Migrate from Poetry to uv, bump Python to >=3.11

Author: astanziola

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

@@ -1,24 +1,25 @@
-name: 'Setup Python + Poetry environment'
-description: 'Setup Python + Poetry environment'
+name: 'Setup Python + uv environment'
+description: 'Setup Python + uv environment'
 
 inputs:
   python-version:
     required: false
     description: 'Python version'
-    default: '3.10'
+    default: '3.13'
 outputs: {}
 runs:
   using: 'composite'
   steps:
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{inputs.python-version}}
-    - name: Install poetry
-      run: python -m pip install poetry
-      shell: bash
-    - name: Create virtual environment
-      run: poetry install --with=dev
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        enable-cache: true
+    - name: Install dependencies
+      run: uv sync --dev
       shell: bash
     - name: Install jaxlib
-      run: poetry run pip install jax[cpu]
+      run: uv pip install jax[cpu]
       shell: bash

.github/workflows/build_docs.yml

@@ -1,7 +1,3 @@
-# This is a workflow that runs whenever a pull request
-# changes some documentation files or the mkdocs.yml file. It
-# checks that the documentation builds correctly.
-
 name: Build Docs
 
 on:
@@ -19,7 +15,7 @@ jobs:
   build-and-publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/python-poetry-env
       - name: Build docs
-        run: poetry run mkdocs build
+        run: uv run mkdocs build

.github/workflows/ci_tests.yml

@@ -1,6 +1,3 @@
-# This workflow runs both the regression tests and the unit/integration tests.
-# It is triggered on push to the main branch.
-
 name: CI
 
 on:
@@ -11,23 +8,23 @@ jobs:
   full_tests:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/python-poetry-env
       - name: Downloading test data
         run: |
           make get_test_data
       - name: Running Regression Tests
         run: |
-          poetry run coverage run --source=jwave -m pytest -xvs ./tests/regression_tests
+          uv run coverage run --source=jwave -m pytest -xvs ./tests/regression_tests
       - name: Remove coverage data from regression tests
         run: |
           rm ./.coverage
       - name: Running Unit and Integration tests
         run: |
-          poetry run coverage run --source=jwave -m pytest -xvs --ignore=tests/regression_tests
-          poetry run coverage xml
+          uv run coverage run --source=jwave -m pytest -xvs --ignore=tests/regression_tests
+          uv run coverage xml
       - name: "Upload coverage to Codecov"
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage.xml

.github/workflows/draft_release.yml

@@ -13,33 +13,38 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Set up SSH agent
-        uses: webfactory/ssh-agent@v0.5.0
+        uses: webfactory/ssh-agent@v0.9.1
         with:
           ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           ssh-key: ${{ secrets.SSH_PRIVATE_KEY }}
       - uses: ./.github/actions/python-poetry-env
       - name: Update version
         id: updated_version
         shell: bash
         run: |
-          poetry version ${{ github.event.inputs.version }}
-          version=$(poetry version --short)
-          echo ::set-output name="version::$version"
+          # Update version in pyproject.toml
+          if [[ "${{ github.event.inputs.version }}" =~ ^[0-9] ]]; then
+            version="${{ github.event.inputs.version }}"
+          else
+            echo "Semantic version bumps (patch/minor/major) require manual edit with uv"
+            exit 1
+          fi
+          sed -i "s/^version = .*/version = \"$version\"/" pyproject.toml
+          echo "version=$version" >> "$GITHUB_OUTPUT"
       - name: Update changelog
         id: changelog
         shell: bash
         run: |
-          poetry run kacl-cli release ${{ steps.updated_version.outputs.version }} --modify --auto-link
+          uv run kacl-cli release ${{ steps.updated_version.outputs.version }} --modify --auto-link
           echo "" >> CHANGELOG.md
-          body=$(poetry run kacl-cli get ${{ steps.updated_version.outputs.version }})
-          body="${body//'%'/'%25'}"
-          body="${body//$'\n'/'%0A'}"
-          body="${body//$'\r'/'%0D'}"
-          echo ::set-output name="body::$body"
+          body=$(uv run kacl-cli get ${{ steps.updated_version.outputs.version }})
+          echo "body<<EOF" >> "$GITHUB_OUTPUT"
+          echo "$body" >> "$GITHUB_OUTPUT"
+          echo "EOF" >> "$GITHUB_OUTPUT"
       - name: Commit changes
-        uses: EndBug/add-and-commit@v7
+        uses: EndBug/add-and-commit@v9
         with:
           add: 'CHANGELOG.md pyproject.toml'
           message: 'Release ${{ steps.updated_version.outputs.version }}'
@@ -48,11 +53,9 @@ jobs:
           git tag ${{ steps.updated_version.outputs.version }}
           git push --tags
       - name: Create a draft release
-        uses: actions/create-release@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        uses: softprops/action-gh-release@v2
         with:
           tag_name: ${{ steps.updated_version.outputs.version }}
-          release_name: Release ${{ steps.updated_version.outputs.version }}
+          name: Release ${{ steps.updated_version.outputs.version }}
           body: ${{ steps.changelog.outputs.body }}
           draft: true

