Merge branch 'pybamm-team:develop' into ocvr_ecm

docs/source/api/parameters/parameter_sets.rst

@@ -33,7 +33,7 @@ package (``cell_parameters``) should consist of the following::
 The actual parameter set is defined within ``cell_alpha.py``, as shown below.
 For an example, see the `Marquis2019`_ parameter sets.
 
-.. _Marquis2019: https://github.com/pybamm-team/PyBaMM/blob/develop/pybamm/input/parameters/lithium_ion/Marquis2019.py
+.. _Marquis2019: https://github.com/pybamm-team/PyBaMM/blob/develop/src/pybamm/input/parameters/lithium_ion/Marquis2019.py
 
 .. code-block:: python
     :linenos:

docs/source/examples/notebooks/getting_started/tutorial-4-setting-parameter-values.ipynb

@@ -573,7 +573,7 @@
    "source": [
     "Note how, when we pass a function as a parameter, we pass the object without calling it, i.e. we pass `cube` rather than `cube(t)`. This new `parameter_values` variable could now be passed to a simulation, but note that it is incomplete as it does not include all the parameters that the model needs to run (see the parameters needed by calling `model.print_parameter_info()`, as done above). \n",
     "\n",
-    "It is often convenient to define the parameter set in a separate file, and then call the parameters into your notebook or script. You can find some examples on how to do so in [PyBaMM's parameter library](https://github.com/pybamm-team/PyBaMM/tree/develop/pybamm/input/parameters/lithium_ion). You can copy one of the parameter sets available into a new file and modify it accordingly for the new parameter set. Then, whenever the set is needed, one can import the `get_parameter_values` method from the corresponding file and call it to obtain a copy of the parameter values."
+    "It is often convenient to define the parameter set in a separate file, and then call the parameters into your notebook or script. You can find some examples on how to do so in [PyBaMM's parameter library](https://github.com/pybamm-team/PyBaMM/tree/develop/src/pybamm/input/parameters/lithium_ion). You can copy one of the parameter sets available into a new file and modify it accordingly for the new parameter set. Then, whenever the set is needed, one can import the `get_parameter_values` method from the corresponding file and call it to obtain a copy of the parameter values."
    ]
   },
   {

src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/Expression.hpp

@@ -47,12 +47,12 @@ class Expression {
   /**
    * @brief Returns row indices in COO format (where the output data represents sparse matrix elements)
    */
-  virtual std::vector<expr_int> get_row() = 0;
+  virtual const std::vector<expr_int>& get_row() = 0;
 
   /**
    * @brief Returns column indices in COO format (where the output data represents sparse matrix elements)
    */
-  virtual std::vector<expr_int> get_col() = 0;
+  virtual const std::vector<expr_int>& get_col() = 0;
 
 public:  // data members
   /**

src/pybamm/solvers/c_solvers/idaklu/Expressions/Casadi/CasadiFunctions.cpp

@@ -19,6 +19,12 @@ CasadiFunction::CasadiFunction(const BaseFunctionType &f) : Expression(), m_func
   m_res.resize(sz_res, nullptr);
   m_iw.resize(sz_iw, 0);
   m_w.resize(sz_w, 0);
+
+  if (m_func.n_out() > 0) {
+    casadi::Sparsity casadi_sparsity = m_func.sparsity_out(0);
+    m_rows = casadi_sparsity.get_row();
+    m_cols = casadi_sparsity.get_col();
+  }
 }
 
 // only call this once m_arg and m_res have been set appropriately
@@ -45,24 +51,14 @@ expr_int CasadiFunction::nnz_out() {
   return static_cast<expr_int>(m_func.nnz_out());
 }
 
-std::vector<expr_int> CasadiFunction::get_row() {
-  return get_row(0);
-}
-
-std::vector<expr_int> CasadiFunction::get_row(expr_int ind) {
+const std::vector<expr_int>& CasadiFunction::get_row() {
   DEBUG("CasadiFunction get_row(): " << m_func.name());
-  casadi::Sparsity casadi_sparsity = m_func.sparsity_out(ind);
-  return casadi_sparsity.get_row();
-}
-
-std::vector<expr_int> CasadiFunction::get_col() {
-  return get_col(0);
+  return m_rows;
 }
 
