Merge branch 'v4-dev' into convert_from_copernicusmarine

erikvansebille · web-flow · commit 0bb62084c141 · 2026-01-15T13:18:38.000+01:00
diff --git a/.github/workflows/cache-pixi-lock.yml b/.github/workflows/cache-pixi-lock.yml
@@ -12,41 +12,41 @@ on:
 
 jobs:
   cache-pixi-lock:
-    name: Generate output
+    name: Pixi lock
     runs-on: ubuntu-latest
     outputs:
       cache-id: ${{ steps.restore.outputs.cache-primary-key }}
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
           submodules: recursive
       - name: Get current date
         id: date
         run: echo "date=$(date +'%Y-%m-%d')" >> "$GITHUB_OUTPUT"
-      - uses: actions/cache/restore@v4
+      - uses: actions/cache/restore@v5
         id: restore
         with:
           path: |
             pixi.lock
-          key: ${{ steps.date.outputs.date }}_${{inputs.pixi-version}}_${{hashFiles('pixi.toml')}}
-      - uses: prefix-dev/setup-pixi@v0.9.0
+          key: ${{ steps.date.outputs.date }}_${{ inputs.pixi-version }}_${{hashFiles('pixi.toml')}}
+      - uses: prefix-dev/setup-pixi@v0.9.3
         if: ${{ !steps.restore.outputs.cache-hit }}
         with:
           pixi-version: ${{ inputs.pixi-version }}
           run-install: false
       - name: Run pixi lock
         if: ${{ !steps.restore.outputs.cache-hit }}
         run: pixi lock
-      - uses: actions/cache/save@v4
+      - uses: actions/cache/save@v5
         if: ${{ !steps.restore.outputs.cache-hit }}
         id: cache
         with:
           path: |
             pixi.lock
           key: ${{ steps.restore.outputs.cache-primary-key }}
       - name: Upload pixi.lock
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@v6
         with:
           name: pixi-lock
           path: pixi.lock
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -16,9 +16,14 @@ defaults:
   run:
     shell: bash -el {0}
 
+env:
+  PIXI_VERSION: "v0.63.0"
+
 jobs:
   cache-pixi-lock:
     uses: ./.github/workflows/cache-pixi-lock.yml
+    with:
+      pixi-version: "v0.62.2" # keep in sync with env var above
   unit-test:
     name: "Unit tests: ${{ matrix.os }} | pixi run -e ${{ matrix.pixi-environment }} tests"
     runs-on: ${{ matrix.os }}-latest
@@ -49,6 +54,7 @@ jobs:
           key: ${{ needs.cache-pixi-lock.outputs.cache-id }}
       - uses: prefix-dev/setup-pixi@v0.9.0
         with:
+          pixi-version: ${{ env.PIXI_VERSION }}
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'v4-dev' }} # TODO: Update v4-dev to main when v4 is released
       # https://github.com/actions/cache/blob/main/tips-and-workarounds.md#update-a-cache
@@ -112,6 +118,7 @@ jobs:
           key: ${{ needs.cache-pixi-lock.outputs.cache-id }}
       - uses: prefix-dev/setup-pixi@v0.9.0
         with:
+          pixi-version: ${{ env.PIXI_VERSION }}
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'v4-dev' }} # TODO: Update v4-dev to main when v4 is released
       - name: Integration test
@@ -159,6 +166,7 @@ jobs:
           key: ${{ needs.cache-pixi-lock.outputs.cache-id }}
       - uses: prefix-dev/setup-pixi@v0.9.0
         with:
+          pixi-version: ${{ env.PIXI_VERSION }}
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'v4-dev' }} # TODO: Update v4-dev to main when v4 is released
       - name: Typechecking
diff --git a/docs/getting_started/explanation_concepts.md b/docs/getting_started/explanation_concepts.md
@@ -164,7 +164,7 @@ We have to be careful with writing kernels for vector fields on Curvilinear grid
 - [Sample fields like temperature](../user_guide/examples/tutorial_sampling.ipynb).
 - [Mimic the behaviour of ARGO floats](../user_guide/examples/tutorial_Argofloats.ipynb).
 - [Add diffusion to approximate subgrid-scale processes and unresolved physics](../user_guide/examples/tutorial_diffusion.ipynb).
-- [Convert between units in m/s and degrees](../user_guide/examples/tutorial_unitconverters.ipynb).
+- [Convert velocities between units in m s<sup>-1</sup> and degrees s<sup>-1</sup>](../user_guide/examples/tutorial_velocityconversion.ipynb).
 ```
 
 ## 4. Execute
diff --git a/docs/user_guide/examples/tutorial_nemo_3D.ipynb b/docs/user_guide/examples/tutorial_nemo_3D.ipynb
@@ -5,7 +5,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Nemo 3D tutorial\n"
+    "# 🖥️ Nemo 3D tutorial\n"
    ]
   },
   {
diff --git a/docs/user_guide/examples/tutorial_velocityconversion.ipynb b/docs/user_guide/examples/tutorial_velocityconversion.ipynb
diff --git a/docs/user_guide/index.md b/docs/user_guide/index.md
@@ -26,8 +26,8 @@ The tutorials written for Parcels v3 are currently being updated for Parcels v4.
 :titlesonly:
 examples/explanation_grids.md
 examples/tutorial_nemo_curvilinear.ipynb
-examples_v3/tutorial_nemo_3D.ipynb  # TODO move to examples folder
-examples/tutorial_unitconverters.ipynb
+examples/tutorial_nemo_3D.ipynb
+examples/tutorial_velocityconversion.ipynb
 examples/tutorial_nestedgrids.ipynb
 ```
 
