Merge branch 'develop' into pytest-migration-4

pybamm-team · Jul 23, 2024 · ba6a5e1 · ba6a5e1
2 parents 6de815f + 668e563
commit ba6a5e1
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diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
@@ -317,7 +317,7 @@ jobs:
         if: github.event.inputs.target == 'testpypi'
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          packages-dir: files/
+          packages-dir: artifacts/
           repository-url: https://test.pypi.org/legacy/
 
   open_failure_issue:

diff --git a/.github/workflows/run_periodic_tests.yml b/.github/workflows/run_periodic_tests.yml
@@ -14,6 +14,8 @@ on:
 
 env:
   FORCE_COLOR: 3
+  PYBAMM_IDAKLU_EXPR_CASADI: ON
+  PYBAMM_IDAKLU_EXPR_IREE: ON
 
 concurrency:
   # github.workflow: name of the workflow, so that we don't cancel other workflows

diff --git a/.github/workflows/scorecard.yml b/.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@b611370bb5703a7efb587f9d136a52ea24c5c38c # v3.25.11
+        uses: github/codeql-action/upload-sarif@2d790406f505036ef40ecba973cc774a50395aac # v3.25.13
         with:
           sarif_file: results.sarif
diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
@@ -6,6 +6,8 @@ on:
 
 env:
   FORCE_COLOR: 3
+  PYBAMM_IDAKLU_EXPR_CASADI: ON
+  PYBAMM_IDAKLU_EXPR_IREE: ON
 
 concurrency:
   # github.workflow: name of the workflow, so that we don't cancel other workflows

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: "v0.5.1"
+    rev: "v0.5.4"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
-# [v24.5rc0](https://github.com/pybamm-team/PyBaMM/tree/v24.5rc0) - 2024-05-01
+# [v24.5rc2](https://github.com/pybamm-team/PyBaMM/tree/v24.5rc2) - 2024-07-12
 
