Merge branch 'develop' into 6-hamiltonian-monte-carlo-hmc

pybop-team · Feb 20, 2024 · 22ad7f0 · 22ad7f0
2 parents 0ba83dd + 209c5dc
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -50,7 +50,9 @@
       "contributions": [
         "ideas",
         "mentoring",
-        "review"
+        "review",
+        "code",
+        "test"
       ]
     },
     {
@@ -79,6 +81,16 @@
       "contributions": [
         "financial"
       ]
+    },
+    {
+      "login": "agriyakhetarpal",
+      "name": "Agriya Khetarpal",
+      "avatar_url": "https://avatars.githubusercontent.com/u/74401230?v=4",
+      "profile": "https://github.com/agriyakhetarpal",
+      "contributions": [
+        "code",
+        "infra"
+      ]
     }
   ],
   "contributorsPerLine": 7,

diff --git a/.github/workflows/release-action.yaml → .github/workflows/release_action.yaml b/.github/workflows/release-action.yaml → .github/workflows/release_action.yaml
diff --git a/.github/workflows/scheduled_tests.yaml b/.github/workflows/scheduled_tests.yaml
@@ -10,54 +10,113 @@ on:
   schedule:
     - cron: '0 9 * * *'
 
+# Check noxfile.py for associated environment variables
+env:
+  PYBOP_SCHEDULED: 1
+
 jobs:
+  # Dynamically create a matrix of OS, Python, and PyBaMM versions
+  create_pybamm_matrix:
+    name: Dynamically create GitHub Actions matrix
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out PyBOP repository
+        uses: actions/checkout@v4
+        with:
+          sparse-checkout-cone-mode: false
+          sparse-checkout: |
+            scripts/ci/build_matrix.sh
+
+      - name: Run script to create matrix
+        id: set-matrix
+        run: |
+          echo "matrix=$(bash scripts/ci/build_matrix.sh)" >> "$GITHUB_OUTPUT"
+    outputs:
+      pybop_matrix: ${{ steps.set-matrix.outputs.matrix }}
+
+  # filter the matrix to only include the macOS-latest entries
+  filter_pybamm_matrix:
+    name: Filter the matrix for macOS-latest entries
+    needs: [create_pybamm_matrix]
+    runs-on: ubuntu-latest
+    outputs:
+      filtered_pybop_matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - name: Filter pybop matrix
+        id: set-matrix
+        run: |
+          import json
+          import os
+
+          # Get the matrix
+          matrix_json = '${{ needs.create_pybamm_matrix.outputs.pybop_matrix }}'
+          matrix = json.loads(matrix_json)
+
+          # Filter the matrix for macOS-latest entries only
+          filtered_entries = [entry for entry in matrix['include'] if entry['os'] == 'macos-latest']
+          filtered_matrix = {'include': filtered_entries}
+
+          # Set the output variable for other jobs to use
+          output_file = os.environ['GITHUB_OUTPUT']
+          with open(output_file, "a", encoding="utf-8") as output_stream:
+              output_stream.write(f"matrix={json.dumps(filtered_matrix)}\n")
+        shell: python
+
   build:
+    needs: [create_pybamm_matrix]
+    name: Build (${{ matrix.os }}, Python ${{ matrix.python_version }}, PyBaMM ${{ matrix.pybamm_version }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+      matrix: ${{fromJson(needs.create_pybamm_matrix.outputs.pybop_matrix)}}
+    env:
+      PYBAMM_VERSION: ${{ matrix.pybamm_version }}
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
+      - name: Set up Python ${{ matrix.python_version }}
         uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.python_version }}
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip nox
+
       - name: Unit tests with nox
-        run: |
-          python -m nox -s unit
-          python -m nox -s notebooks
+        run: python -m nox -s unit
 
