From d78f6ec50a3a73eb49e246eb55c4cc601e96d935 Mon Sep 17 00:00:00 2001
From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com>
Date: Fri, 3 Oct 2025 15:49:04 +0200
Subject: [PATCH 1/9] Add pixi.toml configuration for environment management

- Define workspace with VirtualShip name and pixi-build preview
- Configure multiple test environments (py310, py311, py312)
- Set up feature environments for docs, typing, and pre-commit
- Define pixi tasks for tests, docs, linting, and type checking
- Align dependencies with existing pyproject.toml
---
 pixi.toml | 93 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 93 insertions(+)
 create mode 100644 pixi.toml

diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 000000000..e6d86f158
--- /dev/null
+++ b/pixi.toml
@@ -0,0 +1,93 @@
+[workspace]
+name = "VirtualShip"
+preview = ["pixi-build"]
+channels = ["conda-forge"]
+platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"]
+
+[package]
+name = "virtualship"
+version = "dynamic"
+
+[package.build]
+backend = { name = "pixi-build-python", version = "==0.3.2" }
+
+[package.host-dependencies]
+setuptools = "*"
+setuptools_scm = "*"
+
+[environments]
+test-latest = { features = ["test"], solve-group = "test" }
+test-py310 = { features = ["test", "py310"] }
+test-py311 = { features = ["test", "py311"] }
+test-py312 = { features = ["test", "py312"] }
+test-notebooks = { features = ["test", "notebooks"], solve-group = "test" }
+docs = { features = ["docs"], solve-group = "docs" }
+typing = { features = ["typing"], solve-group = "typing" }
+pre-commit = { features = ["pre-commit"], no-default-feature = true }
+
+[dependencies] # keep section in sync with pyproject.toml dependencies
+python = ">=3.10"
+click = "*"
+parcels = ">3.1.0"
+pyproj = ">=3,<4"
+sortedcontainers = "==2.4.0"
+opensimplex = "==0.4.5"
+numpy = ">=1,<2"
+pydantic = ">=2,<3"
+pyyaml = "*"
+copernicusmarine = ">=2.2.2"
+yaspin = "*"
+textual = "*"
+
+[feature.py310.dependencies]
+python = "3.10.*"
+
+[feature.py311.dependencies]
+python = "3.11.*"
+
+[feature.py312.dependencies]
+python = "3.12.*"
+
+[feature.test.dependencies]
+pytest = "*"
+pytest-cov = "*"
+pytest-asyncio = "*"
+seabird = "*"
+openpyxl = "*"
+
+[feature.test.tasks]
+tests = "pytest -ra --cov --cov-report=xml --cov-report=term --durations=20"
+
+[feature.notebooks.dependencies]
+nbval = "*"
+ipykernel = "*"
+
+[feature.notebooks.tasks]
+tests-notebooks = "pytest --nbval-lax docs/"
+
+[feature.docs.dependencies]
+sphinx = ">=7.0"
+myst-parser = ">=0.13"
+nbsphinx = "*"
+ipykernel = "*"
+pandoc = "*"
+sphinx-copybutton = "*"
+pydata-sphinx-theme = "*"
+sphinx-autobuild = "*"
+
+[feature.docs.tasks]
+docs = "sphinx-build docs docs/_build"
+docs-watch = "sphinx-autobuild docs docs/_build"
+
+[feature.pre-commit.dependencies]
+pre_commit = "*"
+
+[feature.pre-commit.tasks]
+lint = "pre-commit run --all-files"
+
+[feature.typing.dependencies]
+mypy = "*"
+lxml = "*"
+
+[feature.typing.tasks]
+typing = "mypy src/virtualship --install-types"

From 00dc6f5f498ce16d35610f6b58009ec482b7e62d Mon Sep 17 00:00:00 2001
From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com>
Date: Fri, 3 Oct 2025 15:50:36 +0200
Subject: [PATCH 2/9] Update CI workflows to use Pixi

- Replace mamba-org/setup-micromamba with prefix-dev/setup-pixi
- Update test job to use pixi environments (test-py310, test-py312)
- Update typechecking job to use pixi run typing
- Enable pixi caching for faster CI runs
- Simplify workflow by removing manual dependency installation
---
 .github/workflows/ci.yml | 34 +++++++++++-----------------------
 1 file changed, 11 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0ee289de0..bc994fd3d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -22,55 +22,43 @@ env:
 
 jobs:
   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 }}
     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
+      - uses: prefix-dev/setup-pixi@v0.9.0
         with:
-          environment-name: ship
-          environment-file: environment.yml
-          create-args: >-
-            python=${{matrix.python-version}}
-
-      - run: pip install . --no-deps
+          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
-          --durations=20
+        run: pixi run -e ${{ matrix.pixi-environment }} tests
 
