Merge branch 'develop' into joss

.github/workflows/lychee_links.yaml

@@ -0,0 +1,59 @@
+# Lychee Link Checking
+
+name: Links
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  schedule:
+    - cron: '0 6 * * 0'  # Run weekly on Sundays at 06:00 UTC
+
+jobs:
+  Lychee:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Restore lychee cache
+        uses: actions/cache@v4
+        with:
+          path: .lycheecache
+          key: cache-lychee-${{ github.sha }}
+          restore-keys: cache-lychee-
+
+      - name: Set up Lychee
+        uses: lycheeverse/[email protected]
+        with:
+          args: >-
+            --cache
+            --no-progress
+            --max-cache-age 2d
+            --timeout 10
+            --max-retries 5
+            --skip-missing
+            --exclude-loopback
+            --accept 200,429
+            --exclude "https://tiles.stadiamaps.com/*|https://b.tile.openstreetmap.org/*"
+            --exclude "https://cartodb-basemaps-c.global.ssl.fastly.net/*"
+            --exclude "https://events.mapbox.com/*|https://events.mapbox.cn/*|https://api.mapbox.cn/*"
+            --exclude "https://github.com/mikolalysenko/glsl-read-float/*"
+            --exclude "https://fonts.openmaptiles.org/*"
+            --exclude "https://a.tile.openstreetmap.org/*"
+            --exclude "https://openstreetmap.org/*|https://www.openstreetmap.org/*"
+            --exclude "https://cdn.plot.ly/*"
+            --exclude "https://doi.org/*"
+            --exclude-path ./CHANGELOG.md
+            --exclude-path asv.conf.json
+            --exclude-path docs/conf.py
+            './**/*.rst'
+            './**/*.md'
+            './**/*.py'
+            './**/*.ipynb'
+            './**/*.json'
+            './**/*.toml'
+          fail: true
+          jobSummary: true
+          format: markdown

.github/workflows/test_on_push.yaml → .github/workflows/test_on_pull_request.yaml

@@ -105,6 +105,37 @@ jobs:
         run: |
           nox -s examples
 
+  # Quick benchmarks on macos-14
+  benchmarks:
+    needs: style
+    runs-on: macos-14
+    strategy:
+      fail-fast: false
+    name: Benchmarks
+
+    steps:
+      - name: Check out PyBOP repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 2
+
+      - name: Set up Python 3.12
+        id: setup-python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.12
+
+      - name: Install dependencies
+        shell: bash
+        run: |
+          python -m pip install --upgrade pip asv[virtualenv]
+
+      - name: Run quick benchmarks
+        shell: bash
+        run: |
+          asv machine --machine "GitHubRunner"
+          asv run --machine "GitHubRunner" --quick --show-stderr
+
   # Runs only on macos-14 with Python 3.12
   check_coverage:
     needs: style

.gitignore

@@ -315,5 +315,8 @@ $RECYCLE.BIN/
 *.asv/
 results/
 
+# Pycharm
+*.idea/
+
 # JOSS
 jats/

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.5.0"
+    rev: "v0.5.7"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
@@ -32,3 +32,9 @@ repos:
         - id: rst-backticks
         - id: rst-directive-colons
         - id: rst-inline-touching-normal
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
+    hooks:
+      - id: nbstripout
+        args: ['--keep-output', '--drop-empty-cells']