 ## Features
 

diff --git a/CITATION.cff b/CITATION.cff
@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "24.5rc0"
+version: "24.5rc2"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -35,32 +35,76 @@ add_compile_definitions(_GLIBCXX_USE_CXX11_ABI=0)
 if(NOT PYBIND11_DIR)
   set(PYBIND11_DIR pybind11)
 endif()
-
 add_subdirectory(${PYBIND11_DIR})
-# The sources list should mirror the list in setup.py
+
+# Check Casadi build flag
+if(NOT DEFINED PYBAMM_IDAKLU_EXPR_CASADI)
+  set(PYBAMM_IDAKLU_EXPR_CASADI ON)
+endif()
+message("PYBAMM_IDAKLU_EXPR_CASADI: ${PYBAMM_IDAKLU_EXPR_CASADI}")
+
+# Casadi PyBaMM source files
+set(IDAKLU_EXPR_CASADI_SOURCE_FILES "")
+if(${PYBAMM_IDAKLU_EXPR_CASADI} STREQUAL "ON" )
+  add_compile_definitions(CASADI_ENABLE)
+  set(IDAKLU_EXPR_CASADI_SOURCE_FILES
+    pybamm/solvers/c_solvers/idaklu/Expressions/Casadi/CasadiFunctions.cpp
+    pybamm/solvers/c_solvers/idaklu/Expressions/Casadi/CasadiFunctions.hpp
+  )
+endif()
+
+# Check IREE build flag
+if(NOT DEFINED PYBAMM_IDAKLU_EXPR_IREE)
+  set(PYBAMM_IDAKLU_EXPR_IREE OFF)
+endif()
+message("PYBAMM_IDAKLU_EXPR_IREE: ${PYBAMM_IDAKLU_EXPR_IREE}")
+
+# IREE (MLIR expression evaluation) PyBaMM source files
+set(IDAKLU_EXPR_IREE_SOURCE_FILES "")
+if(${PYBAMM_IDAKLU_EXPR_IREE} STREQUAL "ON" )
+  add_compile_definitions(IREE_ENABLE)
+  # Source file list
+  set(IDAKLU_EXPR_IREE_SOURCE_FILES
+    pybamm/solvers/c_solvers/idaklu/Expressions/IREE/iree_jit.cpp
+    pybamm/solvers/c_solvers/idaklu/Expressions/IREE/iree_jit.hpp
+    pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEFunctions.cpp
+    pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEFunctions.hpp
+    pybamm/solvers/c_solvers/idaklu/Expressions/IREE/ModuleParser.cpp
+    pybamm/solvers/c_solvers/idaklu/Expressions/IREE/ModuleParser.hpp
+  )
+endif()
+
+# The complete (all dependencies) sources list should be mirrored in setup.py
 pybind11_add_module(idaklu
-  pybamm/solvers/c_solvers/idaklu/casadi_functions.cpp
-  pybamm/solvers/c_solvers/idaklu/casadi_functions.hpp
-  pybamm/solvers/c_solvers/idaklu/casadi_solver.cpp
-  pybamm/solvers/c_solvers/idaklu/casadi_solver.hpp
-  pybamm/solvers/c_solvers/idaklu/CasadiSolver.cpp
-  pybamm/solvers/c_solvers/idaklu/CasadiSolver.hpp
-  pybamm/solvers/c_solvers/idaklu/CasadiSolverOpenMP.cpp
-  pybamm/solvers/c_solvers/idaklu/CasadiSolverOpenMP.hpp
-  pybamm/solvers/c_solvers/idaklu/CasadiSolverOpenMP_solvers.cpp
-  pybamm/solvers/c_solvers/idaklu/CasadiSolverOpenMP_solvers.hpp
-  pybamm/solvers/c_solvers/idaklu/casadi_sundials_functions.cpp
-  pybamm/solvers/c_solvers/idaklu/casadi_sundials_functions.hpp
-  pybamm/solvers/c_solvers/idaklu/idaklu_jax.cpp
-  pybamm/solvers/c_solvers/idaklu/idaklu_jax.hpp
+  # pybind11 interface
+  pybamm/solvers/c_solvers/idaklu.cpp
+  # IDAKLU solver (SUNDIALS)
+  pybamm/solvers/c_solvers/idaklu/idaklu_solver.hpp
+  pybamm/solvers/c_solvers/idaklu/IDAKLUSolver.cpp
+  pybamm/solvers/c_solvers/idaklu/IDAKLUSolver.hpp
+  pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP.inl
+  pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP.hpp
+  pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP_solvers.cpp
+  pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP_solvers.hpp
+  pybamm/solvers/c_solvers/idaklu/sundials_functions.inl
+  pybamm/solvers/c_solvers/idaklu/sundials_functions.hpp
+  pybamm/solvers/c_solvers/idaklu/IdakluJax.cpp
+  pybamm/solvers/c_solvers/idaklu/IdakluJax.hpp
   pybamm/solvers/c_solvers/idaklu/common.hpp
   pybamm/solvers/c_solvers/idaklu/python.hpp
   pybamm/solvers/c_solvers/idaklu/python.cpp
-  pybamm/solvers/c_solvers/idaklu/solution.cpp
-  pybamm/solvers/c_solvers/idaklu/solution.hpp
-  pybamm/solvers/c_solvers/idaklu/options.hpp
-  pybamm/solvers/c_solvers/idaklu/options.cpp
-  pybamm/solvers/c_solvers/idaklu.cpp
+  pybamm/solvers/c_solvers/idaklu/Solution.cpp
+  pybamm/solvers/c_solvers/idaklu/Solution.hpp
+  pybamm/solvers/c_solvers/idaklu/Options.hpp
+  pybamm/solvers/c_solvers/idaklu/Options.cpp
+  # IDAKLU expressions / function evaluation [abstract]
+  pybamm/solvers/c_solvers/idaklu/Expressions/Expressions.hpp
+  pybamm/solvers/c_solvers/idaklu/Expressions/Base/Expression.hpp
+  pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionSet.hpp
+  pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionTypes.hpp
+  # IDAKLU expressions - concrete implementations
+  ${IDAKLU_EXPR_CASADI_SOURCE_FILES}
+  ${IDAKLU_EXPR_IREE_SOURCE_FILES}
 )
 
