#3611 merge develop

.all-contributorsrc

@@ -793,6 +793,15 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "AlessioBugetti",
+      "name": "Alessio Bugetti",
+      "avatar_url": "https://avatars.githubusercontent.com/u/38499721?v=4",
+      "profile": "https://github.com/AlessioBugetti",
+      "contributions": [
+        "infra"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/workflows/lychee_url_checker.yml

@@ -28,7 +28,7 @@ jobs:
 
       # use stable version for now to avoid breaking changes
       - name: Lychee URL checker
-        uses: lycheeverse/[email protected].0
+        uses: lycheeverse/[email protected].1
         with:
           # arguments with file types to check
           args: >-

.github/workflows/run_periodic_tests.yml

@@ -36,8 +36,7 @@ jobs:
       - name: Check style
         run: |
           python -m pip install pre-commit
-          git add .
-          pre-commit run ruff
+          pre-commit run -a
 
   build:
     needs: style

.github/workflows/test_on_push.yml

@@ -28,8 +28,7 @@ jobs:
       - name: Check style
         run: |
           python -m pip install pre-commit
-          git add .
-          pre-commit run ruff
+          pre-commit run -a
 
   run_unit_tests:
     needs: style

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.1.11"
+    rev: "v0.1.13"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

CHANGELOG.md

@@ -2,15 +2,17 @@
 
 ## Bug fixes
 
+- Fixed a bug where if the first step(s) in a cycle are skipped then the cycle solution started from the model's initial conditions instead of from the last state of the previous cycle ([#3708](https://github.com/pybamm-team/PyBaMM/pull/3708))
 - Fixed a bug where the lumped thermal model conflates cell volume with electrode volume  ([#3707](https://github.com/pybamm-team/PyBaMM/pull/3707))
 
 ## Breaking changes
 - The parameters `GeometricParameters.A_cooling` and `GeometricParameters.V_cell` are now automatically computed from the electrode heights, widths and thicknesses if the "cell geometry" option is "pouch" and from the parameters "Cell cooling surface area [m2]" and "Cell volume [m3]", respectively, otherwise. When using the lumped thermal model we recommend using the "arbitrary" cell geometry and specifying the parameters "Cell cooling surface area [m2]", "Cell volume [m3]" and "Total heat transfer coefficient [W.m-2.K-1]" directly. ([#3707](https://github.com/pybamm-team/PyBaMM/pull/3707))
+
 # [v24.1rc0](https://github.com/pybamm-team/PyBaMM/tree/v24.1rc0) - 2024-01-31
 
 ## Features
 
-- The `pybamm_install_odes` command now includes support for macOS systems and can be used to set up SUNDIALS and install the `scikits.odes` solver on macOS ([#3417](https://github.com/pybamm-team/PyBaMM/pull/3417))
+- The `pybamm_install_odes` command now includes support for macOS systems and can be used to set up SUNDIALS and install the `scikits.odes` solver on macOS ([#3417](https://github.com/pybamm-team/PyBaMM/pull/3417), [#3706](https://github.com/pybamm-team/PyBaMM/3706]))
 - Added support for Python 3.12 ([#3531](https://github.com/pybamm-team/PyBaMM/pull/3531))
 - Added method to get QuickPlot axes by variable ([#3596](https://github.com/pybamm-team/PyBaMM/pull/3596))
 - Added custom experiment terminations ([#3596](https://github.com/pybamm-team/PyBaMM/pull/3596))

README.md

@@ -14,7 +14,7 @@
 [![code style](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-73-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-74-orange.svg)](#-contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 </div>
@@ -279,6 +279,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/prady0t"><img src="https://avatars.githubusercontent.com/u/99216956?v=4?s=100" width="100px;" alt="Pradyot Ranjan"/><br /><sub><b>Pradyot Ranjan</b></sub></a><br /><a href="#infra-prady0t" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/XuboGU"><img src="https://avatars.githubusercontent.com/u/53944452?v=4?s=100" width="100px;" alt="XuboGU"/><br /><sub><b>XuboGU</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=XuboGU" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3AXuboGU" title="Bug reports">🐛</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/cringeyburger"><img src="https://avatars.githubusercontent.com/u/121183876?v=4?s=100" width="100px;" alt="Ankit Meda"/><br /><sub><b>Ankit Meda</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=cringeyburger" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/AlessioBugetti"><img src="https://avatars.githubusercontent.com/u/38499721?v=4?s=100" width="100px;" alt="Alessio Bugetti"/><br /><sub><b>Alessio Bugetti</b></sub></a><br /><a href="#infra-AlessioBugetti" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
     </tr>
   </tbody>
 </table>

docs/source/user_guide/installation/gnu-linux-mac.rst

@@ -119,7 +119,8 @@ Users can install `scikits.odes <https://github.com/bmcage/odes>`__ to utilize i
 
    .. code:: bash
 
-      apt install libopenblas-dev
+      apt-get install libopenblas-dev
+      pip install wget cmake
       pybamm_install_odes
 
    system (under ``~/.local``), before installing ``scikits.odes``. (Alternatively, one can install SUNDIALS without this script and run ``pip install pybamm[odes]`` to install ``pybamm`` with ``scikits.odes``.)
@@ -131,6 +132,7 @@ Users can install `scikits.odes <https://github.com/bmcage/odes>`__ to utilize i
    .. code:: bash
 
       brew install openblas gcc gfortran
+      pip install wget cmake
       pybamm_install_odes
 
 The ``pybamm_install_odes`` command, installed with PyBaMM, automatically downloads and installs the SUNDIALS library on your
@@ -161,7 +163,7 @@ Users can install ``jax`` and ``jaxlib`` to use the Jax solver.
 