-std::vector<expr_int> CasadiFunction::get_col(expr_int ind) {
+const std::vector<expr_int>& CasadiFunction::get_col() {
   DEBUG("CasadiFunction get_col(): " << m_func.name());
-  casadi::Sparsity casadi_sparsity = m_func.sparsity_out(ind);
-  return casadi_sparsity.get_col();
+  return m_cols;
 }
 
 void CasadiFunction::operator()(const std::vector<realtype*>& inputs,

src/pybamm/solvers/c_solvers/idaklu/Expressions/Casadi/CasadiFunctions.hpp

@@ -29,10 +29,8 @@ class CasadiFunction : public Expression
   expr_int out_shape(int k) override;
   expr_int nnz() override;
   expr_int nnz_out() override;
-  std::vector<expr_int> get_row() override;
-  std::vector<expr_int> get_row(expr_int ind);
-  std::vector<expr_int> get_col() override;
-  std::vector<expr_int> get_col(expr_int ind);
+  const std::vector<expr_int>& get_row() override;
+  const std::vector<expr_int>& get_col() override;
 
 public:
   /*
@@ -43,6 +41,8 @@ class CasadiFunction : public Expression
 private:
   std::vector<expr_int> m_iw;  // cppcheck-suppress unusedStructMember
   std::vector<double> m_w;  // cppcheck-suppress unusedStructMember
+  std::vector<expr_int> m_rows;  // cppcheck-suppress unusedStructMember
+  std::vector<expr_int> m_cols;  // cppcheck-suppress unusedStructMember
 };
 
 /**

src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEFunction.hpp

@@ -27,8 +27,8 @@ class IREEFunction : public Expression
   expr_int out_shape(int k) override;
   expr_int nnz() override;
   expr_int nnz_out() override;
-  std::vector<expr_int> get_col() override;
-  std::vector<expr_int> get_row() override;
+  const std::vector<expr_int>& get_col() override;
+  const std::vector<expr_int>& get_row() override;
 
   /*
    * @brief Evaluate the MLIR function

src/pybamm/solvers/c_solvers/idaklu/Expressions/IREE/IREEFunctions.cpp

@@ -203,12 +203,12 @@ expr_int IREEFunction::nnz_out() {
   return m_func.nnz;
 }
 
-std::vector<expr_int> IREEFunction::get_row() {
+const std::vector<expr_int>& IREEFunction::get_row() {
   DEBUG("IreeFunction get_row" << m_func.row.size());
   return m_func.row;
 }
 
-std::vector<expr_int> IREEFunction::get_col() {
+const std::vector<expr_int>& IREEFunction::get_col() {
   DEBUG("IreeFunction get_col" << m_func.col.size());
   return m_func.col;
 }

src/pybamm/solvers/c_solvers/idaklu/IDAKLUSolverOpenMP.inl

@@ -297,7 +297,7 @@ void IDAKLUSolverOpenMP<ExprSet>::CalcVarsSensitivities(
   DEBUG("IDAKLUSolver::CalcVarsSensitivities");
   // Calculate sensitivities
   std::vector<realtype> dens_dvar_dp = std::vector<realtype>(number_of_parameters, 0);
-  for (size_t dvar_k=0; dvar_k<functions->dvar_dy_fcns.size(); dvar_k++) {
+  for (size_t dvar_k = 0; dvar_k < functions->dvar_dy_fcns.size(); dvar_k++) {
     // Isolate functions
     Expression* dvar_dy = functions->dvar_dy_fcns[dvar_k];
     Expression* dvar_dp = functions->dvar_dp_fcns[dvar_k];
@@ -306,15 +306,15 @@ void IDAKLUSolverOpenMP<ExprSet>::CalcVarsSensitivities(
     // Calculate dvar/dp and convert to dense array for indexing
     (*dvar_dp)({tret, yval, functions->inputs.data()}, {&res_dvar_dp[0]});
     for (int k=0; k<number_of_parameters; k++) {
-      dens_dvar_dp[k]=0;
+      dens_dvar_dp[k] = 0;
     }
     for (int k=0; k<dvar_dp->nnz_out(); k++) {
       dens_dvar_dp[dvar_dp->get_row()[k]] = res_dvar_dp[k];
     }
     // Calculate sensitivities
-    for (int paramk=0; paramk<number_of_parameters; paramk++) {
+    for (int paramk = 0; paramk < number_of_parameters; paramk++) {
       yS_return[*ySk] = dens_dvar_dp[paramk];
-      for (int spk=0; spk<dvar_dy->nnz_out(); spk++) {
+      for (int spk = 0; spk < dvar_dy->nnz_out(); spk++) {
         yS_return[*ySk] += res_dvar_dy[spk] * ySval[paramk][dvar_dy->get_col()[spk]];
       }
       (*ySk)++;

