Merge pull request #1650 from KOMPALALOKESH/feature/from_a_grid_dataset

added: FieldSet.from_a_grid_dataset

docs/contributing.rst

@@ -18,7 +18,7 @@ There are two primary groups that contribute to Parcels; oceanographers who brin
 
 .. note::
 
-    The first component of this documentation is geared to those new to open source. Already familiar with GitHub and open source? Skip ahead to `"Editing Parcels code" <https://www.notion.so/Parcels-Contributing-md-c8bc5a057b7f47e885f3eee82ea6fdf6?pvs=21>`_. See the panel on the right hand side for the table of contents.
+    The first component of this documentation is geared to those new to open source. Already familiar with GitHub and open source? Skip ahead to the `Editing Parcels code`_ section.
 
 What is open source?
 --------------------
@@ -53,6 +53,8 @@ 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:
+
 Editing Parcels code
 ---------------------
 

docs/documentation/index.rst

@@ -4,7 +4,7 @@ Documentation and Tutorials
 Parcels has several documentation and tutorial Jupyter notebooks and scripts which go through various aspects of Parcels. Static versions of the notebooks are available below via the gallery in the site, with the interactive notebooks being available either completely online at the following `Binder link <https://mybinder.org/v2/gh/OceanParcels/parcels/master?labpath=docs%2Fexamples%2Fparcels_tutorial.ipynb>`_. Following the gallery of notebooks is a list of scripts which provide additional examples to users. You can work with the example notebooks and scripts locally by downloading :download:`parcels_tutorials.zip </_downloads/parcels_tutorials.zip>` and running with your own Parcels installation.
 
 .. warning::
-   When browsing/downloading the tutorials, it's vital that you are using the documentation corresponding to the version of Parcels that you have installed. You can find which parcels version you have installed by doing ``import parcels`` followed by ``print(parcels.__version__)``. If you don't want to use the latest version of Parcels, you can browse prior versions of the documentation by using the version switcher in the bottom right of this page.
+   When browsing/downloading the tutorials, it's important that you are using the documentation corresponding to the version of Parcels that you have installed. You can find which parcels version you have installed by doing ``import parcels`` followed by ``print(parcels.__version__)``. If you don't want to use the latest version of Parcels, you can browse prior versions of the documentation by using the version switcher in the bottom right of this page.
 
 .. nbgallery::
    :caption: Overview

parcels/fieldset.py

@@ -533,7 +533,7 @@ def from_nemo(cls, filenames, variables, dimensions, indices=None, mesh='spheric
             This flag overrides the allow_time_extrapolation and sets it to False
         tracer_interp_method : str
             Method for interpolation of tracer fields. It is recommended to use 'cgrid_tracer' (default)
-            Note that in the case of from_nemo() and from_cgrid(), the velocity fields are default to 'cgrid_velocity'
+            Note that in the case of from_nemo() and from_c_grid_dataset(), the velocity fields are default to 'cgrid_velocity'
         chunksize :
             size of the chunks in dask loading. Default is None (no chunking)
         **kwargs :
@@ -645,7 +645,7 @@ def from_c_grid_dataset(cls, filenames, variables, dimensions, indices=None, mes
             This flag overrides the allow_time_extrapolation and sets it to False
         tracer_interp_method : str
             Method for interpolation of tracer fields. It is recommended to use 'cgrid_tracer' (default)
-            Note that in the case of from_nemo() and from_cgrid(), the velocity fields are default to 'cgrid_velocity'
+            Note that in the case of from_nemo() and from_c_grid_dataset(), the velocity fields are default to 'cgrid_velocity'
         gridindexingtype : str
             The type of gridindexing. Set to 'nemo' in FieldSet.from_nemo()
             See also the Grid indexing documentation on oceanparcels.org (Default value = 'nemo')
@@ -745,7 +745,7 @@ def from_pop(cls, filenames, variables, dimensions, indices=None, mesh='spherica
             This flag overrides the allow_time_extrapolation and sets it to False
         tracer_interp_method : str
             Method for interpolation of tracer fields. It is recommended to use 'bgrid_tracer' (default)
-            Note that in the case of from_pop() and from_bgrid(), the velocity fields are default to 'bgrid_velocity'
+            Note that in the case of from_pop() and from_b_grid_dataset(), the velocity fields are default to 'bgrid_velocity'
         chunksize :
             size of the chunks in dask loading (Default value = None)
         depth_units :
@@ -855,6 +855,29 @@ def from_mom5(cls, filenames, variables, dimensions, indices=None, mesh='spheric
             fieldset.W.set_scaling_factor(-1)
         return fieldset
 
