Merge branch 'develop' into issue-3200-2D-processed-variables

KwanjuEUN · Aug 7, 2023 · 86f2a09 · 86f2a09
2 parents 26b28fe + f0cc984
commit 86f2a09
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -610,7 +610,9 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/104268427?v=4",
       "profile": "https://github.com/arjxn-py",
       "contributions": [
-        "infra"
+        "infra",
+        "code",
+        "doc"
       ]
     },
     {
@@ -660,6 +662,16 @@
         "code",
         "test"
       ]
+    },
+    {
+      "login": "ejfdickinson",
+      "name": "ejfdickinson",
+      "avatar_url": "https://avatars.githubusercontent.com/u/116663050?v=4",
+      "profile": "https://github.com/ejfdickinson",
+      "contributions": [
+        "ideas",
+        "bug"
+      ]
     }
   ],
   "contributorsPerLine": 7,

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -2,3 +2,5 @@
 0054efe388d2d17301f7e0554449eac9a7d3b7fc
 # activated pre-commit for notebooks - https://github.com/pybamm-team/PyBaMM/pull/3110
 a63e49ece0f9336d1f5c2562f7459e555c6e6693
+# activated standard pre-commits - https://github.com/pybamm-team/PyBaMM/pull/3192
+5273214b585c5a4286609aed40e0b092d0e05f42
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -14,11 +14,11 @@ Please add a line in the relevant section of [CHANGELOG.md](https://github.com/p
 
 # Key checklist:
 
-- [ ] No style issues: `$ pre-commit run` (see [CONTRIBUTING.md](https://github.com/pybamm-team/PyBaMM/blob/develop/CONTRIBUTING.md#installing-and-using-pre-commit) for how to set this up to run automatically when committing locally, in just two lines of code)
-- [ ] All tests pass: `$ python run-tests.py --all`
-- [ ] The documentation builds: `$ python run-tests.py --doctest`
+- [ ] No style issues: `$ pre-commit run` (or `$ nox -s pre-commit`) (see [CONTRIBUTING.md](https://github.com/pybamm-team/PyBaMM/blob/develop/CONTRIBUTING.md#installing-and-using-pre-commit) for how to set this up to run automatically when committing locally, in just two lines of code)
+- [ ] All tests pass: `$ python run-tests.py --all` (or `$ nox -s tests`)
+- [ ] The documentation builds: `$ python run-tests.py --doctest` (or `$ nox -s doctests`)
 
-You can run unit and doctests together at once, using `$ python run-tests.py --quick`.
+You can run integration tests, unit tests, and doctests together at once, using `$ python run-tests.py --quick` (or `$ nox -s quick`).
 
 ## Further checks:
 

diff --git a/.github/workflows/lychee_url_checker.yml b/.github/workflows/lychee_url_checker.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
 
-      # cache Lychee results to avoid hitting rate limits  
+      # cache Lychee results to avoid hitting rate limits
       - name: Restore lychee cache
         uses: actions/cache@v3
         with:
@@ -42,7 +42,7 @@ jobs:
             --exclude https://twitter.com/pybamm_
             --exclude "https://doi\.org|www.sciencedirect\.com/*"
             --accept 200,429
-            --exclude-path ./CHANGELOG.md 
+            --exclude-path ./CHANGELOG.md
             --exclude-path ./scripts/update_version.py
             './**/*.rst'
             './**/*.md'

diff --git a/.github/workflows/need_reply_remove.yml b/.github/workflows/need_reply_remove.yml
@@ -22,4 +22,4 @@ jobs:
           issue: ${{ github.event.issue.number }}
           label: needs-reply
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/needs_reply.yml b/.github/workflows/needs_reply.yml
@@ -13,4 +13,4 @@ jobs:
         uses: dwieeb/needs-reply@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
-          issue-label: needs-reply
+          issue-label: needs-reply
diff --git a/.github/workflows/run_periodic_tests.yml b/.github/workflows/run_periodic_tests.yml
@@ -1,11 +1,11 @@
-# Run all unit tests and integration tests for all Python versions 
+# Run all unit tests and integration tests for all Python versions
 # and platforms at 3am UTC every day and on PRs to the main branch
 name: Scheduled
 
 on:
   workflow_dispatch:
   pull_request:
-    branches: 
+    branches:
     - main
 
