Merge branch 'develop' of https://github.com/pybamm-team/PyBaMM into …

…develop
DrSOKane · Nov 22, 2023 · bcc1a37 · bcc1a37
2 parents 8aa17f9 + 2ee8da2
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diff --git a/.github/release_workflow.md b/.github/release_workflow.md
@@ -1,6 +1,6 @@
 # Release workflow
 
-This file contains the workflow required to make a `PyBaMM` release on GitHub and PyPI by the maintainers.
+This file contains the workflow required to make a `PyBaMM` release on GitHub, PyPI, and conda-forge by the maintainers.
 
 ## rc0 releases (automated)
 
@@ -77,3 +77,5 @@ Some other essential things to check throughout the release process -
   git tag -f <tag_name> <commit_hash>
   git push -f <pybamm-team/PyBaMM_remote_name> <tag_name>  # can only be carried out by the maintainers
   ```
+- If changes are made to the API, console scripts, entry points, new optional dependencies are added, support for major Python versions is dropped or added, or core project information and metadata are modified at the time of the release, make sure to update the `meta.yaml` file in the `recipe/` folder of the [conda-forge/pybamm-feedstock](https://github.com/conda-forge/pybamm-feedstock) repository accordingly by following the instructions in the [conda-forge documentation](https://conda-forge.org/docs/maintainer/updating_pkgs.html#updating-the-feedstock-repository) and re-rendering the recipe
+- The conda-forge release workflow will automatically be triggered following a stable PyPI release, and the aforementioned updates should be carried out directly in the main repository by pushing changes to the automated PR created by the conda-forge-bot. A manual PR can also be created if the updates are not included in the automated PR for some reason. This manual PR **must** bump the build number in `meta.yaml` and **must** be from a personal fork of the repository.
diff --git a/.github/workflows/run_periodic_tests.yml b/.github/workflows/run_periodic_tests.yml
@@ -66,62 +66,54 @@ jobs:
           sudo apt install gfortran gcc libopenblas-dev graphviz pandoc
           sudo apt install texlive-full
 
-      # 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
+      - name: Install macOS system dependencies
         if: matrix.os == 'macos-latest'
         run: |
-          rm -f /usr/local/bin/2to3*
-          rm -f /usr/local/bin/idle3*
-          rm -f /usr/local/bin/pydoc3*
-          rm -f /usr/local/bin/python3*
-          brew update
-          brew install graphviz
-          brew install openblas
+          brew install graphviz openblas
+          brew reinstall gcc
 
       - name: Install Windows system dependencies
         if: matrix.os == 'windows-latest'
         run: choco install graphviz --version=2.38.0.20190211
 
       - name: Install standard Python dependencies
         run: |
-          python -m pip install --upgrade pip wheel setuptools
+          python -m pip install --upgrade pip wheel setuptools nox
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
         if: matrix.os == 'ubuntu-latest'
-        run: pipx run nox -s pybamm-requires
+        run: python -m nox -s pybamm-requires
 
       - name: Run unit tests for GNU/Linux with Python 3.8, 3.9, and 3.10, and for macOS and Windows with all Python versions
         if: (matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11) || (matrix.os != 'ubuntu-latest')
-        run: pipx run nox -s unit
+        run: python -m nox -s unit
 
       - 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: pipx run nox -s coverage
+        run: python -m nox -s coverage
 
       - name: Upload coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         uses: codecov/codecov-action@v3.1.4
 
       - name: Run integration tests
-        run: pipx run nox -s integration
+        run: python -m nox -s integration
 
       - name: Install docs dependencies and run doctests
         if: matrix.os == 'ubuntu-latest'
-        run: pipx run nox -s doctests
+        run: python -m nox -s doctests
 
       - name: Check if the documentation can be built
         if: matrix.os == 'ubuntu-latest'
-        run: pipx run nox -s docs
+        run: python -m nox -s docs
 
       - name: Install dev dependencies and run example tests
         if: matrix.os == 'ubuntu-latest'
-        run: pipx run nox -s examples
+        run: python -m nox -s examples
 
       - name: Run example scripts tests
         if: matrix.os == 'ubuntu-latest'
-        run: pipx run nox -s scripts
+        run: python -m nox -s scripts
 
   #M-series Mac Mini
   build-apple-mseries:

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
@@ -50,7 +50,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@v1.3.0
+        uses: awalsh128/cache-apt-pkgs-action@v1.3.1
         if: matrix.os == 'ubuntu-latest'
         with:
           packages: gfortran gcc graphviz pandoc
@@ -75,7 +75,6 @@ jobs:
           NONINTERACTIVE: 1
         run: |
           brew analytics off
-          brew update
           brew install graphviz openblas
 
       - name: Install Windows system dependencies
@@ -90,10 +89,9 @@ jobs:
           cache: 'pip'
           cache-dependency-path: setup.py
 
-      - name: Install PyBaMM dependencies
+      - name: Install standard Python dependencies
