Add support for ase >= 3.23 and Python 3.13

.github/workflows/architecture-tests.yml

@@ -24,7 +24,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.12"
+        python-version: "3.13"
     - run: pip install tox
 
     - name: run architecture tests

.github/workflows/build.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.12"
+        python-version: "3.13"
     - run: pip install tox
 
     - name: Test build integrity

.github/workflows/docs.yml

@@ -17,7 +17,7 @@ jobs:
       - name: setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
       - name: install dependencies
         run: python -m pip install tox
       - name: build documentation

.github/workflows/lint.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.12"
+        python-version: "3.13"
     - run: pip install tox
 
     - name: Lint the code

.github/workflows/release.yml

@@ -22,7 +22,7 @@ jobs:
     - name: setup Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.12"
+        python-version: "3.13"
     - run: python -m pip install tox
     - name: Build package
       run: tox -e build

.github/workflows/tests.yml

@@ -14,12 +14,12 @@ jobs:
           - os: ubuntu-22.04
             python-version: "3.9"
           - os: ubuntu-22.04
-            python-version: "3.12"
+            python-version: "3.13"
           - os: macos-14
-            python-version: "3.12"
+            python-version: "3.13"
           # To be restored once we figure out the issue with the windows build
           # - os: windows-2019
-          #   python-version: "3.12"
+          #   python-version: "3.13"
 
     runs-on: ${{ matrix.os }}
 

.readthedocs.yml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.12"
+    python: "3.13"
     rust: "1.75"
   jobs:
     pre_build:

docs/requirements.txt

@@ -4,5 +4,5 @@ sphinx >= 7
 sphinxcontrib-bibtex
 sphinx-gallery
 sphinx-toggleprompt
-setuptools  # required for sphinxcontrib-bibtex together with Python 3.12
+setuptools  # required for sphinxcontrib-bibtex together with Python 3.13
 tomli

docs/src/dev-docs/changelog.rst

@@ -12,8 +12,10 @@ Unreleased
 
 .. Possible sections for each release:
 
-.. Added
-.. #####
+Added
+#####
+
+- Added support for Python 3.13 and ase >= 3.23
 
 .. Fixed
 .. #####

docs/src/dev-docs/utils/data/readers.rst

@@ -44,6 +44,7 @@ ASE
 
 This section describes the parsers for the ASE library.
 
+.. autofunction:: metatrain.utils.data.readers.ase.read
 .. autofunction:: metatrain.utils.data.readers.ase.read_systems
 .. autofunction:: metatrain.utils.data.readers.ase.read_energy
 .. autofunction:: metatrain.utils.data.readers.ase.read_generic

pyproject.toml

@@ -9,16 +9,14 @@ description = "Training and evaluating machine learning models for atomistic sys
 authors = [{name = "metatrain developers"}]
 
 dependencies = [
-    "ase < 3.23.0",
+    "ase",
     "metatensor-learn==0.3.1",
     "metatensor-operations==0.3.1",
     "metatensor-torch==0.7.2",
     "jsonschema",
     "omegaconf",
     "python-hostlist",
-    "torch",
     "vesin",
-    "numpy < 2.0.0"
 ]
 
 keywords = ["machine learning", "molecular modeling"]
@@ -44,7 +42,7 @@ homepage = "https://metatensor.github.io/metatrain"
 documentation = "https://metatensor.github.io/metatrain"
 repository = "https://github.com/metatensor/metatrain"
 issues = "https://github.com/metatensor/metatrain/issues"
-changelog = "https://metatensor.github.io/metatrain/latest/references/changelog.html"
+changelog = "https://metatensor.github.io/metatrain/latest/dev-docs/changelog.html"
 
 [project.scripts]
 mtt = "metatrain.__main__:main"
@@ -130,7 +128,7 @@ follow_imports = 'skip'
 ignore_missing_imports = true
 
 [tool.pytest.ini_options]
-# ignore" a bunch of internal warnings with Python 3.12 and PyTorch
+# ignore" a bunch of internal warnings with Python 3.13 and PyTorch
 filterwarnings = [
     "ignore:ast.Str is deprecated and will be removed in Python 3.14:DeprecationWarning",
     "ignore:Attribute s is deprecated and will be removed in Python 3.14:DeprecationWarning",

src/metatrain/gap/tests/test_regression.py

@@ -1,7 +1,6 @@
 import copy
 import random
 
-import ase.io
 import metatensor.torch
 import numpy as np
 import torch
@@ -10,6 +9,7 @@
 from metatrain.gap import GAP, Trainer
 from metatrain.utils.data import Dataset, DatasetInfo
 from metatrain.utils.data.readers import read_systems, read_targets
+from metatrain.utils.data.readers.ase import read
 from metatrain.utils.data.target_info import get_energy_target_info
 
 from . import DATASET_ETHANOL_PATH, DATASET_PATH, DEFAULT_HYPERS
@@ -90,7 +90,7 @@ def test_regression_train_and_invariance():
     assert torch.allclose(output["mtt::U0"].block().values, expected_output, rtol=0.3)
 
