Add-custom-module-functions-functionality

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/workflows/publish_pypi.yml

@@ -1,38 +1,83 @@
 name: Build and publish package to PyPI
 
 on:
-  push:
-    tags:
-    - '*'
+  release:
+    types: [published]
   workflow_dispatch:
     inputs:
       target:
-        description: 'Deployment target. Can be "pypi" or "testpypi"'
-        default: "pypi"
+        description: 'Deployment target. Can be "pypi" or "testpypi", or left as blank to skip publishing. Default is blank.'
+        default: ""
 
 jobs:
-  publish_pypi:
-    name: Build wheels on ubuntu-latest
+  build:
+    name: Build sdist and wheel
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
         with:
-          python-version: 3.8
-      - name: Install dependencies
+          python-version: "3.x"
+
+      - name: Build distributions
+        run: pipx run build
+
+      - name: Build, inspect, and display contents of distributions
+        shell: bash
         run: |
-          python -m pip install --upgrade pip
-          pip install build
-      - name: Build package
-        run: python -m build
-      - name: Publish on PyPI
-        if: github.event.inputs.target == 'pypi'
-        uses: pypa/gh-action-pypi-publish@release/v1
+          mkdir -p output/sdist
+          tar -xf dist/*.tar.gz -C output/sdist
+
+          echo -e '## View source distribution (SDist) contents\n' >> $GITHUB_STEP_SUMMARY
+          echo -e '```\n' >> $GITHUB_STEP_SUMMARY
+          (cd output/sdist && tree -a * | sed 's/^/    /' | tee -a $GITHUB_STEP_SUMMARY)
+          echo -e '\n```\n' >> $GITHUB_STEP_SUMMARY
+
+          mkdir -p output/wheel
+          pipx run wheel unpack dist/*.whl -d output/wheel
+
+          echo -e '## View binary distribution (wheel) contents\n' >> $GITHUB_STEP_SUMMARY
+          echo -e '```\n' >> $GITHUB_STEP_SUMMARY
+          (cd output/wheel && tree -a * | sed 's/^/    /' | tee -a $GITHUB_STEP_SUMMARY)
+          echo -e '\n```\n' >> $GITHUB_STEP_SUMMARY
+
+      - name: Upload sdist and wheel artifacts
+        uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b # v4.5.0
         with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
-      - name: Publish on TestPyPI
+          name: distributions
+          path: dist/*
+
+  publish:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/bpx
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    needs: [build]
+    if: >-
+      github.event_name == 'release' &&
+      github.event.action == 'published' ||
+      github.event_name == 'workflow_dispatch' &&
+      github.event.inputs.target == 'pypi' ||
+      github.event.inputs.target == 'testpypi'
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
+        with:
+          path: dist
+          merge-multiple: true
+
+      - name: Upload to PyPI
+        if: github.event.inputs.target == 'pypi' || github.event_name == 'release' && github.event.action == 'published'
+        uses: pypa/gh-action-pypi-publish@67339c736fd9354cd4f8cb0b744f2b82a74b5c70 # v1.12.3
+        with:
+          packages-dir: dist
+
+      - name: Upload to TestPyPI
         if: github.event.inputs.target == 'testpypi'
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@67339c736fd9354cd4f8cb0b744f2b82a74b5c70 # v1.12.3
         with:
-          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-          repository_url: https://test.pypi.org/legacy/
+          repository-url: https://test.pypi.org/legacy/
+          packages-dir: dist

.github/workflows/test.yml

@@ -3,31 +3,32 @@ name: BPX-tests
 on:
   workflow_dispatch:
   pull_request:
+  push:
+    branches:
+      - main
 
 jobs:
   build:
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
         os: [ubuntu-latest, windows-latest, macos-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install coverage flake8
-          pip install .
-      - name: Lint with flake8
-        run: |
-          flake8 . --count --exit-zero --show-source --statistics
-      - name: Test with unittest 
-        run: |
-          coverage run -m unittest
+          pip install hatch "coverage[toml]"
+      - name: Lint with ruff
+        run: hatch run dev:check
+      - name: Run unit tests 
+        run: hatch run dev:cov
       - name: Upload Coverage to Codecov
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v5

