Various small fixes

docs/conf.py

@@ -121,7 +121,6 @@
     "_build",
     "jupyter_execute",
     "**.ipynb_checkpoints",
-    "user_guide/examples_v3",
     ".jupyter_cache",
 ]
 

pixi.toml

@@ -83,6 +83,9 @@ pytest-cov = "*"
 pytest-reportlog = "*"
 pytest-timeout = "*"
 
+[feature.test.pypi-dependencies]
+re-assert = "*"
+
 [feature.test.tasks]
 tests = { cmd = "pytest", description = "Run the test suite." }
 tests-flaky = { cmd = "pytest -m 'flaky' --run-flaky-tests", description = "Run only flaky tests." }

pyproject.toml

@@ -23,7 +23,7 @@ dependencies = [
   "cftime >=1.6.3",
   "numpy >=2.1.0",
   "dask >=2024.5.1",
-  "netCDF4 >=1.7.2", # TODO: should we use h5netcdf here instead of netCDF4?
+  "netCDF4 >=1.7.2",
   "zarr >=3",
   "tqdm >=4.50.0",
   "xarray >=2024.5.0",
@@ -53,7 +53,6 @@ local_scheme = "no-local-version"
 [tool.pytest.ini_options]
 addopts = ["--strict-config", "--strict-markers"]
 xfail_strict = true
-# testpaths = ["tests", "docs/examples"] # TODO v4: Re-enable once examples are back/fixed
 testpaths = ["tests"]
 python_files = ["test_*.py", "example_*.py", "*tutorial*"]
 minversion = "7"
@@ -101,11 +100,6 @@ select = [
   "NPY201", # numpy 2 deprecations
 ]
 
-exclude = [
-  "tests-v3/**",
-  'docs/user_guide/examples_v3/**',
-] # TODO v4: Remove once folders are gone
-
 ignore = [
   # # Rules intentionally excluded
   # line too long (82 > 79 characters)

src/parcels/_core/field.py

@@ -116,7 +116,7 @@ def time_interval(self):  # TODO PR: Remove in favour of referencing model time_
         return self.model.time_interval
 
     def __repr__(self):
-        return f"Field(name={self.name}, model={self.model})"
+        return f"Field(name={self.name!r}, model={self.model})"
 
     @property
     def interp_method(self):

src/parcels/_datasets/structured/generated.py

@@ -91,7 +91,7 @@ def radial_rotation_dataset(xdim=200, ydim=200):  # Define 2D flat, square field
     )
 
 
-def moving_eddy_dataset(xdim=2, ydim=2):  # TODO check if this also works with xdim=1, ydim=1
+def moving_eddy_dataset(xdim=2, ydim=2):
     """Create a dataset with an eddy moving in time. Note that there is no spatial variation in the flow."""
     f, u_0, u_g = 1.0e-4, 0.3, 0.04  # Some constants
 

src/parcels/_repr_utils.py

@@ -44,7 +44,6 @@ def fieldset_repr(fieldset: FieldSet) -> str:
     return textwrap.dedent(out).strip()
 
 
-# TODO add land_value here after HG #2451 is merged
 def field_repr(field: Field, level: int = 0) -> str:
     """Return a pretty repr for Field"""
     with xr.set_options(display_expand_data=False):
@@ -138,8 +137,7 @@ def particlefile_repr(pfile: Any) -> str:
     out = f"""<{type(pfile).__name__}>
     path                : {pfile.path}
     outputdt            : {pfile.outputdt!r}
-    metadata            :
-{_format_list_items_multiline(pfile.metadata, level=2, with_brackets=False)}
+    metadata            : {_format_list_items_multiline(pfile.metadata, level=2, with_brackets=False)}
 """
     return textwrap.dedent(out).strip()
 

src/parcels/_typing.py

@@ -60,7 +60,7 @@ def _validate_against_pure_literal(value, typing_literal):
 
     Can't be used with ``Literal[...] | None`` etc. as its not a pure literal.
     """
-    # TODO remove once https://github.com/pydata/xarray/issues/11209 is resolved - Xarray objects don't work normally in `in` statements
+    # Xarray objects don't work normally in `in` statements - see https://github.com/pydata/xarray/issues/11209 (this is unlikely to be resolved anytime soon)
     if _is_xarray_object(value):
         raise ValueError(f"Invalid input type {type(value)}")
 

tests/test_field.py

@@ -2,6 +2,7 @@
 
 import numpy as np
 import pytest
+from re_assert import Matches
 
 from parcels import Field, VectorField
 from parcels._core.fieldset import FieldSet
@@ -39,6 +40,14 @@ def test_field_init_param_types():
         Field(name="while", model=model)
 
