Merge branch '177-plotting-capabilities' into 177b-plotting-capabilities

.github/workflows/periodic_benchmarks.yaml

@@ -0,0 +1,100 @@
+# Initial Source: pybop-team/PyBop
+
+# This workflow periodically runs the benchmarks suite in benchmarks/
+# using asv and publish the results, effectively updating
+# the display website hosted in the pybop-bench repo
+
+# Steps:
+# - Benchmark all commits since the last one that was benchmarked
+# - Push results to pybop-bench repo
+# - Publish website
+name: Benchmarks
+on:
+  # Everyday at 12 pm UTC
+  schedule:
+    - cron: "0 12 * * *"
+  # Make it possible to trigger the
+  # workflow manually
+  workflow_dispatch:
+
+jobs:
+  benchmarks:
+    runs-on: [self-hosted, macOS, ARM64]
+    if: github.repository == 'pybop-team/PyBOP'
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install python & create virtualenv
+        shell: bash
+        run: |
+            eval "$(pyenv init -)"
+            pyenv install 3.12 -s
+            pyenv virtualenv 3.12 pybop-312-bench
+
+      - name: Install dependencies & run benchmarks
+        shell: bash
+        run: |
+            eval "$(pyenv init -)"
+            pyenv activate pybop-312-bench
+            python -m pip install -e .[all,dev]
+            python -m pip install asv[virtualenv]
+            python -m asv machine --machine "SelfHostedRunner"
+            python -m asv run --machine "SelfHostedRunner" NEW --show-stderr -v
+
+      - name: Upload results as artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: asv_periodic_results
+          path: results
+
+      - name: Uninstall pyenv-virtualenv & python
+        if: always()
+        shell: bash
+        run: |
+            eval "$(pyenv init -)"
+            pyenv activate pybop-312-bench
+            pyenv uninstall -f $( python --version )
+
+  publish-results:
+    name: Push and publish results
+    needs: benchmarks
+    runs-on: ubuntu-latest
+    if: github.repository == 'pybop-team/PyBOP'
+    steps:
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Install asv
+        run: pip install asv
+
+      - name: Checkout pybop-bench repo
+        uses: actions/checkout@v4
+        with:
+          repository: pybop-team/pybop-bench
+          token: ${{ secrets.PUSH_BENCH_TOKEN }}
+
+      - name: Download results artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: asv_periodic_results
+          path: new_results
+
+      - name: Copy new results and push to pybop-bench repo
+        env:
+          PUSH_BENCH_EMAIL: ${{ secrets.PUSH_BENCH_EMAIL }}
+          PUSH_BENCH_NAME: ${{ secrets.PUSH_BENCH_NAME }}
+        run: |
+          cp -vr new_results/* results
+          git config --global user.email "$PUSH_BENCH_EMAIL"
+          git config --global user.name "$PUSH_BENCH_NAME"
+          git add results
+          git commit -am "Add new benchmark results"
+          git push
+
+      - name: Publish results
+        run: |
+          asv publish
+          git fetch origin gh-pages:gh-pages
+          asv gh-pages

.gitignore

@@ -310,3 +310,7 @@ $RECYCLE.BIN/
 
 # Output JSON files
 **/fit_ecm_parameters.json
+
+# Airspeed Velocity
+*.asv/
+results/

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.2.2"
+    rev: "v0.3.2"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