 if (NOT DEFINED USE_PYTHON_CASADI)
@@ -113,3 +157,16 @@ else()
 endif()
 include_directories(${SuiteSparse_INCLUDE_DIRS})
 target_link_libraries(idaklu PRIVATE ${SuiteSparse_LIBRARIES})
+
+# IREE (MLIR compiler and runtime library) build settings
+if(${PYBAMM_IDAKLU_EXPR_IREE} STREQUAL "ON" )
+  set(IREE_BUILD_COMPILER ON)
+  set(IREE_BUILD_TESTS OFF)
+  set(IREE_BUILD_SAMPLES OFF)
+  add_subdirectory(iree EXCLUDE_FROM_ALL)
+  set(IREE_COMPILER_ROOT "${CMAKE_CURRENT_SOURCE_DIR}/iree/compiler")
+  target_include_directories(idaklu SYSTEM PRIVATE "${IREE_COMPILER_ROOT}/bindings/c/iree/compiler")
+  target_compile_options(idaklu PRIVATE ${IREE_DEFAULT_COPTS})
+  target_link_libraries(idaklu PRIVATE iree_compiler_bindings_c_loader)
+  target_link_libraries(idaklu PRIVATE iree_runtime_runtime)
+endif()
diff --git a/bandit.yml b/bandit.yml
@@ -0,0 +1,2 @@
+# To ignore false flagging of assert statements in tests by Codacy.
+skips: ['B101']
diff --git a/docs/source/examples/notebooks/getting_started/tutorial-5-run-experiments.ipynb b/docs/source/examples/notebooks/getting_started/tutorial-5-run-experiments.ipynb
@@ -25,18 +25,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "\n",
-      "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip is available: \u001b[0m\u001b[31;49m23.3.1\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m24.0\u001b[0m\n",
-      "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n",
       "Note: you may need to restart the kernel to use updated packages.\n"
      ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "An NVIDIA GPU may be present on this machine, but a CUDA-enabled jaxlib is not installed. Falling back to cpu.\n"
-     ]
     }
    ],
    "source": [
@@ -163,18 +153,19 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "At t = 522.66 and h = 1.1556e-13, the corrector convergence failed repeatedly or with |h| = hmin.\n"
+      "At t = 339.952 and h = 1.4337e-18, the corrector convergence failed repeatedly or with |h| = hmin.\n",
+      "At t = 522.687 and h = 4.04917e-14, the corrector convergence failed repeatedly or with |h| = hmin.\n"
      ]
     },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "5ab1f22de6af4878b6ca43d27ffc01c5",
+       "model_id": "93feca98298f4111909ae487e2a1e273",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "interactive(children=(FloatSlider(value=0.0, description='t', max=40.132949019384355, step=0.40132949019384356…"
+       "interactive(children=(FloatSlider(value=0.0, description='t', max=40.13268704803602, step=0.4013268704803602),…"
       ]
      },
      "metadata": {},
@@ -183,7 +174,7 @@
     {
      "data": {
       "text/plain": [
-       "<pybamm.plotting.quick_plot.QuickPlot at 0x7f1a11f76690>"
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x16520e690>"
       ]
      },
      "execution_count": 5,
@@ -211,12 +202,12 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "7cdac234d74241a2814918053454f6a6",
+       "model_id": "4d6e43032f4e4aa6be5843c4916b4b50",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "interactive(children=(FloatSlider(value=0.0, description='t', max=13.076977041121545, step=0.13076977041121546…"
+       "interactive(children=(FloatSlider(value=0.0, description='t', max=13.076887099589111, step=0.1307688709958911)…"
       ]
      },
      "metadata": {},
@@ -225,7 +216,7 @@
     {
      "data": {
       "text/plain": [
-       "<pybamm.plotting.quick_plot.QuickPlot at 0x7f1a105ecb50>"
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x1696cf290>"
       ]
      },
      "execution_count": 6,
@@ -255,7 +246,7 @@
     {
      "data": {
       "text/plain": [