   # Run everyday at 3 am UTC
@@ -119,13 +119,13 @@ jobs:
   build-apple-mseries:
     needs: style
     runs-on: [self-hosted, macOS, ARM64]
-    env: 
+    env:
       GITHUB_PATH: ${PYENV_ROOT/bin:$PATH}
     strategy:
       fail-fast: false
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
-        
+
     steps:
       - uses: actions/checkout@v3
       - name: Install python & create virtualenv

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
@@ -45,12 +45,8 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
-      - id: setup-python
-        name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v3
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
@@ -68,73 +64,59 @@ jobs:
           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
+          HOMEBREW_NO_COLOR: 1
           # Speed up CI
           NONINTERACTIVE: 1
         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 analytics off
           brew update
           brew install graphviz openblas
 
       - name: Install Windows system dependencies
         if: matrix.os == 'windows-latest'
         run: choco install graphviz --version=8.0.5
 
-      - name: Install standard Python dependencies
+      - name: Set up Python ${{ matrix.python-version }}
+        id: setup-python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: setup.py
+
+      - name: Install PyBaMM dependencies
         run: |
-          python -m pip install --upgrade pip wheel setuptools
-          python -m pip install nox
+          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
         if: matrix.os == 'ubuntu-latest'
         with:
           path: |
             # Repository files
-            ${{ github.workspace }}/.nox/pybamm-requires/
             ${{ github.workspace }}/pybind11/
             ${{ github.workspace }}/install_KLU_Sundials/
             # Headers and dynamic library files for SuiteSparse and SUNDIALS
             ${{ env.HOME }}/.local/lib/
             ${{ env.HOME }}/.local/include/
             ${{ env.HOME }}/.local/examples/
-          key: nox-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/noxfile.py', '**/install_KLU_Sundials.py') }}
+          key: nox-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py') }}
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
         if: matrix.os == 'ubuntu-latest'
         run: nox -s pybamm-requires
 
-      - name: Cache unit tests nox environment for GNU/Linux with Python 3.8, 3.9, and 3.10, and for macOS and Windows with all Python versions
-        uses: actions/cache@v3
-        if: (matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11) || (matrix.os != 'ubuntu-latest')
-        with:
-          path: ${{ github.workspace }}/.nox/unit/
-          key: ${{ runner.os }}-nox-unit-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/noxfile.py', '**/setup.py') }}
-
       - 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: nox -s unit
 
-      - name: Cache coverage nox environment for GNU/Linux with Python 3.11
-        uses: actions/cache@v3
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        with:
-          path: ${{ github.workspace }}/.nox/coverage/
-          key: ${{ runner.os }}-nox-coverage-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/noxfile.py', '**/setup.py', '**/.coveragerc') }}
-
       - 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
@@ -143,35 +125,14 @@ jobs:
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         uses: codecov/[email protected]
 
-      - name: Cache integration tests nox environment for GNU/Linux with Python 3.11
-        uses: actions/cache@v3
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        with:
-          path: ${{ github.workspace }}/.nox/integration/
-          key: ${{ runner.os }}-nox-integration-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/noxfile.py', '**/setup.py') }}
-
       - name: Run integration tests for GNU/Linux with Python 3.11
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         run: nox -s integration
 
-      - name: Cache doctests nox environment for GNU/Linux with Python 3.11
-        uses: actions/cache@v3
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        with:
-          path: ${{ github.workspace }}/.nox/doctests/
-          key: ${{ runner.os }}-nox-doctests-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/noxfile.py', '**/setup.py', '**/docs/requirements.txt') }}
-
       - 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: nox -s doctests
 
-      - name: Cache examples nox environment for GNU/Linux with Python 3.11
-        uses: actions/cache@v3
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        with:
-          path: ${{ github.workspace }}/.nox/examples/
-          key: ${{ runner.os }}-nox-examples-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/noxfile.py', '**/setup.py') }}
-
       - 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: nox -s examples
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -21,3 +21,23 @@ repos:
     hooks:
        - id: blacken-docs
          additional_dependencies: [black==22.12.0]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+        - id: check-added-large-files
+        - id: check-case-conflict
+        - id: check-merge-conflict
+        - id: check-yaml
+        - id: debug-statements
+        - id: end-of-file-fixer
+        - id: mixed-line-ending
+        - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+        - id: python-check-blanket-type-ignore
+        - id: rst-backticks
+        - id: rst-directive-colons
+        - id: rst-inline-touching-normal
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -1,4 +1,4 @@
-# .readthedocs.yml
+# .readthedocs.yaml
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
@@ -34,7 +34,9 @@ build:
 
