Merge branch 'pybamm-team:develop' into develop

.github/workflows/periodic_benchmarks.yml

@@ -48,7 +48,7 @@ jobs:
           LD_LIBRARY_PATH: $HOME/.local/lib
 
       - name: Upload results as artifact
-        uses: actions/[email protected].4
+        uses: actions/[email protected].5
         with:
           name: asv_periodic_results
           path: results

.github/workflows/publish_pypi.yml

@@ -88,7 +88,7 @@ jobs:
           CIBW_TEST_COMMAND: python -c "import pybamm; print(pybamm.IDAKLUSolver())"
 
       - name: Upload Windows wheels
-        uses: actions/[email protected].4
+        uses: actions/[email protected].5
         with:
           name: wheels_windows
           path: ./wheelhouse/*.whl
@@ -123,7 +123,7 @@ jobs:
             python -c "import pybamm; print(pybamm.IDAKLUSolver())"
 
       - name: Upload wheels for Linux
-        uses: actions/[email protected].4
+        uses: actions/[email protected].5
         with:
           name: wheels_manylinux
           path: ./wheelhouse/*.whl
@@ -254,7 +254,7 @@ jobs:
             python -c "import pybamm; print(pybamm.IDAKLUSolver())"
 
       - name: Upload wheels for macOS (amd64, arm64)
-        uses: actions/[email protected].4
+        uses: actions/[email protected].5
         with:
           name: wheels_${{ matrix.os }}
           path: ./wheelhouse/*.whl
@@ -274,7 +274,7 @@ jobs:
         run: pipx run build --sdist
 
       - name: Upload SDist
-        uses: actions/[email protected].4
+        uses: actions/[email protected].5
         with:
           name: sdist
           path: ./dist/*.tar.gz

.github/workflows/run_benchmarks_over_history.yml

@@ -46,7 +46,7 @@ jobs:
           ${{ github.event.inputs.commit_start }}..${{ github.event.inputs.commit_end }}
 
       - name: Upload results as artifact
-        uses: actions/[email protected].4
+        uses: actions/[email protected].5
         with:
           name: asv_over_history_results
           path: results

.github/workflows/scorecard.yml

@@ -59,7 +59,7 @@ jobs:
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
       - name: "Upload artifact"
-        uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4.3.4
+        uses: actions/upload-artifact@89ef406dd8d7e03cfd12d9e0a4a378f454709029 # v4.3.5
         with:
           name: SARIF file
           path: results.sarif

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.5.5"
+    rev: "v0.5.6"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

docs/source/user_guide/installation/install-from-docker.rst

@@ -90,11 +90,11 @@ If you want to build the PyBaMM Docker image locally from the PyBaMM source code
 
       docker run -it pybamm
 
-5. Activate PyBaMM development environment inside docker container using:
+5. Activate PyBaMM development virtual environment inside docker container using:
 
 .. code-block:: bash
 
-      conda activate pybamm
+      source /home/pybamm/venv/bin/activate
 
 .. note::
 

pybamm/simulation.py

@@ -218,7 +218,7 @@ def set_parameters(self):
         A method to set the parameters in the model and the associated geometry.
         """
 
-        if self.model_with_set_params:
+        if self._model_with_set_params:
             return
 
         self._model_with_set_params = self._parameter_values.process_model(
@@ -235,7 +235,7 @@ def set_initial_soc(self, initial_soc, inputs=None):
             self.steps_to_built_models = None
             self.steps_to_built_solvers = None
 
-        options = self.model.options
+        options = self._model.options
         param = self._model.param
         if options["open-circuit potential"] == "MSMR":
             self._parameter_values = (
@@ -287,7 +287,7 @@ def build(self, initial_soc=None, inputs=None):
         if initial_soc is not None:
             self.set_initial_soc(initial_soc, inputs=inputs)
 
-        if self.built_model:
+        if self._built_model:
             return
         elif self._model.is_discretised:
             self._model_with_set_params = self._model
@@ -486,7 +486,7 @@ def solve(
                         )
 
             self._solution = solver.solve(
-                self.built_model, t_eval, inputs=inputs, **kwargs
+                self._built_model, t_eval, inputs=inputs, **kwargs
             )
 
         elif self.operating_mode == "with experiment":
@@ -875,17 +875,17 @@ def solve(
                 if feasible is False:
                     break
 
