Merge branch 'develop' into issue-2670-interp2d

michasahre · Apr 28, 2023 · 4b52d2e · 4b52d2e
2 parents 38925e1 + aa80775
commit 4b52d2e
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diff --git a/.github/workflows/benchmark_on_push.yml b/.github/workflows/benchmark_on_push.yml
@@ -38,7 +38,7 @@ jobs:
           HEAD_COMMIT=$(git rev-parse HEAD)
           echo $BASE_COMMIT | tee commits_to_compare.txt
           echo $HEAD_COMMIT | tee -a commits_to_compare.txt
-          asv run HASHFILE:commits_to_compare.txt --m "GitHubRunner" --show-stderr -v
+          asv run HASHFILE:commits_to_compare.txt --m "GitHubRunner" --show-stderr --strict -v
       - name: Compare commits' benchmark results
         run: |
           BASE_COMMIT=$(head -1 commits_to_compare.txt)

diff --git a/.github/workflows/need_reply_remove.yml b/.github/workflows/need_reply_remove.yml
@@ -0,0 +1,24 @@
+name: Remove needs-reply label
+
+on:
+  issue_comment:
+    types:
+      - created
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    if: |
+      github.event.comment.author_association != 'OWNER' &&
+      github.event.comment.author_association != 'COLLABORATOR'
+    steps:
+      - name: Remove needs-reply label
+        uses: octokit/[email protected]
+        continue-on-error: true
+        with:
+          route: DELETE /repos/:repository/issues/:issue/labels/:label
+          repository: ${{ github.repository }}
+          issue: ${{ github.event.issue.number }}
+          label: needs-reply
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/needs_reply.yml b/.github/workflows/needs_reply.yml
@@ -0,0 +1,15 @@
+name: Close old issues that need reply
+
+on:
+  schedule:
+    - cron: "0 0 * * *"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Close old issues that need reply
+        uses: dwieeb/needs-reply@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          issue-label: needs-reply
diff --git a/.github/workflows/periodic_benchmarks.yml b/.github/workflows/periodic_benchmarks.yml
@@ -24,12 +24,22 @@ 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 Linux system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt install gfortran gcc libopenblas-dev
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip wheel setuptools virtualenv asv wget cmake casadi numpy
+      - name: Install SuiteSparse and Sundials
+        run: python scripts/install_KLU_Sundials.py
       - name: Run benchmarks
         run: |
           asv machine --machine "GitHubRunner"
-          asv run --machine "GitHubRunner" NEW
+          asv run --machine "GitHubRunner" NEW --show-stderr --strict -v
+        env:
+          SUNDIALS_INST: $HOME/.local
+          LD_LIBRARY_PATH: $HOME/.local/lib
       - name: Upload results as artifact
         uses: actions/upload-artifact@v2
         with:

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
@@ -46,7 +46,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.8, 3.9]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v3
@@ -89,7 +89,7 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run: tox -e pybamm-requires
 
-      - name: Run unit tests for GNU/Linux with Python 3.8
+      - 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
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,12 +4,12 @@ ci:
 
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.3.0
     hooks:
       - id: black
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: "v0.0.259"
+    rev: "v0.0.261"
     hooks:
       - id: ruff
         args: [--ignore=E741, --exclude=__init__.py]
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,21 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+# 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))
+- 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))
+
+## Bug fixes
+
+- 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))
+
+# Breaking changes
+
+- Made `Jupyter` a development only dependency. Now `Jupyter` would not be a required dependency for users while installing `PyBaMM`. ([#2846](https://github.com/pybamm-team/PyBaMM/pull/2846))
+
 # [v23.3](https://github.com/pybamm-team/PyBaMM/tree/v23.3) - 2023-03-31
 
 ## Features
@@ -14,12 +30,13 @@
 
 ## Bug fixes
 
+- 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 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))
 - Fixed `plot_voltage_components` so that the sum of overpotentials is now equal to the voltage ([#2740](https://github.com/pybamm-team/PyBaMM/pull/2740))
-- Fixed use of last_state as starting_solution in Simulation.solve() ([#2822](https://github.com/pybamm-team/PyBaMM/pull/2822))
 
 ## Optimizations
 

diff --git a/asv.conf.json b/asv.conf.json
@@ -24,6 +24,7 @@
   // "install_command": ["in-dir={env_dir} python -mpip install {wheel_file}"],
   // "uninstall_command": ["return-code=any python -mpip uninstall -y {project}"],
   "build_command": [
+    "/bin/rm -rf pybind11",
     "/usr/bin/git clone --depth 1 --branch v2.6.2 https://github.com/pybind/pybind11.git",
     "python setup.py build",
     "PIP_NO_BUILD_ISOLATION=false python -mpip wheel --no-deps --no-index -w {build_cache_dir} {build_dir}"

diff --git a/benchmarks/different_model_options.py b/benchmarks/different_model_options.py
@@ -124,7 +124,7 @@ class TimeSolveLithiumPlating:
 
     def setup(self, model, params, solver_class):
         SolveModel.solve_setup(
-            self, "OKane2020", model, "lithium plating", params, solver_class
+            self, "OKane2022", model, "lithium plating", params, solver_class
         )
 
     def time_solve_model(self, model, params, solver_class):
@@ -139,12 +139,10 @@ class TimeBuildModelSEI:
             "none",
             "constant",
             "reaction limited",
-            "reaction limited (asymmetric)",
             "solvent-diffusion limited",
             "electron-migration limited",
             "interstitial-diffusion limited",
             "ec reaction limited",
-            "ec reaction limited (asymmetric)",
         ],
     )
 
