Merge branch 'develop' into 327-weighted-cost

.github/workflows/lychee_links.yaml

@@ -0,0 +1,58 @@
+# 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://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

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.5.0"
+    rev: "v0.5.1"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

CHANGELOG.md

@@ -3,6 +3,7 @@
 ## Features
 
 - [#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.
+- [#403](https://github.com/pybop-team/PyBOP/pull/403/) - Adds lychee link checking action.
 
 ## Bug Fixes
 

CONTRIBUTING.md

@@ -62,7 +62,7 @@ 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.
 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).

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.

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:

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:

benchmarks/benchmark_parameterisation.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 BenchmarkParameterisation:

benchmarks/benchmark_track_parameterisation.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 BenchmarkTrackParameterisation:

docs/_extension/gallery_directive.py

@@ -12,7 +12,7 @@
 """
 
 from pathlib import Path
-from typing import Any, Dict, List
+from typing import Any
 
 from docutils import nodes
 from docutils.parsers.rst import directives
@@ -68,7 +68,7 @@ class GalleryGridDirective(SphinxDirective):
         "class-card": directives.unchanged,
     }
 
-    def run(self) -> List[nodes.Node]:
+    def run(self) -> list[nodes.Node]:
         """Create the gallery grid."""
         if self.arguments:
             # If an argument is given, assume it's a path to a YAML file
@@ -129,7 +129,7 @@ def run(self) -> List[nodes.Node]:
         return [container.children[0]]
 
 
-def setup(app: Sphinx) -> Dict[str, Any]:
+def setup(app: Sphinx) -> dict[str, Any]:
     """Add custom configuration to sphinx app.
 
     Args:

docs/conf.py

@@ -7,11 +7,11 @@
 from pathlib import Path
 
 sys.path.append(str(Path(".").resolve()))
-from pybop._version import __version__  # noqa: E402
+from pybop._version import __version__
 
 # -- Project information -----------------------------------------------------
 project = "PyBOP"
-copyright = "2023, The PyBOP Team"
+copyright = "2023, The PyBOP Team"  # noqa A001
 author = "The PyBOP Team"
 release = f"v{__version__}"
 

examples/notebooks/LG_M50_ECM/1-single-pulse-circuit-model.ipynb

@@ -7,7 +7,7 @@
    "source": [
     "## LG M50 Single Pulse Parameter Identification\n",
     "\n",
-    "This example presents an experimental parameter identification method for a two-RC circuit model. The data for this notebook is located within the same directory and was obtained from [[1]](https://github.com/WDWidanage/Simscape-Battery-Library/tree/main/Examples/parameterEstimation_TECMD/Data).\n",
+    "This example presents an experimental parameter identification method for a two-RC circuit model. The data for this notebook is located within the same directory and was obtained from WDWidanage/Simscape-Battery-Library [[1]](https://github.com/WDWidanage/Simscape-Battery-Library/tree/a3842b91b3ccda006bc9be5d59c8bcbd167ceef7/Examples/parameterEstimation_TECMD/Data).\n",
     "\n",
     "\n",
     "### Setting up the Environment\n",
@@ -261,7 +261,7 @@
         {
          "type": "scatter",
          "x": [
-          0.0,
+          0,
           0.01800000004004687,
           0.12100000004284084,
           0.25100000004749745,
@@ -571,7 +571,7 @@
             },
             "colorscale": [
              [
-              0.0,
+              0,
               "#0d0887"
              ],
              [
@@ -607,7 +607,7 @@
               "#fdca26"
              ],
              [
-              1.0,
+              1,
               "#f0f921"
              ]
             ],
@@ -631,7 +631,7 @@
             },
             "colorscale": [
              [
-              0.0,
+              0,
               "#0d0887"
              ],
              [
@@ -667,7 +667,7 @@
               "#fdca26"
              ],
              [
-              1.0,
+              1,
               "#f0f921"
              ]
             ],
@@ -682,7 +682,7 @@
             },
             "colorscale": [
              [
-              0.0,
+              0,
               "#0d0887"
              ],
              [
@@ -718,7 +718,7 @@
               "#fdca26"
              ],
              [
-              1.0,
+              1,
               "#f0f921"
              ]
             ],
@@ -745,7 +745,7 @@
             },
             "colorscale": [
              [
-              0.0,
+              0,
               "#0d0887"
              ],
              [
@@ -781,7 +781,7 @@
               "#fdca26"
              ],
              [
-              1.0,
+              1,
               "#f0f921"
              ]
             ],
@@ -796,7 +796,7 @@
             },
             "colorscale": [
              [
-              0.0,
+              0,
               "#0d0887"
              ],
              [
@@ -832,7 +832,7 @@
               "#fdca26"
              ],
              [
-              1.0,
+              1,
               "#f0f921"
              ]
             ],
@@ -977,7 +977,7 @@
             },
             "colorscale": [
              [
-              0.0,
+              0,
               "#0d0887"
              ],
              [
@@ -1013,7 +1013,7 @@
               "#fdca26"
              ],
              [
-              1.0,
+              1,
               "#f0f921"
              ]
             ],
@@ -1104,7 +1104,7 @@
            ],
            "sequential": [
             [
-             0.0,
+             0,
              "#0d0887"
             ],
             [
@@ -1140,13 +1140,13 @@
              "#fdca26"
             ],
             [
-             1.0,
+             1,
              "#f0f921"
             ]
            ],
            "sequentialminus": [
             [
-             0.0,
+             0,
              "#0d0887"
             ],
             [
@@ -1182,7 +1182,7 @@
              "#fdca26"
             ],
             [
-             1.0,
+             1,
              "#f0f921"
             ]
            ]
@@ -1888,7 +1888,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.2"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,