-       "_Step(C-rate, 1.0, duration=1 hour, period=1 minute, temperature=25oC, tags=['tag1'], description=Discharge at 1C for 1 hour)"
+       "Step(1.0, duration=1 hour, period=1 minute, temperature=25oC, tags=['tag1'], description=Discharge at 1C for 1 hour, direction=Discharge)"
       ]
      },
      "execution_count": 7,
@@ -293,7 +284,7 @@
     {
      "data": {
       "text/plain": [
-       "_Step(current, 1, duration=1 hour, termination=2.5 V)"
+       "Step(1, duration=1 hour, termination=2.5 V, direction=Discharge)"
       ]
      },
      "execution_count": 8,
@@ -321,7 +312,7 @@
     {
      "data": {
       "text/plain": [
-       "_Step(current, 1.0, duration=1 hour, termination=2.5V, description=Discharge at 1A for 1 hour or until 2.5V)"
+       "Step(1.0, duration=1 hour, termination=2.5V, description=Discharge at 1A for 1 hour or until 2.5V, direction=Discharge)"
       ]
      },
      "execution_count": 9,
@@ -348,10 +339,78 @@
    "execution_count": 10,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "2024-07-10 14:41:02.625 - [WARNING] callbacks.on_experiment_infeasible_time(240): \n",
+      "\n",
+      "\tExperiment is infeasible: default duration (1.0 seconds) was reached during 'Step([[ 0.00000000e+00  0.00000000e+00]\n",
+      " [ 1.69491525e-02  5.31467428e-02]\n",
+      " [ 3.38983051e-02  1.05691312e-01]\n",
+      " [ 5.08474576e-02  1.57038356e-01]\n",
+      " [ 6.77966102e-02  2.06606093e-01]\n",
+      " [ 8.47457627e-02  2.53832900e-01]\n",
+      " [ 1.01694915e-01  2.98183679e-01]\n",
+      " [ 1.18644068e-01  3.39155918e-01]\n",
+      " [ 1.35593220e-01  3.76285385e-01]\n",
+      " [ 1.52542373e-01  4.09151388e-01]\n",
+      " [ 1.69491525e-01  4.37381542e-01]\n",
+      " [ 1.86440678e-01  4.60655989e-01]\n",
+      " [ 2.03389831e-01  4.78711019e-01]\n",
+      " [ 2.20338983e-01  4.91342062e-01]\n",
+      " [ 2.37288136e-01  4.98406004e-01]\n",
+      " [ 2.54237288e-01  4.99822806e-01]\n",
+      " [ 2.71186441e-01  4.95576416e-01]\n",
+      " [ 2.88135593e-01  4.85714947e-01]\n",
+      " [ 3.05084746e-01  4.70350133e-01]\n",
+      " [ 3.22033898e-01  4.49656065e-01]\n",
+      " [ 3.38983051e-01  4.23867214e-01]\n",
+      " [ 3.55932203e-01  3.93275778e-01]\n",
+      " [ 3.72881356e-01  3.58228370e-01]\n",
+      " [ 3.89830508e-01  3.19122092e-01]\n",
+      " [ 4.06779661e-01  2.76400033e-01]\n",
+      " [ 4.23728814e-01  2.30546251e-01]\n",
+      " [ 4.40677966e-01  1.82080288e-01]\n",
+      " [ 4.57627119e-01  1.31551282e-01]\n",
+      " [ 4.74576271e-01  7.95317480e-02]\n",
+      " [ 4.91525424e-01  2.66110874e-02]\n",
+      " [ 5.08474576e-01 -2.66110874e-02]\n",
+      " [ 5.25423729e-01 -7.95317480e-02]\n",
+      " [ 5.42372881e-01 -1.31551282e-01]\n",
+      " [ 5.59322034e-01 -1.82080288e-01]\n",
+      " [ 5.76271186e-01 -2.30546251e-01]\n",
+      " [ 5.93220339e-01 -2.76400033e-01]\n",
+      " [ 6.10169492e-01 -3.19122092e-01]\n",
+      " [ 6.27118644e-01 -3.58228370e-01]\n",
+      " [ 6.44067797e-01 -3.93275778e-01]\n",
+      " [ 6.61016949e-01 -4.23867214e-01]\n",
+      " [ 6.77966102e-01 -4.49656065e-01]\n",
+      " [ 6.94915254e-01 -4.70350133e-01]\n",
+      " [ 7.11864407e-01 -4.85714947e-01]\n",
+      " [ 7.28813559e-01 -4.95576416e-01]\n",
+      " [ 7.45762712e-01 -4.99822806e-01]\n",
+      " [ 7.62711864e-01 -4.98406004e-01]\n",
+      " [ 7.79661017e-01 -4.91342062e-01]\n",
+      " [ 7.96610169e-01 -4.78711019e-01]\n",
+      " [ 8.13559322e-01 -4.60655989e-01]\n",
+      " [ 8.30508475e-01 -4.37381542e-01]\n",
+      " [ 8.47457627e-01 -4.09151388e-01]\n",
+      " [ 8.64406780e-01 -3.76285385e-01]\n",