CHANGELOG.md

@@ -2,6 +2,33 @@
 
 ## Features
 
+- [#460](https://github.com/pybop-team/PyBOP/pull/460) - Notebook example files added for ECM and folder structure updated.
+- [#450](https://github.com/pybop-team/PyBOP/pull/450) - Adds support for IDAKLU with output variables, and corresponding examples, tests.
+- [#364](https://github.com/pybop-team/PyBOP/pull/364) - Adds the MultiFittingProblem class and the multi_fitting example script.
+- [#444](https://github.com/pybop-team/PyBOP/issues/444) - Merge `BaseModel` `build()` and `rebuild()` functionality.
+- [#435](https://github.com/pybop-team/PyBOP/pull/435) - Adds SLF001 linting for private members.
+- [#418](https://github.com/pybop-team/PyBOP/issues/418) - Wraps the `get_parameter_info` method from PyBaMM to get a dictionary of parameter names and types.
+- [#413](https://github.com/pybop-team/PyBOP/pull/413) - Adds `DesignCost` functionality to `WeightedCost` class with additional tests.
+- [#357](https://github.com/pybop-team/PyBOP/pull/357) - Adds `Transformation()` class with `LogTransformation()`, `IdentityTransformation()`, and `ScaledTransformation()`, `ComposedTransformation()` implementations with corresponding examples and tests.
+- [#427](https://github.com/pybop-team/PyBOP/issues/427) - Adds the nbstripout pre-commit hook to remove unnecessary metadata from notebooks.
+- [#327](https://github.com/pybop-team/PyBOP/issues/327) - Adds the `WeightedCost` subclass, defines when to evaluate a problem and adds the `spm_weighted_cost` example script.
+- [#393](https://github.com/pybop-team/PyBOP/pull/383) - Adds Minkowski and SumofPower cost classes, with an example and corresponding tests.
+- [#403](https://github.com/pybop-team/PyBOP/pull/403/) - Adds lychee link checking action.
+
+## Bug Fixes
+
+- [#454](https://github.com/pybop-team/PyBOP/issue/454) - Fixes benchmarking suite.
+- [#421](https://github.com/pybop-team/PyBOP/issues/421) - Adds a default value for the initial SOC for design problems.
+
+## Breaking Changes
+
+- [#424](https://github.com/pybop-team/PyBOP/issues/424) - Replaces the `init_soc` input to `FittingProblem` with the option to pass an initial OCV value, updates `BaseModel` and fixes `multi_model_identification.ipynb` and `spm_electrode_design.ipynb`.
+
+# [v24.6.1](https://github.com/pybop-team/PyBOP/tree/v24.6.1) - 2024-07-31
+
+## Features
+
+- [#313](https://github.com/pybop-team/PyBOP/pull/313/) - Fixes for PyBaMM v24.5, drops support for PyBaMM v23.9, v24.1
 
 ## Bug Fixes
 

CITATION.cff

@@ -11,5 +11,5 @@ authors:
     family-names: Courtier
   - given-names: David
     family-names: Howey
-version: "24.6" # Update this when you release a new version
+version: "24.6.1" # Update this when you release a new version
 repository-code: 'https://www.github.com/pybop-team/pybop'

CONTRIBUTING.md

@@ -21,7 +21,7 @@ pip install -e .[all,dev]
 
 Before you commit any code, please perform the following checks using [Nox](https://nox.thea.codes/en/stable/index.html):
 
-- [All tests pass](#testing): `$ nox -s unit`
+- [All tests pass](#testing): `$ nox -s quick`
 
 ### Installing and using pre-commit
 
@@ -62,9 +62,9 @@ You now have everything you need to start making changes!
 
 ### B. Writing your code
 
-6. PyBOP is developed in [Python](https://en.wikipedia.org/wiki/Python_(programming_language)), and makes heavy use of [NumPy](https://en.wikipedia.org/wiki/NumPy) (see also [NumPy for MatLab users](https://numpy.org/doc/stable/user/numpy-for-matlab-users.html) and [Python for R users](http://blog.hackerearth.com/how-can-r-users-learn-python-for-data-science)).
+6. PyBOP is developed in [Python](https://en.wikipedia.org/wiki/Python_(programming_language)), and makes heavy use of [NumPy](https://en.wikipedia.org/wiki/NumPy) (see also [NumPy for MatLab users](https://numpy.org/doc/stable/user/numpy-for-matlab-users.html) and [Python for R users](https://rebeccabarter.com/blog/2023-09-11-from_r_to_python)).
 7. Make sure to follow our [coding style guidelines](#coding-style-guidelines).
-8. Commit your changes to your branch with [useful, descriptive commit messages](https://chris.beams.io/posts/git-commit/): Remember these are publicly visible and should still make sense a few months ahead in time. While developing, you can keep using the GitHub issue you're working on as a place for discussion. [Refer to your commits](https://stackoverflow.com/questions/8910271/how-can-i-reference-a-commit-in-an-issue-comment-on-github) when discussing specific lines of code.
+8. Commit your changes to your branch with [useful, descriptive commit messages](https://chris.beams.io/posts/git-commit/): Remember these are publicly visible and should still make sense a few months ahead in time. While developing, you can keep using the GitHub issue you're working on as a place for discussion. Refer to your commits when discussing specific lines of code. This is achieved by referencing the SHA-hash in the comment. An example of this looks like: `the commit 3e5c1e6 solved the issue...`
 9. If you want to add a dependency on another library, or re-use code you found somewhere else, have a look at [these guidelines](#dependencies-and-reusing-code).
 
 ### C. Merging your changes with PyBOP
@@ -83,16 +83,20 @@ PyBOP follows the [PEP8 recommendations](https://www.python.org/dev/peps/pep-000
 
 ### Ruff
 
-We use [ruff](https://github.com/charliermarsh/ruff) to check our PEP8 adherence. To try this on your system, navigate to the PyBOP directory in a console and type
+We use [ruff](https://github.com/charliermarsh/ruff) to lint and ensure adherence to Python PEP standards. To manually trigger `ruff`, navigate to the PyBOP directory in a console and type
 
 ```bash
 python -m pip install pre-commit
 pre-commit run ruff
 ```
 
-ruff is configured inside the file `pre-commit-config.yaml`, allowing us to ignore some errors. If you think this should be added or removed, please submit an [issue](https://guides.github.com/features/issues/).
+ruff is configured inside the file `pyproject.toml`, allowing us to ignore some errors. If you think a rule should be added or removed, please submit an [issue](https://guides.github.com/features/issues/).
 
