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agriyakhetarpal · Jun 17, 2023 · b5372be · b5372be
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -631,6 +631,15 @@
         "code",
         "bug"
       ]
+    },
+    {
+      "login": "julian-evers",
+      "name": "julian-evers",
+      "avatar_url": "https://avatars.githubusercontent.com/u/133691040?v=4",
+      "profile": "https://github.com/julian-evers",
+      "contributions": [
+        "code"
+      ]
     }
   ],
   "contributorsPerLine": 7,

diff --git a/.coveragerc b/.coveragerc
@@ -0,0 +1,3 @@
+[run]
+source = pybamm
+concurrency = multiprocessing
diff --git a/.github/workflows/periodic_benchmarks.yml b/.github/workflows/periodic_benchmarks.yml
@@ -27,7 +27,7 @@ jobs:
       - name: Install Linux system dependencies
         run: |
           sudo apt-get update
-          sudo apt install gfortran gcc libopenblas-dev
+          sudo apt-get install gfortran gcc libopenblas-dev
       - name: Install python dependencies
         run: |
           python -m pip install --upgrade pip wheel setuptools virtualenv asv wget cmake casadi numpy

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
@@ -40,13 +40,13 @@ jobs:
           .\bootstrap-vcpkg.bat
 
       - name: Cache packages installed through vcpkg on windows
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         env:
           cache-name: vckpg_binary_cache
         with:
           path: C:\Users\runneradmin\AppData\Local\vcpkg\archives
           key: ${{ runner.os }}-build-VS2022-${{ env.cache-name }}-${{ hashFiles('vcpkg*.json') }}
-            
+
       # Enable tmate debugging of manually-triggered workflows if the input option was provided
       - name: Setup tmate session
         uses: mxschmitt/action-tmate@v3
@@ -85,7 +85,7 @@ jobs:
       - name: Clone pybind11 repo (no history)
         run: git clone --depth 1 --branch v2.10.4 https://github.com/pybind/pybind11.git
 
-      - name: Install sundials on macOS
+      - name: Install SUNDIALS on macOS
         if: matrix.os == 'macos-latest'
         run: |
           # https://github.com/actions/virtual-environments/issues/1280
@@ -95,6 +95,7 @@ jobs:
           rm -f /usr/local/bin/python3*
           brew update
           brew reinstall gcc
+          brew install libomp
           python -m pip install cmake wget
           python scripts/install_KLU_Sundials.py
 
@@ -104,7 +105,7 @@ jobs:
           # TODO: openblas no longer available on centos 7 i686 image, use blas instead for now
           CIBW_BEFORE_ALL_LINUX: >
             yum -y install blas-devel lapack-devel &&
-            bash build_manylinux_wheels/install_sundials.sh 5.8.1 5.7.0
+            bash build_manylinux_wheels/install_sundials.sh 5.8.1 6.5.0
 
           CIBW_BEFORE_BUILD_LINUX: "python -m pip install cmake casadi numpy"
           CIBW_BEFORE_BUILD_MACOS: >

diff --git a/.github/workflows/run_benchmarks_over_history.yml b/.github/workflows/run_benchmarks_over_history.yml
@@ -27,8 +27,8 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.8
-      - name: Install tox and asv
-        run: pip install -U pip "tox<4" asv
+      - name: Install nox and asv
+        run: pip install -U pip nox asv
       - name: Fetch develop branch
         # Not required when worklow trigerred
         # on develop, but useful when

diff --git a/.github/workflows/run_periodic_tests.yml b/.github/workflows/run_periodic_tests.yml
@@ -86,41 +86,35 @@ jobs:
 
       - name: Install standard python dependencies
         run: |
-          python -m pip install --upgrade pip wheel setuptools
-          python -m pip install "tox<4"
-
+          python -m pip install --upgrade pip wheel setuptools nox
+  
       - name: Install SuiteSparse and Sundials
         if: matrix.os == 'ubuntu-latest'
-        run: tox -e pybamm-requires
+        run: nox -s pybamm-requires
 
-      - name: Run unit tests for GNU/Linux with Python 3.8, 3.10, and 3.11
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version != 3.9
-        run: python -m tox -e unit
+      - name: Run unit tests for GNU/Linux with Python 3.8, 3.9, and 3.10
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11
+        run: nox -s unit
 
-      - name: Run unit tests for GNU/Linux with Python 3.9 and generate coverage report
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9
-        run: python -m tox -e coverage
+      - name: Run unit tests for GNU/Linux with Python 3.11 and generate coverage report
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
+        run: nox -s coverage
 
       - name: Upload coverage report
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         uses: codecov/codecov-action@v2.1.0
 
-      - name: Run integration tests for GNU/Linux
-        if: matrix.os == 'ubuntu-latest'
-        run: python -m tox -e integration
+      - name: Run integration tests
+        run: nox -s integration
 
       - name: Run unit tests for Windows and MacOS
         if: matrix.os != 'ubuntu-latest'
-        run: python -m tox -e mac-windows-unit
-
-      - name: Run integration tests for Windows and MacOS
-        if: matrix.os != 'ubuntu-latest'
-        run: python -m tox -e mac-windows-integration
+        run: nox -s unit
 