CHANGELOG.md

@@ -4,6 +4,7 @@
 
 - [#198](https://github.com/pybop-team/PyBOP/pull/198) - Adds default subplot trace options, removes `[]` in axis plots as per SI standard, add varying signal length to quick_plot, restores design optimisation execption.
 - [#224](https://github.com/pybop-team/PyBOP/pull/224) - Updated prediction objects to dictionaries, cost class calculations, added `additional_variables` argument to problem class, updated scipy.minimize defualt method to Nelder-Mead, added gradient cost landscape plots with optional argument.
+- [#179](https://github.com/pybop-team/PyBOP/pull/203) - Adds `asv` configuration for benchmarking and initial benchmark suite.
 - [#218](https://github.com/pybop-team/PyBOP/pull/218) - Adds likelihood base class, `GaussianLogLikelihoodKnownSigma`, `GaussianLogLikelihood`, and `ProbabilityBased` cost function. As well as addition of a maximum likelihood estimation (MLE) example.
 - [#185](https://github.com/pybop-team/PyBOP/pull/185) - Adds a pull request template, additional nox sessions `quick` for standard tests + docs, `pre-commit` for pre-commit, `test` to run all standard tests, `doctest` for docs.
 - [#215](https://github.com/pybop-team/PyBOP/pull/215) - Adds `release_workflow.md` and updates `release_action.yaml`
@@ -20,6 +21,7 @@
 
 ## Bug Fixes
 
+- [#233](https://github.com/pybop-team/PyBOP/pull/233) - Enforces model rebuild on initialisation of a Problem to allow a change of experiment, fixes if statement triggering current function update, updates `predictions` to `simulation` to keep distinction between `predict` and `simulate` and adds `test_changes`.
 - [#123](https://github.com/pybop-team/PyBOP/issues/123) - Reinstates check for availability of parameter sets via PyBaMM upon retrieval by `pybop.ParameterSet.pybamm()`.
 - [#196](https://github.com/pybop-team/PyBOP/issues/196) - Fixes failing observer cost tests.
 - [#63](https://github.com/pybop-team/PyBOP/issues/63) - Removes NLOpt Optimiser from future releases. This is to support deployment to the Apple M-Series platform.

README.md

@@ -31,6 +31,9 @@
   <a href="https://colab.research.google.com/github/pybop-team/PyBOP/blob/develop/">
     <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="open In colab" />
   </a>
+  <a href = "https://pybop-team.github.io/pybop-bench/">
+    <img alt="Static Badge" src="https://img.shields.io/badge/https%3A%2F%2Fpybop-team.github.io%2Fpybop-bench%2F?label=Benchmarks">
+  </a>
   <a href = "https://github.com/pybop-team/PyBOP/releases">
     <img src = "https://img.shields.io/github/v/release/pybop-team/PyBOP?color=gold"  alt = releases />
   </a>

asv.conf.json

@@ -0,0 +1,23 @@
+{
+    "version": 1,
+    "project": "PyBOP",
+    "project_url": "https://github.com/pybop-team/pybop",
+    "repo": ".",
+    "build_command": [
+        "python -m pip install build",
+        "python -m build --wheel -o {build_cache_dir} {build_dir}"
+    ],
+    "default_benchmark_timeout": 180,
+    "branches": ["develop"],
+    "environment_type": "virtualenv",
+    "matrix": {
+        "req":{
+           "pybamm": [],
+           "numpy": [],
+           "scipy": [],
+           "pints": []
+       }
+    },
+    "build_cache_dir": ".asv/cache",
+    "build_dir": ".asv/build"
+}

