Merge pull request #4781 from pybamm-team/release/v25.1.1

Release v25.1.1

Author: kratman

.clang-format

@@ -30,7 +30,7 @@ jobs:
             password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build and push Docker image to Docker Hub
-        uses: docker/build-push-action@b32b51a8eda65d6793cd0494a773d4f6bcef32dc # v6.11.0
+        uses: docker/build-push-action@67a2d409c0a876cbe6b11854e3e25193efe4e62d # v6.12.0
         with:
           context: .
           file: scripts/Dockerfile

.github/codecov.yml

@@ -36,7 +36,7 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run: |
           sudo apt-get update
-          sudo dot -c
+          sudo apt-get install gfortran gcc graphviz pandoc
           sudo apt-get install libopenblas-dev texlive-latex-extra dvipng
 
       - name: Install macOS system dependencies
@@ -100,6 +100,7 @@ jobs:
       - name: Install Linux system dependencies
         run: |
           sudo apt-get update
+          sudo apt-get install graphviz pandoc
           sudo apt-get install texlive-latex-extra dvipng
 
       - name: Set up Python
@@ -132,6 +133,7 @@ jobs:
       - name: Install Linux system dependencies
         run: |
           sudo apt-get update
+          sudo apt-get install gfortran gcc graphviz pandoc
           sudo apt-get install libopenblas-dev texlive-latex-extra dvipng
 
       - name: Set up Python 3.12
@@ -161,6 +163,7 @@ jobs:
       - name: Install Linux system dependencies
         run: |
           sudo apt-get update
+          sudo apt-get install gfortran gcc graphviz
           sudo apt-get install libopenblas-dev texlive-latex-extra dvipng
 
       - name: Set up Python 3.12

.github/workflows/docker.yml

@@ -1,11 +1,9 @@
 name: Alert validation repository
 on:
+  workflow_dispatch:
   release:
     types:
       - published
-  push:
-    branches:
-      - develop
 
 jobs:
   build:

.github/workflows/run_periodic_tests.yml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.9.1"
+    rev: "v0.9.2"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

.github/workflows/update_license.yml

@@ -1,5 +1,16 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+# [v25.1.1](https://github.com/pybamm-team/PyBaMM/tree/v25.1.1) - 2025-01-20
+
+## Features
+
+- Added Operators to current and voltage termination events. ([#4770](https://github.com/pybamm-team/PyBaMM/pull/4770))
+
+## Bug fixes
+
+- Fixed a bug which caused the wc-reaction limited SEI model to give
+  incorrect results ([#4774](https://github.com/pybamm-team/PyBaMM/pull/4774))
+
 # [v25.1.0](https://github.com/pybamm-team/PyBaMM/tree/v25.1.0) - 2025-01-14
 
 ## Features

.github/workflows/validation_benchmarks.yml

@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "25.1.0"
+version: "25.1.1"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"

.pre-commit-config.yaml

@@ -422,18 +422,13 @@ wherever code is called that uses that citation (for example, in functions or in
 
 ### Installation
 
-Installation of PyBaMM and its dependencies is handled via [pip](https://pip.pypa.io/en/stable/) and [setuptools](http://setuptools.readthedocs.io/). It uses `CMake` to compile C++ extensions using [`pybind11`](https://pybind11.readthedocs.io/en/stable/) and [`casadi`](https://web.casadi.org/). The installation process is described in detail in the [source installation](https://docs.pybamm.org/en/latest/source/user_guide/installation/install-from-source.html) page and is configured through the `CMakeLists.txt` file.
+Installation of PyBaMM and its dependencies is handled via [pip](https://pip.pypa.io/en/stable/)
 
 Configuration files:
-
 ```
-setup.py
 pyproject.toml
-MANIFEST.in
 ```
 
-Note: `MANIFEST.in` is used to include and exclude non-Python files and auxiliary package data for PyBaMM when distributing it. If a file is not included in `MANIFEST.in`, it will not be included in the source distribution (SDist) and subsequently not be included in the binary distribution (wheel).
-
 ### Continuous Integration using GitHub Actions
 
 Each change pushed to the PyBaMM GitHub repository will trigger the test and benchmark suites to be run, using [GitHub Actions](https://github.com/features/actions).