       - name: Install docs dependencies and run doctests
         if: matrix.os == 'ubuntu-latest'
-        run: tox -e doctests
+        run: nox -s doctests
 
       - name: Install dev dependencies and run example tests
         if: matrix.os == 'ubuntu-latest'
-        run: tox -e examples
+        run: nox -s examples
diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
@@ -51,18 +51,35 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      # Install and cache apt packages
       - name: Install Linux system dependencies
+        uses: awalsh128/cache-apt-pkgs-action@v1.3.0
+        if: matrix.os == 'ubuntu-latest'
+        with:
+          packages: gfortran gcc graphviz
+          execute_install_scripts: true
+
+      # dot -c is for registering graphviz fonts and plugins
+      - name: Install OpenBLAS and TexLive for Linux
         if: matrix.os == 'ubuntu-latest'
         run: |
           sudo apt-get update
-          sudo apt install gfortran gcc libopenblas-dev graphviz
-          sudo apt install texlive-full
+          sudo dot -c 
+          sudo apt-get install libopenblas-dev texlive-latex-extra dvipng
 
       # Added fixes to homebrew installs:
       # rm -f /usr/local/bin/2to3
       # (see https://github.com/actions/virtual-environments/issues/2322)
       - name: Install MacOS system dependencies
         if: matrix.os == 'macos-latest'
+        env:
+          # Homebrew environment variables
+          HOMEBREW_NO_INSTALL_CLEANUP: 1
+          HOMEBREW_NO_ANALYTICS: 1
+          HOMEBREW_NO_GOOGLE_ANALYTICS: 1
+          HOMEBREW_NO_AUTO_UPDATE: 1
+          # Speed up CI
+          NONINTERACTIVE: 1
         run: |
           rm -f /usr/local/bin/2to3*
           rm -f /usr/local/bin/idle3*
@@ -76,39 +93,39 @@ jobs:
         if: matrix.os == 'windows-latest'
         run: choco install graphviz --version=2.38.0.20190211
 
-      - name: Install standard python dependencies
+      - name: Install standard Python dependencies
         run: |
           python -m pip install --upgrade pip wheel setuptools
-          python -m pip install "tox<4"
+          python -m pip install nox
 
       - name: Install SuiteSparse and Sundials
         if: matrix.os == 'ubuntu-latest'
-        run: tox -e pybamm-requires
+        run: nox -s pybamm-requires
 
-      - name: Run unit tests for GNU/Linux with Python 3.8, 3.10, and 3.11
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version != 3.9
-        run: python -m tox -e unit
+      - name: Run unit tests for GNU/Linux with Python 3.8, 3.9, and 3.10
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11
+        run: nox -s unit
 
-      - name: Run unit tests for GNU/Linux with Python 3.9 and generate coverage report
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9
-        run: python -m tox -e coverage
+      - name: Run unit tests for GNU/Linux with Python 3.11 and generate coverage report
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
+        run: nox -s coverage
 
       - name: Upload coverage report
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         uses: codecov/codecov-action@v2.1.0
 
       - name: Run integration tests for GNU/Linux with Python 3.11
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        run: python -m tox -e integration
+        run: nox -s integration
 
       - name: Run unit tests for Windows and MacOS with all Python versions
         if: matrix.os != 'ubuntu-latest'
-        run: python -m tox -e mac-windows-unit
+        run: nox -s unit
 
       - name: Install docs dependencies and run doctests for GNU/Linux with Python 3.11
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        run: tox -e doctests
+        run: nox -s doctests
 
       - name: Install dev dependencies and run example tests for GNU/Linux with Python 3.11
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        run: tox -e examples
+        run: nox -s examples
diff --git a/.github/workflows/update_version.yml b/.github/workflows/update_version.yml
@@ -2,9 +2,6 @@ name: Update version
 
 on:
   workflow_dispatch:
-  schedule:
-    # Run at 10 am UTC on 28th every month
-    - cron: 0 10 28 * *
 
 jobs:
   update-version:

diff --git a/.gitignore b/.gitignore
@@ -113,6 +113,9 @@ test.json
 # tox
 .tox/
 
+# nox
+.nox/
+
 # vcpkg
 vcpkg_installed/
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -9,7 +9,7 @@ repos:
       - id: black
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: "v0.0.269"
+    rev: "v0.0.272"
     hooks:
       - id: ruff
         args: [--ignore=E741, --exclude=__init__.py]
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,23 +1,34 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+# [v23.5](https://github.com/pybamm-team/PyBaMM/tree/v23.5) - 2023-05-31
+
+## Bug fixes
+
+- Realign 'count' increment in CasadiSolver._integrate() ([#2986](https://github.com/pybamm-team/PyBaMM/pull/2986))
+
 ## Features
 
