Merge branch 'develop' into issue-2670-interp2d

Author: valentinsulzer

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
       - id: black
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: "v0.0.261"
+    rev: "v0.0.262"
     hooks:
       - id: ruff
         args: [--ignore=E741, --exclude=__init__.py]

CHANGELOG.md

@@ -9,6 +9,7 @@
 
 ## Bug fixes
 
+- Parameter sets can now contain the key "chemistry", and will ignore its value (this previously would give errors in some cases) ([#2901](https://github.com/pybamm-team/PyBaMM/pull/2901))
 - Fixed a bug in the discretisation of initial conditions of a scaled variable ([#2856](https://github.com/pybamm-team/PyBaMM/pull/2856))
 - Fixed keyerror on "all" when getting sensitivities from IDAKLU solver([#2883](https://github.com/pybamm-team/PyBaMM/pull/2883))
 

README.md

@@ -229,7 +229,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/chuckliu1979"><img src="https://avatars.githubusercontent.com/u/13491954?v=4?s=100" width="100px;" alt="Chuck Liu"/><br /><sub><b>Chuck Liu</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Achuckliu1979" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=chuckliu1979" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/partben"><img src="https://avatars.githubusercontent.com/u/88316576?v=4?s=100" width="100px;" alt="partben"/><br /><sub><b>partben</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=partben" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://gavinw.me"><img src="https://avatars.githubusercontent.com/u/6828967?v=4?s=100" width="100px;" alt="Gavin Wiggins"/><br /><sub><b>Gavin Wiggins</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Awigging" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=wigging" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://wigging.me"><img src="https://avatars.githubusercontent.com/u/6828967?v=4?s=100" width="100px;" alt="Gavin Wiggins"/><br /><sub><b>Gavin Wiggins</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Awigging" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=wigging" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/dion-w"><img src="https://avatars.githubusercontent.com/u/91852142?v=4?s=100" width="100px;" alt="Dion Wilde"/><br /><sub><b>Dion Wilde</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Adion-w" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=dion-w" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://www.ehtec.co"><img src="https://avatars.githubusercontent.com/u/48386220?v=4?s=100" width="100px;" alt="Elias Hohl"/><br /><sub><b>Elias Hohl</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=ehtec" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/KAschad"><img src="https://avatars.githubusercontent.com/u/93784399?v=4?s=100" width="100px;" alt="KAschad"/><br /><sub><b>KAschad</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3AKAschad" title="Bug reports">🐛</a></td>

casadi-headers

@@ -70,12 +70,14 @@ def __init__(self, values, chemistry=None):
                 )
                 self.update_from_chemistry(values)
             else:
+                # Remove chemistry if present
+                values.pop("chemistry", None)
                 self.update(values, check_already_exists=False)
         else:
             # Check if values is a named parameter set
             if isinstance(values, str) and values in pybamm.parameter_sets:
                 values = pybamm.parameter_sets[values]
-                values.pop("chemistry")
+                values.pop("chemistry", None)
                 self.update(values, check_already_exists=False)
 
             else:

pybamm/parameters/parameter_values.py

@@ -8,6 +8,7 @@
 import warnings
 import sys
 from functools import lru_cache
+import tqdm
 
 
 def is_notebook():
@@ -510,6 +511,7 @@ def solve(
         starting_solution=None,
         initial_soc=None,
         callbacks=None,
+        showprogress=False,
         **kwargs,
     ):
         """
@@ -557,6 +559,10 @@ def solve(
         callbacks : list of callbacks, optional
             A list of callbacks to be called at each time step. Each callback must
             implement all the methods defined in :class:`pybamm.callbacks.BaseCallback`.
+        showprogress : bool, optional
+            Whether to show a progress bar for cycling. If true, shows a progress bar
+            for cycles. Has no effect when not used with an experiment.
+            Default is False.
         **kwargs
             Additional key-word arguments passed to `solver.solve`.
             See :meth:`pybamm.BaseSolver.solve`.
@@ -698,7 +704,13 @@ def solve(
             num_cycles = len(self.experiment.cycle_lengths)
             feasible = True  # simulation will stop if experiment is infeasible
             for cycle_num, cycle_length in enumerate(
-                self.experiment.cycle_lengths, start=1
+                # tqdm is the progress bar.
+                tqdm.tqdm(
+                    self.experiment.cycle_lengths,
+                    disable=(not showprogress),
+                    desc="Cycling",
+                ),
+                start=1,
             ):
                 logs["cycle number"] = (
                     cycle_num + cycle_offset,

pybamm/simulation.py

@@ -10,6 +10,7 @@ pybtex>=0.24.0
 sympy >= 1.8
 xarray
 bpx
+tqdm
 # Note: Matplotlib is loaded for debug plots but to ensure pybamm runs
 # on systems without an attached display it should never be imported
 # outside of plot() methods.

requirements.txt

@@ -216,6 +216,7 @@ def compile_KLU():
         "sympy>=1.8",
         "xarray",
         "bpx",
+        "tqdm",
         # Note: Matplotlib is loaded for debug plots, but to ensure pybamm runs
         # on systems without an attached display, it should never be imported
         # outside of plot() methods.

setup.py

@@ -342,6 +342,21 @@ def test_run_experiment_termination_capacity(self):
         # all but the last value should be above the termination condition
         np.testing.assert_array_less(5.04, C[:-1])
 
+    def test_run_experiment_with_pbar(self):
+        # The only thing to test here is for errors.
+        experiment = pybamm.Experiment(
+            [
+                (
+                    "Discharge at 1C for 1 sec",
+                    "Charge at 1C for 1 sec",
+                ),
+            ]
+            * 10,
+        )
+        model = pybamm.lithium_ion.SPM()
+        sim = pybamm.Simulation(model, experiment=experiment)
+        sim.solve(showprogress=True)
+
     def test_run_experiment_termination_voltage(self):
         # with percent
         experiment = pybamm.Experiment(

tests/unit/test_experiments/test_simulation_with_experiment.py

@@ -56,6 +56,10 @@ def test_init(self):
         self.assertIn("a", param.keys())
         self.assertIn(1, param.values())
 
+        # from dict "chemistry" key gets removed
+        param = pybamm.ParameterValues({"a": 1, "chemistry": "lithium-ion"})
+        self.assertNotIn("chemistry", param.keys())
+
         # from file
         param = pybamm.ParameterValues(
             "lithium_ion/testing_only/positive_electrodes/lico2_Ai2020/parameters.csv"