.github/workflows/regression_tests.yml

@@ -1,6 +1,3 @@
-# This is a workflow for Regression Tests.
-# It is triggered by a pull request to the main branch.
-
 name: Regression Tests
 
 on:
@@ -11,10 +8,10 @@ jobs:
   regression_tests:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/python-poetry-env
       - name: Downloading test data
         run: |
           make get_test_data
       - name: Running tests
-        run: poetry run coverage run --source=jwave -m pytest -xvs ./tests/regression_tests
+        run: uv run coverage run --source=jwave -m pytest -xvs ./tests/regression_tests

.github/workflows/release.yml

@@ -8,11 +8,11 @@ jobs:
   build-and-publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/python-poetry-env
-      - name: Publish to pypi
-        run: |
-          poetry config pypi-token.pypi ${{ secrets.PYPI_TOKEN }}
-          poetry publish --build --no-interaction
+      - name: Build package
+        run: uv build
+      - name: Publish to PyPI
+        run: uv publish --token ${{ secrets.PYPI_TOKEN }}
       - name: Deploy docs
-        run: poetry run mkdocs gh-deploy --force
+        run: uv run mkdocs gh-deploy --force

.github/workflows/unit_integration_tests.yml

@@ -1,7 +1,3 @@
-# This is a workflow for Unit, Integration, and Regression Tests
-# It is used to test the code on every pull request, whenever a
-# python, matlab, yaml, makefile, or markdown file is changed.
-
 name: Unit and Integration Tests
 
 on:
@@ -16,17 +12,17 @@ jobs:
   unit_and_integration_tests:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/python-poetry-env
       - name: Downloading test data
         run: |
           make get_test_data
       - name: Running tests
         run: |
-          poetry run coverage run --source=jwave -m pytest -xvs --ignore=tests/regression_tests
-          poetry run coverage xml
+          uv run coverage run --source=jwave -m pytest -xvs --ignore=tests/regression_tests
+          uv run coverage xml
       - name: "Upload coverage to Codecov"
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage.xml

CHANGELOG.md

@@ -1,46 +1,68 @@
 # Changelog
+
 All notable changes to this project will be documented in this file.
 
 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).
 
 ## [Unreleased]
 
+### Changed
+
+- Migrated from Poetry to uv for dependency management and builds
+- Minimum Python version bumped to 3.11
+- Upgraded plumkdocs to >=1.0.0 and mkdocstrings to >=1.0.0
+
 ## [0.2.1] - 2024-09-17
+
 ### Changed
+
 - Upgraded `jaxdf` dependency
 
 ## [0.2.0] - 2023-12-18
+
 ### Fixed
+
 - Fixed arguments error in helmholtz notebook
 
 ### Changed
+
 - `Medium` objects are now `jaxdf.Module`s, which is based on `equinox` modules. It is also a [parametric module for dispatching operators](https://beartype.github.io/plum/parametric.html), meaning that there's a type difference betwee `Medium[FourierSeries]` and `Medium[FiniteDifferences]`, for example.
 - The settings of time domain acoustic simulations are now set using a `TimeWavePropagationSettings`. This also includes an attribute to explicity set the reference sound speed.
 