CHANGELOG.md

@@ -19,19 +19,12 @@ def pytest_addoption(parser):
         default=False,
         help="run integration tests",
     )
-    parser.addoption(
-        "--cibw",
-        action="store_true",
-        default=False,
-        help="test build wheels",
-    )
 
 
 def pytest_configure(config):
     config.addinivalue_line("markers", "scripts: mark test as an example script")
     config.addinivalue_line("markers", "unit: mark test as a unit test")
     config.addinivalue_line("markers", "integration: mark test as an integration test")
-    config.addinivalue_line("markers", "cibw: mark test as build wheel test")
 
 
 def pytest_collection_modifyitems(items):

CITATION.cff

@@ -64,8 +64,7 @@ def run_integration(session):
 @nox.session(name="doctests")
 def run_doctests(session):
     """Run the doctests and generate the output(s) in the docs/build/ directory."""
-    # TODO: Temporary fix for Python 3.12 CI.
-    # See: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
+    # Fix for Python 3.12 CI. This can be removed after pybtex is replaced.
     session.install("setuptools", silent=False)
     session.install("-e", ".[all,dev,docs]", silent=False)
     session.run(
@@ -102,9 +101,7 @@ def run_examples(session):
 def run_scripts(session):
     """Run the scripts tests for Python scripts."""
     set_environment_variables(PYBAMM_ENV, session=session)
-    # Temporary fix for Python 3.12 CI. TODO: remove after
-    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
-    # is fixed
+    # Fix for Python 3.12 CI. This can be removed after pybtex is replaced.
     session.install("setuptools", silent=False)
     session.install("-e", ".[all,dev,jax]", silent=False)
     session.run("python", "-m", "pytest", "-m", "scripts")
@@ -119,9 +116,7 @@ def set_dev(session):
     python = os.fsdecode(VENV_DIR.joinpath("bin/python"))
     components = ["all", "dev", "jax"]
     args = []
-    # Temporary fix for Python 3.12 CI. TODO: remove after
-    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
-    # is fixed
+    # Fix for Python 3.12 CI. This can be removed after pybtex is replaced.
     session.run(python, "-m", "pip", "install", "setuptools", external=True)
     session.run(
         python,
@@ -153,8 +148,7 @@ def run_tests(session):
 def build_docs(session):
     """Build the documentation and load it in a browser tab, rebuilding on changes."""
     envbindir = session.bin
-    # TODO: Temporary fix for Python 3.12 CI.
-    # See: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
+    # Fix for Python 3.12 CI. This can be removed after pybtex is replaced.
     session.install("setuptools", silent=False)
     session.install("-e", ".[all,docs]", silent=False)
     session.chdir("docs")

CONTRIBUTING.md

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pybamm"
-version = "25.1.0"
+version = "25.1.1"
 license = { file = "LICENSE.txt" }
 description = "Python Battery Mathematical Modelling"
 authors = [{name = "The PyBaMM Team", email = "[email protected]"}]
@@ -227,7 +227,6 @@ required_plugins = [
     "pytest-mock",
     "pytest-subtests",
 ]
-norecursedirs = 'pybind11*'
 addopts = [
     "-nauto",
     "-vra",

conftest.py

@@ -1,5 +1,5 @@
 from .steps import *
 from .base_step import BaseStep, BaseStepExplicit, BaseStepImplicit
-from .step_termination import *
+from .step_termination import BaseTermination, CurrentTermination, VoltageTermination, CustomTermination, CrateTermination, _read_termination
 
 __all__ = ['base_step', 'step_termination', 'steps']

noxfile.py

@@ -67,8 +67,14 @@ def __init__(
         tags=None,
         start_time=None,
         description=None,
-        direction=None,
+        direction: str | None = None,
     ):
+        potential_directions = ["charge", "discharge", "rest", None]
+        if direction not in potential_directions:
+            raise ValueError(
+                f"Invalid direction: {direction}. Must be one of {potential_directions}"
+            )
+        self.input_duration = duration
         self.input_duration = duration
         self.input_value = value
         # Check if drive cycle
@@ -386,11 +392,11 @@ def value_based_charge_or_discharge(self):
             init_curr = self.value
         sign = np.sign(init_curr)
         if sign == 0:
-            return "Rest"
+            return "rest"
         elif sign > 0:
-            return "Discharge"
+            return "discharge"
         else:
-            return "Charge"
+            return "charge"
 
     def record_tags(
         self,

pyproject.toml

@@ -14,8 +14,11 @@ class BaseTermination:
         The value at which the event is triggered
     """
 
