Merge branch 'develop' into ocvr_ecm

.github/workflows/publish_pypi.yml

@@ -85,8 +85,10 @@ jobs:
           CIBW_ARCHS: AMD64
           CIBW_BEFORE_BUILD: python -m pip install setuptools wheel delvewheel # skip CasADi and CMake
           CIBW_REPAIR_WHEEL_COMMAND: delvewheel repair -w {dest_dir} {wheel}
-          CIBW_TEST_COMMAND: python -c "import pybamm; print(pybamm.IDAKLUSolver())"
-
+          CIBW_TEST_EXTRAS: "all,dev,jax"
+          CIBW_TEST_COMMAND: |
+            python -c "import pybamm; print(pybamm.IDAKLUSolver())"
+            python -m pytest -m cibw {project}/tests/unit
       - name: Upload Windows wheels
         uses: actions/upload-artifact@v4.3.6
         with:
@@ -118,9 +120,11 @@ jobs:
             bash scripts/install_sundials.sh 6.0.3 6.5.0
           CIBW_BEFORE_BUILD_LINUX: python -m pip install cmake casadi setuptools wheel
           CIBW_REPAIR_WHEEL_COMMAND_LINUX: auditwheel repair -w {dest_dir} {wheel}
+          CIBW_TEST_EXTRAS: "all,dev,jax"
           CIBW_TEST_COMMAND: |
             set -e -x
             python -c "import pybamm; print(pybamm.IDAKLUSolver())"
+            python -m pytest -m cibw {project}/tests/unit
 
       - name: Upload wheels for Linux
         uses: actions/upload-artifact@v4.3.6
@@ -249,9 +253,11 @@ jobs:
               delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel} --require-target-macos-version 11.1
               for file in {dest_dir}/*.whl; do mv "$file" "${file//macosx_11_1/macosx_11_0}"; done
             fi
+          CIBW_TEST_EXTRAS: "all,dev,jax"
           CIBW_TEST_COMMAND: |
             set -e -x
             python -c "import pybamm; print(pybamm.IDAKLUSolver())"
+            python -m pytest -m cibw {project}/tests/unit
 
       - name: Upload wheels for macOS (amd64, arm64)
         uses: actions/upload-artifact@v4.3.6

.github/workflows/scorecard.yml

@@ -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@883d8588e56d1753a8a58c1c86e88976f0c23449 # v3.26.3
+        uses: github/codeql-action/upload-sarif@2c779ab0d087cd7fe7b826087247c2c81f27bfa6 # v3.26.5
         with:
           sarif_file: results.sarif

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.6.1"
+    rev: "v0.6.2"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

CHANGELOG.md

@@ -7,13 +7,20 @@
 
 ## Optimizations
 
+- Improved adaptive time-stepping performance of the (`IDAKLUSolver`). ([#4351](https://github.com/pybamm-team/PyBaMM/pull/4351))
 - Improved performance and reliability of DAE consistent initialization. ([#4301](https://github.com/pybamm-team/PyBaMM/pull/4301))
 - Replaced rounded Faraday constant with its exact value in `bpx.py` for better comparison between different tools. ([#4290](https://github.com/pybamm-team/PyBaMM/pull/4290))
 
 ## Bug Fixes
 
+- Fixed memory issue that caused failure when `output variables` were specified with (`IDAKLUSolver`). ([#4379](https://github.com/pybamm-team/PyBaMM/issues/4379))
 - Fixed bug where IDAKLU solver failed when `output variables` were specified and an event triggered. ([#4300](https://github.com/pybamm-team/PyBaMM/pull/4300))
 
+## Breaking changes
+
+- Remove deprecated function `pybamm_install_jax` ([#4362](https://github.com/pybamm-team/PyBaMM/pull/4362))
+- Removed legacy python-IDAKLU solver. ([#4326](https://github.com/pybamm-team/PyBaMM/pull/4326))
+
 # [v24.5](https://github.com/pybamm-team/PyBaMM/tree/v24.5) - 2024-07-26
 
