Merge branch 'develop' into composite_mechanics

.all-contributorsrc

@@ -970,6 +970,27 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "MarcBerliner",
+      "name": "Marc Berliner",
+      "avatar_url": "https://avatars.githubusercontent.com/u/34451391?v=4",
+      "profile": "http://marcberliner.com",
+      "contributions": [
+        "code",
+        "doc",
+        "infra",
+        "maintenance"
+      ]
+    },
+    {
+      "login": "Aswinr24",
+      "name": "Aswinr24",
+      "avatar_url": "https://avatars.githubusercontent.com/u/135364633?v=4",
+      "profile": "https://github.com/Aswinr24",
+      "contributions": [
+        "test"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/workflows/lychee_url_checker.yml

@@ -28,7 +28,7 @@ jobs:
 
       # use stable version for now to avoid breaking changes
       - name: Lychee URL checker
-        uses: lycheeverse/lychee-action@v1.10.0
+        uses: lycheeverse/lychee-action@v2.0.2
         with:
           # arguments with file types to check
           args: >-

.github/workflows/periodic_benchmarks.yml

@@ -51,7 +51,7 @@ jobs:
           LD_LIBRARY_PATH: $HOME/.local/lib
 
       - name: Upload results as artifact
-        uses: actions/[email protected].1
+        uses: actions/[email protected].3
         with:
           name: asv_periodic_results
           path: results

.github/workflows/publish_pypi.yml

@@ -92,7 +92,7 @@ jobs:
             python -c "import pybamm; print(pybamm.IDAKLUSolver())"
             python -m pytest -m cibw {project}/tests/unit
       - name: Upload Windows wheels
-        uses: actions/[email protected].1
+        uses: actions/[email protected].3
         with:
           name: wheels_windows
           path: ./wheelhouse/*.whl
@@ -129,7 +129,7 @@ jobs:
             python -m pytest -m cibw {project}/tests/unit
 
       - name: Upload wheels for Linux
-        uses: actions/[email protected].1
+        uses: actions/[email protected].3
         with:
           name: wheels_manylinux
           path: ./wheelhouse/*.whl
@@ -261,7 +261,7 @@ jobs:
             python -m pytest -m cibw {project}/tests/unit
 
       - name: Upload wheels for macOS (amd64, arm64)
-        uses: actions/[email protected].1
+        uses: actions/[email protected].3
         with:
           name: wheels_${{ matrix.os }}
           path: ./wheelhouse/*.whl
@@ -281,7 +281,7 @@ jobs:
         run: pipx run build --sdist
 
       - name: Upload SDist
-        uses: actions/[email protected].1
+        uses: actions/[email protected].3
         with:
           name: sdist
           path: ./dist/*.tar.gz

.github/workflows/run_benchmarks_over_history.yml

@@ -46,7 +46,7 @@ jobs:
           ${{ github.event.inputs.commit_start }}..${{ github.event.inputs.commit_end }}
 
       - name: Upload results as artifact
-        uses: actions/[email protected].1
+        uses: actions/[email protected].3
         with:
           name: asv_over_history_results
           path: results

.github/workflows/scorecard.yml

@@ -59,7 +59,7 @@ jobs:
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
       - name: "Upload artifact"
-        uses: actions/upload-artifact@604373da6381bf24206979c74d06a550515601b9 # v4.4.1
+        uses: actions/upload-artifact@184d73b71b93c222403b2e7f1ffebe4508014249 # v4.4.1
         with:
           name: SARIF file
           path: results.sarif
@@ -68,6 +68,6 @@ jobs:
       # Upload the results to GitHub's code scanning dashboard (optional).
       # Commenting out will disable upload of results to your repo's Code Scanning dashboard
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@c36620d31ac7c881962c3d9dd939c40ec9434f2b # v3.26.12
+        uses: github/codeql-action/upload-sarif@f779452ac5af1c261dce0346a8f964149f49322b # v3.26.13
         with:
           sarif_file: results.sarif

.gitignore

@@ -65,6 +65,7 @@ coverage.xml
 htmlcov/
 
 # virtual environment
+.venv
 env/
 venv/
 venv3.5/

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
         types_or: [python, pyi, jupyter]
 
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.18.0"
+    rev: "1.19.0"
     hooks:
        - id: blacken-docs
          additional_dependencies: [black==23.*]