.gitignore

@@ -50,6 +50,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+.ruff_cache/
 
 # Translations
 *.mo
@@ -129,4 +130,8 @@ dmypy.json
 .pyre/
 
 # IDEs
-.vscode
+.vscode
+.idea
+
+# MacOS
+.DS_Store

CHANGELOG.md

@@ -1,3 +1,8 @@
+# [v0.5.0](https://github.com/FaradayInstitution/BPX/releases/tag/v0.5.0)
+
+- Bug fixes for Pydantic ([#81](https://github.com/FaradayInstitution/BPX/pull/81))
+- Updated to Pydantic V2 and the hatch build system ([#79](https://github.com/FaradayInstitution/BPX/pull/79))
+
 # [v0.4.0](https://github.com/FaradayInstitution/BPX/releases/tag/v0.4.0)
 
 - Added five parametrisation examples (two DFN parametrisation examples from About:Energy open-source release, blended electrode definition, user-defined 0th-order hysteresis, and SPM parametrisation). ([#45](https://github.com/FaradayInstitution/BPX/pull/45))

CODE-OF-CONDUCT.md

@@ -0,0 +1,135 @@
+[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](https://www.contributor-covenant.org/version/2/1/code_of_conduct.html)
+
+
+# BPX Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[bpx@faraday.ac.uk](mailto:bpx@faraday.ac.uk).
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

README.md

@@ -6,16 +6,23 @@ An implementation of the Battery Parameter eXchange (BPX) format in Pydantic. BP
 
 This repository features a Pydantic-based parser for JSON files in the BPX format, which validates your file against the schema.
 
-To support the new open standard, [About:Energy](https://www.aboutenergy.io/) have supplied two parameters sets for an NMC and LFP cell. The BPX files and associated examples and information can be found on the [A:E BPX Parameterisation repository](https://github.com/About-Energy-OpenSource/About-Energy-BPX-Parameterisation/).
+To support the new open standard, [About:Energy](https://www.aboutenergy.io/) have supplied two parameter sets for an NMC and LFP cell. The BPX files and associated examples and information can be found on the [A:E BPX Parameterisation repository](https://github.com/About-Energy-OpenSource/About-Energy-BPX-Parameterisation/).
 
-To see how to use BPX with [PyBaMM](https://www.pybamm.org/), check out the [BPX example repository](https://github.com/pybamm-team/bpx-example).
+To see how to use BPX with [PyBaMM](https://www.pybamm.org/), check out the [BPX example notebook]([https://github.com/pybamm-team/bpx-example](https://github.com/pybamm-team/PyBaMM/blob/1ead6c512a6cff3effaa35f47efb354ec4a3c8c8/docs/source/examples/notebooks/parameterization/bpx.ipynb)).
 
 ## 🚀 Installation
 The BPX package can be installed using pip
+
 ```bash
 pip install bpx
 ```
 
+or conda
+
+```bash
+conda install -c conda-forge bpx
+```
+
 BPX is available on GNU/Linux, MacOS and Windows. We strongly recommend to install PyBaMM within a python [virtual environment](https://docs.python.org/3/tutorial/venv.html), in order not to alter any distribution python files.
 
 ## 💻 Usage
@@ -26,7 +33,7 @@ import bpx
 filename = 'path/to/my/file.json'
 my_params = bpx.parse_bpx_file(filename)
 ```
-`my_params` will now be of type `BPX`, which acts like a python dataclass with the same attributes as the BPX format. To obatin example files, see the `examples` folder, the [A:E BPX Parameterisation repository](https://github.com/About-Energy-OpenSource/About-Energy-BPX-Parameterisation/), or the [BPX example repository](https://github.com/pybamm-team/bpx-example).
+`my_params` will now be of type `BPX`, which acts like a python dataclass with the same attributes as the BPX format. To obtain example files, see the `examples` folder, the [A:E BPX Parameterisation repository](https://github.com/About-Energy-OpenSource/About-Energy-BPX-Parameterisation/), or the [BPX example repository](https://github.com/pybamm-team/bpx-example).
 
 Attributes of the class can be printed out using the standard Python dot notation, for example, you can print out the initial temperature of the cell using
 ```python
@@ -39,7 +46,7 @@ my_params_dict = my_params.dict(by_alias=True)
 print('Initial temperature of cell:', my_params_dict["Parameterisation"]["Cell"]["Initial temperature [K]"])
 ```
 
-The entire BPX object can be pretty printed using the `devtools` package 
+The entire BPX object can be pretty-printed using the `devtools` package 
 ```python
 from devtools import pprint
 pprint(my_params)