-When you commit your changes they will be checked against ruff automatically (see [Pre-commit checks](#pre-commit-checks)).
+When you commit your changes they will be checked against ruff automatically (see [Pre-commit checks](#pre-commit-checks)). If you are having issues getting your commit to pass the linting, it
+is possible to skip linting for single lines (this should only be done as a **last resort**) by adding a line comment of `#noqa: $ruff_rule` where the `$ruff_rule` is replaced with the rule in question.
+It is also possible to skip linting altogether by committing your changes by using the
+`--no-verify` command-line flag.
+These rules can be found in the ruff configuration in `pyproject.toml` or in the failed pre-commit output. Please note the lint skipping in the pull request for reviewers.
 
 ### Naming
 
@@ -105,7 +109,7 @@ Class names are CamelCase, and start with an upper case letter, for example `MyO
 While it's a bad idea for developers to "reinvent the wheel", it's important for users to get a _reasonably sized download and an easy install_. In addition, external libraries can sometimes cease to be supported, and when they contain bugs it might take a while before fixes become available as automatic downloads to PyBOP users.
 For these reasons, all dependencies in PyBOP should be thought about carefully and discussed on GitHub.
 
-Direct inclusion of code from other packages is possible, as long as their license permits it and is compatible with ours, but again should be considered carefully and discussed in the group. Snippets from blogs and [stackoverflow](https://stackoverflow.com/) can often be included but must include attribution to the original by commenting with a link in the source code.
+Direct inclusion of code from other packages is possible, as long as their license permits it and is compatible with ours, but again should be considered carefully and discussed in the group. Snippets from blogs and stackoverflow can often be included but must include attribution to the original by commenting with a link in the source code.
 
 ### Separating dependencies
 

README.md

@@ -9,7 +9,7 @@
   [![Contributors](https://img.shields.io/github/contributors/pybop-team/PyBOP)](https://github.com/pybop-team/PyBOP/graphs/contributors)
   [![Last Commit](https://img.shields.io/github/last-commit/pybop-team/PyBOP/develop?color=purple)](https://github.com/pybop-team/PyBOP/commits/develop)
   [![Python Versions from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Fpybop-team%2FPyBOP%2Fdevelop%2Fpyproject.toml&label=Python)](https://pypi.org/project/pybop/)
-  [![Forks](https://img.shields.io/github/forks/pybop-team/PyBOP?style=flat)](https://github.com/pybop-team/PyBOPe/network/members)
+  [![Forks](https://img.shields.io/github/forks/pybop-team/PyBOP?style=flat)](https://github.com/pybop-team/PyBOP/network/members)
   [![Stars](https://img.shields.io/github/stars/pybop-team/PyBOP?style=flat&color=gold)](https://github.com/pybop-team/PyBOP/stargazers)
   [![Codecov](https://codecov.io/gh/pybop-team/PyBOP/branch/develop/graph/badge.svg)](https://codecov.io/gh/pybop-team/PyBOP)
   [![Open Issues](https://img.shields.io/github/issues/pybop-team/PyBOP)](https://github.com/pybop-team/PyBOP/issues/)
@@ -74,7 +74,7 @@ Additional script-based examples can be found in the [examples directory](https:
 - [Unscented Kalman filter parameter identification of a SPM](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/spm_UKF.py)
 - [Import and export parameters using Faraday's BPX format](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/BPX_spm.py)
 - [Maximum a posteriori parameter identification of a SPM](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/BPX_spm.py)
-- [Gradient based parameter identification of a SPM](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/spm_adam.py)
+- [Gradient based parameter identification of a SPM](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/spm_AdamW.py)
 
 ### Supported Methods
 The table below lists the currently supported [models](https://github.com/pybop-team/PyBOP/tree/develop/pybop/models), [optimisers](https://github.com/pybop-team/PyBOP/tree/develop/pybop/optimisers), and [cost functions](https://github.com/pybop-team/PyBOP/tree/develop/pybop/costs) in PyBOP.

