Merge branch 'develop' into pybop-team#282-restructure-example-directory

.all-contributorsrc

@@ -62,7 +62,8 @@
       "profile": "https://www.brosaplanella.xyz",
       "contributions": [
         "review",
-        "code"
+        "code",
+        "example"
       ]
     },
     {
@@ -97,7 +98,7 @@
     {
       "login": "IntelLiGent",
       "name": "Horizon Europe IntelLiGent Consortium",
-      "avatar_url": "assets/logo-farger.pdf",
+      "avatar_url": "assets/logo-farger.svg",
       "profile": "https://heuintelligent.eu/",
       "contributions": [
         "financial"
@@ -111,6 +112,33 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "MarkBlyth",
+      "name": "MarkBlyth",
+      "avatar_url": "https://avatars.githubusercontent.com/u/20501619?v=4",
+      "profile": "https://github.com/MarkBlyth",
+      "contributions": [
+        "code"
+      ]
+    },
+    {
+      "login": "f-g-r-i-m-m",
+      "name": "f-g-r-i-m-m",
+      "avatar_url": "https://avatars.githubusercontent.com/u/137511310?v=4",
+      "profile": "https://github.com/f-g-r-i-m-m",
+      "contributions": [
+        "example"
+      ]
+    },
+    {
+      "login": "Dibyendu-IITKGP",
+      "name": "Dibyendu-IITKGP",
+      "avatar_url": "https://avatars.githubusercontent.com/u/32595915?v=4",
+      "profile": "https://github.com/Dibyendu-IITKGP",
+      "contributions": [
+        "example"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/release_workflow.md

@@ -11,6 +11,7 @@ To create a new release, follow these steps:
    -  Increment the following;
          -  The version number in the `pyproject.toml` and `CITATION.cff` files following CalVer versioning.
          -  The`CHANGELOG.md` version with the changes for the new version.
+         -  Add a new entry for the documentation site version switcher located at `docs/_static/switcher.json`
    -  Open a PR to the `main` branch. Once the PR is merged, proceed to the next step.
 
 2. **Tag the Release:**

.github/workflows/lychee_links.yaml

@@ -0,0 +1,61 @@
+# 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 200,403,429,999
+            --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 "http://www.w3.org/*|https://www.w3.org/*"
+            --exclude "https://doi.org/*"
+            --exclude "https://raw.githubusercontent.com/paramm-team/pybamm-param/develop/pbparam/input/data/"
+            --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/release_action.yaml

@@ -72,7 +72,7 @@ jobs:
           ./dist/*.tar.gz
           ./dist/*.whl
     - name: Publish artifacts and signatures to GitHub Releases
-      uses: softprops/action-gh-release@9d7c94cfd0a1f3ed45544c887983e9fa900f0564  # v2.0.4
+      uses: softprops/action-gh-release@v2
       with:
         # `dist/` contains the built packages, and the
         # sigstore-produced signatures and certificates.

.github/workflows/scheduled_tests.yaml

@@ -6,13 +6,14 @@ on:
     branches:
       - main
 
-  # runs every day at 09:00 UTC
+  # runs every day at 03:00 UTC
   schedule:
-    - cron: '0 9 * * *'
+    - cron: '0 3 * * *'
 
 # Check noxfile.py for associated environment variables
 env:
   PYBOP_SCHEDULED: 1
+  FORCE_COLOR: 3
 
 jobs:
   # Dynamically create a matrix of OS, Python, and PyBaMM versions

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

@@ -4,6 +4,10 @@ on:
   workflow_dispatch:
   pull_request:
 
+# Add colors to nox/pytest
+env:
+  FORCE_COLOR: 3
+
 concurrency:
   # github.workflow: name of the workflow, so that we don't cancel other workflows
   # github.event.pull_request.number || github.ref: pull request number or branch name if not a pull request
@@ -105,6 +109,37 @@ 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

@@ -314,3 +314,6 @@ $RECYCLE.BIN/
 # Airspeed Velocity
 *.asv/
 results/
+
+# Pycharm
+*.idea/

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.4.10"
+    rev: "v0.7.4"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
@@ -13,7 +13,7 @@ repos:
         types_or: [python, pyi, jupyter]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
         - id: check-added-large-files
           args: ['--maxkb=2000']
@@ -32,3 +32,9 @@ repos:
         - id: rst-backticks
         - id: rst-directive-colons
         - id: rst-inline-touching-normal
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.8.1
+    hooks:
+      - id: nbstripout
+        args: ['--keep-output', '--drop-empty-cells']

