Merge remote-tracking branch 'upstream/main' into update-convert

Author: VeckoTheGecko

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,14 @@
+<!-- Feel free to remove check-list items aren't relevant to your change -->
+
+- [ ] Closes #xxxx
+- [ ] Tests added
+- [ ] This PR targets the correct branch (`main` for normal development, `v3-support` for v3 support)
+
+### AI Disclosure
+
+<!--- Please review our AI & contribution guidelines (https://docs.oceanparcels.org/en/main/development/policies.html#use-of-ai-in-development). Remove this section if your PR does not contain AI-generated content. --->
+
+- [ ] This PR contains AI-generated content.
+  - [ ] I have tested any AI-generated content in my PR.
+  - [ ] I take responsibility for any AI-generated content in my PR.
+  - Describe how you used it (e.g., by pasting your prompt):

.github/workflows/ci.yml

@@ -77,6 +77,7 @@ jobs:
       - uses: prefix-dev/setup-pixi@v0.9.0
         with:
           pixi-version: ${{ needs.cache-pixi-lock.outputs.pixi-version }}
+          locked: false # TODO: Remove once v7 of the lock file is removed, or once we stop having external source dependencies https://github.com/Parcels-code/Parcels/pull/2550#issuecomment-4088660238
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
       # https://github.com/actions/cache/blob/main/tips-and-workarounds.md#update-a-cache
@@ -137,6 +138,7 @@ jobs:
       - uses: prefix-dev/setup-pixi@v0.9.0
         with:
           pixi-version: ${{ needs.cache-pixi-lock.outputs.pixi-version }}
+          locked: false # TODO: Remove once v7 of the lock file is removed, or once we stop having external source dependencies https://github.com/Parcels-code/Parcels/pull/2550#issuecomment-4088660238
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
       - name: Integration test
@@ -180,6 +182,7 @@ jobs:
       - uses: prefix-dev/setup-pixi@v0.9.0
         with:
           pixi-version: ${{ needs.cache-pixi-lock.outputs.pixi-version }}
+          locked: false # TODO: Remove once v7 of the lock file is removed, or once we stop having external source dependencies https://github.com/Parcels-code/Parcels/pull/2550#issuecomment-4088660238
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
       - name: Typechecking
@@ -202,6 +205,7 @@ jobs:
       - uses: prefix-dev/setup-pixi@v0.9.0
         with:
           pixi-version: ${{ needs.cache-pixi-lock.outputs.pixi-version }}
+          locked: false # TODO: Remove once v7 of the lock file is removed, or once we stop having external source dependencies https://github.com/Parcels-code/Parcels/pull/2550#issuecomment-4088660238
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
       - name: Find the alpha version of Parcels
@@ -212,7 +216,7 @@ jobs:
         run: |
           for pkg in $(find output -type f \( -name "*.conda" -o -name "*.tar.bz2" \) ); do
             echo "Uploading ${pkg}"
-            pixi run -e rattler-build rattler-build upload prefix -c parcels "${pkg}"
+            pixi run -e build rattler-build upload prefix -c parcels "${pkg}"
           done
         env:
           PREFIX_API_KEY: ${{ secrets.PREFIX_API_KEY }}

CITATION.cff

@@ -4,6 +4,9 @@ authors:
   - family-names: "Van Sebille"
     given-names: "Erik"
     orcid: "https://orcid.org/0000-0003-2041-0704"
+  - family-names: "Hodgskin"
+    given-names: "Nick"
+    orcid: "https://orcid.org/0009-0003-0778-3183"
   - family-names: "Kehl"
     given-names: "Christian"
     orcid: "https://orcid.org/0000-0003-4200-1450"

docs/getting_started/tutorial_output.ipynb

@@ -162,9 +162,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Note that if you are running Parcels on multiple processors with `mpirun`, you will need to concatenate the files of each processor, see also the [MPI documentation](https://docs.oceanparcels.org/en/latest/examples/documentation_MPI.html#Reading-in-the-ParticleFile-data-in-zarr-format).\n",
-    "\n",
-    "Also, once you have loaded the data as an `xarray` DataSet using `xr.open_zarr()`, you can always save the file to NetCDF if you prefer with the `.to_netcdf()` method.\n"
+    "Once you have loaded the data as an `xarray` DataSet using `xr.open_zarr()`, you can always save the file to NetCDF if you prefer with the `.to_netcdf()` method.\n"
    ]
   },
   {

docs/user_guide/examples_v3/documentation_LargeRunsOutput.ipynb

@@ -60,7 +60,7 @@
    "id": "4",
    "metadata": {},
    "source": [
-    "## How to save the output of an MPI ocean parcels run to a single zarr dataset\n"
+    "## (TODO: Remove section now that we don't support MPI) How to save the output of an MPI ocean parcels run to a single zarr dataset\n"
    ]
   },
   {

docs/user_guide/examples_v3/documentation_MPI.ipynb

@@ -88,11 +88,6 @@ def AgeP(particle, fieldset, time):  # pragma: no cover
         particle.delete()
 
