Merge branch 'develop' into feat-eval-at-edge

Author: martinjrobins

.github/workflows/benchmark_on_push.yml

@@ -24,7 +24,7 @@ jobs:
         with:
           persist-credentials: false
       - name: Set up Python 3.12
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: 3.12
 

.github/workflows/periodic_benchmarks.yml

@@ -33,7 +33,7 @@ jobs:
           persist-credentials: false
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: 3.12
 
@@ -70,7 +70,7 @@ jobs:
       contents: write
     steps:
       - name: Set up Python 3.12
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: 3.12
 

.github/workflows/publish_pypi.yml

@@ -16,7 +16,7 @@ jobs:
       - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: true
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: 3.12
 
@@ -45,6 +45,6 @@ jobs:
           merge-multiple: true
 
       - name: Publish on PyPI
-        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc # v1.12.4
+        uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0
         with:
           packages-dir: deploy/

.github/workflows/run_benchmarks_over_history.yml

@@ -41,7 +41,7 @@ jobs:
         with:
           persist-credentials: false
       - name: Set up Python 3.12
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: 3.12
 
@@ -58,7 +58,7 @@ jobs:
 
       - name: Validate commit_start
         id: validate_start
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7.0.1
+        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8.0.0
         with:
           script: |
             const input = context.payload.inputs.commit_start;
@@ -70,7 +70,7 @@ jobs:
 
       - name: Validate commit_end
         id: validate_end
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7.0.1
+        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8.0.0
         with:
           script: |
             const input = context.payload.inputs.commit_end;
@@ -82,7 +82,7 @@ jobs:
 
       - name: Validate ncommits
         id: validate_ncommits
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7.0.1
+        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8.0.0
         with:
           script: |
             const input = context.payload.inputs.ncommits;
@@ -132,7 +132,7 @@ jobs:
       contents: write
     steps:
       - name: Set up Python 3.12
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: 3.12
 

.github/workflows/run_periodic_tests.yml

@@ -66,7 +66,7 @@ jobs:
         run: choco install graphviz --version=8.0.5
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -86,7 +86,7 @@ jobs:
 
       - name: Upload coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
-        uses: codecov/codecov-action@fdcc8476540edceab3de004e990f80d881c6cc00 # v5.5.0
+        uses: codecov/codecov-action@5a1091511ad55cbe89839c7260b706298ca349f7 # v5.5.1
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 
@@ -115,7 +115,7 @@ jobs:
           sudo apt-get install texlive-latex-extra dvipng
 
       - name: Set up Python
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: 3.11
 
@@ -152,7 +152,7 @@ jobs:
           sudo apt-get install libopenblas-dev texlive-latex-extra dvipng
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: 3.12
 
@@ -186,7 +186,7 @@ jobs:
           sudo apt-get install libopenblas-dev texlive-latex-extra dvipng
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: 3.12
 

.github/workflows/scorecard.yml

@@ -65,6 +65,6 @@ jobs:
       # Upload the results to GitHub's code scanning dashboard (optional).
       # Commenting out will disable upload of results to your repo's Code Scanning dashboard
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@3c3833e0f8c1c83d449a7478aa59c036a9165498 # v3.29.5
+        uses: github/codeql-action/upload-sarif@f1f6e5f6af878fb37288ce1c627459e94dbf7d01 # v3.29.5
         with:
           sarif_file: results.sarif

.github/workflows/test_on_push.yml

@@ -28,7 +28,7 @@ jobs:
         with:
           persist-credentials: false
       - name: Setup Python
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: 3.12
 
@@ -93,7 +93,7 @@ jobs:
 
       - name: Set up Python ${{ matrix.python-version }}
         id: setup-python
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
@@ -114,7 +114,7 @@ jobs:
 
       - name: Upload coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
-        uses: codecov/codecov-action@fdcc8476540edceab3de004e990f80d881c6cc00 # v5.5.0
+        uses: codecov/codecov-action@5a1091511ad55cbe89839c7260b706298ca349f7 # v5.5.1
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 
@@ -152,7 +152,7 @@ jobs:
 
       - name: Set up Python
         id: setup-python
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: 3.11
           cache: 'pip'
@@ -198,7 +198,7 @@ jobs:
 
       - name: Set up Python 3.12
         id: setup-python
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: 3.12
           cache: 'pip'
@@ -241,7 +241,7 @@ jobs:
 
       - name: Set up Python 3.12
         id: setup-python
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
         with:
           python-version: 3.12
           cache: 'pip'

CHANGELOG.md

@@ -9,6 +9,7 @@
 
 ## Bug fixes
 
+- Fix a bug in setting initial stoichiometries where the reference temperature was used instead of the initial temperature. ([#5189](https://github.com/pybamm-team/PyBaMM/pull/5189))
 - Fix a bug in the calculation of "Bulk" OCP terms in hysteresis models ([#5169](https://github.com/pybamm-team/PyBaMM/pull/5169))
 - Fixed a bug where the final duration of a drive cycle would not be inferred correctly. ([#5153](https://github.com/pybamm-team/PyBaMM/pull/5153))
 

src/pybamm/input/parameters/lithium_ion/Chen2020_composite.py

@@ -82,7 +82,7 @@ def silicon_ocp_lithiation_Mark2016(sto):
         + p6 * sto**2
         + p7 * sto
         + p8
-    )
+    ) + 1e-4 * (1 / sto + 1 / (sto - 1))
     return U_lithiation
 
 
@@ -205,7 +205,7 @@ def nmc_LGM50_ocp_Chen2020(sto):
         - 0.0428 * np.tanh(18.5138 * (sto - 0.5542))
         - 17.7326 * np.tanh(15.7890 * (sto - 0.3117))
         + 17.5842 * np.tanh(15.9308 * (sto - 0.3120))
-    )
+    ) + 1e-4 * (1 / sto + 1 / (sto - 1))
 
     return u_eq
 

src/pybamm/models/full_battery_models/equivalent_circuit/initial_state.py

@@ -6,6 +6,7 @@
 def set_initial_state(
     initial_value,
     parameter_values,
+    direction=None,
     param=None,
     inplace=True,
     options=None,