Merge branch 'v4-dev' into removing_applyconversion_from_vectorinterpolation

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/01_feature.md

@@ -2,6 +2,6 @@
 name: 🔼 Parcels feature requests, and other enhancements
 about: Suggest an improvement to the parcels codebase.
 title: ""
-labels: ""
+labels: ["needs-triage"]
 assignees: ""
 ---

.github/ISSUE_TEMPLATE/02_bug.yaml

@@ -1,6 +1,6 @@
 name: "🐛 Bug Report"
 description: Describe a bug in the parcels codebase. For support related to your specific use case, please post in Q&A in our Discussions tab.
-labels: ["bug"]
+labels: ["bug", "needs-triage"]
 body:
   - type: "input"
     attributes:

.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/cache-pixi-lock.yml

@@ -17,7 +17,6 @@ jobs:
       - uses: actions/checkout@v5
         with:
           fetch-depth: 0
-          sparse-checkout: pixi.toml
       - name: Get current date
         id: date
         run: echo "date=$(date +'%Y-%m-%d')" >> "$GITHUB_OUTPUT"
@@ -30,7 +29,7 @@ jobs:
       - uses: prefix-dev/[email protected]
         if: ${{ !steps.restore.outputs.cache-hit }}
         with:
-          pixi-version: v0.49.0
+          pixi-version: v0.56.0
           run-install: false
       - name: Run pixi lock
         if: ${{ !steps.restore.outputs.cache-hit }}

.github/workflows/ci.yml

@@ -33,6 +33,8 @@ jobs:
         include:
           - os: ubuntu
             pixi-environment: "test-py311"
+          - os: ubuntu
+            pixi-environment: "test-minimum"
     steps:
       - uses: actions/checkout@v4
       - name: Restore cached pixi lockfile

.github/workflows/pypi-release.yml

@@ -11,7 +11,7 @@ on:
 jobs:
   build-artifacts:
     runs-on: ubuntu-latest
-    if: github.repository == 'OceanParcels/parcels'
+    if: github.repository == 'Parcels-code/parcels'
     steps:
       - uses: actions/checkout@v4
         with:
@@ -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

@@ -20,7 +20,7 @@ Profile.prof
 .eggs/*
 parcels.egg-info/*
 dist/parcels*.egg
-parcels/_version_setup.py
+src/parcels/_version_setup.py
 .pytest_cache
 .hypothesis
 .coverage
@@ -29,5 +29,8 @@ 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

CITATION.cff

@@ -14,9 +14,9 @@ authors:
     given-names: "Philippe"
     orcid: "https://orcid.org/0000-0003-0100-5834"
   - name: "The Parcels contributors"
-    website: "https://github.com/OceanParcels/parcels/graphs/contributors"
+    website: "https://github.com/Parcels-code/parcels/graphs/contributors"
 title: "Parcels"
 version: 3.1.2
 doi: 10.5281/zenodo.14845686
 date-released: 2025-02-10
-url: "https://github.com/OceanParcels/parcels"
+url: "https://github.com/Parcels-code/parcels"