Merge branch 'v4-dev' into runge-kutta2

Author: erikvansebille

.github/CONTRIBUTING.md

@@ -1 +1 @@
-See https://docs.oceanparcels.org/en/latest/contributing.html
+See https://docs.parcels-code.org/en/latest/contributing.html

.github/ISSUE_TEMPLATE/config.yml

@@ -1,7 +1,7 @@
 contact_links:
   - name: 🙏 Parcels use question, help, or support
-    url: https://github.com/OceanParcels/parcels/discussions/new?category=q-a
+    url: https://github.com/Parcels-code/parcels/discussions/new?category=q-a
     about: Have a question about Parcels? Or do you need troubleshooting for a specific usecase? Then start a Q&A Discussion thread instead, and we'll be happy to help.
   - name: 💬 Other Parcels discussion
-    url: https://github.com/OceanParcels/parcels/discussions
+    url: https://github.com/Parcels-code/parcels/discussions
     about: For general discussion about Parcels, or to share your work with the community, please use the Discussions tab.

.github/ci/recipe.yaml

@@ -29,43 +29,35 @@ requirements:
     - wheel
   run:
     - python >=3.11
-    - cftime
-    - dask
-    - matplotlib-base >=2.0.2
-    - netcdf4 >=1.1.9
-    - numpy >=1.11
-    - platformdirs
-    - pytest
-    - scipy >=0.16.0
-    - trajan
-    - tqdm
-    - xarray >=0.10.8
-    - cf_xarray
-    - xgcm
-    - zarr >=2.11.0,!=2.18.0,<3
+    - cftime >=1.6.3
+    - dask >=2024.5.1
+    - netcdf4 >=1.7.2
+    - numpy >=2.1.0
+    - tqdm >=4.50.0
+    - xarray >=2024.5.0
+    - cf_xarray >=0.8.6
+    - xgcm >=0.9.0
+    - zarr >=2.15.0,!=2.18.0,<3
     - uxarray>=2025.3.0
     - pyogrio # needed for geopandas (uxarray -> geoviews -> geopandas -> pyogrio, but for some reason conda doesn't pick it up automatically)
-    - pooch
+    - pooch >=1.8.0
 
 tests:
   - python:
       imports:
         - parcels
 
 about:
-  homepage: https://github.com/OceanParcels/parcels
+  homepage: https://github.com/Parcels-code/parcels
   license: MIT
   license_file: LICENSE.md
-  summary: Probably A Really Computationally Efficient Lagrangian Simulator
+  summary: Parcels - A highly customisable Lagrangian simulation framework
   description: |
-    Parcels (Probably A Really Computationally Efficient Lagrangian Simulator)
-    is a set of Python classes and methods to create customisable particle
-    tracking simulations using output from Ocean Circulation models.
-    Parcels can be used to track passive and active particulates such as
-    water, nutrients, plankton, plastic and fish.
-  documentation: https://oceanparcels.org/
-  repository: https://github.com/OceanParcels/parcels
+    Parcels provides a set of Python classes and methods to create customisable particle tracking simulations using gridded output from (ocean) circulation models.
+  documentation: https://parcels-code.org/
+  repository: https://github.com/Parcels-code/parcels
 
 extra:
   recipe-maintainers:
     - VeckoTheGecko
+    - erikvansebille

.github/workflows/additional.yml

@@ -13,7 +13,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Setup micromamba
         uses: mamba-org/setup-micromamba@v2
         with:
@@ -36,7 +36,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
+      - uses: actions/checkout@v5
       - uses: prefix-dev/[email protected]
       - run: pixi run docs-linkcheck

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

@@ -2,6 +2,9 @@ name: Generate and cache Pixi lockfile
 
 on:
   workflow_call:
+    inputs:
+      pixi-version:
+        type: string
     outputs:
       cache-id:
         description: "The lock file contents"
@@ -17,6 +20,7 @@ jobs:
       - 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"
@@ -25,11 +29,11 @@ jobs:
         with:
           path: |
             pixi.lock
-          key: ${{ steps.date.outputs.date }}_${{hashFiles('pixi.toml')}}
+          key: ${{ steps.date.outputs.date }}_${{inputs.pixi-version}}_${{hashFiles('pixi.toml')}}
       - uses: prefix-dev/[email protected]
         if: ${{ !steps.restore.outputs.cache-hit }}
         with:
-          pixi-version: v0.56.0
+          pixi-version: ${{ inputs.pixi-version }}
           run-install: false
       - name: Run pixi lock
         if: ${{ !steps.restore.outputs.cache-hit }}
@@ -42,7 +46,7 @@ jobs:
             pixi.lock
           key: ${{ steps.restore.outputs.cache-primary-key }}
       - name: Upload pixi.lock
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: pixi-lock
           path: pixi.lock