 - Enable multithreading in IDAKLU solver ([#2947](https://github.com/pybamm-team/PyBaMM/pull/2947))
 - If a solution contains cycles and steps, the cycle number and step number are now saved when `solution.save_data()` is called ([#2931](https://github.com/pybamm-team/PyBaMM/pull/2931))
+- Experiments can now be given a `start_time` to define when each step should be triggered ([#2616](https://github.com/pybamm-team/PyBaMM/pull/2616)) 
 
 ## Optimizations
 
 - Test `JaxSolver`'s compatibility with Python `3.8`, `3.9`, `3.10`, and `3.11` ([#2958](https://github.com/pybamm-team/PyBaMM/pull/2958))
 - Update Jax (0.4.8) and JaxLib (0.4.7) compatibility ([#2927](https://github.com/pybamm-team/PyBaMM/pull/2927))
+- Migrate from `tox=3.28` to `nox` ([#3005](https://github.com/pybamm-team/PyBaMM/pull/3005))
 
 ## Bug fixes
 
 - Fix `pybamm_install_odes` and update the required SUNDIALS version ([#2958](https://github.com/pybamm-team/PyBaMM/pull/2958))
+- Fixed a bug where all data included in a BPX was incorrectly assumed to be given as a function of time.([#2957](https://github.com/pybamm-team/PyBaMM/pull/2957))
 - Remove brew install for Mac from the recommended developer installation options for SUNDIALS ([#2925](https://github.com/pybamm-team/PyBaMM/pull/2925))
+- Fix `bpx.py` to correctly generate parameters for "lumped" thermal model ([#2860](https://github.com/pybamm-team/PyBaMM/issues/2860))
 
 ## Breaking changes
 
 - Deprecate functionality to load parameter set from a csv file. Parameter sets must now be provided as python dictionaries ([#2959](https://github.com/pybamm-team/PyBaMM/pull/2959))
+- Tox support for Installation & testing has now been replaced by Nox ([#3005](https://github.com/pybamm-team/PyBaMM/pull/3005))
 
 # [v23.4.1](https://github.com/pybamm-team/PyBaMM/tree/v23.4) - 2023-05-01
 
@@ -30,20 +41,21 @@
 ## Features
 
 - Added verbose logging to `pybamm.print_citations()` and citation tags for the `pybamm.Citations` class so that users can now see where the citations were registered when running simulations ([#2862](https://github.com/pybamm-team/PyBaMM/pull/2862))
+- Updated to casadi 3.6, which required some changes to the casadi integrator ([#2859](https://github.com/pybamm-team/PyBaMM/pull/2859))
 - PyBaMM is now natively supported on Apple silicon chips (`M1/M2`) ([#2435](https://github.com/pybamm-team/PyBaMM/pull/2435))
 - PyBaMM is now supported on Python `3.10` and `3.11` ([#2435](https://github.com/pybamm-team/PyBaMM/pull/2435))
-- Updated to casadi 3.6, which required some changes to the casadi integrator. ([#2859](https://github.com/pybamm-team/PyBaMM/pull/2859))
+
 
 ## Optimizations
 
 - Fixed deprecated `interp2d` method by switching to `xarray.DataArray` as the backend for `ProcessedVariable` ([#2907](https://github.com/pybamm-team/PyBaMM/pull/2907))
 
 ## Bug fixes
 
+- Initial conditions for sensitivity equations calculated correctly ([#2920](https://github.com/pybamm-team/PyBaMM/pull/2920))
 - 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))
-- Initial conditions for sensitivity equations calculated correctly ([#2920](https://github.com/pybamm-team/PyBaMM/pull/2920))
+- Fixed a bug in the discretisation of initial conditions of a scaled variable ([#2856](https://github.com/pybamm-team/PyBaMM/pull/2856))
 
 ## Breaking changes
 
@@ -65,7 +77,7 @@
 
 - Fix non-deteministic outcome of some tests in the test suite ([#2844](https://github.com/pybamm-team/PyBaMM/pull/2844))
 - Fixed excessive RAM consumption when running multiple simulations ([#2823](https://github.com/pybamm-team/PyBaMM/pull/2823))
-- Fixed use of last_state as starting_solution in Simulation.solve() ([#2822](https://github.com/pybamm-team/PyBaMM/pull/2822))
+- Fixed use of `last_state` as `starting_solution` in `Simulation.solve()` ([#2822](https://github.com/pybamm-team/PyBaMM/pull/2822))
 - Fixed a bug where variable bounds could not contain `InputParameters` ([#2795](https://github.com/pybamm-team/PyBaMM/pull/2795))
 - Improved `model.latexify()` to have a cleaner and more readable output ([#2764](https://github.com/pybamm-team/PyBaMM/pull/2764))
 - Fixed electrolyte conservation in the case of concentration-dependent transference number ([#2758](https://github.com/pybamm-team/PyBaMM/pull/2758))

diff --git a/CITATION.cff b/CITATION.cff
@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "23.4.1"
+version: "23.5"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"
-Original file line number
+Diff line change
@@ Expand Up / @@ -113,6 +113,9 @@ test.json @@
     # tox
     .tox/
+    # nox
+    .nox/
     # vcpkg
     vcpkg_installed/
@@ Expand Down @@