Merge branch 'v4-dev' into swap_space_and_time_interpolation_order

Author: erikvansebille

.github/workflows/ci.yml

@@ -76,9 +76,9 @@ jobs:
         with:
           environment-file: environment.yml
       - name: Integration test
-        # TODO v4: Re-enable `tutorial_periodic_boundaries` and `tutorial_timevaryingdepthdimensions` notebooks
+        # TODO v4: Re-enable `tutorial_periodic_boundaries`, `tutorial_timevaryingdepthdimensions` and `tutorial_croco_3D` notebooks
         run: |
-          coverage run -m pytest -v -s --nbval-lax -k "not documentation and not tutorial_periodic_boundaries and not tutorial_timevaryingdepthdimensions" --html="${{ matrix.os }}_${{ matrix.python-version }}_integration_test_report.html" --self-contained-html docs/examples
+          coverage run -m pytest -v -s --nbval-lax -k "not documentation and not tutorial_periodic_boundaries and not tutorial_timevaryingdepthdimensions and not tutorial_croco_3D" --html="${{ matrix.os }}_${{ matrix.python-version }}_integration_test_report.html" --self-contained-html docs/examples
           coverage xml
       - name: Codecov
         uses: codecov/[email protected]

docs/documentation/index.rst

@@ -25,7 +25,6 @@ Parcels has several documentation and tutorial Jupyter notebooks and scripts whi
    ../examples/tutorial_periodic_boundaries.ipynb
    ../examples/tutorial_interpolation.ipynb
    ../examples/tutorial_unitconverters.ipynb
-   ../examples/tutorial_timestamps.ipynb
 
 
 .. nbgallery::

docs/examples/documentation_unstuck_Agrid.ipynb

@@ -809,7 +809,7 @@
     "dimensions = {\"U\": dims, \"V\": dims}\n",
     "\n",
     "indices = {\n",
-    "    \"lon\": range(lonmin, lonmax),\n",
+    "    \"lon\": range(lonmin, lonmax),  # TODO v4: Remove `indices` argument from this cell\n",
     "    \"lat\": range(latmin, latmax),\n",
     "}  # to load only a small part of the domain\n",
     "\n",
@@ -874,7 +874,10 @@
    "outputs": [],
    "source": [
     "fieldset = parcels.FieldSet.from_netcdf(\n",
-    "    filenames, variables, dimensions, indices=indices\n",
+    "    filenames,\n",
+    "    variables,\n",
+    "    dimensions,\n",
+    "    indices=indices,  # TODO v4: Remove `indices` argument from this cell\n",
     ")\n",
     "u_displacement = v_x\n",
     "v_displacement = v_y\n",
@@ -1401,7 +1404,7 @@
     "    filenames,\n",
     "    variables,\n",
     "    dimensions,\n",
-    "    indices=indices,\n",
+    "    indices=indices,  # TODO v4: Remove `indices` argument from this cell\n",
     "    interp_method={\n",
     "        \"U\": \"partialslip\",\n",
     "        \"V\": \"partialslip\",\n",
@@ -1439,7 +1442,7 @@
     "    filenames,\n",
     "    variables,\n",
     "    dimensions,\n",
-    "    indices=indices,\n",
+    "    indices=indices,  # TODO v4: Remove `indices` argument from this cell\n",
     "    interp_method={\n",
     "        \"U\": \"freeslip\",\n",
     "        \"V\": \"freeslip\",\n",

docs/examples/example_globcurrent.py

@@ -10,9 +10,6 @@
 
 def set_globcurrent_fieldset(
     filename=None,
-    indices=None,
-    use_xarray=False,
-    timestamps=None,
 ):
     if filename is None:
         data_folder = parcels.download_example_dataset("GlobCurrent_example_data")
@@ -23,38 +20,32 @@ def set_globcurrent_fieldset(
         "U": "eastward_eulerian_current_velocity",
         "V": "northward_eulerian_current_velocity",
     }
-    if timestamps is None:
-        dimensions = {"lat": "lat", "lon": "lon", "time": "time"}
-    else:
-        dimensions = {"lat": "lat", "lon": "lon"}
-    if use_xarray:
-        ds = xr.open_mfdataset(filename, combine="by_coords")
-        return parcels.FieldSet.from_xarray_dataset(
-            ds,
-            variables,
-            dimensions,
-        )
-    else:
-        return parcels.FieldSet.from_netcdf(
-            filename,
-            variables,
-            dimensions,
-            indices,
-            timestamps=timestamps,
-        )
+    dimensions = {"lat": "lat", "lon": "lon", "time": "time"}
+    ds = xr.open_mfdataset(filename, combine="by_coords")
+
+    return parcels.FieldSet.from_xarray_dataset(
+        ds,
+        variables,
+        dimensions,
+    )
 