.github/workflows/ci.yml

@@ -28,17 +28,22 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu] #, mac, windows] # TODO v4: Re-enable windows and mac
+        os: [ubuntu, mac, windows]
         pixi-environment: [test-latest]
         include:
           - os: ubuntu
             pixi-environment: "test-py311"
+          - os: ubuntu
+            pixi-environment: "test-py313"
+          - os: ubuntu
+            pixi-environment: "test-minimum"
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Restore cached pixi lockfile
         uses: actions/cache/restore@v4
         id: restore-pixi-lock
         with:
+          enableCrossOsArchive: true
           path: |
             pixi.lock
           key: ${{ needs.cache-pixi-lock.outputs.cache-id }}
@@ -50,14 +55,14 @@ jobs:
         run: |
           pixi run -e ${{ matrix.pixi-environment }} tests -v -s --cov=parcels --cov-report=xml --html="${{ env.COVERAGE_REPORT }}" --self-contained-html
       - name: Codecov
-        uses: codecov/codecov-action@v5.3.1
+        uses: codecov/codecov-action@v5.5.1
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
           flags: unit-tests
       - name: Upload test results
         if: ${{ always() }} # Always run this step, even if tests fail
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: Unittest report ${{ matrix.os }}-${{ matrix.pixi-environment }}
           path: ${{ env.COVERAGE_REPORT }}
@@ -78,11 +83,12 @@ jobs:
           - os: ubuntu
             python-version: "3.11"
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Restore cached pixi lockfile
         uses: actions/cache/restore@v4
         id: restore-pixi-lock
         with:
+          enableCrossOsArchive: true
           path: |
             pixi.lock
           key: ${{ needs.cache-pixi-lock.outputs.cache-id }}
@@ -94,14 +100,14 @@ jobs:
         run: |
           pixi run test-notebooks -v -s --html="${{ env.COVERAGE_REPORT }}" --self-contained-html --cov=parcels --cov-report=xml
       - name: Codecov
-        uses: codecov/codecov-action@v5.3.1
+        uses: codecov/codecov-action@v5.5.1
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
           flags: integration-tests
       - name: Upload test results
         if: ${{ always() }} # Always run this step, even if tests fail
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: Integration test report ${{ matrix.os }}-${{ matrix.pixi-environment }}
           path: ${{ env.COVERAGE_REPORT }}
@@ -113,7 +119,7 @@ jobs:
       - typechecking
     steps:
       - name: Merge Artifacts
-        uses: actions/upload-artifact/merge@v4
+        uses: actions/upload-artifact/merge@v5
         with:
           name: Testing reports
           pattern: "* report *"
@@ -125,7 +131,7 @@ jobs:
     needs: [cache-pixi-lock]
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Restore cached pixi lockfile
         uses: actions/cache/restore@v4
         id: restore-pixi-lock
@@ -142,7 +148,7 @@ jobs:
           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
+        uses: actions/upload-artifact@v5
         with:
           name: Mypy report
           path: mypy-report

.github/workflows/nightly.yml

@@ -11,9 +11,9 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Build conda package
-        uses: prefix-dev/[email protected].19
+        uses: prefix-dev/[email protected].34
         with:
           recipe-path: .github/ci/recipe.yaml
 

.github/workflows/pypi-release.yml

@@ -11,12 +11,12 @@ on:
 jobs:
   build-artifacts:
     runs-on: ubuntu-latest
-    if: github.repository == 'OceanParcels/parcels'
+    if: github.repository == 'Parcels-code/parcels'
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         name: Install Python
         with:
           python-version: "3.11"
@@ -42,7 +42,7 @@ jobs:
           else
             echo "✅ Looks good"
           fi
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         with:
           name: releases
           path: dist
@@ -51,11 +51,11 @@ jobs:
     needs: build-artifacts
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         name: Install Python
         with:
           python-version: "3.11"
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v6
         with:
           name: releases
           path: dist
@@ -84,7 +84,7 @@ jobs:
     if: github.event_name == 'release'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v6
         with:
           name: releases
           path: dist
@@ -102,5 +102,5 @@ jobs:
           channels: conda-forge
       - run: conda install -c conda-forge pip
       - run: pip install parcels --no-cache
-      - run: curl https://raw.githubusercontent.com/OceanParcels/parcels/main/docs/examples/example_peninsula.py > example_peninsula.py
+      - run: curl https://raw.githubusercontent.com/Parcels-code/parcels/main/docs/examples/example_peninsula.py > example_peninsula.py
       - run: python example_peninsula.py

.gitignore

@@ -29,5 +29,8 @@ src/parcels/_version_setup.py
 .pixi
 *.egg-info
 
-# Ignore pixi.lock file for now as Vecko is the only one using pixi for development. This should be checked into VCS if it becomes a more common tool.
+# 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

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -10,7 +10,7 @@ repos:
         types: [text]
         files: \.(json|ipynb)$
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.5
+    rev: v0.14.2
     hooks:
       - id: ruff
         name: ruff lint (.py)