tests/integration/test_experiments.py

@@ -1,13 +1,11 @@
 #
 # Test some experiments
 #
-
 import pybamm
 import numpy as np
-import unittest
 
 
-class TestExperiments(unittest.TestCase):
+class TestExperiments:
     def test_discharge_rest_charge(self):
         experiment = pybamm.Experiment(
             [
@@ -78,7 +76,7 @@ def test_infeasible(self):
         )
         sol = sim.solve()
         # this experiment fails during the third cycle (i.e. is infeasible)
-        self.assertEqual(len(sol.cycles), 3)
+        assert len(sol.cycles) == 3
 
     def test_drive_cycle(self):
         drive_cycle = np.array([np.arange(100), 5 * np.ones(100)]).T
@@ -100,13 +98,3 @@ def test_drive_cycle(self):
         )
         sol = sim.solve()
         assert np.all(sol["Terminal voltage [V]"].entries >= 4.00)
-
-
-if __name__ == "__main__":
-    print("Add -v for more debug output")
-    import sys
-
-    if "-v" in sys.argv:
-        debug = True
-    pybamm.settings.debug_mode = True
-    unittest.main()

tests/integration/test_models/test_full_battery_models/test_lithium_ion/test_basic_models.py

@@ -21,24 +21,24 @@ def test_with_experiment(self):
 
 class TestBasicSPM(BaseBasicModelTest):
     @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup(self):
         self.model = pybamm.lithium_ion.BasicSPM()
 
 
 class TestBasicDFN(BaseBasicModelTest):
     @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup(self):
         self.model = pybamm.lithium_ion.BasicDFN()
 
 
 class TestBasicDFNComposite(BaseBasicModelTest):
     @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup(self):
         self.model = pybamm.lithium_ion.BasicDFNComposite()
 
 
 class TestBasicDFNHalfCell(BaseBasicModelTest):
     @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup(self):
         options = {"working electrode": "positive"}
         self.model = pybamm.lithium_ion.BasicDFNHalfCell(options)

tests/integration/test_models/test_full_battery_models/test_lithium_ion/test_compare_outputs_two_phase.py

@@ -3,10 +3,9 @@
 #
 import pybamm
 import numpy as np
-import unittest
 
 
-class TestCompareOutputsTwoPhase(unittest.TestCase):
+class TestCompareOutputsTwoPhase:
     def compare_outputs_two_phase_graphite_graphite(self, model_class):
         """
         Check that a two-phase graphite-graphite model gives the same results as a
@@ -158,7 +157,7 @@ def compare_outputs_two_phase_silicon_graphite(self, model_class):
             )
 
         # More silicon means longer sim
-        self.assertLess(sol[0]["Time [s]"].data[-1], sol[1]["Time [s]"].data[-1])
+        assert sol[0]["Time [s]"].data[-1] < sol[1]["Time [s]"].data[-1]
 
     def test_compare_SPM_silicon_graphite(self):
         model_class = pybamm.lithium_ion.SPM
@@ -171,12 +170,3 @@ def test_compare_SPMe_silicon_graphite(self):
     def test_compare_DFN_silicon_graphite(self):
         model_class = pybamm.lithium_ion.DFN
         self.compare_outputs_two_phase_silicon_graphite(model_class)
-
-
-if __name__ == "__main__":
-    print("Add -v for more debug output")
-    import sys
-
-    if "-v" in sys.argv:
-        debug = True
-    unittest.main()