+    @classmethod
+    def from_a_grid_dataset(cls, filenames, variables, dimensions, **kwargs):
+        """
+        Load a FieldSet from an A-grid dataset, which is the default grid type.
+
+        Parameters
+        ----------
+        filenames :
+            Path(s) to the input files.
+        variables :
+            Dictionary of the variables in the NetCDF file.
+        dimensions :
+            Dictionary of the dimensions in the NetCDF file.
+        **kwargs :
+            Additional keyword arguments for `from_netcdf()`.
+
+        Returns
+        -------
+        FieldSet
+            A FieldSet object.
+        """
+        return cls.from_netcdf(filenames, variables, dimensions, **kwargs)
+
     @classmethod
     def from_b_grid_dataset(cls, filenames, variables, dimensions, indices=None, mesh='spherical',
                             allow_time_extrapolation=None, time_periodic=False,

tests/test_advection.py

@@ -503,12 +503,9 @@ def test_analyticalAgrid(mode):
     V = np.ones((lat.size, lon.size), dtype=np.float32)
     fieldset = FieldSet.from_data({'U': U, 'V': V}, {'lon': lon, 'lat': lat}, mesh='flat')
     pset = ParticleSet(fieldset, pclass=ptype[mode], lon=1, lat=1)
-    failed = False
-    try:
+
+    with pytest.raises(NotImplementedError):
         pset.execute(AdvectionAnalytical, runtime=1)
-    except NotImplementedError:
-        failed = True
-    assert failed
 
 
 @pytest.mark.parametrize('mode', ['scipy'])  # JIT not implemented

tests/test_fieldset.py

@@ -68,12 +68,9 @@ def test_fieldset_from_data(xdim, ydim):
 def test_fieldset_extra_syntax():
     """Simple test for fieldset initialisation from data."""
     data, dimensions = generate_fieldset(10, 10)
-    failed = False
-    try:
+
+    with pytest.raises(SyntaxError):
         FieldSet.from_data(data, dimensions, unknown_keyword=5)
-    except SyntaxError:
-        failed = True
-    assert failed
 
 
 def test_fieldset_vmin_vmax():
@@ -152,13 +149,9 @@ def test_field_from_netcdf_variables():
     assert np.allclose(f1.data, f2.data, atol=1e-12)
     assert np.allclose(f1.data, f3.data, atol=1e-12)
 
-    failed = False
-    try:
+    with pytest.raises(AssertionError):
         variable = {'U': 'vozocrtx', 'nav_lat': 'nav_lat'}  # multiple variables will fail
         f3 = Field.from_netcdf(filename, variable, dims)
-    except AssertionError:
-        failed = True
-    assert failed
 
 
 @pytest.mark.parametrize('calendar, cftime_datetime',
@@ -237,6 +230,17 @@ def test_field_from_netcdf_fieldtypes():
     fset = FieldSet.from_nemo(filenames, variables, dimensions, fieldtype={'varU': 'U', 'varV': 'V'})
     assert isinstance(fset.varU.units, GeographicPolar)
 
+def test_fieldset_from_agrid_dataset():
+    data_path = os.path.join(os.path.dirname(__file__), 'test_data/')
+
+    filenames = {
+        'lon': data_path + 'mask_nemo_cross_180lon.nc',
+        'lat': data_path + 'mask_nemo_cross_180lon.nc',
+        'data': data_path + 'Uu_eastward_nemo_cross_180lon.nc'
+    }
+    variable = {'U': 'U'}
+    dimensions = {'lon': 'glamf', 'lat': 'gphif'}
+    FieldSet.from_a_grid_dataset(filenames, variable, dimensions)
 
 def test_fieldset_from_cgrid_interpmethod():
     data_path = os.path.join(os.path.dirname(__file__), 'test_data/')
@@ -246,13 +250,10 @@ def test_fieldset_from_cgrid_interpmethod():
                  'data': data_path + 'Uu_eastward_nemo_cross_180lon.nc'}
     variable = 'U'
     dimensions = {'lon': 'glamf', 'lat': 'gphif'}
-    failed = False
-    try:
+
+    with pytest.raises(TypeError):
         # should fail because FieldSet.from_c_grid_dataset does not support interp_method
         FieldSet.from_c_grid_dataset(filenames, variable, dimensions, interp_method='partialslip')
-    except TypeError:
-        failed = True
-    assert failed
 
 
 @pytest.mark.parametrize('cast_data_dtype', ['float32', 'float64'])
@@ -951,12 +952,8 @@ def SampleField(particle, fieldset, time):
     pset = ParticleSet(fieldset, pclass=SampleParticle, time=[0, time2], lon=[0.5, 0.5], lat=[0.5, 0.5], depth=[0.5, 0.5])
 
     if time2 > 1:
-        failed = False
-        try:
+        with pytest.raises(TimeExtrapolationError):
             pset.execute(SampleField, runtime=10)
-        except TimeExtrapolationError:
-            failed = True
-        assert failed
     else:
         pset.execute(SampleField, runtime=1)
         assert np.allclose([p.u_kernel for p in pset], [p.u_scipy for p in pset], atol=1e-5)