Merge branch 'develop' into single-layer-sei

pybamm-team · Oct 9, 2024 · 5e1a46b · 5e1a46b
2 parents 482f5f8 + e4eb82a
commit 5e1a46b
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diff --git a/.github/workflows/periodic_benchmarks.yml b/.github/workflows/periodic_benchmarks.yml
@@ -51,7 +51,7 @@ jobs:
           LD_LIBRARY_PATH: $HOME/.local/lib
 
       - name: Upload results as artifact
-        uses: actions/upload-artifact@v4.4.0
+        uses: actions/upload-artifact@v4.4.1
         with:
           name: asv_periodic_results
           path: results

diff --git a/.github/workflows/publish_pypi.yml b/.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/upload-artifact@v4.4.0
+        uses: actions/upload-artifact@v4.4.1
         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/upload-artifact@v4.4.0
+        uses: actions/upload-artifact@v4.4.1
         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/upload-artifact@v4.4.0
+        uses: actions/upload-artifact@v4.4.1
         with:
           name: wheels_${{ matrix.os }}
           path: ./wheelhouse/*.whl
@@ -281,7 +281,7 @@ jobs:
         run: pipx run build --sdist
 
       - name: Upload SDist
-        uses: actions/upload-artifact@v4.4.0
+        uses: actions/upload-artifact@v4.4.1
         with:
           name: sdist
           path: ./dist/*.tar.gz

diff --git a/.github/workflows/run_benchmarks_over_history.yml b/.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/upload-artifact@v4.4.0
+        uses: actions/upload-artifact@v4.4.1
         with:
           name: asv_over_history_results
           path: results

diff --git a/.github/workflows/run_periodic_tests.yml b/.github/workflows/run_periodic_tests.yml
@@ -89,7 +89,7 @@ jobs:
 
       - name: Upload coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v4.6.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 

diff --git a/.github/workflows/scorecard.yml b/.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@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
+        uses: actions/upload-artifact@604373da6381bf24206979c74d06a550515601b9 # 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@294a9d92911152fe08befb9ec03e240add280cb3 # v3.26.8
+        uses: github/codeql-action/upload-sarif@c36620d31ac7c881962c3d9dd939c40ec9434f2b # v3.26.12
         with:
           sarif_file: results.sarif
diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
@@ -123,7 +123,7 @@ jobs:
 
       - name: Upload coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v4.6.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.6.7"
+    rev: "v0.6.9"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
@@ -19,7 +19,7 @@ repos:
          additional_dependencies: [black==23.*]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
         - id: check-added-large-files
         - id: check-case-conflict

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,11 +2,14 @@
 
 ## Features
 
+- Added Hermite interpolation to the (`IDAKLUSolver`) that improves the accuracy and performance of post-processing variables. ([#4464](https://github.com/pybamm-team/PyBaMM/pull/4464))
+- Added `BasicDFN` model for sodium-ion batteries ([#4451](https://github.com/pybamm-team/PyBaMM/pull/4451))
 - Added sensitivity calculation support for `pybamm.Simulation` and `pybamm.Experiment` ([#4415](https://github.com/pybamm-team/PyBaMM/pull/4415))
 - Added OpenMP parallelization to IDAKLU solver for lists of input parameters ([#4449](https://github.com/pybamm-team/PyBaMM/pull/4449))
 - Added phase-dependent particle options to LAM
   ([#4369](https://github.com/pybamm-team/PyBaMM/pull/4369))
 - Added a lithium ion equivalent circuit model with split open circuit voltages for each electrode (`SplitOCVR`). ([#4330](https://github.com/pybamm-team/PyBaMM/pull/4330))
+- Added the `pybamm.DiscreteTimeSum` expression node to sum an expression over a sequence of data times, and accompanying `pybamm.DiscreteTimeData` class to store the data times and values ([#4501](https://github.com/pybamm-team/PyBaMM/pull/4501))
 
 ## Optimizations
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -105,6 +105,8 @@ pybind11_add_module(idaklu
   src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/Expression.hpp
   src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionSet.hpp
   src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionTypes.hpp
+  src/pybamm/solvers/c_solvers/idaklu/observe.hpp
+  src/pybamm/solvers/c_solvers/idaklu/observe.cpp
   # IDAKLU expressions - concrete implementations
   ${IDAKLU_EXPR_CASADI_SOURCE_FILES}
   ${IDAKLU_EXPR_IREE_SOURCE_FILES}

diff --git a/docs/conf.py b/docs/conf.py
@@ -341,7 +341,7 @@
 
 {% set github_docname =
 'github/pybamm-team/pybamm/blob/develop/docs/' +
-env.doc2path(env.docname, base=None) %}
+env.doc2path(env.docname, base=None) | string() %}
 