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

@@ -1,16 +1,16 @@
 #
 # Tests for the lithium-ion DFN model
 #
-
 import pybamm
 import tests
 import numpy as np
-import unittest
 from tests import BaseIntegrationTestLithiumIon
+import pytest
 
 
-class TestDFN(BaseIntegrationTestLithiumIon, unittest.TestCase):
-    def setUp(self):
+class TestDFN(BaseIntegrationTestLithiumIon):
+    @pytest.fixture(autouse=True)
+    def setup(self):
         self.model = pybamm.lithium_ion.DFN
 
     def test_particle_distribution_in_x(self):
@@ -35,8 +35,9 @@ def positive_radius(x):
         self.run_basic_processing_test({}, parameter_values=param)
 
 
-class TestDFNWithSizeDistribution(unittest.TestCase):
-    def setUp(self):
+class TestDFNWithSizeDistribution:
+    @pytest.fixture(autouse=True)
+    def setup(self):
         params = pybamm.ParameterValues("Marquis2019")
         self.params = pybamm.get_size_distribution_parameters(params)
 
@@ -120,12 +121,3 @@ def test_conservation_each_electrode(self):
         # compare
         np.testing.assert_array_almost_equal(neg_Li[0], neg_Li[1], decimal=12)
         np.testing.assert_array_almost_equal(pos_Li[0], pos_Li[1], decimal=12)
-
-
-if __name__ == "__main__":
-    print("Add -v for more debug output")
-    import sys
-
-    if "-v" in sys.argv:
-        debug = True
-    unittest.main()

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

@@ -8,5 +8,5 @@
 
 class TestDFNHalfCell(BaseIntegrationTestLithiumIonHalfCell):
     @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup(self):
         self.model = pybamm.lithium_ion.DFN

tests/integration/test_models/test_full_battery_models/test_lithium_ion/test_mpm.py

@@ -1,14 +1,12 @@
 #
 # Tests for the lithium-ion MPM model
 #
-
 import pybamm
 import tests
 import numpy as np
-import unittest
 
 
-class TestMPM(unittest.TestCase):
+class TestMPM:
     def test_basic_processing(self):
         options = {"thermal": "isothermal"}
         model = pybamm.lithium_ion.MPM(options)
@@ -124,12 +122,3 @@ def test_conservation_each_electrode(self):
         # compare
         np.testing.assert_array_almost_equal(neg_Li[0], neg_Li[1], decimal=13)
         np.testing.assert_array_almost_equal(pos_Li[0], pos_Li[1], decimal=13)
-
-
-if __name__ == "__main__":
-    print("Add -v for more debug output")
-    import sys
-
-    if "-v" in sys.argv:
-        debug = True
-    unittest.main()

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

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

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

@@ -8,5 +8,5 @@
 
 class TestSPM(BaseIntegrationTestLithiumIon):
     @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup(self):
         self.model = pybamm.lithium_ion.SPM

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

@@ -8,5 +8,5 @@
 
 class TestSPMHalfCell(BaseIntegrationTestLithiumIonHalfCell):
     @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup(self):
         self.model = pybamm.lithium_ion.SPM

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

@@ -8,7 +8,7 @@
 
 class TestSPMe(BaseIntegrationTestLithiumIon):
     @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup(self):
         self.model = pybamm.lithium_ion.SPMe
 
     def test_integrated_conductivity(self):

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

@@ -8,5 +8,5 @@
 
 class TestSPMeHalfCell(BaseIntegrationTestLithiumIonHalfCell):
     @pytest.fixture(autouse=True)
-    def setUp(self):
+    def setup(self):
         self.model = pybamm.lithium_ion.SPMe