       - name: Upload coverage report
         uses: codecov/codecov-action@v5.4.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
   typechecking:
-    name: mypy
+    name: "TypeChecking: pixi run typing"
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: mamba-org/setup-micromamba@v2
+      - uses: prefix-dev/setup-pixi@v0.9.0
         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
+          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

From 65edf75f0f0fe47a8c814a0a175b1c2b5003a53a Mon Sep 17 00:00:00 2001
From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com>
Date: Fri, 3 Oct 2025 15:51:23 +0200
Subject: [PATCH 3/9] Update contributing guidelines for Pixi

- Replace Conda-based development setup with Pixi
- Add comprehensive Pixi workflows section with examples
- Document testing, docs, and code quality commands
- Include tips for environment management and CI reproduction
- Update dependency management instructions to reference pixi.toml
---
 docs/contributing/index.md | 72 +++++++++++++++++++++++++++-----------
 1 file changed, 51 insertions(+), 21 deletions(-)

diff --git a/docs/contributing/index.md b/docs/contributing/index.md
index 27d6d40c3..171d714e9 100644
--- a/docs/contributing/index.md
+++ b/docs/contributing/index.md
@@ -8,36 +8,66 @@ 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 and `cd` into the repository.
+
+**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.
+
+### Pixi workflows
+
+You can use the following Pixi commands to run common development tasks.
 
-- core dependencies
-- development dependencies (e.g., for testing)
-- documentation dependencies
+**Testing**
 
-then installs the package in editable mode.
+- `pixi run tests` - Run the full test suite using pytest with coverage reporting
+- `pixi run tests-notebooks` - Run notebook tests
 
-### Useful commands
+**Documentation**
 
-The following commands are useful for local development:
+- `pixi run docs` - Build the documentation using Sphinx
+- `pixi run docs-watch` - Build and auto-rebuild documentation when files change (useful for live editing)
 
-- `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
+**Code quality**
 
-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 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-py310 tests` - Run tests using Python 3.10
+- `pixi run -e test-py311 tests` - Run tests using Python 3.11
+- `pixi run -e test-py312 tests` - Run tests using Python 3.12
+
+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 +82,5 @@ 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)

From 66085c9705b8f77abc87bbf40264f333915e6c6f Mon Sep 17 00:00:00 2001
From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com>
Date: Fri, 3 Oct 2025 15:51:45 +0200
Subject: [PATCH 4/9] Add Pixi badge to README

Add Pixi badge to indicate project uses Pixi for environment management
---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index b9a59e706..2444bc700 100644
--- a/README.md
+++ b/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)

From b074772a6f1a164c77b2858e4cf21478e54499b1 Mon Sep 17 00:00:00 2001
From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com>
Date: Fri, 3 Oct 2025 15:52:39 +0200
Subject: [PATCH 5/9] Remove environment.yml

Environment management is now handled by pixi.toml. The environment.yml
file is no longer needed as all dependencies are defined in pixi.toml.
---
 environment.yml | 40 ----------------------------------------
 1 file changed, 40 deletions(-)
 delete mode 100644 environment.yml

diff --git a/environment.yml b/environment.yml
deleted file mode 100644
index e15b21d0f..000000000
--- a/environment.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-name: ship
-channels:
-  - conda-forge
-dependencies:
-  - click
-  - parcels >3.1.0
-  - pyproj >= 3, < 4
-  - sortedcontainers == 2.4.0
-  - opensimplex == 0.4.5
-  - numpy >=1, < 2
-  - pydantic >=2, <3
-  - pip
-  - pyyaml
-  - copernicusmarine >= 2.2.2
-  - openpyxl
-  - yaspin
-  - textual
-
-  # linting
-  - pre-commit
-  - mypy
-
-  # Testing
-  - pytest
-  - pytest-cov
-  - pytest-asyncio
-  - codecov
-  - seabird
-  - setuptools
-
-  # Docs
-  - sphinx>=7.0
-  - myst-parser>=0.13
-  - nbsphinx
-  - ipykernel
-  - pandoc
-  - sphinx-copybutton
-  # - sphinx-autodoc-typehints # https://github.com/OceanParcels/virtualship/pull/125#issuecomment-2668766302
-  - pydata-sphinx-theme
-  - sphinx-autobuild