 {% set notebooks_version = env.config.html_context.notebooks_version %}
 {% set github_download_url = env.config.html_context.github_download_url %}

diff --git a/docs/source/examples/index.rst b/docs/source/examples/index.rst
@@ -68,6 +68,7 @@ The notebooks are organised into subfolders, and can be viewed in the galleries
     notebooks/models/SEI-on-cracks.ipynb
     notebooks/models/simulate-3E-cell.ipynb
     notebooks/models/simulating-ORegan-2022-parameter-set.ipynb
+    notebooks/models/sodium-ion.ipynb
     notebooks/models/SPM.ipynb
     notebooks/models/SPMe.ipynb
     notebooks/models/submodel_cracking_DFN_or_SPM.ipynb

diff --git a/docs/source/examples/notebooks/models/sodium-ion.ipynb b/docs/source/examples/notebooks/models/sodium-ion.ipynb
diff --git a/docs/source/user_guide/installation/index.rst b/docs/source/user_guide/installation/index.rst
@@ -145,8 +145,8 @@ Dependency
 `pre-commit <https://pre-commit.com/index.html>`__                               \-                 dev                For managing and maintaining multi-language pre-commit hooks.
 `ruff <https://beta.ruff.rs/docs/>`__                                            \-                 dev                For code formatting.
 `nox <https://nox.thea.codes/en/stable/>`__                                      \-                 dev                For running testing sessions in multiple environments.
+`pytest-subtests <https://github.com/pytest-dev/pytest-subtests/>`__             \-                 dev                For subtests pytest fixture.
 `pytest-cov <https://pytest-cov.readthedocs.io/en/stable/>`__                    \-                 dev                For calculating test coverage.
-`parameterized <https://github.com/wolever/parameterized>`__                     \-                 dev                For test parameterization.
 `pytest <https://docs.pytest.org/en/stable/>`__                                  6.0.0              dev                For running the test suites.
 `pytest-doctestplus <https://github.com/scientific-python/pytest-doctestplus>`__ \-                 dev                For running doctests.
 `pytest-xdist <https://pytest-xdist.readthedocs.io/en/latest/>`__                \-                 dev                For running tests in parallel across distributed workers.

diff --git a/pyproject.toml b/pyproject.toml
@@ -84,6 +84,7 @@ plot = [
     "matplotlib>=3.6.0",
 ]
 cite = [
+    "setuptools", # Fix for a pybtex issue
     "pybtex>=0.24.0",
 ]
 # Battery Parameter eXchange format
@@ -105,12 +106,11 @@ dev = [
     "pytest-cov",
     # For doctest
     "pytest-doctestplus",
-    # For test parameterization
-    "parameterized>=0.9",
     # pytest and its plugins
     "pytest>=6",
     "pytest-xdist",
     "pytest-mock",
+    "pytest-subtests",
     # For testing Jupyter notebooks
     "nbmake",
     # To access the metadata for python packages
@@ -152,6 +152,7 @@ Ramadass2004 = "pybamm.input.parameters.lithium_ion.Ramadass2004:get_parameter_v
 Xu2019 = "pybamm.input.parameters.lithium_ion.Xu2019:get_parameter_values"
 ECM_Example = "pybamm.input.parameters.ecm.example_set:get_parameter_values"
 MSMR_Example = "pybamm.input.parameters.lithium_ion.MSMR_example_set:get_parameter_values"
+Chayambuka2022 = "pybamm.input.parameters.sodium_ion.Chayambuka2022:get_parameter_values"
 
 [tool.setuptools]
 include-package-data = true
@@ -197,6 +198,8 @@ extend-select = [
     "YTT",           # flake8-2020
     "TID252",        # relative-imports
     "S101",          # to identify use of assert statement
+    "PT027",         # remove unittest style assertion
+    "PT009",         # Use pytest.raises instead of unittest-style
 ]
 ignore = [
     "E741",        # Ambiguous variable name
@@ -230,6 +233,7 @@ minversion = "8"
 required_plugins = [
     "pytest-xdist",
     "pytest-mock",
+    "pytest-subtests",
 ]
 norecursedirs = 'pybind11*'
 addopts = [

diff --git a/setup.py b/setup.py
@@ -327,6 +327,8 @@ def compile_KLU():
         "src/pybamm/solvers/c_solvers/idaklu/Solution.hpp",
         "src/pybamm/solvers/c_solvers/idaklu/Options.hpp",
         "src/pybamm/solvers/c_solvers/idaklu/Options.cpp",
+        "src/pybamm/solvers/c_solvers/idaklu/observe.hpp",
+        "src/pybamm/solvers/c_solvers/idaklu/observe.cpp",
         "src/pybamm/solvers/c_solvers/idaklu.cpp",
     ],
 )