-    def __init__(self, value):
+    def __init__(self, value, operator=None):
         self.value = value
+        if operator not in ["<", ">", None]:
+            raise ValueError(f"Invalid operator: {operator}")
+        self.operator = operator
 
     def get_event(self, variables, step):
         """
@@ -67,9 +70,19 @@ def get_event(self, variables, step):
         """
         See :meth:`BaseTermination.get_event`
         """
+        operator = self.operator
+        if operator == ">":
+            expr = self.value - variables["Current [A]"]
+            event_string = f"Current [A] > {self.value} [A] [experiment]"
+        elif operator == "<":
+            expr = variables["Current [A]"] - self.value
+            event_string = f"Current [A] < {self.value} [A] [experiment]"
+        else:
+            expr = abs(variables["Current [A]"]) - self.value
+            event_string = f"abs(Current [A]) < {self.value} [A] [experiment]"
         event = pybamm.Event(
-            "Current cut-off [A] [experiment]",
-            abs(variables["Current [A]"]) - self.value,
+            event_string,
+            expr,
         )
         return event
 
@@ -89,24 +102,48 @@ def get_event(self, variables, step):
         # figure out whether the voltage event is greater than the starting
         # voltage (charge) or less (discharge) and set the sign of the
         # event accordingly
-        direction = step.direction.capitalize()
-        if direction == "Charge":
+        operator = self.operator
+        if operator is None:
+            direction = step.direction
+            if direction == "charge":
+                operator = ">"
+            elif direction == "discharge":
+                operator = "<"
+            else:
+                # No event for rest steps
+                return None
+
+        if operator == ">":
             sign = -1
-        elif direction == "Discharge":
+        else:
+            # operator can only be "<" or ">"
             sign = 1
-        elif direction == "Rest":
-            # No event for rest steps
-            return None
 
         # Event should be positive at initial conditions for both
         # charge and discharge
         event = pybamm.Event(
-            f"{direction} voltage cut-off [V] [experiment]",
+            f"Voltage {operator} {self.value} [V] [experiment]",
             sign * (variables["Battery voltage [V]"] - self.value),
         )
         return event
 
 
+class Voltage:
+    def __gt__(self, value):
+        return VoltageTermination(value, operator=">")
+
+    def __lt__(self, value):
+        return VoltageTermination(value, operator="<")
+
+
+class Current:
+    def __gt__(self, value):
+        return CurrentTermination(value, operator=">")
+
+    def __lt__(self, value):
+        return CurrentTermination(value, operator="<")
+
+
 class CustomTermination(BaseTermination):
     """
     Define a custom termination event using a function. This can be used to create an

src/pybamm/experiment/step/__init__.py

@@ -45,7 +45,7 @@ def graphite_electrolyte_exchange_current_density_Dualfoil1998(
 
     References
     ----------
-    .. [2] http://www.cchem.berkeley.edu/jsngrp/fortran.html
+    .. [2] John Newman, Dualfoil
 
     Parameters
     ----------
@@ -219,7 +219,7 @@ def lico2_diffusivity_Dualfoil1998(sto, T):
 
     References
     ----------
-    .. [1] http://www.cchem.berkeley.edu/jsngrp/fortran.html
+    .. [1] John Newman, Dualfoil
 
     Parameters
     ----------
@@ -247,7 +247,7 @@ def lico2_electrolyte_exchange_current_density_Dualfoil1998(c_e, c_s_surf, c_s_m
 
     References
     ----------
-    .. [2] http://www.cchem.berkeley.edu/jsngrp/fortran.html
+    .. [2] John Newman, Dualfoil
 
     Parameters
     ----------