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Cleanup for pypi release (#172)
* moved install method to poetry * updated contributing guidelines * moved changelog to kacl * updated github actions * updated doc scripts * updated doc action and styling * removed markdown katex * reverted checkpoint functionality * update test workflow * added type hints and increased coverage to part of geometry.py
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‎.flake8‎

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‎.github/actions/python-poetry-env/action.yml‎

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name: 'Setup Python + Poetry environment'
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description: 'Setup Python + Poetry environment'
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inputs:
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python-version:
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required: false
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description: 'Python version'
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default: '3.10'
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outputs: {}
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runs:
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using: 'composite'
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steps:
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- uses: actions/setup-python@v4
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with:
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python-version: ${{inputs.python-version}}
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- name: Install poetry
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run: python -m pip install poetry
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shell: bash
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- name: Create virtual environment
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run: poetry install --with=dev
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shell: bash

‎.github/dependabot.yml‎

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directory: "/" # Location of package manifests
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schedule:
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interval: "daily"
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ignore:
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# Ignore updates to "black" because we'd need to reformat everything
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- dependency-name: "black"

‎.github/workflows/build_docs.yml‎

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name: Documentation
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name: Update Documentation
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on:
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push:
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tags:
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- '*'
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release:
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types: [ published ]
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jobs:
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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- uses: ./.github/actions/python-poetry-env
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- name: Building docs
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run: |
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python -m pip install --upgrade pip
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pip install -e .[docs]
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- name: Test and get accuracy file
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run: |
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echo "Testing and saving accuracy file..."
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make get_test_data
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coverage run --source=jwave -m pytest -vs
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mkdocs build
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- name: Build documentation
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run: mkdocs gh-deploy --force

‎.github/workflows/draft_release.yml‎

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name: Draft a release
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on:
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workflow_dispatch:
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inputs:
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version:
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description: 'The version number (e.g. 1.2.3) OR one of: patch|minor|major|prepatch|preminor|premajor|prerelease'
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required: true
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default: 'patch'
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jobs:
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draft-release:
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runs-on: ubuntu-latest
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steps:
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- name: Set up SSH agent
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uses: webfactory/ssh-agent@v0.5.0
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with:
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ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
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- uses: actions/checkout@v2
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with:
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ssh-key: ${{ secrets.SSH_PRIVATE_KEY }}
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- uses: ./.github/actions/python-poetry-env
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- name: Update version
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id: updated_version
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shell: bash
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run: |
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poetry version ${{ github.event.inputs.version }}
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version=$(poetry version --short)
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echo ::set-output name="version::$version"
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- name: Update changelog
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id: changelog
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shell: bash
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run: |
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poetry run kacl-cli release ${{ steps.updated_version.outputs.version }} --modify --auto-link
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echo "" >> CHANGELOG.md
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body=$(poetry run kacl-cli get ${{ steps.updated_version.outputs.version }})
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body="${body//'%'/'%25'}"
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body="${body//$'\n'/'%0A'}"
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body="${body//$'\r'/'%0D'}"
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echo ::set-output name="body::$body"
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- name: Commit changes
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uses: EndBug/add-and-commit@v7
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with:
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add: 'CHANGELOG.md pyproject.toml'
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message: 'Release ${{ steps.updated_version.outputs.version }}'
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- name: Create tag
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run: |
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git tag ${{ steps.updated_version.outputs.version }}
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git push --tags
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- name: Create a draft release
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uses: actions/create-release@v1
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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tag_name: ${{ steps.updated_version.outputs.version }}
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release_name: Release ${{ steps.updated_version.outputs.version }}
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body: ${{ steps.changelog.outputs.body }}
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draft: true

‎.github/workflows/release.yml‎

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name: Release
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on:
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release:
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types: [ published ]
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jobs:
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build-and-publish:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: ./.github/actions/python-poetry-env
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- name: Publish to pypi
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run: |
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poetry config pypi-token.pypi ${{ secrets.PYPI_TOKEN }}
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poetry publish --build --no-interaction
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- name: Deploy docs
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run: poetry run mkdocs gh-deploy --force