 ## Features

CMakeLists.txt

@@ -91,8 +91,7 @@ pybind11_add_module(idaklu
   src/pybamm/solvers/c_solvers/idaklu/IdakluJax.cpp
   src/pybamm/solvers/c_solvers/idaklu/IdakluJax.hpp
   src/pybamm/solvers/c_solvers/idaklu/common.hpp
-  src/pybamm/solvers/c_solvers/idaklu/python.hpp
-  src/pybamm/solvers/c_solvers/idaklu/python.cpp
+  src/pybamm/solvers/c_solvers/idaklu/common.cpp
   src/pybamm/solvers/c_solvers/idaklu/Solution.cpp
   src/pybamm/solvers/c_solvers/idaklu/Solution.hpp
   src/pybamm/solvers/c_solvers/idaklu/Options.hpp

conftest.py

@@ -19,12 +19,19 @@ def pytest_addoption(parser):
         default=False,
         help="run integration tests",
     )
+    parser.addoption(
+        "--cibw",
+        action="store_true",
+        default=False,
+        help="test build wheels",
+    )
 
 
 def pytest_configure(config):
     config.addinivalue_line("markers", "scripts: mark test as an example script")
     config.addinivalue_line("markers", "unit: mark test as a unit test")
     config.addinivalue_line("markers", "integration: mark test as an integration test")
+    config.addinivalue_line("markers", "cibw: mark test as build wheel test")
 
 
 def pytest_collection_modifyitems(items):

docs/source/api/util.rst

@@ -16,8 +16,6 @@ Utility functions
 
 .. autofunction:: pybamm.load
 
-.. autofunction:: pybamm.install_jax
-
 .. autofunction:: pybamm.have_jax
 
 .. autofunction:: pybamm.is_jax_compatible

docs/source/user_guide/installation/gnu-linux-mac.rst

@@ -99,7 +99,7 @@ Users can install ``jax`` and ``jaxlib`` to use the Jax solver.
 
 	  pip install "pybamm[jax]"
 
-The ``pip install "pybamm[jax]"`` command automatically downloads and installs ``pybamm`` and the compatible versions of ``jax`` and ``jaxlib`` on your system. (``pybamm_install_jax`` is deprecated.)
+The ``pip install "pybamm[jax]"`` command automatically downloads and installs ``pybamm`` and the compatible versions of ``jax`` and ``jaxlib`` on your system.
 
 .. _optional-iree-mlir-support:
 

docs/source/user_guide/installation/windows.rst

@@ -75,7 +75,7 @@ Users can install ``jax`` and ``jaxlib`` to use the Jax solver.
 
 	  pip install "pybamm[jax]"
 
-The ``pip install "pybamm[jax]"`` command automatically downloads and installs ``pybamm`` and the compatible versions of ``jax`` and ``jaxlib`` on your system. (``pybamm_install_jax`` is deprecated.)
+The ``pip install "pybamm[jax]"`` command automatically downloads and installs ``pybamm`` and the compatible versions of ``jax`` and ``jaxlib`` on your system.
 