diff --git a/pixi.toml b/pixi.toml
@@ -10,7 +10,7 @@ version = "dynamic" # dynamic versioning needs better support in pixi https://gi
 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 = "==0.4.0" }
+backend = { name = "pixi-build-python", version = "0.4.*" }
 
 [package.host-dependencies]
 setuptools = "*"
diff --git a/pyproject.toml b/pyproject.toml
@@ -87,6 +87,12 @@ select = [
   "T100", # Checks for the presence of debugger calls and imports
   "N", # pep8 naming conventions
   "PGH004", # ensures no blanket noqa's are used
+  "W", # Pycodestyle warnings
+  "YTT", # checks for misuse of sys.version or sys.version_info
+  # "FBT", # checks for boolean traps (which result in poor function API)
+  # "A", # check for python builtins being used as variables or parameters
+  # "T20", # disallows printing in code - parcels source code should not have dev debugging statements, or should use logging statements instead of prints
+  "NPY201", # numpy 2 deprecations
 ]
 
 exclude = [
@@ -95,6 +101,7 @@ exclude = [
 ] # TODO v4: Remove once folders are gone
 
 ignore = [
+  # # Rules intentionally excluded
   # line too long (82 > 79 characters)
   "E501",
   # ‘from module import *’ used; unable to detect undefined names
@@ -109,7 +116,6 @@ ignore = [
   "UP038",
   # Pattern passed to `match=` contains metacharacters but is neither escaped nor raw
   "RUF043",
-  "RUF046", # Value being cast to `int` is already an integer
 
   # Parcels specific deviations from PEP8 naming
   'N802', # We use function names that are camelcased to denote functions
@@ -118,10 +124,7 @@ ignore = [
   'N816', # TODO: Enable for `src` and consider disabling for notebooks
   'N818', # Not all Parcels exceptions should have an "Error" suffix
 
-  # TODO: Move this ignore so that it only applies in the tests folder. Do in conjunction with any doc related rules
-  "RUF059", # Unpacked variable `coords` is never used
-
-  # TODO: ignore for now (requires more work). Remove ignore once fixed
+  # # TODO: ignore for now (requires more work). Remove ignore once fixed
   # Missing docstring in public module
   "D100",
   # Missing docstring in public package
@@ -136,7 +139,6 @@ ignore = [
   "D404",
   # 1 blank line required between summary line and description (requires writing of summaries)
   "D205",
-  "F811",
 ]
 
 [tool.ruff.lint.per-file-ignores]
diff --git a/src/parcels/_core/fieldset.py b/src/parcels/_core/fieldset.py
@@ -136,7 +136,6 @@ def add_constant_field(self, name: str, value, mesh: Mesh = "spherical"):
             Value of the constant field
         mesh : str
             String indicating the type of mesh coordinates,
-            see also `this tutorial <../examples/tutorial_unitconverters.ipynb>`__:
 
             1. spherical (default): Lat and lon in degree, with a
                correction for zonal velocity U near the poles.
diff --git a/src/parcels/_datasets/structured/generated.py b/src/parcels/_datasets/structured/generated.py
@@ -10,7 +10,6 @@
     _attach_sgrid_metadata,
 )
 from parcels._core.utils.time import timedelta_to_float
-from parcels._datasets.utils import _attach_sgrid_metadata
 
 
 def simple_UV_dataset(dims=(360, 2, 30, 4), maxdepth=1, mesh="spherical"):
diff --git a/src/parcels/_datasets/structured/generic.py b/src/parcels/_datasets/structured/generic.py
@@ -10,7 +10,6 @@
 from parcels._core.utils.sgrid import (
     rename as sgrid_rename,
 )
-from parcels._datasets.utils import _attach_sgrid_metadata
 
 from . import T, X, Y, Z
 
diff --git a/src/parcels/_datasets/utils.py b/src/parcels/_datasets/utils.py
@@ -4,26 +4,9 @@
 import numpy as np
 import xarray as xr
 
-from parcels._core.utils.sgrid import (
-    Grid2DMetadata,
-    Grid3DMetadata,
-)
-
 _SUPPORTED_ATTR_TYPES = int | float | str | np.ndarray
 