‎.github/workflows/tests.yml‎

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# This is a workflow for Unit, Integration, and Regression Tests
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name: Unit, Integration and Regression Tests
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name: CI
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on:
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jobs:
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unit_and_integration_tests:
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strategy:
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matrix:
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python-version: [3.11]
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os: [ubuntu-latest]
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runs-on: ${{ matrix.os }}
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Making virtual environment, linting
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run: |
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make testenv
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- uses: ./.github/actions/python-poetry-env
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- name: Downloading test data
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run: |
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make get_test_data
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- name: Running tests
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run: |
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source .venv/bin/activate
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coverage run --source=jwave -m pytest -xvs --ignore=tests/regression_tests
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run: poetry run coverage run --source=jwave -m pytest -xvs --ignore=tests/regression_tests
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- name: "Upload coverage data for unit and integration tests"
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uses: actions/upload-artifact@v2
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with:
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name: coverage-unit
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path: ./.coverage
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regression_tests:
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strategy:
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matrix:
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python-version: [3.11]
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os: [ubuntu-latest]
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runs-on: ${{ matrix.os }}
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Making virtual environment, linting
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run: |
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make testenv
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- uses: ./.github/actions/python-poetry-env
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- name: Downloading test data
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run: |
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make get_test_data
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- name: Running tests
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run: |
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source .venv/bin/activate
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coverage run --source=jwave -m pytest -xvs ./tests/regression_tests
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run: poetry run coverage run --source=jwave -m pytest -xvs ./tests/regression_tests
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- name: "Upload coverage data for regression tests"
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uses: actions/upload-artifact@v2
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with:

‎.gitignore‎

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# Project
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*.ipynb_checkpoints
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*.pytest_cache
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*.vscode
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site/*
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build/*
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# Nodejs
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node_modules
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package-lock.json
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package.json
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# poetry
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poetry.lock
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# Testing
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.coverage
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#k-wave outputs
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docs/benchmarks/kwave/*.png
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# Profiling
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profiling/*
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# Misc
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*.DS_Store
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*.env.local
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*.env.development.local
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*.env.test.local
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*.env.production.local
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*npm-debug.log*
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*yarn-debug.log*
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*yarn-error.log*

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.0.1
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hooks:
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- id: check-ast
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- id: check-added-large-files
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- id: check-merge-conflict
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- id: check-case-conflict
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- id: check-yaml
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- id: check-toml
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- id: debug-statements
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- id: end-of-file-fixer
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- id: no-commit-to-branch
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- id: trailing-whitespace
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- id: mixed-line-ending
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- repo: https://github.com/hadialqattan/pycln
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rev: 'v1.1.0'
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hooks:
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- id: pycln
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args: [--config=pyproject.toml]
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- repo: https://github.com/google/yapf
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rev: v0.40.0
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hooks:
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- id: yapf
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args: ['--style=pyproject.toml', '--parallel', '--in-place']
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- repo: https://github.com/pycqa/isort
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rev: '5.12.0'
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hooks:
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- id: isort
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files: "\\.(py)$"
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args: [--settings-path=pyproject.toml]
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- repo: https://github.com/psf/black
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rev: 22.12.0
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hooks:
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- id: black
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language_version: python3.10

‎CHANGELOG.md‎

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# Changelog
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All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [Unreleased]
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### Added
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- `k0` is automatically calculated in the Convergent Born Series, if not given, using the fromula from Osnabrugge et al.
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### Fixed
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- updated for new `Array` type in `jax` 0.4.x
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### Changed
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- reverted checkpoint to only step checkpoints for time varying simulations. Soon jwave will use diffrax for advanced checkpointing
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## [0.0.4] - 2022-11-04
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### Added
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- Convergent Born series.
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### Fixed
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- Correctly handles Nyquist frequency for Helmholtz operator, to improve agreement with k-Wave.
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- Fixed incorrect domain size for angular spectrum.
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- Angular spectrum is only dispatched on `pressure` types.
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## [0.0.3] - 2022-07-05
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### Added
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- Angular spectrum method for single frequency sources.
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- Differentiable rayleigh integral (from a plane)
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## [0.0.2] - 2022-06-23
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### Added
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- Generate `TimeHarmonicSource` from point sources.
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### Fixed
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- Helmholtz notebook parameters bug.
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## [0.0.1] - 2022-06-07
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### Added
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- Finite differences helmholtz tested.
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- Extract time varying params without running the simulation.
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- Windows one-line installer
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### Fixed
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- Using numpy operations in TimeAxis for static fields.
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- Pml for 1D and 3D simulations.
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- Plotting functions of `jwave.utils` now work with both `Field`s and arrays.
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[Unreleased]: https://github.com/ucl-bug/jwave/compare/0.0.5...master
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[0.0.4]: https://github.com/ucl-bug/jwave/compare/0.0.3...0.0.4
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[0.0.3]: https://github.com/ucl-bug/jwave/compare/0.0.2...0.0.3
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[0.0.2]: https://github.com/ucl-bug/jwave/compare/0.0.1...0.0.2
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[0.0.1]: https://github.com/ucl-bug/jwave/releases/tag/0.0.1

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