-  #M-series Mac Mini
+      - name: Run notebooks with nox
+        run: python -m nox -s notebooks
+
+  # M-series Mac Mini
   build-apple-mseries:
+    needs: [filter_pybamm_matrix]
+    name: Build (MacOS M-series, Python ${{ matrix.python_version }}, PyBaMM ${{ matrix.pybamm_version }})
     runs-on: [self-hosted, macOS, ARM64]
+    if: github.repository == 'pybop-team/PyBOP'
     env:
       GITHUB_PATH: ${PYENV_ROOT/bin:$PATH}
+      PYBAMM_VERSION: ${{ matrix.pybamm_version }}
     strategy:
       fail-fast: false
-      matrix:
-        python-version: ["3.10"]
+      matrix: ${{fromJson(needs.filter_pybamm_matrix.outputs.filtered_pybop_matrix)}}
 
     steps:
       - uses: actions/checkout@v4
       - name: Install python & create virtualenv
         shell: bash
         run: |
           eval "$(pyenv init -)"
-          pyenv install ${{ matrix.python-version }} -s
-          pyenv virtualenv ${{ matrix.python-version }} pybop-${{ matrix.python-version }}
+          pyenv install ${{ matrix.python_version }} -s
+          pyenv virtualenv ${{ matrix.python_version }} pybop-${{ matrix.python_version }}-${{ matrix.pybamm_version }}
 
-      - name: Install dependencies & run unit tests
+      - name: Install dependencies & run unit + notebook tests
         shell: bash
         run: |
           eval "$(pyenv init -)"
-          pyenv activate pybop-${{ matrix.python-version }}
-          python -m pip install --upgrade pip wheel setuptools nox
+          pyenv activate pybop-${{ matrix.python_version }}-${{ matrix.pybamm_version }}
+          python -m pip install --upgrade pip nox
           python -m nox -s unit
           python -m nox -s notebooks
 
@@ -66,5 +125,5 @@ jobs:
         shell: bash
         run: |
           eval "$(pyenv init -)"
-          pyenv activate pybop-${{ matrix.python-version }}
+          pyenv activate pybop-${{ matrix.python_version }}-${{ matrix.pybamm_version }}
           pyenv uninstall -f $( python --version )
diff --git a/.github/workflows/test_on_push.yaml b/.github/workflows/test_on_push.yaml
@@ -29,12 +29,22 @@ jobs:
 
 
   build:
+    needs: style
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: ["3.8", "3.9", "3.10", "3.11"]
+        exclude: # We run the coverage tests on Ubuntu with Python 3.11
+          - os: ubuntu-latest
+            python-version: "3.11"
+        # Include MacOS M-series Runners
+        include:
+          - os: macos-14
+            python-version: "3.10"
+          - os: macos-14
+            python-version: "3.11"
 
     steps:
       - uses: actions/checkout@v4
@@ -45,9 +55,10 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip nox
-      - name: Unit tests with nox
+      - name: Unit and notebook tests with nox
         run: |
           nox -s unit
+          nox -s notebooks
 
   # Runs only on Ubuntu with Python 3.11
   check_coverage:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,17 +4,19 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.1.9"
+    rev: "v0.2.2"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
         types_or: [python, pyi, jupyter]
       - id: ruff-format
+        types_or: [python, pyi, jupyter]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:
         - id: check-added-large-files
+          args: ['--maxkb=1000']
         - id: check-case-conflict
         - id: check-merge-conflict
         - id: check-yaml

