Merge branch 'v4-dev' into API_change_pset_depth_to_z

Author: erikvansebille

.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/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 }}

docs/community/contributing.md

@@ -49,8 +49,6 @@ If you're having trouble using Parcels, feel free to create a discussion in our
 
 In the [Projects panel](https://github.com/OceanParcels/parcels/projects?query=is%3Aopen), you'll see the "Parcels development" project. This is used by the core development team for project management, as well as drafting up new ideas for the codebase that aren't mature enough to be issues themselves. Everything in "backlog" is not being actively worked on and is fair game for open source contributions.
 
-(editing-parcels-code)=
-
 ## Development
 
 ### Environment setup
@@ -77,7 +75,19 @@ Now you have a development installation of Parcels, as well as a bunch of develo
 
 ### Pixi workflows
 
-You can use the following Pixi commands to run common development tasks.
+**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.
+```
+
+See below for more Pixi commands relevant to development.
 
 **Testing**
 
@@ -99,21 +109,13 @@ You can use the following Pixi commands to run common development tasks.
 
 Parcels 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-py311 tests` - Run tests in the environment containing Python 3.11
+- `pixi run -e test-py312 tests` - Run tests in the environment containing 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 those familiar with Conda, you are used to activating an environment. With Pixi, you can do the same by doing `pixi shell <env-name>`. For example, `pixi shell test-latest` will drop you into a shell where you can run commands such as `pytest` like normal. You can exit the shell with `exit` or `Ctrl+D`.
 ```
 
 ### Changing code

docs/documentation/index.md

@@ -2,71 +2,76 @@
 
 Shown below are several documentation and tutorial Jupyter notebooks and scripts which go through various aspects of Parcels.
 
+```{note}
+The tutorials written for Parcels v3 are currently being updated for Parcels v4. Shown below are only the notebooks which have been updated.
+[Feel free to post a Discussion on GitHub](https://github.com/OceanParcels/Parcels/discussions/categories/ideas) if you feel like v4 needs a specific tutorial that wasn't in v3, or [post an issue](https://github.com/OceanParcels/Parcels/issues/new?template=01_feature.md) if you feel that the notebooks below can be improved!
+```
+
 ```{nbgallery}
 :caption: Overview
 :name: tutorial-overview
 
-../examples/tutorial_parcels_structure.ipynb
-../examples/parcels_tutorial.ipynb
-../examples/tutorial_output.ipynb
+<!-- ../examples/tutorial_parcels_structure.ipynb -->
+<!-- ../examples/parcels_tutorial.ipynb -->
+<!-- ../examples/tutorial_output.ipynb -->
 ```
 
 ```{nbgallery}
 :caption: Setting up FieldSets
 :name: tutorial-fieldsets
 
-../examples/documentation_indexing.ipynb
-../examples/tutorial_nemo_curvilinear.ipynb
-../examples/tutorial_nemo_3D.ipynb
-../examples/tutorial_croco_3D.ipynb
-../examples/tutorial_timevaryingdepthdimensions.ipynb
-../examples/tutorial_periodic_boundaries.ipynb
-../examples/tutorial_interpolation.ipynb
-../examples/tutorial_unitconverters.ipynb
+<!-- ../examples/documentation_indexing.ipynb -->
+<!-- ../examples/tutorial_nemo_curvilinear.ipynb -->
+<!-- ../examples/tutorial_nemo_3D.ipynb -->
+<!-- ../examples/tutorial_croco_3D.ipynb -->
+<!-- ../examples/tutorial_timevaryingdepthdimensions.ipynb -->
+<!-- ../examples/tutorial_periodic_boundaries.ipynb -->
+<!-- ../examples/tutorial_interpolation.ipynb -->
+<!-- ../examples/tutorial_unitconverters.ipynb -->
 ```
 
 ```{nbgallery}
 :caption: Creating ParticleSets
 :name: tutorial-particlesets
 
-../examples/tutorial_delaystart.ipynb
+<!-- ../examples/tutorial_delaystart.ipynb -->
 ```
 
 ```{nbgallery}
 :caption: Writing kernels to be executed on each particle
 :name: tutorial-kernels
 
-../examples/tutorial_diffusion.ipynb
-../examples/tutorial_sampling.ipynb
-../examples/tutorial_particle_field_interaction.ipynb
-../examples/tutorial_interaction.ipynb
-../examples/tutorial_analyticaladvection.ipynb
-../examples/tutorial_kernelloop.ipynb
+<!-- ../examples/tutorial_diffusion.ipynb -->
+<!-- ../examples/tutorial_sampling.ipynb -->
+<!-- ../examples/tutorial_particle_field_interaction.ipynb -->
+<!-- ../examples/tutorial_interaction.ipynb -->
+<!-- ../examples/tutorial_analyticaladvection.ipynb -->
+<!-- ../examples/tutorial_kernelloop.ipynb -->
 ```
 
 ```{nbgallery}
 :caption: Other tutorials
 :name: tutorial-other
 
-../examples/tutorial_peninsula_AvsCgrid.ipynb
-../examples/documentation_MPI.ipynb
-../examples/documentation_stuck_particles.ipynb
-../examples/documentation_unstuck_Agrid.ipynb
-../examples/documentation_LargeRunsOutput.ipynb
-../examples/documentation_geospatial.ipynb
-../examples/documentation_advanced_zarr.ipynb
+<!-- ../examples/tutorial_peninsula_AvsCgrid.ipynb -->
+<!-- ../examples/documentation_MPI.ipynb -->
+<!-- ../examples/documentation_stuck_particles.ipynb -->
+<!-- ../examples/documentation_unstuck_Agrid.ipynb -->
+<!-- ../examples/documentation_LargeRunsOutput.ipynb -->
+<!-- ../examples/documentation_geospatial.ipynb -->
+<!-- ../examples/documentation_advanced_zarr.ipynb -->
 ```
 
 ```{nbgallery}
 :caption: Worked examples
 :name: tutorial-examples
 
 ../examples/tutorial_Argofloats.ipynb
-../examples/documentation_homepage_animation.ipynb
+<!-- ../examples/documentation_homepage_animation.ipynb -->
 ```
 
 ## Python Example Scripts
 
-```{toctree}
+<!-- ```{toctree}
 additional_examples
-```
+``` -->

pixi.toml

@@ -7,9 +7,10 @@ platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"]
 [package]
 name = "parcels"
 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 = "*"
@@ -26,6 +27,7 @@ pre-commit = { features = ["pre-commit"], no-default-feature = true }
 
 [dependencies] # keep section in sync with pyproject.toml dependencies
 python = ">=3.11,<3.13"
+parcels = { path = "." }
 netcdf4 = ">=1.1.9"
 numpy = ">=1.9.1"
 tqdm = "*"