README.md

@@ -15,7 +15,7 @@
 [![OpenSSF Scorecard](https://api.scorecard.dev/projects/github.com/pybamm-team/PyBaMM/badge)](https://scorecard.dev/viewer/?uri=github.com/pybamm-team/PyBaMM)
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-91-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-93-orange.svg)](#-contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 </div>

all_contributors.md

@@ -122,6 +122,10 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/pipliggins"><img src="https://avatars.githubusercontent.com/u/55396775?v=4?s=100" width="100px;" alt="Pip Liggins"/><br /><sub><b>Pip Liggins</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=pipliggins" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=pipliggins" title="Tests">⚠️</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/medha-14"><img src="https://avatars.githubusercontent.com/u/143182673?v=4?s=100" width="100px;" alt="Medha Bhardwaj"/><br /><sub><b>Medha Bhardwaj</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=medha-14" title="Code">💻</a></td>
     </tr>
+    <tr>
+      <td align="center" valign="top" width="14.28%"><a href="http://marcberliner.com"><img src="https://avatars.githubusercontent.com/u/34451391?v=4?s=100" width="100px;" alt="Marc Berliner"/><br /><sub><b>Marc Berliner</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=MarcBerliner" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=MarcBerliner" title="Documentation">📖</a> <a href="#infra-MarcBerliner" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-MarcBerliner" title="Maintenance">🚧</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/Aswinr24"><img src="https://avatars.githubusercontent.com/u/135364633?v=4?s=100" width="100px;" alt="Aswinr24"/><br /><sub><b>Aswinr24</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=Aswinr24" title="Tests">⚠️</a></td>
+    </tr>
   </tbody>
 </table>
 

src/pybamm/CITATIONS.bib

@@ -291,7 +291,7 @@ @article{Hindmarsh2005
 @misc{jax2018,
   author = {James Bradbury and Roy Frostig and Peter Hawkins and Matthew James Johnson and Chris Leary and Dougal Maclaurin and Skye Wanderman-Milne},
   title = {{JAX: composable transformations of Python+NumPy programs}},
-  url = {http://github.com/google/jax},
+  url = {http://github.com/jax-ml/jax},
   version = {0.2.5},
   year = {2018},
 }

src/pybamm/solvers/jax_bdf_solver.py

@@ -28,7 +28,7 @@
     MIN_FACTOR = 0.2
     MAX_FACTOR = 10
 
-    # https://github.com/google/jax/issues/4572#issuecomment-709809897
+    # https://github.com/jax-ml/jax/issues/4572#issuecomment-709809897
     def some_hash_function(x):
         return hash(str(x))
 
@@ -711,7 +711,7 @@ def block_fun(i, j, Ai, Aj):
         return onp.block(blocks)
 
     # NOTE: the code below (except the docstring on jax_bdf_integrate and other minor
-    # edits), has been modified from the JAX library at https://github.com/google/jax.
+    # edits), has been modified from the JAX library at https://github.com/jax-ml/jax.
     # The main difference is the addition of support for semi-explicit dae index 1
     # problems via the addition of a mass matrix.
     # This is under an Apache license, a short form of which is given here:

src/pybamm/solvers/jax_solver.py

@@ -46,7 +46,7 @@ class JaxSolver(pybamm.BaseSolver):
     extra_options : dict, optional
         Any options to pass to the solver.
         Please consult `JAX documentation
-        <https://github.com/google/jax/blob/master/jax/experimental/ode.py>`_
+        <https://github.com/jax-ml/jax/blob/master/jax/experimental/ode.py>`_
         for details.
     """
 
@@ -263,8 +263,8 @@ async def solve_model_async(inputs_v):
         # sparse matrix support in JAX resulting in high memory usage, or a bug
         # in the BDF solver.
         #
-        # This issue on guthub appears related:
-        # https://github.com/google/jax/discussions/13930
+        # This issue on GitHub appears related:
+        # https://github.com/jax-ml/jax/discussions/13930
         #
         #     # Split input list based on the number of available xla devices
         #     device_count = jax.local_device_count()

tests/unit/test_models/test_full_battery_models/test_lithium_ion/test_dfn.py

@@ -7,8 +7,7 @@
 
 
 class TestDFN(BaseUnitTestLithiumIon):
-    @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup_method(self):
         self.model = pybamm.lithium_ion.DFN
 
     def test_electrolyte_options(self):

tests/unit/test_models/test_full_battery_models/test_lithium_ion/test_dfn_half_cell.py

@@ -4,10 +4,8 @@
 
 import pybamm
 from tests import BaseUnitTestLithiumIonHalfCell
-import pytest
 
 
 class TestDFNHalfCell(BaseUnitTestLithiumIonHalfCell):
-    @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup_method(self):
         self.model = pybamm.lithium_ion.DFN

tests/unit/test_models/test_full_battery_models/test_lithium_ion/test_newman_tobias.py

@@ -7,8 +7,7 @@
 
 
 class TestNewmanTobias(BaseUnitTestLithiumIon):
-    @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup_method(self):
         self.model = pybamm.lithium_ion.NewmanTobias
 
     def test_electrolyte_options(self):

tests/unit/test_models/test_full_battery_models/test_lithium_ion/test_spm.py

@@ -7,8 +7,7 @@
 
 
 class TestSPM(BaseUnitTestLithiumIon):
-    @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup_method(self):
         self.model = pybamm.lithium_ion.SPM
 
     def test_electrolyte_options(self):

tests/unit/test_models/test_full_battery_models/test_lithium_ion/test_spm_half_cell.py

