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

…develop

.all-contributorsrc

@@ -1,6 +1,6 @@
 {
   "files": [
-    "README.md"
+    "all_contributors.md"
   ],
   "imageSize": 100,
   "commit": false,

.git-blame-ignore-revs

@@ -10,3 +10,5 @@ a63e49ece0f9336d1f5c2562f7459e555c6e6693
 ff6d81c01331c7d269303b4a8321d9881bdf98fa
 # migrated to ruff-format - https://github.com/pybamm-team/PyBaMM/pull/3655
 60ebd4148059a95428a496f4f55c1175ead362d3
+# implemented cleaner string formatting via f-strings - https://github.com/pybamm-team/PyBaMM/pull/3890
+f395819d1c874071b7e76e32ec4f0bbe42462b48

.github/workflows/benchmark_on_push.yml

@@ -2,7 +2,6 @@ name: Run benchmarks on push
 on:
   push:
     branches: [main, develop]
-  pull_request:
 
 concurrency:
   # Cancel intermediate builds always

.github/workflows/lychee_url_checker.yml

@@ -47,6 +47,7 @@ jobs:
             --exclude-path ./scripts/update_version.py
             --exclude-path asv.conf.json
             --exclude-path docs/conf.py
+            --exclude-path all_contributors.md
             './**/*.rst'
             './**/*.md'
             './**/*.py'

.github/workflows/need_reply_remove.yml

@@ -1,6 +1,8 @@
 name: Remove needs-reply label
 
 on:
+  schedule:
+      - cron:  '0 3 * * 1'
   issue_comment:
     types:
       - created
@@ -11,7 +13,8 @@ jobs:
     if: |
       github.event.comment.author_association != 'OWNER' &&
       github.event.comment.author_association != 'COLLABORATOR' &&
-      github.repository_owner == 'pybamm-team'
+      github.repository_owner == 'pybamm-team' &&
+      github.event_name != 'pull_request'
     steps:
       - name: Remove needs-reply label
         uses: octokit/[email protected]

.github/workflows/periodic_benchmarks.yml

@@ -8,7 +8,7 @@
 # - Publish website
 name: Benchmarks
 on:
-  # Everyday at 3 am UTC
+  # Every day at 3 am UTC
   schedule:
     - cron: "0 3 * * *"
   # Make it possible to trigger the

.github/workflows/run_periodic_tests.yml

@@ -8,7 +8,7 @@ on:
     branches:
     - main
 
-  # Run everyday at 3 am UTC
+  # Run every day at 3 am UTC
   schedule:
     - cron: "0 3 * * *"
 

.github/workflows/test_on_push.yml

@@ -59,7 +59,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/[email protected].1
+        uses: awalsh128/[email protected].2
         if: matrix.os == 'ubuntu-latest'
         with:
           packages: gfortran gcc graphviz pandoc
@@ -138,7 +138,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/[email protected].1
+        uses: awalsh128/[email protected].2
         with:
           packages: gfortran gcc graphviz pandoc
           execute_install_scripts: true
@@ -208,7 +208,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/[email protected].1
+        uses: awalsh128/[email protected].2
         if: matrix.os == 'ubuntu-latest'
         with:
           packages: gfortran gcc graphviz pandoc
@@ -279,7 +279,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
-    name: Doctests (ubuntu-latest / Python 3.12)
+    name: Doctests (ubuntu-latest / Python 3.11)
 
     steps:
       - name: Check out PyBaMM repository
@@ -289,7 +289,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/[email protected].1
+        uses: awalsh128/[email protected].2
         with:
           packages: graphviz pandoc
           execute_install_scripts: true
@@ -301,20 +301,20 @@ jobs:
           sudo dot -c
           sudo apt-get install texlive-latex-extra dvipng
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.11
         id: setup-python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.11
           cache: 'pip'
 
       - name: Install nox
         run: python -m pip install nox
 
-      - name: Install docs dependencies and run doctests for GNU/Linux with Python 3.12
+      - name: Install docs dependencies and run doctests for GNU/Linux with Python 3.11
         run: python -m nox -s doctests
 
-      - name: Check if the documentation can be built for GNU/Linux with Python 3.12
+      - name: Check if the documentation can be built for GNU/Linux with Python 3.11
         run: python -m nox -s docs
 
