Merge pull request #2497 from pybamm-team/develop

Make release v22.11
pybamm-team · Dec 4, 2022 · efd426c · efd426c
2 parents c544b6d + c17756f
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -528,7 +528,8 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/74401230?v=4",
       "profile": "https://github.com/agriyakhetarpal",
       "contributions": [
-        "infra"
+        "infra",
+        "code"
       ]
     },
     {

diff --git a/.gitignore b/.gitignore
@@ -13,6 +13,7 @@
 !CMakeLists.txt
 !pybamm/CITATIONS.txt
 !pybamm/input/**/*.csv
+!tests/unit/test_parameters/*.csv
 !benchmarks/benchmark_images/*.png
 
 # running files

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.3
+    rev: v3.0.0-alpha.4
     hooks:
       - id: prettier
         exclude: assets/js/webapp\.js
@@ -15,6 +15,6 @@ repos:
       - id: black
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
+    rev: 6.0.0
     hooks:
       - id: flake8
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,14 +1,45 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+# [v22.11](https://github.com/pybamm-team/PyBaMM/tree/v22.11) - 2022-11-30
+
+## Features
+
+- Updated parameter sets so that interpolants are created explicitly in the parameter set python file. This does not change functionality but allows finer control, e.g. specifying a "cubic" interpolator instead of the default "linear" ([#2510](https://github.com/pybamm-team/PyBaMM/pull/2510))
+- Equivalent circuit models ([#2478](https://github.com/pybamm-team/PyBaMM/pull/2478))
+- New Idaklu solver options for jacobian type and linear solver, support Sundials v6 ([#2444](https://github.com/pybamm-team/PyBaMM/pull/2444))
+- Added `scale` and `reference` attributes to `Variable` objects, which can be use to make the ODE/DAE solver better conditioned ([#2440](https://github.com/pybamm-team/PyBaMM/pull/2440))
+- SEI reactions can now be asymmetric ([#2425](https://github.com/pybamm-team/PyBaMM/pull/2425))
+
+## Bug fixes
+
+- Switched from `pkg_resources` to `importlib_metadata` for handling entry points ([#2500](https://github.com/pybamm-team/PyBaMM/pull/2500))
+- Fixed some bugs related to processing `FunctionParameter` to `Interpolant` ([#2494](https://github.com/pybamm-team/PyBaMM/pull/2494))
+
+## Optimizations
+
+- `ParameterValues` now avoids trying to process children if a function parameter is an object that doesn't depend on its children ([#2477](https://github.com/pybamm-team/PyBaMM/pull/2477))
+- Implemented memoization via `cache` and `cached_property` from functools ([#2465](https://github.com/pybamm-team/PyBaMM/pull/2465))
+- Added more rules for simplifying expressions, especially around Concatenations. Also, meshes constructed from multiple domains are now cached ([#2443](https://github.com/pybamm-team/PyBaMM/pull/2443))
+- Added more rules for simplifying expressions. Constants in binary operators are now moved to the left by default (e.g. `x*2` returns `2*x`) ([#2424](https://github.com/pybamm-team/PyBaMM/pull/2424))
+
+## Breaking changes
+
+- Interpolants created from parameter data are now "linear" by default (was "cubic") ([#2494](https://github.com/pybamm-team/PyBaMM/pull/2494))
+- Renamed entry point for parameter sets to `pybamm_parameter_sets` ([#2475](https://github.com/pybamm-team/PyBaMM/pull/2475))
+- Removed code for generating `ModelingToolkit` problems ([#2432](https://github.com/pybamm-team/PyBaMM/pull/2432))
+- Removed `FirstOrder` and `Composite` lead-acid models, and some submodels specific to those models ([#2431](https://github.com/pybamm-team/PyBaMM/pull/2431))
+
 # [v22.10.post1](https://github.com/pybamm-team/PyBaMM/tree/v22.10.post1) - 2022-10-31
 
+## Breaking changes
+
 - Removed all julia generation code ([#2453](https://github.com/pybamm-team/PyBaMM/pull/2453)). Julia code will be hosted at [PyBaMM.jl](https://github.com/tinosulzer/PyBaMM.jl) from now on.
 