 
-@pytest.mark.parametrize("use_xarray", [True, False])
+@pytest.mark.v4remove(
+    reason="indices keryword is not supported in v4. Subsetting should be done on xarray level."
+)
+@pytest.mark.parametrize(
+    "use_xarray", [True, pytest.param(False, marks=pytest.mark.xfail)]
+)
 def test_globcurrent_fieldset(use_xarray):
-    fieldset = set_globcurrent_fieldset(use_xarray=use_xarray)
+    fieldset = set_globcurrent_fieldset()
     assert fieldset.U.lon.size == 81
     assert fieldset.U.lat.size == 41
     assert fieldset.V.lon.size == 81
     assert fieldset.V.lat.size == 41
 
     if not use_xarray:
         indices = {"lon": [5], "lat": range(20, 30)}
-        fieldsetsub = set_globcurrent_fieldset(indices=indices, use_xarray=use_xarray)
+        fieldsetsub = set_globcurrent_fieldset(indices=indices)
         assert np.allclose(fieldsetsub.U.lon, fieldset.U.lon[indices["lon"]])
         assert np.allclose(fieldsetsub.U.lat, fieldset.U.lat[indices["lat"]])
         assert np.allclose(fieldsetsub.V.lon, fieldset.V.lon[indices["lon"]])
@@ -64,21 +55,20 @@ def test_globcurrent_fieldset(use_xarray):
 @pytest.mark.parametrize(
     "dt, lonstart, latstart", [(3600.0, 25, -35), (-3600.0, 20, -39)]
 )
-@pytest.mark.parametrize("use_xarray", [True, False])
-def test_globcurrent_fieldset_advancetime(dt, lonstart, latstart, use_xarray):
+def test_globcurrent_fieldset_advancetime(dt, lonstart, latstart):
     data_folder = parcels.download_example_dataset("GlobCurrent_example_data")
     basepath = str(data_folder / "20*-GLOBCURRENT-L4-CUReul_hs-ALT_SUM-v02.0-fv01.0.nc")
     files = sorted(glob(str(basepath)))
 
-    fieldsetsub = set_globcurrent_fieldset(files[0:10], use_xarray=use_xarray)
+    fieldsetsub = set_globcurrent_fieldset(files[0:10])
     psetsub = parcels.ParticleSet.from_list(
         fieldset=fieldsetsub,
         pclass=parcels.Particle,
         lon=[lonstart],
         lat=[latstart],
     )
 
-    fieldsetall = set_globcurrent_fieldset(files[0:10], use_xarray=use_xarray)
+    fieldsetall = set_globcurrent_fieldset(files[0:10])
     psetall = parcels.ParticleSet.from_list(
         fieldset=fieldsetall,
         pclass=parcels.Particle,
@@ -95,9 +85,8 @@ def test_globcurrent_fieldset_advancetime(dt, lonstart, latstart, use_xarray):
     assert abs(psetsub[0].lon - psetall[0].lon) < 1e-4
 
 
-@pytest.mark.parametrize("use_xarray", [True, False])
-def test_globcurrent_particles(use_xarray):
-    fieldset = set_globcurrent_fieldset(use_xarray=use_xarray)
+def test_globcurrent_particles():
+    fieldset = set_globcurrent_fieldset()
 
     lonstart = [25]
     latstart = [-35]
@@ -114,6 +103,10 @@ def test_globcurrent_particles(use_xarray):
     assert abs(pset[0].lat - -35.3) < 1
 
 
+@pytest.mark.v4remove
+@pytest.mark.xfail(
+    reason="Can't patch metadata without using xarray. v4 will natively use xarray anyway. GH1919."
+)
 @pytest.mark.parametrize("dt", [-300, 300])
 def test_globcurrent_xarray_vs_netcdf(dt):
     fieldsetNetcdf = set_globcurrent_fieldset(use_xarray=False)
@@ -134,6 +127,10 @@ def test_globcurrent_xarray_vs_netcdf(dt):
     assert np.allclose(psetN[0].lat, psetX[0].lat)
 
 
+@pytest.mark.v4remove
+@pytest.mark.xfail(
+    reason="Timeslices will be removed in v4, as users will be able to use xarray directly."
+)
 @pytest.mark.parametrize("dt", [-300, 300])
 def test_globcurrent_netcdf_timestamps(dt):
     fieldsetNetcdf = set_globcurrent_fieldset()
@@ -195,9 +192,8 @@ def test__particles_init_time():
     assert pset[0].time - pset4[0].time == 0
 
 
-@pytest.mark.parametrize("use_xarray", [True, False])
-def test_globcurrent_time_extrapolation_error(use_xarray):
-    fieldset = set_globcurrent_fieldset(use_xarray=use_xarray)
+def test_globcurrent_time_extrapolation_error():
+    fieldset = set_globcurrent_fieldset()
     pset = parcels.ParticleSet(
         fieldset,
         pclass=parcels.Particle,

docs/examples/tutorial_timestamps.ipynb

@@ -5,5 +5,7 @@ List of tasks that are important to do before the release of version 4 (but can'
 - [ ] Make migration guide for v3 to v4
 - [ ] Just prior to release: Update conda feedstock recipe dependencies (remove cgen and compiler dependencies). Make sure that recipe is up-to-date.
 - [ ] Revamp the oceanparcels.org landing page, and perhaps also consider new logo/branding?
-- [ ] Look into xarray and whether users can create periodic datasets without increasing the size of the original dataset (i.e., no compromise alternative to `time_periodic` param in v3). Update docs accordingly.
 - [ ] Rerun all the tutorials so that their output is in line with new v4 print statements etc
+- Documentation
+  - [ ] Look into xarray and whether users can create periodic datasets without increasing the size of the original dataset (i.e., no compromise alternative to `time_periodic` param in v3). Update docs accordingly.
+  - [ ] Look into xarray and whether users can create datasets from snapshots assigning different time dimensions without increasing the size of the original dataset (i.e., no compromise alternative to `timestamps` param in v3). Update docs accordingly.