Merge branch 'develop' into issue-3495-separator

.all-contributorsrc

@@ -1,6 +1,6 @@
 {
   "files": [
-    "README.md"
+    "all_contributors.md"
   ],
   "imageSize": 100,
   "commit": false,
@@ -836,6 +836,16 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "lorenzofavaro",
+      "name": "Lorenzo",
+      "avatar_url": "https://avatars.githubusercontent.com/u/44714920?v=4",
+      "profile": "https://github.com/lorenzofavaro",
+      "contributions": [
+        "code",
+        "test"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.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/request-action@v2.x

.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/publish_pypi.yml

@@ -218,6 +218,12 @@ jobs:
     name: Upload package to PyPI
     needs: [build_macos_and_linux_wheels, build_macos_arm64_wheels, build_windows_wheels, build_sdist]
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pybamm
+    permissions:
+      id-token: write
+
     steps:
       - name: Download all artifacts
         uses: actions/download-artifact@v4
@@ -231,8 +237,6 @@ jobs:
         if: github.event.inputs.target == 'pypi' || github.event_name == 'release'
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          user: __token__
-          password: ${{ secrets.PYPI_TOKEN }}
           packages-dir: files/
 
       - name: Publish on TestPyPI

.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

@@ -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
@@ -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

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.2.2"
+    rev: "v0.3.3"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

CHANGELOG.md

@@ -3,9 +3,10 @@
 ## Features
 
 - Added support for macOS arm64 (M-series) platforms. ([#3789](https://github.com/pybamm-team/PyBaMM/pull/3789))
+- Added the ability to specify a custom solver tolerance in `get_initial_stoichiometries` and related functions ([#3714](https://github.com/pybamm-team/PyBaMM/pull/3714))
+- Modified `step` function to take an array of time `t_eval` as an argument and deprecated use of `npts`. ([#3627](https://github.com/pybamm-team/PyBaMM/pull/3627))
 - Renamed "electrode diffusivity" to "particle diffusivity" as a non-breaking change with a deprecation warning ([#3624](https://github.com/pybamm-team/PyBaMM/pull/3624))
 - Add support for BPX version 0.4.0 which allows for blended electrodes and user-defined parameters in BPX([#3414](https://github.com/pybamm-team/PyBaMM/pull/3414))
-- Added the ability to specify a custom solver tolerance in `get_initial_stoichiometries` and related functions ([#3714](https://github.com/pybamm-team/PyBaMM/pull/3714))
 
 ## Bug Fixes
 
@@ -23,6 +24,7 @@
 
 ## Breaking changes
 
+- Integrated the `[pandas]` extra into the core PyBaMM package, deprecating the `pybamm[pandas]` optional dependency. Pandas is now a required dependency and will be installed upon installing PyBaMM ([#3892](https://github.com/pybamm-team/PyBaMM/pull/3892))
 - 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))

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