   # Runs only on Ubuntu with Python 3.12
@@ -331,7 +331,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/[email protected].1
+        uses: awalsh128/[email protected].2
         with:
           packages: gfortran gcc graphviz pandoc
           execute_install_scripts: true
@@ -386,7 +386,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/[email protected].1
+        uses: awalsh128/[email protected].2
         with:
           packages: gfortran gcc graphviz
           execute_install_scripts: true

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.2.2"
+    rev: "v0.3.2"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

CHANGELOG.md

@@ -16,8 +16,14 @@
 - Updated `plot_voltage_components.py` to support both `Simulation` and `Solution` objects. Added new methods in both `Simulation` and `Solution` classes for allow the syntax `simulation.plot_voltage_components` and `solution.plot_voltage_components`. Updated `test_plot_voltage_components.py` to reflect these changes ([#3723](https://github.com/pybamm-team/PyBaMM/pull/3723)).
 - The SEI thickness decreased at some intervals when the 'electron-migration limited' model was used. It has been corrected ([#3622](https://github.com/pybamm-team/PyBaMM/pull/3622))
 
+## Optimizations
+
+- Sped up initialization of a `ProcessedVariable` by making the internal `xarray.DataArray` initialization lazy (only gets created if interpolation is needed) ([#3862](https://github.com/pybamm-team/PyBaMM/pull/3862))
+
 ## Breaking changes
 
+- Renamed "have_optional_dependency" to "import_optional_dependency" ([#3866](https://github.com/pybamm-team/PyBaMM/pull/3866))
+- Integrated the `[latexify]` extra into the core PyBaMM package, deprecating the `pybamm[latexify]` set of optional dependencies. SymPy is now a required dependency and will be installed upon installing PyBaMM ([#3848](https://github.com/pybamm-team/PyBaMM/pull/3848))
 - Renamed "testing" argument for plots to "show_plot" and flipped its meaning (show_plot=True is now the default and shows the plot) ([#3842](https://github.com/pybamm-team/PyBaMM/pull/3842))
 - Dropped support for BPX version 0.3.0 and below ([#3414](https://github.com/pybamm-team/PyBaMM/pull/3414))
 

CONTRIBUTING.md

@@ -104,21 +104,21 @@ Only 'core pybamm' is installed by default. The others have to be specified expl
 
 PyBaMM utilizes optional dependencies to allow users to choose which additional libraries they want to use. Managing these optional dependencies and their imports is essential to provide flexibility to PyBaMM users.
 
-PyBaMM provides a utility function `have_optional_dependency`, to check for the availability of optional dependencies within methods. This function can be used to conditionally import optional dependencies only if they are available. Here's how to use it:
+PyBaMM provides a utility function `import_optional_dependency`, to check for the availability of optional dependencies within methods. This function can be used to conditionally import optional dependencies only if they are available. Here's how to use it:
 
 Optional dependencies should never be imported at the module level, but always inside methods. For example:
 
 ```
 def use_pybtex(x,y,z):
-    pybtex = have_optional_dependency("pybtex")
+    pybtex = import_optional_dependency("pybtex")
     ...
 ```
 
 While importing a specific module instead of an entire package/library:
 
 ```python
 def use_parse_file(x, y, z):
-    parse_file = have_optional_dependency("pybtex.database", "parse_file")
+    parse_file = import_optional_dependency("pybtex.database", "parse_file")
     ...
 ```
 
@@ -143,7 +143,7 @@ class TestUtil(TestCase):
             pybamm.function_using_pybtex(x, y, z)
 
         # Test that the function works when pybtex is available
-        sys.modules["pybtex"] = pybamm.util.have_optional_dependency("pybtex")
+        sys.modules["pybtex"] = pybamm.util.import_optional_dependency("pybtex")
         pybamm.function_using_pybtex(x, y, z)
 ```
 

MANIFEST.in

@@ -2,6 +2,6 @@ graft pybamm
 include CITATION.cff
 prune tests
 
-exclude CHANGELOG.md CODE-OF-CONDUCT.md CONTRIBUTING.md CMakeLists.txt
+exclude CHANGELOG.md CODE-OF-CONDUCT.md CONTRIBUTING.md CMakeLists.txt all_contributors.md
 
 global-exclude __pycache__ *.py[cod] .venv