, 1, 1]],
-                   [[1, 0, 1],
-                    [0, 0, 0],
-                    [0, 0, 0],
+                    [1, 0, 0],
+                    [1, 1, 1],
+                    [1, 1, 1]],
+                   [[1, 0, 0],
+                    [1, 1, 1],
+                    [0, 0, 1],
                     [1, 1, 0],
                     [0, 0, 1],
-                    [0, 1, 1]]], dtype=int32)
+                    [1, 0, 0]]], dtype=int32)
             >>> paths = Paths(vertices, objects)
             >>> groups = paths.group_by_objects()
             >>> groups
-            Array([[ 0,  0,  2,  3,  4,  2],
-                   [ 3,  7,  7,  9, 10,  2]], dtype=int32)
+            Array([[0, 1, 2, 3, 4, 4],
+                   [3, 4, 1, 0, 1, 3]], dtype=int32)
         """
         *batch, path_length = self.objects.shape
 

differt/src/differt/utils.py

@@ -88,11 +88,11 @@ def sorted_array2(array: Shaped[Array, "m n"]) -> Shaped[Array, "m n"]:
         ... ) = jax.random.split(key, 2)
         >>> arr = jax.random.permutation(key1, arr)
         >>> arr
-        Array([[4, 5],
-               [8, 9],
+        Array([[6, 7],
                [0, 1],
-               [2, 3],
-               [6, 7]], dtype=int32)
+               [8, 9],
+               [4, 5],
+               [2, 3]], dtype=int32)
         >>>
         >>> sorted_array2(arr)
         Array([[0, 1],
@@ -108,18 +108,18 @@ def sorted_array2(array: Shaped[Array, "m n"]) -> Shaped[Array, "m n"]:
         ...     2,
         ... )
         >>> arr
-        Array([[1, 1, 1, 0, 1],
-               [1, 0, 1, 1, 1],
-               [1, 0, 0, 1, 1],
-               [1, 0, 0, 0, 0],
-               [1, 1, 0, 1, 0]], dtype=int32)
+        Array([[1, 1, 0, 0, 0],
+               [1, 1, 0, 1, 1],
+               [0, 0, 1, 1, 1],
+               [1, 1, 1, 1, 0],
+               [0, 1, 1, 1, 0]], dtype=int32)
         >>>
         >>> sorted_array2(arr)
-        Array([[1, 0, 0, 0, 0],
-               [1, 0, 0, 1, 1],
-               [1, 0, 1, 1, 1],
-               [1, 1, 0, 1, 0],
-               [1, 1, 1, 0, 1]], dtype=int32)
+        Array([[0, 0, 1, 1, 1],
+               [0, 1, 1, 1, 0],
+               [1, 1, 0, 0, 0],
+               [1, 1, 0, 1, 1],
+               [1, 1, 1, 1, 0]], dtype=int32)
     """
     if array.size == 0:
         return array

differt/tests/em/test_constants.py

@@ -18,7 +18,8 @@
 )
 def test_constants(constant_name: str, value: float | None) -> None:
     got = getattr(_constants, constant_name)
-    if value:
-        assert abs(got - value) < 1e-6
-    else:
-        assert got == getattr(scipy.constants, constant_name)
+    expected: float = (
+        value if value is not None else getattr(scipy.constants, constant_name)
+    )
+
+    assert abs(got - expected) < 1e-6

differt/tests/geometry/test_triangle_mesh.py

@@ -438,9 +438,7 @@ def test_plot(self, sphere_mesh: TriangleMesh) -> None:
     def test_sample(self, two_buildings_mesh: TriangleMesh, key: PRNGKeyArray) -> None:
         assert two_buildings_mesh.sample(10, key=key).num_triangles == 10
 
-        with pytest.raises(
-            ValueError, match="Cannot take a larger sample than population"
-        ):
+        with pytest.raises(ValueError, match="Cannot take a larger sample"):
             assert two_buildings_mesh.sample(30, key=key)
 
         assert two_buildings_mesh.sample(30, replace=True, key=key).num_triangles == 30

differt/tests/geometry/test_utils.py

@@ -276,7 +276,7 @@ def test_cartesian_to_spherial_roundtrip(key: PRNGKeyArray) -> None:
     sph = cartesian_to_spherical(xyz)
     got = spherical_to_cartesian(sph)
 