 # [v22.10](https://github.com/pybamm-team/PyBaMM/tree/v22.10) - 2022-10-31
 
 ## Features
 
-- Third-party parameter sets can be added by registering entry points to `pybamm_parameter_set` ([#2396](https://github.com/pybamm-team/PyBaMM/pull/2396))
+- Third-party parameter sets can be added by registering entry points to ~~`pybamm_parameter_set`~~`pybamm_parameter_sets` ([#2396](https://github.com/pybamm-team/PyBaMM/pull/2396), changed in [#2475](https://github.com/pybamm-team/PyBaMM/pull/2475))
 - Added three-dimensional interpolation ([#2380](https://github.com/pybamm-team/PyBaMM/pull/2380))
 
 ## Bug fixes

diff --git a/CITATION.cff b/CITATION.cff
@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "22.10"
+version: "22.11"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"
diff --git a/CMakeBuild.py b/CMakeBuild.py
@@ -82,7 +82,10 @@ def run(self):
             use_python_casadi = False
         else:
             use_python_casadi = True
+
+        build_type = os.getenv("PYBAMM_CPP_BUILD_TYPE", "RELEASE")
         cmake_args = [
+            "-DCMAKE_BUILD_TYPE={}".format(build_type),
             "-DPYTHON_EXECUTABLE={}".format(sys.executable),
             "-DUSE_PYTHON_CASADI={}".format("TRUE" if use_python_casadi else "FALSE"),
         ]

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -35,14 +35,20 @@ endif()
 
 add_subdirectory(${PYBIND11_DIR})
 pybind11_add_module(idaklu 
-  pybamm/solvers/c_solvers/idaklu_python.cpp
-  pybamm/solvers/c_solvers/idaklu_python.hpp
+  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/casadi_sundials_functions.hpp
+  pybamm/solvers/c_solvers/idaklu/casadi_sundials_functions.cpp
+  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.hpp
-  pybamm/solvers/c_solvers/idaklu_casadi.cpp
-  pybamm/solvers/c_solvers/idaklu_casadi.hpp
-  pybamm/solvers/c_solvers/solution.cpp
-  pybamm/solvers/c_solvers/solution.hpp
 )
 
 if (NOT DEFINED USE_PYTHON_CASADI)

diff --git a/FindSUNDIALS.cmake b/FindSUNDIALS.cmake
@@ -8,6 +8,8 @@
 #
 #    * sundials_ida
 #    * sundials_sunlinsolklu
+#    * sundials_sunlinsoldense
+#    * sundials_sunlinsollapackdense
 #    * sundials_sunmatrix_sparse
 #    * sundials_nvecserial
 #
@@ -31,6 +33,9 @@ find_path(SUNDIALS_INCLUDE_DIR
     sundials/sundials_math.h
     sundials/sundials_types.h
     sunlinsol/sunlinsol_klu.h
+    sunlinsol/sunlinsol_dense.h
+    sunlinsol/sunlinsol_spbcgs.h
+    sunlinsol/sunlinsol_lapackdense.h
     sunmatrix/sunmatrix_sparse.h
   PATH_SUFFIXES
     include
@@ -41,6 +46,9 @@ find_path(SUNDIALS_INCLUDE_DIR
 set(SUNDIALS_WANT_COMPONENTS
   sundials_idas
   sundials_sunlinsolklu
+  sundials_sunlinsoldense
+  sundials_sunlinsolspbcgs
+  sundials_sunlinsollapackdense
   sundials_sunmatrixsparse
   sundials_nvecserial
   )

diff --git a/README.md b/README.md
@@ -68,7 +68,9 @@ Additional supporting material can be found
 
 Note that the examples on the default `develop` branch are tested on the latest `develop` commit. This may sometimes cause errors when running the examples on the pybamm pip package, which is synced to the `main` branch. You can switch to the `main` branch on github to see the version of the examples that is compatible with the latest pip release.
 