benchmarks/README.md

@@ -0,0 +1,104 @@
+# Benchmarking Directory for PyBOP
+
+Welcome to the benchmarking directory for PyBOP. We use `asv` (airspeed velocity) for benchmarking, which is a tool for running Python benchmarks over time in a consistent environment. This document will guide you through the setup, execution, and viewing of benchmarks.
+
+## Quick Links
+
+- [Airspeed Velocity (asv) Documentation](https://asv.readthedocs.io/)
+
+## Prerequisites
+
+Before you can run benchmarks, you need to ensure that `asv` is installed and that you have a working Python environment. It is also recommended to run benchmarks in a clean, dedicated virtual environment to avoid any side-effects from your local environment.
+
+### Installing `asv`
+
+You can install `asv` using `pip`. It's recommended to do this within a virtual environment:
+
+```bash
+pip install asv
+```
+
+## Setting Up Benchmarks
+
+The `benchmarks` directory already contains a set of benchmarks for the package. To add or modify benchmarks, edit the `.py` files within this directory.
+
+Each benchmark file should contain one or more classes with methods that `asv` will automatically recognize as benchmarks. Here's an example structure for a benchmark file:
+
+```python
+class ExampleBenchmarks:
+    def setup(self):
+        # Code to run before each benchmark method is executed
+        pass
+
+    def time_example_benchmark(self):
+        # The actual benchmark code
+        pass
+
+    def teardown(self):
+        # Code to run after each benchmark method is executed
+        pass
+```
+
+## Running Benchmarks
+
+With `asv` installed and your benchmarks set up, you can now run benchmarks using the following standard `asv` commands:
+
+### Running All Benchmarks
+
+To run all benchmarks in your python env:
+
+```bash
+asv run
+```
+
+This will test the current state of your codebase by default. You can specify a range of commits to run benchmarks against by appending a commit range to the command, like so:
+
+```bash
+asv run <commit-hash-1>..<commit-hash-2>
+```
+
+For quick benchmarking, pass the `--quick` argument to `asv run`. This runs each benchmark once and returns the singular value.
+
+```bash
+asv run --quick
+```
+
+### Running Specific Benchmarks
+
+To run a specific benchmark, use:
+
+```bash
+asv run --bench <benchmark name>
+```
+
+### Running Benchmarks for a Specific Environment
+
+To run benchmarks against a specific Python version:
+
+```bash
+asv run --python=same  # To use the same Python version as the current environment
+asv run --python=3.8  # To specify the Python version
+```
+
+## Viewing Benchmark Results
+
+After running benchmarks, `asv` will generate results which can be viewed as a web page:
+
+```bash
+asv publish
+asv preview
+```
+
+Now you can open your web browser to the URL provided by `asv` to view the results.
+
+## Continuous Benchmarking
+
+You can also set up `asv` for continuous benchmarking where it will track the performance over time. This typically involves integration with a continuous integration (CI) system.
+
+For more detailed instructions on setting up continuous benchmarking, consult the [asv documentation](https://asv.readthedocs.io/en/stable/using.html#continuous-benchmarking).
+
+## Reporting Issues
+
+If you encounter any issues or have suggestions for improving the benchmarks, please open an issue or a pull request in the project repository.
+
+Thank you for contributing to the performance of the package!

benchmarks/benchmark_model.py

@@ -0,0 +1,81 @@
+import pybop
+import numpy as np
+from .benchmark_utils import set_random_seed
+
+
+class BenchmarkModel:
+    param_names = ["model", "parameter_set"]
+    params = [
+        [pybop.lithium_ion.SPM, pybop.lithium_ion.SPMe],
+        ["Chen2020"],
+    ]
+
+    def setup(self, model, parameter_set):
+        """
+        Setup the model and problem for predict and simulate benchmarks.
+
+        Args:
+            model (pybop.Model): The model class to be benchmarked.
+            parameter_set (str): The name of the parameter set to be used.
+        """
+        # Set random seed
+        set_random_seed()
+
+        # Create model instance
+        self.model = model(parameter_set=pybop.ParameterSet.pybamm(parameter_set))
+
+        # Define fitting parameters
+        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)
+        corrupt_values = values["Voltage [V]"].data + np.random.normal(
+            0, sigma, len(self.t_eval)
+        )
+
+        self.inputs = {
+            "Current function [A]": 0.4,
+        }
+
+        # Create dataset
+        dataset = pybop.Dataset(
+            {
+                "Time [s]": self.t_eval,
+                "Current function [A]": values["Current [A]"].data,
+                "Voltage [V]": corrupt_values,
+            }
+        )
+
+        # Create fitting problem
+        self.problem = pybop.FittingProblem(
+            model=self.model, dataset=dataset, parameters=parameters, init_soc=0.5
+        )
+
+    def time_model_predict(self, model, parameter_set):
+        """
+        Benchmark the predict method of the model.
+
+        Args:
+            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)
+
+    def time_model_simulate(self, model, parameter_set):
+        """
+        Benchmark the simulate method of the model.
+
+        Args:
+            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)