+      " [ 8.81355932e-01 -3.39155918e-01]\n",
+      " [ 8.98305085e-01 -2.98183679e-01]\n",
+      " [ 9.15254237e-01 -2.53832900e-01]\n",
+      " [ 9.32203390e-01 -2.06606093e-01]\n",
+      " [ 9.49152542e-01 -1.57038356e-01]\n",
+      " [ 9.66101695e-01 -1.05691312e-01]\n",
+      " [ 9.83050847e-01 -5.31467428e-02]\n",
+      " [ 1.00000000e+00 -1.22464680e-16]], duration=1.0, period=0.016949152542372836, direction=Rest)'. The returned solution only contains up to step 1 of cycle 1. Please specify a duration in the step instructions.\n"
+     ]
+    },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "730d5e19b17e447ebde5679de68c46ef",
+       "model_id": "6364b4579fc447e2a607f2f8414172ba",
        "version_major": 2,
        "version_minor": 0
       },
@@ -365,7 +424,7 @@
     {
      "data": {
       "text/plain": [
-       "<pybamm.plotting.quick_plot.QuickPlot at 0x7f1a1a4c2ed0>"
+       "<pybamm.plotting.quick_plot.QuickPlot at 0x16a1d8d90>"
       ]
      },
      "execution_count": 10,
@@ -419,13 +478,14 @@
      "output_type": "stream",
      "text": [
       "[1] Joel A. E. Andersson, Joris Gillis, Greg Horn, James B. Rawlings, and Moritz Diehl. CasADi – A software framework for nonlinear optimization and optimal control. Mathematical Programming Computation, 11(1):1–36, 2019. doi:10.1007/s12532-018-0139-4.\n",
-      "[2] Marc Doyle, Thomas F. Fuller, and John Newman. Modeling of galvanostatic charge and discharge of the lithium/polymer/insertion cell. Journal of the Electrochemical society, 140(6):1526–1533, 1993. doi:10.1149/1.2221597.\n",
-      "[3] Charles R. Harris, K. Jarrod Millman, Stéfan J. van der Walt, Ralf Gommers, Pauli Virtanen, David Cournapeau, Eric Wieser, Julian Taylor, Sebastian Berg, Nathaniel J. Smith, and others. Array programming with NumPy. Nature, 585(7825):357–362, 2020. doi:10.1038/s41586-020-2649-2.\n",
-      "[4] Scott G. Marquis, Valentin Sulzer, Robert Timms, Colin P. Please, and S. Jon Chapman. An asymptotic derivation of a single particle model with electrolyte. Journal of The Electrochemical Society, 166(15):A3693–A3706, 2019. doi:10.1149/2.0341915jes.\n",
-      "[5] Peyman Mohtat, Suhak Lee, Jason B Siegel, and Anna G Stefanopoulou. Towards better estimability of electrode-specific state of health: decoding the cell expansion. Journal of Power Sources, 427:101–111, 2019.\n",
-      "[6] Valentin Sulzer, Scott G. Marquis, Robert Timms, Martin Robinson, and S. Jon Chapman. Python Battery Mathematical Modelling (PyBaMM). Journal of Open Research Software, 9(1):14, 2021. doi:10.5334/jors.309.\n",
-      "[7] Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland, Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson, Warren Weckesser, Jonathan Bright, and others. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nature Methods, 17(3):261–272, 2020. doi:10.1038/s41592-019-0686-2.\n",
-      "[8] Andrew Weng, Jason B Siegel, and Anna Stefanopoulou. Differential voltage analysis for battery manufacturing process control. arXiv preprint arXiv:2303.07088, 2023.\n",
+      "[2] Von DAG Bruggeman. Berechnung verschiedener physikalischer konstanten von heterogenen substanzen. i. dielektrizitätskonstanten und leitfähigkeiten der mischkörper aus isotropen substanzen. Annalen der physik, 416(7):636–664, 1935.\n",
+      "[3] Marc Doyle, Thomas F. Fuller, and John Newman. Modeling of galvanostatic charge and discharge of the lithium/polymer/insertion cell. Journal of the Electrochemical society, 140(6):1526–1533, 1993. doi:10.1149/1.2221597.\n",
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       "\n"
      ]
     }

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