CHANGELOG.md

@@ -2,12 +2,102 @@
 
 ## Features
 
+- [#282](https://github.com/pybop-team/PyBOP/issues/282) - Restructures the examples directory.
+- [#396](https://github.com/pybop-team/PyBOP/issues/396) - Adds `ecm_with_tau.py` example script.
+- [#452](https://github.com/pybop-team/PyBOP/issues/452) - Extends `cell_mass` and `approximate_capacity` for half-cell models.
+- [#544](https://github.com/pybop-team/PyBOP/issues/544) - Allows iterative plotting using `StandardPlot`.
+- [#541](https://github.com/pybop-team/PyBOP/pull/541) - Adds `ScaledLogLikelihood` and `BaseMetaLikelihood` classes.
+- [#409](https://github.com/pybop-team/PyBOP/pull/409) - Adds plotting and convergence methods for Monte Carlo sampling. Includes open-access Tesla 4680 dataset for Bayesian inference example. Fixes transformations for sampling.
+- [#531](https://github.com/pybop-team/PyBOP/pull/531) - Adds Voronoi optimiser surface plot (`pybop.plot.surface`) for fast optimiser aligned cost visualisation.
+- [#532](https://github.com/pybop-team/PyBOP/issues/532) - Adds `linked_parameters` example script which shows how to update linked parameters during design optimisation.
+- [#529](https://github.com/pybop-team/PyBOP/issues/529) - Adds `GravimetricPowerDensity` and `VolumetricPowerDensity` costs, along with the mathjax extension for Sphinx.
+
+## Optimisations
+
+- [#512](https://github.com/pybop-team/PyBOP/pull/513) - Refactors `LogPosterior` with attributes pointing to composed likelihood object.
+- [#551](https://github.com/pybop-team/PyBOP/pull/551) - Refactors Optimiser arguments, `population_size` and `max_iterations` as default args, improves optimiser docstrings
+
+## Bug Fixes
+
+- [#505](https://github.com/pybop-team/PyBOP/pull/505) - Bug fixes for `LogPosterior` with transformed `GaussianLogLikelihood` likelihood.
+
+## Breaking Changes
+
+- [#531](https://github.com/pybop-team/PyBOP/pull/531) - Plot methods moved to `pybop.plot` with mostly minimal renaming. For example, `pybop.plot_parameters` is now `pybop.plot.parameters`. Other breaking changes include: `pybop.plot2d` to `pybop.plot.contour`.
+- [#526](https://github.com/pybop-team/PyBOP/pull/526) - Refactor `OptimisationResults` classes, with `optim.run()` now return the full object. Adds finite cost value check for optimised parameters.
+
+# [v24.9.1](https://github.com/pybop-team/PyBOP/tree/v24.9.0) - 2024-09-16
+
+## Features
+
+## Bug Fixes
+
+- [#495](https://github.com/pybop-team/PyBOP/pull/495) - Bugfixes for Transformation class, adds `apply_transform` optional arg to `BaseCost` for transformation functionality.
+
+## Breaking Changes
+
+# [v24.9.0](https://github.com/pybop-team/PyBOP/tree/v24.9.0) - 2024-09-10
+
+## Features
+
+- [#462](https://github.com/pybop-team/PyBOP/pull/462) - Enables multidimensional learning rate for `pybop.AdamW` with updated (more robust) integration testing. Fixes bug in `Minkowski` and `SumofPower` cost functions for gradient-based optimisers.
+- [#411](https://github.com/pybop-team/PyBOP/pull/411) - Updates notebooks with README in `examples/` directory, removes kaleido dependency and moves to nbviewer rendering, displays notebook figures with `notebook_connected` plotly renderer
+- [#6](https://github.com/pybop-team/PyBOP/issues/6) - Adds Monte Carlo functionality, with methods based on Pints' algorithms. A base class is added `BaseSampler`, in addition to `PintsBaseSampler`.
+- [#353](https://github.com/pybop-team/PyBOP/issues/353) - Allow user-defined check_params functions to enforce nonlinear constraints, and enable SciPy constrained optimisation methods
+- [#222](https://github.com/pybop-team/PyBOP/issues/222) - Adds an example for performing and electrode balancing.
+- [#441](https://github.com/pybop-team/PyBOP/issues/441) - Adds an example for estimating constants within a `pybamm.FunctionalParameter`.
+- [#405](https://github.com/pybop-team/PyBOP/pull/405) - Adds frequency-domain based EIS prediction methods via `model.simulateEIS` and updates to `problem.evaluate` with examples and tests.
+- [#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
+
+- [#473](https://github.com/pybop-team/PyBOP/pull/473) - Bugfixes for transformation class, adds optional `apply_transform` arg to `BaseCost.__call__()`, adds `log_update()` method to `BaseOptimiser`
+- [#464](https://github.com/pybop-team/PyBOP/issues/464) - Fix order of design `parameter_set` updates and refactor `update_capacity`.
+- [#468](https://github.com/pybop-team/PyBOP/issue/468) - Renames `quick_plot.py` to `standard_plots.py`.
+- [#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
+
+- [#499](https://github.com/pybop-team/PyBOP/pull/499) - BPX is added as an optional dependency.
+- [#483](https://github.com/pybop-team/PyBOP/pull/483) - Replaces `pybop.MAP` with `pybop.LogPosterior` with an updated call args and bugfixes.
+- [#436](https://github.com/pybop-team/PyBOP/pull/436) - **API Change:** The functionality from `BaseCost.evaluate/S1` & `BaseCost._evaluate/S1` is represented in `BaseCost.__call__` & `BaseCost.compute`. `BaseCost.compute` directly acts on the predictions, while `BaseCost.__call__` calls `BaseProblem.evaluate/S1` before `BaseCost.compute`. `compute` has optional args for gradient cost calculations.
+- [#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
+
+## Breaking Changes
+
+# [v24.6](https://github.com/pybop-team/PyBOP/tree/v24.6) - 2024-07-08
+
+## Features
+
+- [#319](https://github.com/pybop-team/PyBOP/pull/319/) - Adds `CuckooSearch` optimiser with corresponding tests.
+- [#359](https://github.com/pybop-team/PyBOP/pull/359/) - Aligning Inputs between problem, observer and model.
 - [#379](https://github.com/pybop-team/PyBOP/pull/379) - Adds model.simulateS1 to weekly benchmarks.
 - [#174](https://github.com/pybop-team/PyBOP/issues/174) - Adds new logo and updates Readme for accessibility.
 - [#316](https://github.com/pybop-team/PyBOP/pull/316) - Adds Adam with weight decay (AdamW) optimiser, adds depreciation warning for pints.Adam implementation.
 - [#271](https://github.com/pybop-team/PyBOP/issues/271) - Aligns the output of the optimisers via a generalisation of Result class.
 - [#315](https://github.com/pybop-team/PyBOP/pull/315) - Updates __init__ structure to remove circular import issues and minimises dependancy imports across codebase for faster PyBOP module import. Adds type-hints to BaseModel and refactors rebuild parameter variables.
 - [#236](https://github.com/pybop-team/PyBOP/issues/236) - Restructures the optimiser classes, adds a new optimisation API through direct construction and keyword arguments, and fixes the setting of `max_iterations`, and `_minimising`. Introduces `pybop.BaseOptimiser`, `pybop.BasePintsOptimiser`, and `pybop.BaseSciPyOptimiser` classes.
+- [#322](https://github.com/pybop-team/PyBOP/pull/322) - Add `Parameters` class to store and access multiple parameters in one object.
 - [#321](https://github.com/pybop-team/PyBOP/pull/321) - Updates Prior classes with BaseClass, adds a `problem.sample_initial_conditions` method to improve stability of SciPy.Minimize optimiser.
 - [#249](https://github.com/pybop-team/PyBOP/pull/249) - Add WeppnerHuggins model and GITT example.
 - [#304](https://github.com/pybop-team/PyBOP/pull/304) - Decreases the testing suite completion time.
@@ -25,6 +115,11 @@
 