@@ -3,10 +3,8 @@
 #
 import pybamm
 from tests import BaseUnitTestLithiumIonHalfCell
-import pytest
 
 
 class TestSPMHalfCell(BaseUnitTestLithiumIonHalfCell):
-    @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup_method(self):
         self.model = pybamm.lithium_ion.SPM

tests/unit/test_models/test_full_battery_models/test_lithium_ion/test_spme.py

@@ -7,8 +7,7 @@
 
 
 class TestSPMe(BaseUnitTestLithiumIon):
-    @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup_method(self):
         self.model = pybamm.lithium_ion.SPMe
 
     # def test_external_variables(self):

tests/unit/test_models/test_full_battery_models/test_lithium_ion/test_spme_half_cell.py

@@ -4,10 +4,8 @@
 #
 import pybamm
 from tests import BaseUnitTestLithiumIonHalfCell
-import pytest
 
 
 class TestSPMeHalfCell(BaseUnitTestLithiumIonHalfCell):
-    @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup_method(self):
         self.model = pybamm.lithium_ion.SPMe

tests/unit/test_parameters/test_bpx.py

@@ -7,8 +7,7 @@
 
 
 class TestBPX:
-    @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup_method(self):
         self.base = {
             "Header": {
                 "BPX": 1.0,

tests/unit/test_parameters/test_process_parameter_data.py

@@ -2,56 +2,48 @@
 # Tests for the parameter processing functions
 #
 
-
-import os
 import numpy as np
 import pybamm
-
 import pytest
+from pathlib import Path
 
 
-class TestProcessParameterData:
-    def test_process_1D_data(self):
-        name = "lico2_ocv_example"
-        path = os.path.abspath(os.path.dirname(__file__))
-        processed = pybamm.parameters.process_1D_data(name, path)
-        assert processed[0] == name
-        assert isinstance(processed[1], tuple)
-        assert isinstance(processed[1][0][0], np.ndarray)
-        assert isinstance(processed[1][1], np.ndarray)
+@pytest.fixture
+def parameters_path():
+    return Path(__file__).parent.resolve()
 
-    def test_process_2D_data(self):
-        name = "lico2_diffusivity_Dualfoil1998_2D"
-        path = os.path.abspath(os.path.dirname(__file__))
-        processed = pybamm.parameters.process_2D_data(name, path)
-        assert processed[0] == name
-        assert isinstance(processed[1], tuple)
-        assert isinstance(processed[1][0][0], np.ndarray)
-        assert isinstance(processed[1][0][1], np.ndarray)
-        assert isinstance(processed[1][1], np.ndarray)
 
-    def test_process_2D_data_csv(self):
-        name = "data_for_testing_2D"
-        path = os.path.abspath(os.path.dirname(__file__))
-        processed = pybamm.parameters.process_2D_data_csv(name, path)
+@pytest.fixture(
+    params=[
+        ("lico2_ocv_example", pybamm.parameters.process_1D_data),
+        ("lico2_diffusivity_Dualfoil1998_2D", pybamm.parameters.process_2D_data),
+        ("data_for_testing_2D", pybamm.parameters.process_2D_data_csv),
+        ("data_for_testing_3D", pybamm.parameters.process_3D_data_csv),
+    ]
+)
+def parameter_data(request, parameters_path):
+    name, processing_function = request.param
+    processed = processing_function(name, parameters_path)
+    return name, processed
+
 
+class TestProcessParameterData:
+    def test_processed_name(self, parameter_data):
+        name, processed = parameter_data
         assert processed[0] == name
+
+    def test_processed_structure(self, parameter_data):
+        name, processed = parameter_data
         assert isinstance(processed[1], tuple)
         assert isinstance(processed[1][0][0], np.ndarray)
-        assert isinstance(processed[1][0][1], np.ndarray)
         assert isinstance(processed[1][1], np.ndarray)
 
-    def test_process_3D_data_csv(self):
-        name = "data_for_testing_3D"
-        path = os.path.abspath(os.path.dirname(__file__))
-        processed = pybamm.parameters.process_3D_data_csv(name, path)
+        if len(processed[1][0]) > 1:
+            assert isinstance(processed[1][0][1], np.ndarray)
 
-        assert processed[0] == name
-        assert isinstance(processed[1], tuple)
-        assert isinstance(processed[1][0][0], np.ndarray)
-        assert isinstance(processed[1][0][1], np.ndarray)
-        assert isinstance(processed[1][0][2], np.ndarray)
-        assert isinstance(processed[1][1], np.ndarray)
+        elif len(processed[1]) == 3:
+            assert isinstance(processed[1][0][1], np.ndarray)
+            assert isinstance(processed[1][0][2], np.ndarray)
 
     def test_error(self):
         with pytest.raises(FileNotFoundError, match="Could not find file"):