-<!-- For further examples, see the list of repositories that use PyBaMM [here](https://github.com/pybamm-team/pybamm-example-results). -->
+## Versioning
+
+PyBaMM uses [CalVer](https://calver.org/), which means that we make new releases every month with the version number `YY.MM`. There is no difference between releases that increment the year and releases that increment the month; in particular, releases that increment the month may introduce breaking changes. Breaking changes for each release are communicated via the [CHANGELOG](CHANGELOG.md), and come with deprecation warnings or errors that are kept for at least one year (12 releases). If you find a breaking change that is not documented, or think it should be undone, please open an issue on [GitHub](https://github.com/pybamm-team/pybamm).
 
 ## 🚀 Installing PyBaMM
 
@@ -214,7 +216,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center"><a href="https://github.com/ndrewwang"><img src="https://avatars.githubusercontent.com/u/56122552?v=4?s=100" width="100px;" alt="ndrewwang"/><br /><sub><b>ndrewwang</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Andrewwang" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=ndrewwang" title="Code">💻</a></td>
       <td align="center"><a href="https://github.com/MichaPhilipp"><img src="https://avatars.githubusercontent.com/u/58085966?v=4?s=100" width="100px;" alt="MichaPhilipp"/><br /><sub><b>MichaPhilipp</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3AMichaPhilipp" title="Bug reports">🐛</a></td>
       <td align="center"><a href="https://github.com/abillscmu"><img src="https://avatars.githubusercontent.com/u/48105066?v=4?s=100" width="100px;" alt="Alec Bills"/><br /><sub><b>Alec Bills</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=abillscmu" title="Code">💻</a></td>
-      <td align="center"><a href="https://github.com/agriyakhetarpal"><img src="https://avatars.githubusercontent.com/u/74401230?v=4?s=100" width="100px;" alt="Agriya Khetarpal"/><br /><sub><b>Agriya Khetarpal</b></sub></a><br /><a href="#infra-agriyakhetarpal" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
+      <td align="center"><a href="https://github.com/agriyakhetarpal"><img src="https://avatars.githubusercontent.com/u/74401230?v=4?s=100" width="100px;" alt="Agriya Khetarpal"/><br /><sub><b>Agriya Khetarpal</b></sub></a><br /><a href="#infra-agriyakhetarpal" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=agriyakhetarpal" title="Code">💻</a></td>
       <td align="center"><a href="https://github.com/awadell1"><img src="https://avatars.githubusercontent.com/u/5857298?v=4?s=100" width="100px;" alt="Alex Wadell"/><br /><sub><b>Alex Wadell</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=awadell1" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=awadell1" title="Tests">⚠️</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=awadell1" title="Documentation">📖</a></td>
     </tr>
   </tbody>

diff --git a/benchmarks/different_model_options.py b/benchmarks/different_model_options.py
@@ -124,10 +124,12 @@ class TimeBuildModelSEI:
             "none",
             "constant",
             "reaction limited",
+            "reaction limited (asymmetric)",
             "solvent-diffusion limited",
             "electron-migration limited",
             "interstitial-diffusion limited",
             "ec reaction limited",
+            "ec reaction limited (asymmetric)",
         ],
     )
 
@@ -143,10 +145,12 @@ class TimeSolveSEI:
             "none",
             "constant",
             "reaction limited",
+            "reaction limited (asymmetric)",
             "solvent-diffusion limited",
             "electron-migration limited",
             "interstitial-diffusion limited",
             "ec reaction limited",
+            "ec reaction limited (asymmetric)",
         ],
     )
 

diff --git a/build-pure-wheel.sh b/build-pure-wheel.sh
diff --git a/build-wheel.sh b/build-wheel.sh
diff --git a/docs/conf.py b/docs/conf.py
@@ -27,7 +27,7 @@
 author = "The PyBaMM Team"
 
