Bump dependencies to the newest compatible versions

.github/workflows/python-app.yml

@@ -26,8 +26,8 @@ jobs:
         cache: 'pip'
     - name: Install dependencies and package
       run: |
-        python -m pip install pip==26.2.2 setuptools==80.10.2 wheel==0.48.0
-        pip install flake8==7.4.1 pytest==9.1.1
+        python -m pip install pip==26.3 setuptools==84.2.1 wheel==0.48.0
+        pip install flake8==7.5.0 pytest==9.2.0
 
         # install this package (pulls dependencies from pyproject.toml)
         pip install -e .

pyproject.toml

@@ -18,33 +18,33 @@ classifiers = [
 ]
 
 dependencies = [
-  "ase==3.27.0",
+  "ase==3.29.0",
   "torch==2.13.0",
   "torch-sim-atomistic==0.6.2",
-  "fairchem-core==2.24.0",
+  "fairchem-core==2.25.0",
   "morfeus-ml==0.8.0",
-  "rdkit==2026.3.1",
+  "rdkit==2026.3.6",
   "tables==3.11.1",
-  "scipy==1.17.1",
-  "hf_xet==1.2.0",
+  "scipy==1.18.1",
+  "hf_xet==1.8.0",
   "pyyaml==6.0.3",
-  "orb-models==0.6.1",
+  "orb-models==0.6.2",
   "nvalchemi-toolkit-ops==0.5.0",
   "warp-lang==1.17.0",
   "sevenn[torchsim]==0.13.0",
-  "nvmolkit==0.5.1",
+  "nvmolkit==0.7.0",
   "aimnet[ase,torchsim]==0.2.6"
 ]
 
 [project.optional-dependencies]
 dev = [
-    "pytest==9.1.1",
+    "pytest==9.2.0",
     "build==1.6.1",
     "twine==6.2.0",
     "pip-tools==7.6.2",
-    "ruff==0.17.2",
+    "ruff==0.17.4",
     "mkdocs==1.6.1",
-    "mkdocs-material==9.7.7",
+    "mkdocs-material==9.8.1",
     "mkdocstrings[python]==1.0.8",
     "mkdocstrings-python==2.0.10",
     "mkdocs-llmstxt==0.5.1"
@@ -58,7 +58,7 @@ Documentation = "https://niklashoelter.github.io/gpuma/"
 gpuma = "gpuma.cli:main"
 
 [build-system]
-requires = ["setuptools==80.10.2", "wheel==0.48.0"]
+requires = ["setuptools==84.2.1", "wheel==0.48.0"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools]

tests/test_embed.py

@@ -8,6 +8,7 @@
 
 import copy
 
+import numpy as np
 import pytest
 
 from gpuma.config import Config, load_config_from_file
@@ -359,7 +360,7 @@ def test_generate_ensembles_keep_all_is_reproducible(cpu_config):
     assert len(first) == len(second)
     for a, b in zip(first, second, strict=True):
         assert a.symbols == b.symbols
-        assert a.coordinates == pytest.approx(b.coordinates)
+        assert np.array(a.coordinates) == pytest.approx(np.array(b.coordinates))
 
 
 def test_generate_ensembles_keep_all_first_agrees_with_generate_structures(cpu_config):
@@ -369,7 +370,7 @@ def test_generate_ensembles_keep_all_first_agrees_with_generate_structures(cpu_c
     (ensemble,) = generate_ensembles([ETHANOL], None, cpu_config, **kwargs)
 
     assert single.symbols == ensemble[0].symbols
-    assert single.coordinates == pytest.approx(ensemble[0].coordinates)
+    assert np.array(single.coordinates) == pytest.approx(np.array(ensemble[0].coordinates))
 
 
 # ---------------------------------------------------------------------------
@@ -545,7 +546,7 @@ def test_prune_symmetry_is_off_by_default(cpu_config):
 
     assert len(absent) == len(explicit)
     for one, other in zip(absent, explicit, strict=True):
-        assert one.coordinates == pytest.approx(other.coordinates)
+        assert np.array(one.coordinates) == pytest.approx(np.array(other.coordinates))
 
 
 def test_prune_symmetry_keeps_the_lowest_energy_conformer_first(cpu_config):
@@ -558,7 +559,7 @@ def test_prune_symmetry_keeps_the_lowest_energy_conformer_first(cpu_config):
         [ROTOR_RICH], None, cpu_config, prune_symmetry=True, **kwargs
     )
 
-    assert symmetric[0].coordinates == pytest.approx(unpruned[0].coordinates)
+    assert np.array(symmetric[0].coordinates) == pytest.approx(np.array(unpruned[0].coordinates))
 
 
 def test_prune_symmetry_survivors_are_a_subsequence_of_the_ensemble(cpu_config):
@@ -577,7 +578,7 @@ def test_prune_symmetry_survivors_are_a_subsequence_of_the_ensemble(cpu_config):
             next(
                 i
                 for i, candidate in enumerate(unpruned)
-                if candidate.coordinates == pytest.approx(structure.coordinates)
+                if np.array(candidate.coordinates) == pytest.approx(np.array(structure.coordinates))
             )
         )
     assert positions == sorted(positions)