@@ -160,12 +158,10 @@ class TimeSolveSEI:
             "none",
             "constant",
             "reaction limited",
-            "reaction limited (asymmetric)",
             "solvent-diffusion limited",
             "electron-migration limited",
             "interstitial-diffusion limited",
             "ec reaction limited",
-            "ec reaction limited (asymmetric)",
         ],
         [pybamm.CasadiSolver, pybamm.IDAKLUSolver],
     )
@@ -263,6 +259,12 @@ class TimeSolveSurfaceForm:
     )
 
     def setup(self, model, params, solver_class):
+        if (model, params, solver_class) == (
+            pybamm.lithium_ion.SPM,
+            "differential",
+            pybamm.IDAKLUSolver,
+        ):
+            raise NotImplementedError
         SolveModel.solve_setup(
             self, "Marquis2019", model, "surface form", params, solver_class
         )

diff --git a/benchmarks/time_setup_models_and_sims.py b/benchmarks/time_setup_models_and_sims.py
@@ -9,7 +9,7 @@
     "Ramadass2004",
     "Mohtat2020",
     "Chen2020",
-    "Chen2020_plating",
+    "OKane2022",
     "Ecker2015",
 ]
 

diff --git a/benchmarks/time_sims_experiments.py b/benchmarks/time_sims_experiments.py
@@ -21,6 +21,13 @@ class TimeSimulation:
     }
 
     def setup(self, experiment, parameters, model_class, solver_class):
+        if (experiment, parameters, model_class, solver_class) == (
+            "GITT",
+            "Marquis2019",
+            pybamm.lithium_ion.DFN,
+            pybamm.CasadiSolver,
+        ):
+            raise NotImplementedError
         self.param = pybamm.ParameterValues(parameters)
         self.model = model_class()
         self.solver = solver_class()

diff --git a/benchmarks/time_solve_models.py b/benchmarks/time_solve_models.py
@@ -145,6 +145,12 @@ class TimeSolveDFN:
     )
 
     def setup(self, solve_first, parameters, solver_class):
+        if (solve_first, parameters, solver_class) == (
+            True,
+            "ORegan2022",
+            pybamm.CasadiSolver,
+        ):
+            raise NotImplementedError
         self.solver = solver_class()
         self.model = pybamm.lithium_ion.DFN()
         c_rate = 1

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -5,7 +5,7 @@ pandas >= 0.24
 anytree >= 2.4.3
 autograd >= 1.2
 scikit-fem >= 0.2.0
-casadi >= 3.5.0
+casadi >= 3.6.0
 imageio>=2.9.0
 jupyter  # For example notebooks
 pybtex

diff --git a/docs/source/user_guide/installation/GNU-linux.rst b/docs/source/user_guide/installation/GNU-linux.rst
@@ -7,7 +7,7 @@
 Prerequisites
 =============
 
-To use and/or contribute to PyBaMM, you must have Python 3.8 or 3.9 installed.
+To use and/or contribute to PyBaMM, you must have Python 3.8, 3.9, 3.10, or 3.11 installed.
 
 To install Python 3 on Debian-based distribution (Debian, Ubuntu, Linux
 mint), open a terminal and run
@@ -46,7 +46,7 @@ User install
 
 We recommend to install PyBaMM within a virtual environment, in order
 not to alter any distribution Python files.
-First, make sure you are using Python 3.8 or 3.9.
+First, make sure you are using Python 3.8, 3.9, 3.10, or 3.11.
 To create a virtual environment ``env`` within your current directory type:
 
 .. code:: bash

diff --git a/docs/source/user_guide/installation/install-from-source.rst b/docs/source/user_guide/installation/install-from-source.rst
@@ -25,7 +25,7 @@ or download the source archive on the repository's homepage.
 
 To install PyBaMM, you will need:
 
-- Python 3 (PyBaMM supports versions 3.8 and 3.9)
+- Python 3 (PyBaMM supports versions 3.8, 3.9, 3.10, and 3.11)
 - The Python headers file for your current Python version.
 - A BLAS library (for instance `openblas <https://www.openblas.net/>`_).
 - A C compiler (ex: ``gcc``).

diff --git a/docs/source/user_guide/installation/windows.rst b/docs/source/user_guide/installation/windows.rst
@@ -6,7 +6,7 @@ Windows
 Prerequisites
 -------------
 
-To use and/or contribute to PyBaMM, you must have Python 3.8 or 3.9 installed.
+To use and/or contribute to PyBaMM, you must have Python 3.8, 3.9, 3.10, or 3.11 installed.
 
 To install Python 3 download the installation files from `Python’s
 website <https://www.python.org/downloads/windows/>`__. Make sure to