         run: |
-          pip install --upgrade pip wheel setuptools
-          pip install -e .[all,docs]
+          pip install --upgrade pip wheel setuptools nox
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3
@@ -111,10 +109,10 @@ jobs:
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
         if: matrix.os == 'ubuntu-latest'
-        run: pipx run nox -s pybamm-requires
+        run: python -m nox -s pybamm-requires
 
       - name: Run unit tests for ${{ matrix.os }} with Python ${{ matrix.python-version }}
-        run: pipx run nox -s unit
+        run: python -m nox -s unit
 
   # Runs only on Ubuntu with Python 3.11
   check_coverage:
@@ -130,7 +128,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@v1.3.0
+        uses: awalsh128/cache-apt-pkgs-action@v1.3.1
         with:
           packages: gfortran gcc graphviz pandoc
           execute_install_scripts: true
@@ -150,10 +148,9 @@ jobs:
           cache: 'pip'
           cache-dependency-path: setup.py
 
-      - name: Install PyBaMM dependencies
+      - name: Install standard Python dependencies
         run: |
           pip install --upgrade pip wheel setuptools nox
-          pip install -e .[all,docs]
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3
@@ -169,10 +166,10 @@ jobs:
           key: nox-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py') }}
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
-        run: pipx run nox -s pybamm-requires
+        run: python -m nox -s pybamm-requires
 
       - name: Run unit tests for Ubuntu with Python 3.11 and generate coverage report
-        run: pipx run nox -s coverage
+        run: python -m nox -s coverage
 
       - name: Upload coverage report
         uses: codecov/codecov-action@v3.1.4
@@ -193,7 +190,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@v1.3.0
+        uses: awalsh128/cache-apt-pkgs-action@v1.3.1
         if: matrix.os == 'ubuntu-latest'
         with:
           packages: gfortran gcc graphviz pandoc
@@ -218,7 +215,6 @@ jobs:
           NONINTERACTIVE: 1
         run: |
           brew analytics off
-          brew update
           brew install graphviz openblas
 
       - name: Install Windows system dependencies
@@ -233,10 +229,9 @@ jobs:
           cache: 'pip'
           cache-dependency-path: setup.py
 
-      - name: Install PyBaMM dependencies
+      - name: Install standard Python dependencies
         run: |
-          pip install --upgrade pip wheel setuptools
-          pip install -e .[all,docs]
+          pip install --upgrade pip wheel setuptools nox
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3
@@ -254,10 +249,10 @@ jobs:
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
         if: matrix.os == 'ubuntu-latest'
-        run: pipx run nox -s pybamm-requires
+        run: python -m nox -s pybamm-requires
 
       - name: Run integration tests for ${{ matrix.os }} with Python ${{ matrix.python-version }}
-        run: pipx run nox -s integration
+        run: python -m nox -s integration
 
 # Runs only on Ubuntu with Python 3.11. Skips IDAKLU module compilation
 # for speedups, which is already tested in other jobs.
@@ -274,7 +269,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@v1.3.0
+        uses: awalsh128/cache-apt-pkgs-action@v1.3.1
         with:
           packages: gfortran gcc graphviz pandoc
           execute_install_scripts: true
@@ -294,16 +289,15 @@ jobs:
           cache: 'pip'
           cache-dependency-path: setup.py
 
-      - name: Install PyBaMM dependencies
+      - name: Install standard Python dependencies
         run: |
-          pip install --upgrade pip wheel setuptools
-          pip install -e .[all,docs]
+          pip install --upgrade pip wheel setuptools nox
 
       - name: Install docs dependencies and run doctests for GNU/Linux with Python 3.11
-        run: pipx run nox -s doctests
+        run: python -m nox -s doctests
 
       - name: Check if the documentation can be built for GNU/Linux with Python 3.11
-        run: pipx run nox -s docs
+        run: python -m nox -s docs
 
   # Runs only on Ubuntu with Python 3.11
   run_example_tests:
@@ -319,7 +313,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@v1.3.0
+        uses: awalsh128/cache-apt-pkgs-action@v1.3.1
         with:
           packages: gfortran gcc graphviz pandoc
           execute_install_scripts: true
@@ -339,10 +333,9 @@ jobs:
           cache: 'pip'
           cache-dependency-path: setup.py
 
-      - name: Install PyBaMM dependencies
+      - name: Install standard Python dependencies
         run: |
-          pip install --upgrade pip wheel setuptools
-          pip install -e .[all,docs]
+          pip install --upgrade pip wheel setuptools nox
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3
@@ -358,10 +351,10 @@ jobs:
           key: nox-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py') }}
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
-        run: pipx run nox -s pybamm-requires
+        run: python -m nox -s pybamm-requires
 
       - name: Install dev dependencies and run example tests for GNU/Linux with Python 3.11
-        run: pipx run nox -s examples
+        run: python -m nox -s examples
 