 # The short X.Y version
-version = "22.10"
+version = "22.11"
 # The full version, including alpha/beta/rc tags
 release = version
 

diff --git a/docs/source/models/equivalent_circuit/index.rst b/docs/source/models/equivalent_circuit/index.rst
@@ -0,0 +1,7 @@
+Equivalent Circuit Models
+=========================
+
+.. toctree::
+  :maxdepth: 1
+
+  thevenin
diff --git a/docs/source/models/equivalent_circuit/thevenin.rst b/docs/source/models/equivalent_circuit/thevenin.rst
@@ -0,0 +1,5 @@
+Thevenin Model
+==============
+
+.. autoclass:: pybamm.equivalent_circuit.Thevenin
+    :members:
diff --git a/docs/source/models/index.rst b/docs/source/models/index.rst
@@ -14,4 +14,5 @@ to see how these models can be solved, and compared, using PyBaMM.
   base_models/index
   lithium_ion/index
   lead_acid/index
+  equivalent_circuit/index
   submodels/index
diff --git a/docs/source/models/lead_acid/higher_order.rst b/docs/source/models/lead_acid/higher_order.rst
diff --git a/docs/source/models/lead_acid/index.rst b/docs/source/models/lead_acid/index.rst
@@ -6,5 +6,4 @@ Lead Acid Models
 
   base_lead_acid_model
   loqs
-  higher_order
   full
diff --git a/docs/source/models/submodels/current_collector/composite_potential_pair.rst b/docs/source/models/submodels/current_collector/composite_potential_pair.rst
diff --git a/docs/source/models/submodels/current_collector/index.rst b/docs/source/models/submodels/current_collector/index.rst
@@ -5,8 +5,6 @@ Current Collector
   :maxdepth: 1
 
   base_current_collector
-  composite_potential_pair
   effective_resistance_current_collector
   homogeneous_current_collector
   potential_pair
-  quite_conductive_potential_pair
diff --git a/docs/source/models/submodels/current_collector/quite_conductive_potential_pair.rst b/docs/source/models/submodels/current_collector/quite_conductive_potential_pair.rst
diff --git a/docs/source/models/submodels/electrolyte_diffusion/composite_diffusion.rst b/docs/source/models/submodels/electrolyte_diffusion/composite_diffusion.rst
diff --git a/docs/source/models/submodels/electrolyte_diffusion/index.rst b/docs/source/models/submodels/electrolyte_diffusion/index.rst
@@ -6,5 +6,4 @@ Electrolyte Diffusion
   base_electrolyte_diffusion
   constant_concentration
   leading_order_diffusion
-  composite_diffusion
   full_diffusion
diff --git a/docs/source/models/submodels/equivalent_circuit_elements/index.rst b/docs/source/models/submodels/equivalent_circuit_elements/index.rst
@@ -0,0 +1,10 @@
+Equivalent Circuit Elements
+===========================
+
+.. toctree::
+
+  ocv_element
+  resistor_element
+  rc_element
+  thermal
+  voltage_model
diff --git a/docs/source/models/submodels/equivalent_circuit_elements/ocv_element.rst b/docs/source/models/submodels/equivalent_circuit_elements/ocv_element.rst
@@ -0,0 +1,6 @@
+OCV Element
+===========
+
+.. autoclass:: pybamm.equivalent_circuit_elements.OCVElement
+    :members:
+
diff --git a/docs/source/models/submodels/equivalent_circuit_elements/rc_element.rst b/docs/source/models/submodels/equivalent_circuit_elements/rc_element.rst
@@ -0,0 +1,6 @@
+RC Element
+==========
+
+.. autoclass:: pybamm.equivalent_circuit_elements.RCElement
+    :members:
+