     # Tests that the model is rotationally invariant
-    system = ase.io.read(DATASET_PATH)
+    system = read(DATASET_PATH)
     system.numbers = np.ones(len(system.numbers))
 
     original_system = copy.deepcopy(system)
@@ -167,7 +167,7 @@ def test_ethanol_regression_train_and_invariance():
 
     # Predict on the first five systems
     output = gap(systems[:5], {"energy": gap.outputs["energy"]})
-    data = ase.io.read(DATASET_ETHANOL_PATH, ":5", format="extxyz")
+    data = read(DATASET_ETHANOL_PATH, ":5", format="extxyz")
 
     expected_output = torch.tensor([[i.info["energy"]] for i in data])
     assert torch.allclose(output["energy"].block().values, expected_output, rtol=0.1)
@@ -176,7 +176,7 @@ def test_ethanol_regression_train_and_invariance():
     # expected_forces = torch.vstack([torch.Tensor(i.arrays["forces"]) for i in data])
 
     # Tests that the model is rotationally invariant
-    system = ase.io.read(DATASET_ETHANOL_PATH)
+    system = read(DATASET_ETHANOL_PATH)
 
     original_system = copy.deepcopy(system)
     system.rotate(48, "y")

src/metatrain/pet/tests/test_pet_compatibility.py

@@ -1,4 +1,3 @@
-import ase
 import pytest
 import torch
 from metatensor.torch.atomistic import (
@@ -18,6 +17,7 @@
 from metatrain.pet.utils import systems_to_batch_dict
 from metatrain.utils.architectures import get_default_hypers
 from metatrain.utils.data import DatasetInfo
+from metatrain.utils.data.readers.ase import read
 from metatrain.utils.data.target_info import get_energy_target_info
 from metatrain.utils.neighbor_lists import get_system_with_neighbor_lists
 
@@ -57,7 +57,7 @@ def test_batch_dicts_compatibility(cutoff):
     """Tests that the batch dict computed with internal MTM routines
     is consitent with PET implementation."""
 
-    structure = ase.io.read(DATASET_PATH)
+    structure = read(DATASET_PATH)
     atomic_types = sorted(set(structure.numbers))
     system = systems_to_torch(structure)
     options = NeighborListOptions(cutoff=cutoff, full_list=True, strict=True)
@@ -93,7 +93,7 @@ def test_predictions_compatibility(cutoff):
     """Tests that predictions of the MTM implemetation of PET
     are consistent with the predictions of the original PET implementation."""
 
-    structure = ase.io.read(DATASET_PATH)
+    structure = read(DATASET_PATH)
 
     dataset_info = DatasetInfo(
         length_unit="Angstrom",

src/metatrain/soap_bpnn/tests/test_equivariance.py

@@ -1,13 +1,13 @@
 import copy
 
-import ase.io
 import numpy as np
 import pytest
 import torch
 from metatensor.torch.atomistic import System, systems_to_torch
 
 from metatrain.soap_bpnn import SoapBpnn
 from metatrain.utils.data import DatasetInfo
+from metatrain.utils.data.readers.ase import read
 from metatrain.utils.data.target_info import (
     get_energy_target_info,
     get_generic_target_info,
@@ -31,7 +31,7 @@ def test_rotational_invariance():
     )
     model = SoapBpnn(MODEL_HYPERS, dataset_info)
 
-    system = ase.io.read(DATASET_PATH)
+    system = read(DATASET_PATH)
     original_system = copy.deepcopy(system)
     system.rotate(48, "y")
 
@@ -77,7 +77,7 @@ def test_equivariance_rotations(o3_lambda, o3_sigma):
     )
     model = SoapBpnn(MODEL_HYPERS, dataset_info)
 
-    system = ase.io.read(DATASET_PATH)
+    system = read(DATASET_PATH)
     original_system = systems_to_torch(system)
     rotation = get_random_rotation()
     rotated_system = rotate_system(original_system, rotation)
@@ -128,7 +128,7 @@ def test_equivariance_inversion(o3_lambda, o3_sigma):
     )
     model = SoapBpnn(MODEL_HYPERS, dataset_info)
 
-    system = ase.io.read(DATASET_PATH)
+    system = read(DATASET_PATH)
     original_system = systems_to_torch(system)
     inverted_system = System(
         positions=original_system.positions * (-1),