   # Runs only on Ubuntu with Python 3.11
   run_scripts_tests:
@@ -377,7 +370,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@v1.3.0
+        uses: awalsh128/cache-apt-pkgs-action@v1.3.1
         with:
           packages: gfortran gcc graphviz
           execute_install_scripts: true
@@ -397,10 +390,9 @@ jobs:
           cache: 'pip'
           cache-dependency-path: setup.py
 
-      - name: Install PyBaMM dependencies
+      - name: Install standard Python dependencies
         run: |
-          pip install --upgrade pip wheel setuptools
-          pip install -e .[all,docs]
+          pip install --upgrade pip wheel setuptools nox
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3
@@ -416,7 +408,7 @@ jobs:
           key: nox-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py') }}
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
-        run: pipx run nox -s pybamm-requires
+        run: python -m nox -s pybamm-requires
 
       - name: Install dev dependencies and run example scripts tests for GNU/Linux with Python 3.11
-        run: pipx run nox -s scripts
+        run: python -m nox -s scripts
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,17 +4,11 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.1.1"
+    rev: "v0.1.6"
     hooks:
       - id: ruff
-        args: [--fix, --ignore=E741, --exclude=__init__.py]
-
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
-    hooks:
-      - id: nbqa-ruff
-        additional_dependencies: [ruff==0.0.284]
-        args: ["--fix","--ignore=E501,E402"]
+        args: [--fix, --show-fixes]
+        types_or: [python, pyi, jupyter]
 
   - repo: https://github.com/adamchainz/blacken-docs
     rev: "1.16.0"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,12 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
-# [v23.9rc0](https://github.com/pybamm-team/PyBaMM/tree/v23.9rc0) - 2023-10-31
+## Bug fixes
+
+- Fixed bug that made identical Experiment steps with different end times crash ([#3516](https://github.com/pybamm-team/PyBaMM/pull/3516))
+- Fixed bug in calculation of theoretical energy that made it very slow ([#3506](https://github.com/pybamm-team/PyBaMM/pull/3506))
+- The irreversible plating model now increments `f"{Domain} dead lithium concentration [mol.m-3]"`, not `f"{Domain} lithium plating concentration [mol.m-3]"` as it did previously. ([#3485](https://github.com/pybamm-team/PyBaMM/pull/3485))
+
+# [v23.9](https://github.com/pybamm-team/PyBaMM/tree/v23.9) - 2023-10-31
 
 ## Features
 
@@ -19,6 +25,9 @@
 
 ## Bug fixes
 
+- Fixed a bug where the JaxSolver would fails when using GPU support with no input parameters ([#3423](https://github.com/pybamm-team/PyBaMM/pull/3423))
+- Make pybamm importable with minimal dependencies ([#3044](https://github.com/pybamm-team/PyBaMM/pull/3044), [#3475](https://github.com/pybamm-team/PyBaMM/pull/3475))
+- Fixed a bug where supplying an initial soc did not work with half cell models ([#3456](https://github.com/pybamm-team/PyBaMM/pull/3456))
 - Fixed a bug where empty lists passed to QuickPlot resulted in an IndexError and did not return a meaningful error message ([#3359](https://github.com/pybamm-team/PyBaMM/pull/3359))
 - Fixed a bug where there was a missing thermal conductivity in the thermal pouch cell models ([#3330](https://github.com/pybamm-team/PyBaMM/pull/3330))
 - Fixed a bug that caused incorrect results of “{Domain} electrode thickness change [m]” due to the absence of dimension for the variable `electrode_thickness_change`([#3329](https://github.com/pybamm-team/PyBaMM/pull/3329)).
@@ -37,7 +46,6 @@
 - Error generated when invalid parameter values are passed ([#3132](https://github.com/pybamm-team/PyBaMM/pull/3132))
 - Parameters in `Prada2013` have been updated to better match those given in the paper, which is a 2.3 Ah cell, instead of the mix-and-match with the 1.1 Ah cell from Lain2019 ([#3096](https://github.com/pybamm-team/PyBaMM/pull/3096))
 - 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 supplying an initial soc did not work with half cell models ([#3456](https://github.com/pybamm-team/PyBaMM/pull/3456))
 
 ## Optimizations
 
@@ -57,7 +65,7 @@
 - Added option to use an empirical hysteresis model for the diffusivity and exchange-current density ([#3194](https://github.com/pybamm-team/PyBaMM/pull/3194))
 - Double-layer capacity can now be provided as a function of temperature ([#3174](https://github.com/pybamm-team/PyBaMM/pull/3174))
 - `pybamm_install_jax` is deprecated. It is now replaced with `pip install pybamm[jax]` ([#3163](https://github.com/pybamm-team/PyBaMM/pull/3163))
-- PyBaMM now has optional dependencies that can be installed with the pattern `pip install pybamm[option]` e.g. `pybamm[plot]` ([#3044](https://github.com/pybamm-team/PyBaMM/pull/3044))
+- PyBaMM now has optional dependencies that can be installed with the pattern `pip install pybamm[option]` e.g. `pybamm[plot]` ([#3044](https://github.com/pybamm-team/PyBaMM/pull/3044), [#3475](https://github.com/pybamm-team/PyBaMM/pull/3475))
 
 # [v23.5](https://github.com/pybamm-team/PyBaMM/tree/v23.5) - 2023-06-18
 

diff --git a/CITATION.cff b/CITATION.cff
@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "23.9rc0"
+version: "23.9"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"