 ## Bug Fixes
 
+- [#393](https://github.com/pybop-team/PyBOP/pull/393) - General integration test fixes. Adds UserWarning when using Plot2d with prior generated bounds.
+- [#338](https://github.com/pybop-team/PyBOP/pull/338) - Fixes GaussianLogLikelihood class, adds integration tests, updates non-bounded parameter implementation by applying bounds from priors and `boundary_multiplier` argument. Bugfixes to CMAES construction.
+- [#339](https://github.com/pybop-team/PyBOP/issues/339) - Updates the calculation of the cyclable lithium capacity in the spme_max_energy example.
+- [#387](https://github.com/pybop-team/PyBOP/issues/387) - Adds keys to ParameterSet and updates ECM OCV check.
+- [#380](https://github.com/pybop-team/PyBOP/pull/380) - Restore self._boundaries construction for `pybop.PSO`
 - [#372](https://github.com/pybop-team/PyBOP/pull/372) - Converts `np.array` to `np.asarray` for Numpy v2.0 support.
 - [#165](https://github.com/pybop-team/PyBOP/issues/165) - Stores the attempted and best parameter values and the best cost for each iteration in the log attribute of the optimiser and updates the associated plots.
 - [#354](https://github.com/pybop-team/PyBOP/issues/354) - Fixes the calculation of the gradient in the `RootMeanSquaredError` cost.
@@ -39,6 +134,13 @@
 - [#270](https://github.com/pybop-team/PyBOP/pull/270) - Updates PR template.
 - [#91](https://github.com/pybop-team/PyBOP/issues/91) - Adds a check on the number of parameters for CMAES and makes XNES the default optimiser.
 
+## Breaking Changes
+
+- [#322](https://github.com/pybop-team/PyBOP/pull/322) - Add `Parameters` class to store and access multiple parameters in one object (API change).
+- [#285](https://github.com/pybop-team/PyBOP/pull/285) - Drop support for Python 3.8.
+- [#251](https://github.com/pybop-team/PyBOP/pull/251) - Drop support for PyBaMM v23.5
+- [#236](https://github.com/pybop-team/PyBOP/issues/236) - Restructures the optimiser classes (API change).
+
 # [v24.3.1](https://github.com/pybop-team/PyBOP/tree/v24.3.1) - 2024-06-17
 
 ## Features

CITATION.cff

@@ -11,5 +11,5 @@ authors:
     family-names: Courtier
   - given-names: David
     family-names: Howey
-version: "24.3.1" # Update this when you release a new version
+version: "24.9.1" # Update this when you release a new version
 repository-code: 'https://www.github.com/pybop-team/pybop'