 ### Added
+
 - Added a logger in `jwave.logger`
 
 ### Removed
+
 - Removed `pressure_from_density` from `jwave.acoustics.conversion`, as it was a duplicate
 
 ## [0.1.5] - 2023-09-27
+
 ### Added
+
 - Added `numbers_with_smallest_primes` utility to find grids with small primes for efficient FFT when using FourierSeries
 
 ### Fixed
+
 - Restored `default_params` for the helmholtz operators that wen missing since the last jaxdf update
 
 ## [0.1.4] - 2023-06-29
+
 ### Changed
+
 - Refactored `save_video` to use opencv.
 
 ### Deprecated
+
 - `plot_complex_field` has been deprecated in favor of `display_complex_field`
 
 ### Removed
+
 - Removed the uncertainty propagation notebook example. For a more in depth example of using linear uncertainty propagation see [this repository](https://github.com/ucl-bug/linear-uncertainty)
 
 ### Added
+
 - Exposed `points_on_circle` function to generate points on a circle
 - Exposed `unit_fibonacci_sphere` function
 - Exposed `fibonacci_sphere` function
@@ -49,56 +71,77 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Exposed bli_function that is used to compute the band limited interpolant
 
 ## [0.1.3] - 2023-06-28
+
 ### Added
+
 - Added off grid sensors [@tomelse]
 
 ## [0.1.2] - 2023-06-22
+
 ### Changed
+
 - updated documentation
 - made imageio and tqdm optional dependencies
 
 ## [0.1.1] - 2023-06-22
+
 ### Fixed
+
 - fixed pypi classifiers
 
 ## [0.1.0] - 2023-06-22
+
 ### Added
+
 - `k0` is automatically calculated in the Convergent Born Series, if not given, using the fromula from Osnabrugge et al.
 
 ### Fixed
+
 - updated for new `Array` type in `jax` 0.4.x
 
 ### Changed
+
 - reverted checkpoint to only step checkpoints for time varying simulations. Soon jwave will use diffrax for advanced checkpointing
 
 ## [0.0.4] - 2022-11-04
+
 ### Added
+
 - Convergent Born series.
 
 ### Fixed
+
 - Correctly handles Nyquist frequency for Helmholtz operator, to improve agreement with k-Wave.
 - Fixed incorrect domain size for angular spectrum.
 - Angular spectrum is only dispatched on `pressure` types.
 
 ## [0.0.3] - 2022-07-05
+
 ### Added
+
 - Angular spectrum method for single frequency sources.
 - Differentiable rayleigh integral (from a plane)
 
 ## [0.0.2] - 2022-06-23
+
 ### Added
+
 - Generate `TimeHarmonicSource` from point sources.
 
 ### Fixed
+
 - Helmholtz notebook parameters bug.
 
 ## [0.0.1] - 2022-06-07
+
 ### Added
+
 - Finite differences helmholtz tested.
 - Extract time varying params without running the simulation.
 - Windows one-line installer
 
 ### Fixed
+
 - Using numpy operations in TimeAxis for static fields.
 - Pml for 1D and 3D simulations.
 - Plotting functions of `jwave.utils` now work with both `Field`s and arrays.
@@ -116,4 +159,3 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 [0.0.3]: https://github.com/ucl-bug/jwave/compare/0.0.2...0.0.3
 [0.0.2]: https://github.com/ucl-bug/jwave/compare/0.0.1...0.0.2
 [0.0.1]: https://github.com/ucl-bug/jwave/releases/tag/0.0.1
-