Update installation of Parcels to be source installation

.github/workflows/cache-pixi-lock.yml

@@ -0,0 +1,50 @@
+# Adapted from https://raw.githubusercontent.com/Parcels-code/Parcels/58cdd6185b3af03785c567914a070288ffd804e0/.github/workflows/cache-pixi-lock.yml
+name: Generate and cache Pixi lockfile
+
+on:
+  workflow_call:
+    outputs:
+      cache-id:
+        description: "The lock file contents"
+        value: ${{ jobs.cache-pixi-lock.outputs.cache-id }}
+
+jobs:
+  cache-pixi-lock:
+    name: Generate output
+    runs-on: ubuntu-latest
+    outputs:
+      cache-id: ${{ steps.restore.outputs.cache-primary-key }}
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+          submodules: recursive
+      - name: Get current date
+        id: date
+        run: echo "date=$(date +'%Y-%m-%d')" >> "$GITHUB_OUTPUT"
+      - uses: actions/cache/restore@v4
+        id: restore
+        with:
+          path: |
+            pixi.lock
+          key: ${{ steps.date.outputs.date }}_${{hashFiles('pixi.toml')}}
+      - uses: prefix-dev/[email protected]
+        if: ${{ !steps.restore.outputs.cache-hit }}
+        with:
+          pixi-version: v0.56.0
+          run-install: false
+      - name: Run pixi lock
+        if: ${{ !steps.restore.outputs.cache-hit }}
+        run: pixi lock
+      - uses: actions/cache/save@v4
+        if: ${{ !steps.restore.outputs.cache-hit }}
+        id: cache
+        with:
+          path: |
+            pixi.lock
+          key: ${{ steps.restore.outputs.cache-primary-key }}
+      - name: Upload pixi.lock
+        uses: actions/upload-artifact@v4
+        with:
+          name: pixi-lock
+          path: pixi.lock

.github/workflows/ci.yml

@@ -21,56 +21,61 @@ env:
   FORCE_COLOR: 3
 
 jobs:
+  cache-pixi-lock:
+    uses: ./.github/workflows/cache-pixi-lock.yml
+
   tests:
-    name: tests (${{ matrix.runs-on }} | Python ${{ matrix.python-version }})
+    name: "Unit tests: ${{ matrix.runs-on }} | pixi run -e ${{ matrix.pixi-environment }} tests"
     runs-on: ${{ matrix.runs-on }}
+    needs: cache-pixi-lock
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.12"]
+        pixi-environment: ["test-py310", "test-py312"]
         runs-on: [ubuntu-latest, windows-latest, macos-14]
 
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: mamba-org/setup-micromamba@v2
+          submodules: recursive
+      - uses: actions/cache/restore@v4
         with:
-          environment-name: ship
-          environment-file: environment.yml
-          create-args: >-
-            python=${{matrix.python-version}}
-
-      - run: pip install . --no-deps
+          path: pixi.lock
+          key: ${{ needs.cache-pixi-lock.outputs.cache-id }}
+      - uses: prefix-dev/[email protected]
+        with:
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
 
       - name: Test package
-        run: >-
-          python -m pytest -ra --cov --cov-report=xml --cov-report=term
+        run:
+          pixi run -e ${{ matrix.pixi-environment }} tests -ra --cov --cov-report=xml --cov-report=term
           --durations=20
 
       - name: Upload coverage report
         uses: codecov/[email protected]
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
   typechecking:
-    name: mypy
+    name: "TypeChecking: pixi run typing"
     runs-on: ubuntu-latest
+    needs: cache-pixi-lock
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: mamba-org/setup-micromamba@v2
+          submodules: recursive
+      - uses: actions/cache/restore@v4
         with:
-          environment-name: ship
-          environment-file: environment.yml
-          create-args: >-
-            python=3.12
-
-      - run: pip install . --no-deps
-      - run: conda install lxml # dep for report generation
+          path: pixi.lock
+          key: ${{ needs.cache-pixi-lock.outputs.cache-id }}
+      - uses: prefix-dev/[email protected]
+        with:
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
       - name: Typechecking
-        run: |
-          mypy --install-types --non-interactive src/virtualship --html-report mypy-report
+        run: pixi run typing --non-interactive --html-report mypy-report
       - name: Upload test results
         if: ${{ always() }} # Upload even on mypy error
         uses: actions/upload-artifact@v4

.gitignore

@@ -178,3 +178,9 @@ src/virtualship/_version_setup.py
 
 .vscode/
 .DS_Store
+
+# Ignore pixi.lock file for this project. The con of 22k lines of noise it adds to diffs is not worth
+# the minor benefit of perfectly reproducible environments for all developers (and all the tooling that would
+# be required to support that - see https://github.com/pydata/xarray/issues/10732#issuecomment-3327780806
+# for more details)
+pixi.lock

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "Parcels"]
+	path = Parcels
+	url = [email protected]:Parcels-code/Parcels.git

.readthedocs.yaml

@@ -1,18 +1,17 @@
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
 version: 2
-sphinx:
-  configuration: docs/conf.py
 build:
-  os: ubuntu-22.04
+  os: ubuntu-lts-latest
   tools:
-    python: mambaforge-22.9
+    python: "latest" # just so RTD stops complaining
   jobs:
-    pre_build:
-      - pip install .
-      - sphinx-build -b linkcheck docs/ _build/linkcheck
-      - sphinx-apidoc -o docs/api/ --module-first --no-toc --force src/virtualship
-
-conda:
-  environment: environment.yml
+    create_environment:
+      - asdf plugin add pixi
+      - asdf install pixi latest
+      - asdf global pixi latest
+    install:
+      - pixi install -e docs
+    build:
+      html:
+        - pixi run -e docs sphinx-build -T -b html docs $READTHEDOCS_OUTPUT/html
+sphinx:
+  configuration: docs/conf.py

