Merge branch 'v4-dev' into gsw_tutorial

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/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

@@ -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

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"

LICENSE.md

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2019, OceanParcels team
+Copyright (c) 2025, Parcels team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -7,20 +7,20 @@
 [![EffVer Versioning](https://img.shields.io/badge/version_scheme-EffVer-0097a7)](https://jacobtomlinson.dev/effver)
 [![Xarray](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/pydata/xarray/refs/heads/main/doc/badge.json)](https://xarray.dev)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
-[![unit-tests](https://github.com/OceanParcels/parcels/actions/workflows/ci.yml/badge.svg)](https://github.com/OceanParcels/parcels/actions/workflows/ci.yml)
-[![codecov](https://codecov.io/gh/OceanParcels/parcels/branch/main/graph/badge.svg)](https://codecov.io/gh/OceanParcels/parcels)
+[![unit-tests](https://github.com/Parcels-code/parcels/actions/workflows/ci.yml/badge.svg)](https://github.com/Parcels-code/parcels/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/Parcels-code/parcels/branch/main/graph/badge.svg)](https://codecov.io/gh/Parcels-code/parcels)
 [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/5353/badge)](https://bestpractices.coreinfrastructure.org/projects/5353)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/OceanParcels/parcels/main?labpath=docs%2Fexamples%2Fparcels_tutorial.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/Parcels-code/parcels/main?labpath=docs%2Fexamples%2Fparcels_tutorial.ipynb)
 [![LinkedIn](https://custom-icon-badges.demolab.com/badge/LinkedIn-0A66C2?logo=linkedin-white&logoColor=fff)](https://www.linkedin.com/company/parcelscode/)
 
 > [!WARNING]
 > This branch is `v4-dev` - version 4 of Parcels which is in active development. See `main` (or the tags) to browse stable versions of Parcels.
 
-**Parcels** (**P**robably **A** **R**eally **C**omputationally **E**fficient **L**agrangian **S**imulator) 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, plankton, [plastic](http://www.topios.org/) and [fish](https://github.com/Jacketless/IKAMOANA).
+**Parcels** provides a set of Python classes and methods to create customisable particle tracking simulations using gridded output from (ocean) circulation models. Parcels can be used to track passive and active particulates such as water, plankton, [plastic](http://www.topios.org/) and [fish](https://github.com/Jacketless/IKAMOANA).
 
-![Arctic-SO-medusaParticles](https://github.com/OceanParcels/oceanparcels_website/blob/main/images/homepage.gif)
+![Arctic-SO-medusaParticles](https://github.com/Parcels-code/oceanparcels_website/blob/main/images/homepage.gif)
 
-_Animation of virtual particles carried by ocean surface flow in the global oceans. The particles are advected with [Parcels](http://oceanparcels.org/) in data from the [NEMO Ocean Model](https://www.nemo-ocean.eu/)._
+_Animation of virtual particles carried by ocean surface flow in the global oceans. The particles are advected with [Parcels](http://parcels-code.org/) in data from the [NEMO Ocean Model](https://www.nemo-ocean.eu/)._
 
 ### Parcels manuscript and code
 
@@ -38,13 +38,13 @@ _Kehl, C, PD Nooteboom, MLA Kaandorp and E van Sebille (2023) Efficiently simula
 
 ### Further information
 
-See [oceanparcels.org](http://oceanparcels.org/) for further information about [installing](https://docs.oceanparcels.org/en/latest/installation.html) and [running](https://docs.oceanparcels.org/en/latest/documentation.html) the Parcels code, as well as extended [documentation](https://docs.oceanparcels.org/en/latest/reference.html) of the methods and classes.
+See [parcels-code.org](http://parcels-code.org/) for further information about [installing](https://docs.parcels-code.org/en/latest/installation.html) and [running](https://docs.parcels-code.org/en/latest/documentation.html) the Parcels code, as well as extended [documentation](https://docs.parcels-code.org/en/latest/reference.html) of the methods and classes.
 
 ### Contributors
 
-<a href="https://github.com/oceanparcels/parcels/graphs/contributors">
-  <img src="https://contrib.rocks/image?repo=oceanparcels/parcels" />
+<a href="https://github.com/parcels-code/parcels/graphs/contributors">
+  <img src="https://contrib.rocks/image?repo=parcels-code/parcels" />
 </a>
 
-**All contributions are welcome! See the [contributing page](https://docs.oceanparcels.org/en/latest/contributing.html) in our documentation to see how to get involved.**
+**All contributions are welcome! See the [contributing page](https://docs.parcels-code.org/en/latest/contributing.html) in our documentation to see how to get involved.**
 Image made with [contrib.rocks](https://contrib.rocks).