-            if self.solution is not None and len(all_cycle_solutions) > 0:
-                self.solution.cycles = all_cycle_solutions
-                self.solution.set_summary_variables(all_summary_variables)
-                self.solution.all_first_states = all_first_states
+            if self._solution is not None and len(all_cycle_solutions) > 0:
+                self._solution.cycles = all_cycle_solutions
+                self._solution.set_summary_variables(all_summary_variables)
+                self._solution.all_first_states = all_first_states
 
             callbacks.on_experiment_end(logs)
 
             # record initial_start_time of the solution
-            self.solution.initial_start_time = initial_start_time
+            self._solution.initial_start_time = initial_start_time
 
-        return self.solution
+        return self._solution
 
     def run_padding_rest(self, kwargs, rest_time, step_solution, inputs):
         model = self.steps_to_built_models["Rest for padding"]
@@ -951,15 +951,15 @@ def step(
 
         self._solution = solver.step(
             starting_solution,
-            self.built_model,
+            self._built_model,
             dt,
             t_eval=t_eval,
             save=save,
             inputs=inputs,
             **kwargs,
         )
 
-        return self.solution
+        return self._solution
 
     def _get_esoh_solver(self, calc_esoh):
         if (
@@ -1019,7 +1019,7 @@ def create_gif(self, number_of_images=80, duration=0.1, output_filename="plot.gi
             Name of the generated GIF file.
 
         """
-        if self.solution is None:
+        if self._solution is None:
             raise ValueError("The simulation has not been solved yet.")
         if self.quick_plot is None:
             self.quick_plot = pybamm.QuickPlot(self._solution)
@@ -1128,14 +1128,14 @@ def save_model(
             be available when the model is read back in and solved.
         variables: bool
             The discretised variables. Not required to solve a model, but if false
-            tools will not be availble. Will automatically save meshes as well, required
+            tools will not be available. Will automatically save meshes as well, required
             for plotting tools.
         filename: str, optional
             The desired name of the JSON file. If no name is provided, one will be
             created based on the model name, and the current datetime.
         """
-        mesh = self.mesh if (mesh or variables) else None
-        variables = self.built_model.variables if variables else None
+        mesh = self._mesh if (mesh or variables) else None
+        variables = self._built_model.variables if variables else None
 
         if self.operating_mode == "with experiment":
             raise NotImplementedError(
@@ -1144,9 +1144,9 @@ def save_model(
                 """
             )
 
-        if self.built_model:
+        if self._built_model:
             Serialise().save_model(
-                self.built_model, filename=filename, mesh=mesh, variables=variables
+                self._built_model, filename=filename, mesh=mesh, variables=variables
             )
         else:
             raise NotImplementedError(
@@ -1183,11 +1183,11 @@ def plot_voltage_components(
             Keyword arguments, passed to ax.fill_between.
 
         """
-        if self.solution is None:
+        if self._solution is None:
             raise ValueError("The simulation has not been solved yet.")
 
         return pybamm.plot_voltage_components(
-            self.solution,
+            self._solution,
             ax=ax,
             show_legend=show_legend,
             split_by_electrode=split_by_electrode,

scripts/Dockerfile

@@ -1,4 +1,5 @@
-FROM continuumio/miniconda3:latest
+FROM python:3.12-slim-bullseye
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/uv
 
 WORKDIR /
 
@@ -21,17 +22,17 @@ ENV CMAKE_CXX_COMPILER=/usr/bin/g++
 ENV CMAKE_MAKE_PROGRAM=/usr/bin/make
 ENV LD_LIBRARY_PATH=/home/pybamm/.local/lib
 
-RUN conda create -n pybamm python=3.11
-RUN conda init --all
-SHELL ["conda", "run", "-n", "pybamm", "/bin/bash", "-c"]
-RUN conda install -y pip
+# Create a virtual environment
+ENV VIRTUAL_ENV=/home/pybamm/venv
+RUN uv venv $VIRTUAL_ENV
+RUN #!/bin/bash && source /home/pybamm/venv/bin/activate;
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
 
-RUN pip install --upgrade --user pip setuptools wheel wget
-RUN pip install cmake
+RUN uv pip install --upgrade setuptools wheel wget cmake
 
 RUN python scripts/install_KLU_Sundials.py && \
-    rm -rf pybind11 && \
-    git clone https://github.com/pybind/pybind11.git && \
-    pip install --user -e ".[all,dev,docs,jax]";
+rm -rf pybind11 && \
+git clone https://github.com/pybind/pybind11.git && \
+uv pip install -e ".[all,dev,docs,jax]";
 
 ENTRYPOINT ["/bin/bash"]