 
+def test_field_repr(fieldset):
+    Matches(r"Field\(name=.*, model=.*\)").assert_matches(repr(fieldset.U))
+
+
+def test_vectorfield_repr(fieldset):
+    Matches(r"\<.*VectorField object at.*\>").assert_matches(repr(fieldset.UV))
+
+
 # TODO: Move to test_model.py ?
 def test_field_init_fail_on_float_time_dim():
     """Test that accessing time_interval fails when dataset has float time dimension.

tests/test_fieldset.py

@@ -7,6 +7,7 @@
 import pandas as pd
 import pytest
 import xarray as xr
+from re_assert import Matches
 
 import parcels.tutorial
 import tests
@@ -40,6 +41,10 @@ def test_fieldset_init_wrong_types():
         FieldSet([1.0, 2.0, 3.0])
 
 
+def test_fieldset_repr(fieldset):
+    Matches(r"\<.*FieldSet object at.*\>").assert_matches(repr(fieldset))
+
+
 def test_fieldset_add_context(fieldset):
     fieldset.add_context("test_context", 1.0)
     assert fieldset.test_context == 1.0

tests/test_particlefile.py

@@ -9,19 +9,21 @@
 import pyarrow.parquet as pq
 import pytest
 import xarray as xr
+from re_assert import Matches
 
 import parcels.tutorial
 from parcels import (
     Field,
     FieldSet,
+    Particle,
     ParticleFile,
     ParticleSet,
     ParticleSetWarning,
     StatusCode,
     Variable,
     convert,
 )
-from parcels._core.particle import Particle, get_default_particle
+from parcels._core.particle import get_default_particle
 from parcels._core.particlefile import get_schema
 from parcels._core.utils.time import TimeInterval, timedelta_to_float
 from parcels._datasets.structured.generated import peninsula_dataset
@@ -30,6 +32,17 @@
 from tests.common_kernels import DoNothing
 
 
+def test_particlefile_repr(tmp_parquet):
+    pfile_repr = repr(ParticleFile(tmp_parquet, outputdt=np.timedelta64(1, "s")))
+    match = Matches(
+        r"""\<ParticleFile\>
+    path                : .*
+    outputdt            : 1.0
+    metadata            : .*""",
+    )
+    match.assert_matches(pfile_repr)
+
+
 def test_metadata(fieldset, tmp_parquet):
     pset = ParticleSet(fieldset, pclass=Particle, x=0, y=0)
 

tests/test_particleset.py

@@ -5,6 +5,7 @@
 import numpy as np
 import pytest
 import xarray as xr
+from re_assert import Matches
 
 from parcels import (
     FieldSet,
@@ -35,6 +36,10 @@ def test_create_empty_pset(fieldset):
     assert pset.size == 0
 
 
+def test_particleset_repr(fieldset):
+    Matches(r"\<.*ParticleSet object at.*\>").assert_matches(repr(ParticleSet(fieldset, pclass=Particle)))
+
+
 @pytest.mark.parametrize("offset", [0, 1, 200])
 def test_pset_with_pids(fieldset, offset, npart=100):
     lon = np.linspace(0, 1, npart)

tests/test_xgrid.py

@@ -5,6 +5,7 @@
 import pytest
 import xarray as xr
 from numpy.testing import assert_allclose
+from re_assert import Matches
 
 from parcels import FieldSet
 from parcels._core.index_search import (
@@ -56,6 +57,10 @@ def test_grid_init_param_types(ds):
         XGrid.from_dataset(ds, mesh="invalid")
 
 
+def test_xgrid_repr(fieldset):
+    Matches(r"\<.*XGrid object at.*\>").assert_matches(repr(fieldset.U.grid))
+
+
 @pytest.mark.parametrize("ds, attr, expected", test_cases)
 def test_xgrid_properties_ground_truth(ds, attr, expected):
     grid = FieldSet.from_sgrid_conventions(ds, mesh="flat").data_g.grid