asv.conf.json

@@ -8,7 +8,7 @@
         "python -m build --wheel -o {build_cache_dir} {build_dir}"
     ],
     "default_benchmark_timeout": 180,
-    "branches": ["develop"],
+    "branches": ["HEAD"],
     "environment_type": "virtualenv",
     "matrix": {
         "req":{

benchmarks/benchmark_model.py

@@ -1,8 +1,7 @@
 import numpy as np
 
 import pybop
-
-from .benchmark_utils import set_random_seed
+from benchmarks.benchmark_utils import set_random_seed
 
 
 class BenchmarkModel:
@@ -27,19 +26,20 @@ def setup(self, model, parameter_set):
         self.model = model(parameter_set=pybop.ParameterSet.pybamm(parameter_set))
 
         # Define fitting parameters
-        parameters = [
+        parameters = pybop.Parameters(
             pybop.Parameter(
                 "Current function [A]",
                 prior=pybop.Gaussian(0.4, 0.02),
                 bounds=[0.2, 0.7],
                 initial_value=0.4,
             )
-        ]
+        )
 
         # Generate synthetic data
         sigma = 0.001
         self.t_eval = np.arange(0, 900, 2)
-        values = self.model.predict(t_eval=self.t_eval)
+        self.init_state = {"Initial SoC": 0.5}
+        values = self.model.predict(t_eval=self.t_eval, initial_state=self.init_state)
         corrupt_values = values["Voltage [V]"].data + np.random.normal(
             0, sigma, len(self.t_eval)
         )
@@ -59,7 +59,7 @@ def setup(self, model, parameter_set):
 
         # Create fitting problem
         self.problem = pybop.FittingProblem(
-            model=self.model, dataset=dataset, parameters=parameters, init_soc=0.5
+            model=self.model, dataset=dataset, parameters=parameters
         )
 
     def time_model_predict(self, model, parameter_set):
@@ -70,7 +70,9 @@ def time_model_predict(self, model, parameter_set):
             model (pybop.Model): The model class being benchmarked.
             parameter_set (str): The name of the parameter set being used.
         """
-        self.model.predict(inputs=self.inputs, t_eval=self.t_eval)
+        self.model.predict(
+            inputs=self.inputs, t_eval=self.t_eval, initial_state=self.init_state
+        )
 
     def time_model_simulate(self, model, parameter_set):
         """
@@ -80,7 +82,7 @@ def time_model_simulate(self, model, parameter_set):
             model (pybop.Model): The model class being benchmarked.
             parameter_set (str): The name of the parameter set being used.
         """
-        self.problem._model.simulate(inputs=self.inputs, t_eval=self.t_eval)
+        self.problem.model.simulate(inputs=self.inputs, t_eval=self.t_eval)
 
     def time_model_simulateS1(self, model, parameter_set):
         """
@@ -90,4 +92,4 @@ def time_model_simulateS1(self, model, parameter_set):
             model (pybop.Model): The model class being benchmarked.
             parameter_set (str): The name of the parameter set being used.
         """
-        self.problem._model.simulateS1(inputs=self.inputs, t_eval=self.t_eval)
+        self.problem.model.simulateS1(inputs=self.inputs, t_eval=self.t_eval)

benchmarks/benchmark_optim_construction.py

@@ -1,8 +1,7 @@
 import numpy as np
 
 import pybop
-
-from .benchmark_utils import set_random_seed
+from benchmarks.benchmark_utils import set_random_seed
 
 
 class BenchmarkOptimisationConstruction:
@@ -29,7 +28,7 @@ def setup(self, model, parameter_set, optimiser):
         model_instance = model(parameter_set=pybop.ParameterSet.pybamm(parameter_set))
 
         # Define fitting parameters
-        parameters = [
+        parameters = pybop.Parameters(
             pybop.Parameter(
                 "Negative electrode active material volume fraction",
                 prior=pybop.Gaussian(0.6, 0.02),
@@ -42,7 +41,7 @@ def setup(self, model, parameter_set, optimiser):
                 bounds=[0.375, 0.625],
                 initial_value=0.51,
             ),
-        ]
+        )
 
         # Generate synthetic data
         sigma = 0.001
@@ -76,7 +75,7 @@ def time_optimisation_construction(self, model, parameter_set, optimiser):
         Args:
             model (pybop.Model): The model class being benchmarked.
             parameter_set (str): The name of the parameter set being used.
-            optimiser (pybop.Optimiser): The optimizer class being used.
+            optimiser (pybop.Optimiser): The optimiser class being used.
         """
         self.optim = pybop.Optimisation(self.cost, optimiser=optimiser)
 
@@ -87,6 +86,6 @@ def time_cost_evaluate(self, model, parameter_set, optimiser):
         Args:
             model (pybop.Model): The model class being benchmarked.
             parameter_set (str): The name of the parameter set being used.
-            optimiser (pybop.Optimiser): The optimizer class being used.
+            optimiser (pybop.Optimiser): The optimiser class being used.
         """
         self.cost([0.63, 0.51])