 Uninstall PyBaMM
 ----------------

examples/scripts/compare_surface_temperature.py

@@ -0,0 +1,61 @@
+#
+# Compare lithium-ion battery models
+#
+import pybamm
+
+pybamm.set_logging_level("INFO")
+
+# load models
+models = [
+    pybamm.lithium_ion.SPMe(
+        {"thermal": "lumped", "surface temperature": "ambient"},
+        name="ambient surface temperature",
+    ),
+    pybamm.lithium_ion.SPMe(
+        {"thermal": "lumped", "surface temperature": "lumped"},
+        name="lumped surface temperature",
+    ),
+]
+
+experiment = pybamm.Experiment(
+    [
+        "Discharge at 1C until 2.5V",
+        "Rest for 1 hour",
+    ]
+)
+
+parameter_values = pybamm.ParameterValues("Chen2020")
+parameter_values.update(
+    {
+        "Casing heat capacity [J.K-1]": 30,
+        "Environment thermal resistance [K.W-1]": 10,
+    },
+    check_already_exists=False,
+)
+
+# create and run simulations
+sols = []
+for model in models:
+    model.variables["Bulk temperature [°C]"] = (
+        model.variables["Volume-averaged cell temperature [K]"] - 273.15
+    )
+    model.variables["Surface temperature [°C]"] = (
+        model.variables["Surface temperature [K]"] - 273.15
+    )
+    sim = pybamm.Simulation(
+        model, parameter_values=parameter_values, experiment=experiment
+    )
+    sol = sim.solve([0, 3600])
+    sols.append(sol)
+
+# plot
+pybamm.dynamic_plot(
+    sols,
+    [
+        "Voltage [V]",
+        "Bulk temperature [°C]",
+        "Surface temperature [°C]",
+        "Surface total cooling [W]",
+        "Environment total cooling [W]",
+    ],
+)

pyproject.toml

@@ -134,9 +134,6 @@ all = [
     "pybamm[examples,plot,cite,bpx,tqdm]",
 ]
 
-[project.scripts]
-pybamm_install_jax = "pybamm.util:install_jax"
-
 [project.entry-points."pybamm_parameter_sets"]
 Sulzer2019 = "pybamm.input.parameters.lead_acid.Sulzer2019:get_parameter_values"
 Ai2020 = "pybamm.input.parameters.lithium_ion.Ai2020:get_parameter_values"
@@ -234,6 +231,7 @@ required_plugins = [
     "pytest-xdist",
     "pytest-mock",
 ]
+norecursedirs = 'pybind11*'
 addopts = [
     "-nauto",
     "-vra",

setup.py

@@ -322,8 +322,7 @@ def compile_KLU():
         "src/pybamm/solvers/c_solvers/idaklu/IdakluJax.cpp",
         "src/pybamm/solvers/c_solvers/idaklu/IdakluJax.hpp",
         "src/pybamm/solvers/c_solvers/idaklu/common.hpp",
-        "src/pybamm/solvers/c_solvers/idaklu/python.hpp",
-        "src/pybamm/solvers/c_solvers/idaklu/python.cpp",
+        "src/pybamm/solvers/c_solvers/idaklu/common.cpp",
         "src/pybamm/solvers/c_solvers/idaklu/Solution.cpp",
         "src/pybamm/solvers/c_solvers/idaklu/Solution.hpp",
         "src/pybamm/solvers/c_solvers/idaklu/Options.hpp",

src/pybamm/CITATIONS.bib

@@ -252,6 +252,16 @@ @article{Lain2019
   doi = {10.3390/batteries5040064},
 }
 
+@article{lin2014lumped,
+  title={A lumped-parameter electro-thermal model for cylindrical batteries},
+  author={Lin, Xinfan and Perez, Hector E and Mohan, Shankar and Siegel, Jason B and Stefanopoulou, Anna G and Ding, Yi and Castanier, Matthew P},
+  journal={Journal of Power Sources},
+  volume={257},
+  pages={1--11},
+  year={2014},
+  publisher={Elsevier}
+}
+
 @article{Marquis2019,
   title = {{An asymptotic derivation of a single particle model with electrolyte}},
   author = {Marquis, Scott G. and Sulzer, Valentin and Timms, Robert and Please, Colin P. and Chapman, S. Jon},

src/pybamm/__init__.py

@@ -16,7 +16,6 @@
 from .util import (
     get_parameters_filepath,
     have_jax,
-    install_jax,
     import_optional_dependency,
     is_jax_compatible,
     get_git_commit_info,

src/pybamm/batch_study.py

@@ -106,6 +106,7 @@ def solve(
         calc_esoh=True,
         starting_solution=None,
         initial_soc=None,
+        t_interp=None,
         **kwargs,
     ):
         """