-    chex.assert_trees_all_close(got, xyz, atol=1e-5)
+    chex.assert_trees_all_close(got, xyz, atol=2e-5)
 
     key_r, key_polar, key_azim = jax.random.split(key_sph, 3)
 

differt/tests/plotting/test_core.py

@@ -125,7 +125,10 @@ def test_draw_contour(
     if (backend == "vispy" and (fill or isinstance(levels, int))) or (
         backend == "plotly" and isinstance(levels, np.ndarray)
     ):
-        expectation = pytest.warns(UserWarning)
+        expectation = pytest.warns(
+            UserWarning,
+            match=f"{'VisPy' if backend == 'vispy' else 'Plotly'} does not support",
+        )
     else:
         expectation = does_not_raise()
 
@@ -162,7 +165,12 @@ def test_draw_surface(
     Z = X * Y  # noqa: N806
 
     if backend in {"vispy", "matplotlib"} and pass_colors:
-        expectation = pytest.warns(UserWarning)
+        expectation = pytest.warns(
+            UserWarning,
+            match="VisPy does not currently support coloring like we would like"
+            if backend == "vispy"
+            else "Matplotlib requires 'colors' to be RGB or RGBA values",
+        )
     else:
         expectation = does_not_raise()
 

differt/tests/rt/test_utils.py

@@ -273,9 +273,9 @@ def test_rays_intersect_any_triangle(
 @pytest.mark.parametrize(
     ("vertex", "expected_number"),
     [
-        (jnp.array([4.0, 0.0, 0.0]), 2),  # Sees one face of the cude
-        (jnp.array([4.0, 4.0, 0.0]), 4),  # Sees two faces
-        (jnp.array([4.0, 4.0, 4.0]), 6),  # Sees three faces
+        (jnp.array([2.0, 0.0, 0.0]), 2),  # Sees one face of the cude
+        (jnp.array([2.0, 2.0, 0.0]), 4),  # Sees two faces
+        (jnp.array([2.0, 2.0, 2.0]), 6),  # Sees three faces
     ],
 )
 @pytest.mark.parametrize(

justfile

@@ -100,8 +100,3 @@ test-python *ARGS:
 [group('test')]
 test-rust *ARGS:
     cargo test {{ ARGS }}
-
-# Run jupyter-lab with a server that supports reconnecting to running sessions
-[group('dev')]
-remote-jupyter *ARGS:
-    uv run --extra remote-jupyter jupyverse --set kernels.require_yjs=true --set jupyterlab.server_side_execution=true --set auth.mode=noauth {{ ARGS }}

pyproject.toml

@@ -7,7 +7,7 @@ version = "1.0.0"
 
 [project.optional-dependencies]
 cuda = [
-  "jax[cuda]>=0.4.32",
+  "jax[cuda]>=0.5.0",
 ]
 docs = [
   "differt[all]",
@@ -32,15 +32,11 @@ icmlcn2025 = [
 prof = [
   "line-profiler[ipython]>=4.1.3",
 ]
-remote-jupyter = [
-  # This makes sure cell outputs and widgets are kept, see https://github.com/jupyterlab/jupyter-collaboration/pull/279
-  "jupyterlab>=4.2",
-  "jupyverse[auth,jupyterlab]>=0.4.2",
-]
 tests = [
   "differt[all]",
   "beartype>=0.19.0",
   "chex>=0.1.84",
+  "jax>=0.5.0",  # Random number output has changed between 0.4 and 0.5
   "pytest>=7.4.3",
   "pytest-benchmark>=4.0.0",
   "pytest-codspeed>=2.2.0",
@@ -243,12 +239,22 @@ extend-ignore-names = ["T"]
 convention = "google"
 
 [tool.uv]
+conflicts = [
+  [
+    {extra = "cuda"},
+    {extra = "tests-extended"},
+  ],
+]
 dev-dependencies = [
-  "differt_dev[docs,tests]",
+  "differt-dev[docs,tests]",
   "bump-my-version>=0.20.3",
   "maturin-import-hook>=0.2.0",
   "pre-commit>=3.5.0",
 ]
+override-dependencies = [
+  "tensorflow>=2.18,<2.19",  # To support NumPy 2
+]
+required-version = ">=0.5.26"  # See: https://github.com/astral-sh/uv/pull/11075
 
 [tool.uv.sources]
 differt = {workspace = true}