 
-def simple_partition_function(coords, mpi_size=1):
-    """A very simple partition function that assigns particles to processors (for MPI testing purposes))"""
-    return np.linspace(0, mpi_size, coords.shape[0], endpoint=False, dtype=np.int32)
-
-
 def stommel_example(
     npart=1,
     verbose=False,
@@ -101,7 +96,6 @@ def stommel_example(
     outfile="StommelParticle.zarr",
     repeatdt=None,
     maxage=None,
-    custom_partition_function=False,
 ):
     parcels.timer.fieldset = parcels.timer.Timer(
         "FieldSet", parent=parcels.timer.stommel
@@ -125,27 +119,15 @@ def stommel_example(
     ]
     MyParticle = parcels.Particle.add_variables(extra_vars)
 
-    if custom_partition_function:
-        pset = parcels.ParticleSet.from_line(
-            fieldset,
-            size=npart,
-            pclass=MyParticle,
-            repeatdt=repeatdt,
-            start=(10e3, 5000e3),
-            finish=(100e3, 5000e3),
-            time=0,
-            partition_function=simple_partition_function,
-        )
-    else:
-        pset = parcels.ParticleSet.from_line(
-            fieldset,
-            size=npart,
-            pclass=MyParticle,
-            repeatdt=repeatdt,
-            start=(10e3, 5000e3),
-            finish=(100e3, 5000e3),
-            time=0,
-        )
+    pset = parcels.ParticleSet.from_line(
+        fieldset,
+        size=npart,
+        pclass=MyParticle,
+        repeatdt=repeatdt,
+        start=(10e3, 5000e3),
+        finish=(100e3, 5000e3),
+        time=0,
+    )
 
     if verbose:
         print(f"Initial particle positions:\n{pset}")
@@ -245,12 +227,6 @@ def main(args=None):
         type=int,
         help="max age of the particles (after which particles are deleted)",
     )
-    p.add_argument(
-        "-cpf",
-        "--custom_partition_function",
-        default=False,
-        help="Use a custom partition_function (for MPI testing purposes)",
-    )
     args = p.parse_args(args)
 
     parcels.timer.args.stop()
@@ -262,7 +238,6 @@ def main(args=None):
         outfile=args.outfile,
         repeatdt=args.repeatdt,
         maxage=args.maxage,
-        custom_partition_function=args.custom_partition_function,
     )
     parcels.timer.stommel.stop()
     parcels.timer.root.stop()

docs/user_guide/examples_v3/example_stommel.py

@@ -27,7 +27,7 @@ holoviews = ">=1.22.0" # https://github.com/prefix-dev/rattler-build/issues/2326
 uxarray = ">=2025.3.0"
 dask = ">=2024.5.1"
 zarr = ">=2.15.0,!=2.18.0,<3"
-xgcm = ">=0.9.0"
+xgcm = { git = "https://github.com/xgcm/xgcm", rev = "master" } # TODO: Switch to release version after release is cut
 cf_xarray = ">=0.8.6"
 cftime = ">=1.6.3"
 pooch = ">=1.8.0"
@@ -54,7 +54,7 @@ xarray = "2024.5.*"
 uxarray = "2025.3.*"
 dask = "2024.5.*"
 zarr = "2.15.*"
-xgcm = "0.9.*"
+xgcm = { version = "0.9.*", channel = "conda-forge" }
 cf_xarray = "0.8.*"
 cftime = "1.6.*"
 pooch = "1.8.*"
@@ -102,6 +102,9 @@ memray = "*"
 [feature.devtools.target.osx-arm64.dependencies]
 memray = "*"
 
+[feature.devtools.pypi-dependencies]
+tuna = ">=0.5.11"
+
 [feature.docs.dependencies]
 parcels = { path = "." }
 numpydoc = "*"