Merge branch 'develop' into issue3051-BPX-diffusivity-activation-ener…

…gies

.github/workflows/benchmark_on_push.yml

@@ -13,7 +13,7 @@ jobs:
   benchmarks:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
@@ -23,8 +23,9 @@ jobs:
           sudo apt-get update
           sudo apt install gfortran gcc libopenblas-dev
       - name: Install python dependencies
+      # Pin asv==0.5.1 to fix failing benchmarks. Related to https://github.com/airspeed-velocity/asv/issues/1323
         run: |
-          python -m pip install --upgrade pip wheel setuptools virtualenv asv wget cmake casadi numpy
+          python -m pip install --upgrade pip wheel setuptools virtualenv asv==0.5.1 wget cmake casadi numpy
       - name: Install SuiteSparse and Sundials
         run: python scripts/install_KLU_Sundials.py
       - name: Fetch base branch

.github/workflows/create_release.yml

@@ -17,7 +17,7 @@ jobs:
         python-version: [3.8]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Get current date
         run: |

.github/workflows/lychee_url_checker.yml

@@ -24,7 +24,7 @@ jobs:
           restore-keys: cache-lychee-
 
       # check URLs with Lychee
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       # use stable version for now to avoid breaking changes
       - name: Lychee URL checker

.github/workflows/periodic_benchmarks.yml

@@ -19,7 +19,7 @@ jobs:
   benchmarks:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
@@ -58,7 +58,7 @@ jobs:
       - name: Install asv
         run: pip install asv
       - name: Checkout pybamm-bench repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: pybamm-team/pybamm-bench
           token: ${{ secrets.BENCH_PAT }}

.github/workflows/publish_pypi.yml

@@ -19,7 +19,7 @@ jobs:
     name: Build wheels on windows-latest
     runs-on: windows-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: 3.8
@@ -74,7 +74,7 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: 3.8
@@ -135,7 +135,7 @@ jobs:
         python-version: [3.8]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}

.github/workflows/run_benchmarks_over_history.yml

@@ -22,7 +22,7 @@ jobs:
   benchmarks:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
@@ -59,7 +59,7 @@ jobs:
       - name: Install asv
         run: pip install asv
       - name: Checkout pybamm-bench repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: pybamm-team/pybamm-bench
           token: ${{ secrets.BENCH_PAT }}

.github/workflows/run_periodic_tests.yml

@@ -32,7 +32,7 @@ jobs:
     if: ${{ needs.pre_job.outputs.should_skip != 'true' }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Setup python
         uses: actions/setup-python@v4
         with:
@@ -53,7 +53,7 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
@@ -127,7 +127,7 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install python & create virtualenv
         shell: bash
         run: |

.github/workflows/test_on_push.yml

@@ -16,7 +16,7 @@ jobs:
   style:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
@@ -43,7 +43,7 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
@@ -123,7 +123,7 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
@@ -186,7 +186,7 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
@@ -266,7 +266,7 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
@@ -327,7 +327,7 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Install and cache apt packages
       - name: Install Linux system dependencies

.github/workflows/update_license.yml

@@ -13,7 +13,7 @@ jobs:
     if: github.repository_owner == 'pybamm-team'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Update year in license
@@ -28,7 +28,7 @@ jobs:
     needs: license
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Update year in docs

.github/workflows/update_version.yml

@@ -13,7 +13,7 @@ jobs:
         python-version: [3.8]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4

.github/workflows/work_precision_sets.yml

@@ -9,7 +9,7 @@ jobs:
   benchmarks_on_release:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Setup python
         uses: actions/setup-python@v4
         with:

CHANGELOG.md

@@ -10,6 +10,7 @@
 ## Bug fixes
 
 - Fixed bug causing incorrect activation energies using `create_from_bpx()` ([#3242](https://github.com/pybamm-team/PyBaMM/pull/3242))
+- Fixed a bug that occured in `check_ys_are_not_too_large` when trying to reference `y-slice` where the referenced variable was not a `pybamm.StateVector` ([#3313](https://github.com/pybamm-team/PyBaMM/pull/3313)
 - Fixed a bug with `_Heaviside._evaluate_for_shape` which meant some expressions involving heaviside function and subtractions did not work ([#3306](https://github.com/pybamm-team/PyBaMM/pull/3306))
 - The `OneDimensionalX` thermal model has been updated to account for edge/tab cooling and account for the current collector volumetric heat capacity. It now gives the correct behaviour compared with a lumped model with the correct total heat transfer coefficient and surface area for cooling. ([#3042](https://github.com/pybamm-team/PyBaMM/pull/3042))
 - Fixed a bug where the "basic" lithium-ion models gave incorrect results when using nonlinear particle diffusivity ([#3207](https://github.com/pybamm-team/PyBaMM/pull/3207))

docs/source/user_guide/installation/windows-wsl.rst

@@ -22,13 +22,13 @@ Get PyBaMM's Source Code
 
      sudo apt install git-core
 
-3. Clone the PyBaMM repository::
+3. Clone the PyBaMM repository:
 
 .. code:: bash
 
      git clone https://github.com/pybamm-team/PyBaMM.git
 
-4. Enter the PyBaMM Directory by running::
+4. Enter the PyBaMM Directory by running:
 
 .. code:: bash
 

pybamm/solvers/solution.py

@@ -308,7 +308,20 @@ def check_ys_are_not_too_large(self):
         y = y[:, -1]
         if np.any(y > pybamm.settings.max_y_value):
             for var in [*model.rhs.keys(), *model.algebraic.keys()]:
-                y_var = y[model.variables[var.name].y_slices[0]]
+                var = model.variables[var.name]
+                # find the statevector corresponding to this variable
+                statevector = None
+                for node in var.pre_order():
+                    if isinstance(node, pybamm.StateVector):
+                        statevector = node
+
+                # there will always be a statevector, but just in case
+                if statevector is None:  # pragma: no cover
+                    raise RuntimeError(
+                        "Cannot find statevector corresponding to variable {}"
+                        .format(var.name)
+                    )
+                y_var = y[statevector.y_slices[0]]
                 if np.any(y_var > pybamm.settings.max_y_value):
                     pybamm.logger.error(
                         f"Solution for '{var}' exceeds the maximum allowed value "