From 7b6b74ccf50f13cb96b47057174e6095c68f8d5b Mon Sep 17 00:00:00 2001
From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com>
Date: Mon, 6 Oct 2025 14:20:49 +0200
Subject: [PATCH 6/9] Add virtualship source dependency

---
 pixi.toml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/pixi.toml b/pixi.toml
index e6d86f158..4b755b408 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -6,10 +6,11 @@ platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"]
 
 [package]
 name = "virtualship"
-version = "dynamic"
+version = "dynamic" # dynamic versioning needs better support in pixi https://github.com/prefix-dev/pixi/issues/2923#issuecomment-2598460666 . Putting `version = "dynamic"` here for now until pixi recommends something else.
+license = "MIT" # can remove this once https://github.com/prefix-dev/pixi-build-backends/issues/397 is resolved
 
 [package.build]
-backend = { name = "pixi-build-python", version = "==0.3.2" }
+backend = { name = "pixi-build-python", version = "==0.4.0" }
 
 [package.host-dependencies]
 setuptools = "*"
@@ -38,6 +39,7 @@ pyyaml = "*"
 copernicusmarine = ">=2.2.2"
 yaspin = "*"
 textual = "*"
+virtualship = { path = "." }
 
 [feature.py310.dependencies]
 python = "3.10.*"

From e4d39360061f51cdfee23a016582cc3e62ceb87b Mon Sep 17 00:00:00 2001
From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com>
Date: Mon, 6 Oct 2025 14:44:57 +0200
Subject: [PATCH 7/9] Move pytest args to CI call

---
 .github/workflows/ci.yml | 4 +++-
 pixi.toml                | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index bc994fd3d..ac6720f58 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -40,7 +40,9 @@ jobs:
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
 
       - name: Test package
-        run: pixi run -e ${{ matrix.pixi-environment }} tests
+        run:
+          pixi run -e ${{ matrix.pixi-environment }} tests -ra --cov --cov-report=xml --cov-report=term
+          --durations=20
 
       - name: Upload coverage report
         uses: codecov/codecov-action@v5.4.0
diff --git a/pixi.toml b/pixi.toml
index 4b755b408..8164d2d47 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -58,7 +58,7 @@ seabird = "*"
 openpyxl = "*"
 
 [feature.test.tasks]
-tests = "pytest -ra --cov --cov-report=xml --cov-report=term --durations=20"
+tests = "pytest"
 
 [feature.notebooks.dependencies]
 nbval = "*"

From 7c95aa5bb4d6c698a31bd486abb9ae584d8f0182 Mon Sep 17 00:00:00 2001
From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com>
Date: Mon, 6 Oct 2025 14:46:43 +0200
Subject: [PATCH 8/9] Update RTD config

---
 .readthedocs.yaml | 27 +++++++++++++--------------
 1 file changed, 13 insertions(+), 14 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 1c13b28aa..a8b751be8 100644
--- a/.readthedocs.yaml
+++ b/.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

From 00ec92978f082872d283e2224fcd5df6b8d78653 Mon Sep 17 00:00:00 2001
From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com>
Date: Thu, 23 Oct 2025 10:12:34 +0200
Subject: [PATCH 9/9] Add caching of Pixi lock

---
 .github/workflows/ci.yml | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ac6720f58..fe5ee154a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -21,9 +21,13 @@ env:
   FORCE_COLOR: 3
 
 jobs:
+  cache-pixi-lock:
+    uses: Parcels-code/Parcels/.github/workflows/cache-pixi-lock.yml@58cdd6185b3af03785c567914a070288ffd804e0
+
   tests:
     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:
@@ -34,6 +38,10 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+      - uses: actions/cache/restore@v4
+        with:
+          path: pixi.lock
+          key: ${{ needs.cache-pixi-lock.outputs.cache-id }}
       - uses: prefix-dev/setup-pixi@v0.9.0
         with:
           cache: true
@@ -51,10 +59,15 @@ jobs:
   typechecking:
     name: "TypeChecking: pixi run typing"
     runs-on: ubuntu-latest
+    needs: cache-pixi-lock
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+      - uses: actions/cache/restore@v4
+        with:
+          path: pixi.lock
+          key: ${{ needs.cache-pixi-lock.outputs.cache-id }}
       - uses: prefix-dev/setup-pixi@v0.9.0
         with:
           cache: true