 
-def _attach_sgrid_metadata(ds, grid: Grid2DMetadata | Grid3DMetadata):
-    """Copies the dataset and attaches the SGRID metadata in 'grid' variable. Modifies 'conventions' attribute."""
-    ds = ds.copy()
-    ds["grid"] = (
-        [],
-        0,
-        grid.to_attrs(),
-    )
-    ds.attrs["Conventions"] = "SGRID"
-    return ds
-
-
 def _print_mismatched_keys(d1: dict[Any, Any], d2: dict[Any, Any]) -> None:
     k1 = set(d1.keys())
     k2 = set(d2.keys())
diff --git a/tests/test_field.py b/tests/test_field.py
@@ -110,7 +110,7 @@ def test_field_init_fail_on_float_time_dim():
     grid = XGrid.from_dataset(ds, mesh="flat")
     with pytest.raises(
         ValueError,
-        match="Error getting time interval.*. Are you sure that the time dimension on the xarray dataset is stored as timedelta, datetime or cftime datetime objects\?",
+        match=r"Error getting time interval.*. Are you sure that the time dimension on the xarray dataset is stored as timedelta, datetime or cftime datetime objects\?",
     ):
         Field(
             name="test_field",
diff --git a/tests/test_particle.py b/tests/test_particle.py
@@ -20,7 +20,7 @@ def test_variable_init():
 
 
 def test_variable_invalid_init():
-    with pytest.raises(ValueError, match="to_write must be one of .*\. Got to_write="):
+    with pytest.raises(ValueError, match=r"to_write must be one of .*\. Got to_write="):
         Variable("name", to_write="test")
 
     with pytest.raises(TypeError, match="Expected a string for variable name, got int instead."):
diff --git a/tests/test_particlefile.py b/tests/test_particlefile.py
@@ -11,7 +11,6 @@
 from parcels import (
     Field,
     FieldSet,
-    Particle,
     ParticleFile,
     ParticleSet,
     ParticleSetWarning,
diff --git a/tests/test_spatialhash.py b/tests/test_spatialhash.py
@@ -15,7 +15,7 @@ def test_invalid_positions():
     ds = datasets["2d_left_rotated"]
     grid = XGrid.from_dataset(ds, mesh="flat")
 
-    j, i, coords = grid.get_spatial_hash().query([np.nan, np.inf], [np.nan, np.inf])
+    j, i, _ = grid.get_spatial_hash().query([np.nan, np.inf], [np.nan, np.inf])
     assert np.all(j == -3)
     assert np.all(i == -3)
 
@@ -27,7 +27,7 @@ def test_mixed_positions():
     lon = grid.lon.mean()
     y = [lat, np.nan]
     x = [lon, np.nan]
-    j, i, coords = grid.get_spatial_hash().query(y, x)
+    j, i, _ = grid.get_spatial_hash().query(y, x)
     assert j[0] == 29  # Actual value for 2d_left_rotated center
     assert i[0] == 14  # Actual value for 2d_left_rotated center
     assert j[1] == -3
diff --git a/tests/test_xgrid.py b/tests/test_xgrid.py
@@ -113,15 +113,15 @@ def test_invalid_lon_lat():
 
     with pytest.raises(
         ValueError,
-        match=".*is defined on the center of the grid, but must be defined on the F points\.",
+        match=r".*is defined on the center of the grid, but must be defined on the F points\.",
     ):
         XGrid.from_dataset(ds, mesh="flat")
 
     ds = datasets["ds_2d_left"].copy()
     ds["lon"], _ = xr.broadcast(ds["YG"], ds["XG"])
     with pytest.raises(
         ValueError,
-        match=".*have different dimensionalities\.",
+        match=r".*have different dimensionalities\.",
     ):
         XGrid.from_dataset(ds, mesh="flat")
 
@@ -131,7 +131,7 @@ def test_invalid_lon_lat():
 
     with pytest.raises(
         ValueError,
-        match=".*must be defined on the X and Y axes and transposed to have dimensions in order of Y, X\.",
+        match=r".*must be defined on the X and Y axes and transposed to have dimensions in order of Y, X\.",
     ):
         XGrid.from_dataset(ds, mesh="flat")
 
@@ -238,7 +238,7 @@ def test_search_1d_array(array, x, expected_xi, expected_xsi):
     ],
 )
 def test_search_1d_array_out_of_bounds(array, x, expected_xi):
-    xi, xsi = _search_1d_array(array, x)
+    xi, _xsi = _search_1d_array(array, x)
     assert xi == expected_xi
 
 

Original file line number	Diff line number	Diff line change
`@@ -5,7 +5,7 @@`
`5`	`5`	`"cell_type": "markdown",`
`6`	`6`	`"metadata": {},`
`7`	`7`	`"source": [`
`8`		`- "# Nemo 3D tutorial\n"`
	`8`	`+ "# 🖥️ Nemo 3D tutorial\n"`
`9`	`9`	`]`
`10`	`10`	`},`
`11`	`11`	`{`
Original file line number	Diff line number	Diff line change
`@@ -10,7 +10,6 @@`
`10`	`10`	`_attach_sgrid_metadata,`
`11`	`11`	`)`
`12`	`12`	`from parcels._core.utils.time import timedelta_to_float`
`13`		`-from parcels._datasets.utils import _attach_sgrid_metadata`
`14`	`13`
`15`	`14`
`16`	`15`	`def simple_UV_dataset(dims=(360, 2, 30, 4), maxdepth=1, mesh="spherical"):`