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,11 +3,23 @@
 ## Features
 
 - [#6](https://github.com/pybop-team/PyBOP/issues/6) - Adds bayesian sampling class with NUTS example via Pyro + Torch probabilistic libraries.
-- [#38](https://github.com/pybop-team/PyBOP/issues/38) - Updates tests and adds a design optimisation example script `spme_max_energy`
+- [#203](https://github.com/pybop-team/PyBOP/pull/203) - Adds support for modern Python packaging via a `pyproject.toml` file and configures the `pytest` test runner and `ruff` linter to use their configurations stored as declarative metadata.
+- [#123](https://github.com/pybop-team/PyBOP/issues/123) - Configures scheduled tests to run against the last three PyPI releases of PyBaMM via dynamic GitHub Actions matrix generation.
+- [#187](https://github.com/pybop-team/PyBOP/issues/187) - Adds M1 Github runner to `test_on_push` workflow, updt. self-hosted supported python versions in scheduled tests.
+- [#118](https://github.com/pybop-team/PyBOP/issues/118) - Adds example jupyter notebooks.
+- [#151](https://github.com/pybop-team/PyBOP/issues/151) - Adds a standalone version of the Problem class.
+- [#12](https://github.com/pybop-team/PyBOP/issues/12) - Adds initial implementation of an Observer class and an unscented Kalman filter.
+- [#190](https://github.com/pybop-team/PyBOP/issues/190) - Adds a second example design cost, namely the VolumetricEnergyDensity.
 
 ## Bug Fixes
 
+- [#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.
+- [#164](https://github.com/pybop-team/PyBOP/issues/164) - Fixes convergence issues with gradient-based optimisers, changes default `model.check_params()` to allow infeasible solutions during optimisation iterations. Adds a feasibility check on the optimal parameters.
+
 # [v23.12](https://github.com/pybop-team/PyBOP/tree/v23.12) - 2023-12-19
+
 ## Features
 
 - [#141](https://github.com/pybop-team/PyBOP/pull/141) - Adds documentation with Sphinx and PyData Sphinx Theme. Updates docstrings across package, relocates `costs` and `dataset` to top-level of package. Adds noxfile session and deployment workflow for docs.
@@ -24,6 +36,8 @@
 
 ## Bug Fixes
 
+- [#182](https://github.com/pybop-team/PyBOP/pull/182) - Allow square-brackets indexing of Dataset
+
 # [v23.11](https://github.com/pybop-team/PyBOP/releases/tag/v23.11)
 - Initial release
 - Adds Pints, NLOpt, and SciPy optimisers

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -4,17 +4,19 @@ If you'd like to contribute to PyBOP, please have a look at the guidelines below
 
 ## Developer-Installation
 
-To install PyBOP for development purposes, which includes the testing and plotting dependencies, use the `[all]` flag as demonstrated below:
+To install PyBOP for development purposes, which includes the plotting dependencies, use the `[all]` and the `[dev]` flags as demonstrated below:
 
 For `zsh`:
 
 ```sh
-pip install -e '.[all]'
+pip install -e '.[all,dev]'
 ```
+
 For `bash`:
 ```sh
-pip install -e .[all]
+pip install -e .[all,dev]
 ```
+
 ## Pre-commit checks
 
 Before you commit any code, please perform the following checks using [Nox](https://nox.thea.codes/en/stable/index.html):
@@ -40,7 +42,7 @@ If you would like to skip the failing checks and push the code for further discu
 
 ## Workflow
 
-We use [GIT](https://en.wikipedia.org/wiki/Git) and [GitHub](https://en.wikipedia.org/wiki/GitHub) to coordinate our work. When making any kind of update, we try to follow the procedure below.
+We use [Git](https://en.wikipedia.org/wiki/Git) and [GitHub](https://en.wikipedia.org/wiki/GitHub) to coordinate our work. When making any kind of update, we try to follow the procedure below.
 
 ### A. Before you begin
 
@@ -105,8 +107,8 @@ On the other hand... We _do_ want to compare several tools, to generate document
 
 1. Core PyBOP: A minimal set, including things like NumPy, SciPy, etc. All infrastructure should run against this set of dependencies, as well as any numerical methods we implement ourselves.
 2. Extras: Other inference packages and their dependencies. Methods we don't want to implement ourselves, but do want to provide an interface to can have their dependencies added here.
-3. Documentation generating code: Everything you need to generate and work on the docs.
-4. Development code: Everything you need to do PyBOP development (so all of the above packages, plus ruff and other testing tools).
+3. Documentation generating code: Everything you need to generate and work on the docs. This is managed by the `[docs]` set of extras.
+4. Development code: Everything you need to do PyBOP development (so all of the above packages, plus ruff and other testing tools). This is managed by the `[dev]` set of extras.
 