 # Optionally declare the Python requirements required to build your docs
 python:
-    install:
-      - requirements: docs/requirements.txt
-      - method: pip
-        path: .
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+        - all
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,14 +1,12 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
 ## Features
+
 - Processed variables now get the spatial variables automatically, allowing plotting of more generic models ([#3234](https://github.com/pybamm-team/PyBaMM/pull/3234))
 
 ## Breaking changes
 
-- 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))
+- Numpy functions now work with PyBaMM symbols (e.g. `np.exp(pybamm.Symbol("a"))` returns `pybamm.Exp(pybamm.Symbol("a"))`). This means that parameter functions can be specified using numpy functions instead of pybamm functions. Additionally, combining numpy arrays with pybamm objects now works (the numpy array is converted to a pybamm array) ([#3205](https://github.com/pybamm-team/PyBaMM/pull/3205))
 
 ## Bug fixes
 
@@ -20,6 +18,13 @@
 - Thevenin() model is now constructed with standard variables: `Time [s], Time [min], Time [h]` ([#3143](https://github.com/pybamm-team/PyBaMM/pull/3143))
 - Fix SEI Example Notebook ([#3166](https://github.com/pybamm-team/PyBaMM/pull/3166))
 
+## Breaking changes
+
+- 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))
+
 # [v23.5](https://github.com/pybamm-team/PyBaMM/tree/v23.5) - 2023-06-18
 
 ## Features

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -34,7 +34,7 @@ if(NOT PYBIND11_DIR)
 endif()
 
 add_subdirectory(${PYBIND11_DIR})
-pybind11_add_module(idaklu 
+pybind11_add_module(idaklu
   pybamm/solvers/c_solvers/idaklu/casadi_functions.cpp
   pybamm/solvers/c_solvers/idaklu/casadi_functions.hpp
   pybamm/solvers/c_solvers/idaklu/casadi_solver.cpp
@@ -56,7 +56,7 @@ if (NOT DEFINED USE_PYTHON_CASADI)
 endif()
 
 execute_process(
-    COMMAND "${PYTHON_EXECUTABLE}" -c 
+    COMMAND "${PYTHON_EXECUTABLE}" -c
     "import casadi as _; print(_.__path__[0])"
     OUTPUT_VARIABLE CASADI_DIR
     OUTPUT_STRIP_TRAILING_WHITESPACE)
@@ -67,7 +67,7 @@ endif()
 message("Found python casadi path: ${CASADI_DIR}")
 
 if(${USE_PYTHON_CASADI})
-  message("Trying to link against python casadi package")   
+  message("Trying to link against python casadi package")
   find_package(casadi CONFIG PATHS ${CASADI_DIR} REQUIRED)
 else()
   message("Trying to link against any casadi package apart from the python one")
@@ -78,7 +78,7 @@ endif()
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR})
 # Sundials
 find_package(SUNDIALS REQUIRED)
-message("sundials ${SUNDIALS_INCLUDE_DIR} ${SUNDIALS_LIBRARIES}") 
+message("sundials ${SUNDIALS_INCLUDE_DIR} ${SUNDIALS_LIBRARIES}")
 target_include_directories(idaklu PRIVATE ${SUNDIALS_INCLUDE_DIR})
 target_link_libraries(idaklu PRIVATE ${SUNDIALS_LIBRARIES} casadi)
 

diff --git a/FindSuiteSparse.cmake b/FindSuiteSparse.cmake
@@ -1,4 +1,4 @@
-# This CMakeFile is adapted from that in dune-common: 
+# This CMakeFile is adapted from that in dune-common:
 
 # .. cmake_module::
 #
@@ -239,4 +239,3 @@ endif()
 #set HAVE_SUITESPARSE for config.h
 set(HAVE_SUITESPARSE ${SuiteSparse_FOUND})
 set(HAVE_UMFPACK ${SuiteSparse_UMFPACK_FOUND})
-