 .. note::
 
-   The Jax solver is not supported on Python 3.8. It is supported on Python 3.9, 3.10, and 3.11.
+   The Jax solver is only supported for Python versions 3.9 through 3.12.
 
 .. code:: bash
 

docs/source/user_guide/installation/windows.rst

@@ -73,7 +73,7 @@ Users can install ``jax`` and ``jaxlib`` to use the Jax solver.
 
 .. note::
 
-   The Jax solver is not supported on Python 3.8. It is supported on Python 3.9, 3.10, and 3.11.
+   The Jax solver is only supported for Python versions 3.9 through 3.12.
 
 .. code:: bash
 

pybamm/install_odes.py

@@ -190,7 +190,12 @@ def main(arguments=None):
     # see https://scikits-odes.readthedocs.io/en/latest/installation.html#id1
     os.environ["SUNDIALS_INST"] = SUNDIALS_LIB_DIR
     env = os.environ.copy()
-    subprocess.run(["pip", "install", "scikits.odes"], env=env, check=True)
+    logger.info("Installing scikits.odes via pip")
+    subprocess.run(
+        [f"{sys.executable}", "-m", "pip", "install", "scikits.odes", "--verbose"],
+        env=env,
+        check=True,
+    )
 
 
 if __name__ == "__main__":

pybamm/simulation.py

@@ -839,7 +839,20 @@ def solve(
 
                     steps.append(step_solution)
 
-                    cycle_solution = cycle_solution + step_solution
+                    # If there haven't been any successful steps yet in this cycle, then
+                    # carry the solution over from the previous cycle (but
+                    # `step_solution` should still be an EmptySolution so that in the
+                    # list of returned step solutions we can see which steps were
+                    # skipped)
+                    if (
+                        cycle_solution is None
+                        and isinstance(step_solution, pybamm.EmptySolution)
+                        and not isinstance(current_solution, pybamm.EmptySolution)
+                    ):
+                        cycle_solution = current_solution.last_state
+                    else:
+                        cycle_solution = cycle_solution + step_solution
+
                     current_solution = cycle_solution
 
                     callbacks.on_step_end(logs)

scripts/install_KLU_Sundials.py

@@ -1,3 +1,15 @@
+# /// pyproject
+# [run]
+# requires-python = "">=3.8, <3.13""
+# dependencies = [
+#   "wget",
+#   "cmake",
+# ]
+#
+# [additional-info]
+# repository = "https://github.com/pybamm-team/PyBaMM"
+# documentation = "https://docs.pybamm.org"
+# ///
 import os
 import subprocess
 import tarfile

test.ipynb

@@ -0,0 +1,78 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pybamm"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<pybamm.solvers.solution.Solution at 0x14fc50ad0>"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "model = pybamm.lithium_ion.DFN()\n",
+    "sim = pybamm.Simulation(model)\n",
+    "sim.solve([0, 3600])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sim.plot()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "bppenv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.6"
+  },
+  "orig_nbformat": 4,
+  "vscode": {
+   "interpreter": {
+    "hash": "938a56cf8cc78a970178b6cd91dbc2084cfe03b4ddf365fda3eb6d44738b4092"
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

tests/unit/test_experiments/test_simulation_with_experiment.py

@@ -519,6 +519,25 @@ def test_run_experiment_skip_steps(self):
                 decimal=5,
             )
 
+    def test_skipped_step_continuous(self):
+        model = pybamm.lithium_ion.SPM({"SEI": "solvent-diffusion limited"})
+        experiment = pybamm.Experiment(
+            [
+                ("Rest for 24 hours (1 hour period)",),
+                (
+                    "Charge at C/3 until 4.1 V",
+                    "Hold at 4.1V until C/20",
+                    "Discharge at C/3 until 2.5 V",
+                ),
+            ]
+        )
+        sim = pybamm.Simulation(model, experiment=experiment)
+        sim.solve(initial_soc=1)
+        np.testing.assert_array_almost_equal(
+            sim.solution.cycles[0].last_state.y.full(),
+            sim.solution.cycles[1].steps[-1].first_state.y.full(),
+        )
+
     def test_all_empty_solution_errors(self):
         model = pybamm.lithium_ion.SPM()
         parameter_values = pybamm.ParameterValues("Chen2020")