 Only 'core pybop' is installed by default. The others have to be specified explicitly when running the installation command.
 
@@ -283,14 +285,14 @@ as above, and then use some of the profiling tools. In order of increasing detai
 
 ## Infrastructure
 
-### Setuptools
+### Installation via `pip`
 
-Installation of PyBOP _and dependencies_ is handled via [setuptools](http://setuptools.readthedocs.io/)
+Installation of PyBOP and its dependencies is handled via [`pip`](https://pip.pypa.io/) through the [setuptools](http://setuptools.readthedocs.io/) build-backend.
 
 Configuration files:
 
 ```
-setup.py
+pyproject.toml
 ```
 
 Note that this file must be kept in sync with the version number in [pybop/**init**.py](https://github.com/pybop-team/PyBOP/blob/develop/pybop/__init__.py).

diff --git a/README.md b/README.md
@@ -111,13 +111,13 @@ These general cases encompass a wide variety of optimisation problems that requi
 
 PyBOP comes with a number of [example notebooks and scripts](https://github.com/pybop-team/PyBOP/blob/develop/examples) which can be found in the examples folder.
 
-The [spm_descent.py](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/spm_descent.py) script illustrates a straightforward example that starts by generating artificial data from a single particle model (SPM). The unknown parameter values are identified by implementing a sum-of-square error cost function using the terminal voltage as the observed signal and a gradient descent optimiser. To run this example:
+The [spm_pso.py](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/spm_pso.py) script illustrates a straightforward example that starts by generating artificial data from a single particle model (SPM). The unknown parameter values are identified by employing a sum-of-squared errors cost function using the terminal voltage as the observed signal and a particle swarm optimisation algorithm. To run this example:
 
 ```bash
-python examples/scripts/spm_descent.py
+python examples/scripts/spm_pso.py
 ```
 
-In addition, [spm_nlopt.ipynb](https://github.com/pybop-team/PyBOP/blob/develop/examples/notebooks/spm_nlopt.ipynb) provides a second example in notebook form. This example estimates the SPM parameters based on an RMSE cost function and a BOBYQA optimiser.
+Alternatively, [spm_CMAES.ipynb](https://github.com/pybop-team/PyBOP/blob/develop/examples/notebooks/spm_CMAES.ipynb) provides an example in notebook form. This example estimates SPM parameters based on a sum-of-squared errors cost function and a CMA-ES optimiser.
 