README.md

@@ -7,6 +7,7 @@
 
 <!-- Badges -->
 
+[![Pixi Badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json)](https://pixi.sh)
 [![Anaconda-release](https://anaconda.org/conda-forge/virtualship/badges/version.svg)](https://anaconda.org/conda-forge/virtualship/)
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/virtualship)
 [![DOI](https://zenodo.org/badge/682478059.svg)](https://doi.org/10.5281/zenodo.14013931)

docs/contributing/index.md

@@ -8,36 +8,75 @@ We have a design document providing a conceptual overview of VirtualShip. This d
 
 ### Development installation
 
-We use `conda` to manage our development installation. Make sure you have `conda` installed by following [the instructions here](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) and then run the following commands:
+```{note}
+VirtualShip uses [Pixi](https://pixi.sh) to manage environments and run developer tooling. Pixi is a modern alternative to Conda and also includes other powerful tooling useful for a project like VirtualShip. It is our sole development workflow - we do not offer a Conda development workflow. Give Pixi a try, you won't regret it!
+```
+
+To get started contributing to VirtualShip:
+
+**Step 1:** [Install Pixi](https://pixi.sh/latest/).
+
+**Step 2:** [Fork the repository](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo#forking-a-repository)
+
+**Step 3:** Clone your fork with submodules and `cd` into the repository.
+
+```bash
+git clone --recurse-submodules [email protected]:YOUR_USERNAME/virtualship.git
+cd virtualship
+```
+
+```{note}
+The `--recurse-submodules` flag is required to clone the Parcels submodule, which is used for testing and development.
+```
+
+**Step 4:** Install the Pixi environment
 
 ```bash
-conda create -n ship python=3.10
-conda activate ship
-conda env update --file environment.yml
-pip install -e . --no-deps --no-build-isolation
+pixi install
 ```
 
-This creates an environment, and installs all the dependencies that you need for development, including:
+Now you have a development installation of VirtualShip, as well as a bunch of developer tooling to run tests, check code quality, and build the documentation! Simple as that.
 
-- core dependencies
-- development dependencies (e.g., for testing)
-- documentation dependencies
+### Pixi workflows
 
-then installs the package in editable mode.
+You can use the following Pixi commands to run common development tasks.
 
-### Useful commands
+**Testing**
 
-The following commands are useful for local development:
+- `pixi run tests` - Run the full test suite using pytest with coverage reporting
+- `pixi run tests-notebooks` - Run notebook tests
 
-- `pytest` to run tests
-- `pre-commit run --all-files` to run pre-commit checks
-- `pre-commit install` (optional) to install pre-commit hooks
-  - this means that every time you commit, pre-commit checks will run on the files you changed
-- `sphinx-autobuild docs docs/_build` to build and serve the documentation
-- `sphinx-apidoc -o docs/api/ --module-first --no-toc --force src/virtualship` (optional) to generate the API documentation
-- `sphinx-build -b linkcheck docs/ _build/linkcheck` to check for broken links in the documentation
+**Documentation**
 
-The running of these commands is useful for local development and quick iteration, but not _vital_ as they will be run automatically in the CI pipeline (`pre-commit` by pre-commit.ci, `pytest` by GitHub Actions, and `sphinx` by ReadTheDocs).
+- `pixi run docs` - Build the documentation using Sphinx
+- `pixi run docs-watch` - Build and auto-rebuild documentation when files change (useful for live editing)
+
+**Code quality**
+
+- `pixi run lint` - Run pre-commit hooks on all files (includes formatting, linting, and other code quality checks)
+- `pixi run typing` - Run mypy type checking on the codebase
+
+**Different environments**
+
+VirtualShip supports testing against different environments (e.g., different Python versions) with different feature sets. In CI we test against these environments, and you can too locally. For example:
+
+- `pixi run -e test-py311 tests` - Run tests using Python 3.11
+- `pixi run -e test-py312 tests` - Run tests using Python 3.12
+- `pixi run -e test-latest tests` - Run tests using latest Python
+
+The name of the workflow on GitHub contains the command you have to run locally to recreate the workflow - making it super easy to reproduce CI failures locally.
+
+**Typical development workflow**
+
+1. Make your code changes
+2. Run `pixi run lint` to ensure code formatting and style compliance
+3. Run `pixi run tests` to verify your changes don't break existing functionality
+4. If you've added new features, run `pixi run typing` to check type annotations
+5. If you've modified documentation, run `pixi run docs` to build and verify the docs
+
+```{tip}
+You can run `pixi info` to see all available environments and `pixi task list` to see all available tasks across environments.
+```
 
 ## For maintainers
 
@@ -52,5 +91,5 @@ The running of these commands is useful for local development and quick iteratio
 
 When adding a dependency, make sure to modify the following files where relevant:
 
-- `environment.yml` for core and development dependencies (important for the development environment, and CI)
+- `pixi.toml` for core and development dependencies (important for the development environment, and CI)
 - `pyproject.toml` for core dependencies (important for the pypi package, this should propagate through automatically to `recipe/meta.yml` in the conda-forge feedstock)