 <!-- Code of Conduct -->
 ## Code of Conduct
@@ -145,10 +145,13 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center" valign="top" width="14.28%"><a href="http://bradyplanden.github.io"><img src="https://avatars.githubusercontent.com/u/55357039?v=4?s=100" width="100px;" alt="Brady Planden"/><br /><sub><b>Brady Planden</b></sub></a><br /><a href="#infra-BradyPlanden" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/pybop-team/PyBOP/commits?author=BradyPlanden" title="Tests">⚠️</a> <a href="https://github.com/pybop-team/PyBOP/commits?author=BradyPlanden" title="Code">💻</a> <a href="#example-BradyPlanden" title="Examples">💡</a> <a href="https://github.com/pybop-team/PyBOP/pulls?q=is%3Apr+reviewed-by%3ABradyPlanden" title="Reviewed Pull Requests">👀</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/NicolaCourtier"><img src="https://avatars.githubusercontent.com/u/45851982?v=4?s=100" width="100px;" alt="NicolaCourtier"/><br /><sub><b>NicolaCourtier</b></sub></a><br /><a href="https://github.com/pybop-team/PyBOP/commits?author=NicolaCourtier" title="Code">💻</a> <a href="https://github.com/pybop-team/PyBOP/pulls?q=is%3Apr+reviewed-by%3ANicolaCourtier" title="Reviewed Pull Requests">👀</a> <a href="#example-NicolaCourtier" title="Examples">💡</a> <a href="https://github.com/pybop-team/PyBOP/commits?author=NicolaCourtier" title="Tests">⚠️</a></td>
       <td align="center" valign="top" width="14.28%"><a href="http://howey.eng.ox.ac.uk"><img src="https://avatars.githubusercontent.com/u/2247552?v=4?s=100" width="100px;" alt="David Howey"/><br /><sub><b>David Howey</b></sub></a><br /><a href="#ideas-davidhowey" title="Ideas, Planning, & Feedback">🤔</a> <a href="#mentoring-davidhowey" title="Mentoring">🧑‍🏫</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="http://www.rse.ox.ac.uk"><img src="https://avatars.githubusercontent.com/u/1148404?v=4?s=100" width="100px;" alt="Martin Robinson"/><br /><sub><b>Martin Robinson</b></sub></a><br /><a href="#ideas-martinjrobins" title="Ideas, Planning, & Feedback">🤔</a> <a href="#mentoring-martinjrobins" title="Mentoring">🧑‍🏫</a> <a href="https://github.com/pybop-team/PyBOP/pulls?q=is%3Apr+reviewed-by%3Amartinjrobins" title="Reviewed Pull Requests">👀</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="http://www.rse.ox.ac.uk"><img src="https://avatars.githubusercontent.com/u/1148404?v=4?s=100" width="100px;" alt="Martin Robinson"/><br /><sub><b>Martin Robinson</b></sub></a><br /><a href="#ideas-martinjrobins" title="Ideas, Planning, & Feedback">🤔</a> <a href="#mentoring-martinjrobins" title="Mentoring">🧑‍🏫</a> <a href="https://github.com/pybop-team/PyBOP/pulls?q=is%3Apr+reviewed-by%3Amartinjrobins" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/pybop-team/PyBOP/commits?author=martinjrobins" title="Code">💻</a> <a href="https://github.com/pybop-team/PyBOP/commits?author=martinjrobins" title="Tests">⚠️</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://www.brosaplanella.xyz"><img src="https://avatars.githubusercontent.com/u/28443643?v=4?s=100" width="100px;" alt="Ferran Brosa Planella"/><br /><sub><b>Ferran Brosa Planella</b></sub></a><br /><a href="https://github.com/pybop-team/PyBOP/pulls?q=is%3Apr+reviewed-by%3Abrosaplanella" title="Reviewed Pull Requests">👀</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://www.ukri.org/"><img src="assets/UKRI.png" width="100px;" alt="UKRI"/><br /><sub><b>UKRI</b></sub></a><br /><a href="#financial-UKRI" title="Financial">💵</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://faraday.ac.uk"><img src="https://avatars2.githubusercontent.com/u/42166506?v=4?s=100" width="100px;" alt="Faraday Institution"/><br /><sub><b>Faraday Institution</b></sub></a><br /><a href="#financial-FaradayInstitution" title="Financial">💵</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://www.ukri.org/"><img src="assets/UKRI.png" width="100px;" alt="UK Research and Innovation"/><br /><sub><b>UK Research and Innovation</b></sub></a><br /><a href="#financial-UKRI" title="Financial">💵</a></td>
+    </tr>
+    <tr>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/agriyakhetarpal"><img src="https://avatars.githubusercontent.com/u/74401230?v=4?s=100" width="100px;" alt="Agriya Khetarpal"/><br /><sub><b>Agriya Khetarpal</b></sub></a><br /><a href="https://github.com/pybop-team/PyBOP/commits?author=agriyakhetarpal" title="Code">💻</a> <a href="#infra-agriyakhetarpal" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
     </tr>
   </tbody>
 </table>

diff --git a/assets/roadmap_logo.png b/assets/roadmap_logo.png
diff --git a/docs/conf.py b/docs/conf.py
@@ -8,7 +8,7 @@
 root_path = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
 sys.path.insert(0, root_path)
 
-from pybop.version import __version__  # noqa: E402
+from pybop._version import __version__  # noqa: E402
 
 # -- Project information -----------------------------------------------------
 project = "PyBOP"