From 68a17a0ab37514d4ada7af0bb7d3cd87a0dbefe0 Mon Sep 17 00:00:00 2001 From: Dongdong Tian Date: Thu, 3 Oct 2024 14:03:20 +0800 Subject: [PATCH] data_kind: Add more tests to demonstrate the data kind of various data types (#3480) Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- pygmt/helpers/utils.py | 84 +++++++++++++++++++++++--------- pygmt/tests/test_blockm.py | 3 +- pygmt/tests/test_blockmedian.py | 3 +- pygmt/tests/test_geopandas.py | 16 ++++++ pygmt/tests/test_grdtrack.py | 10 ++-- pygmt/tests/test_grdview.py | 6 +-- pygmt/tests/test_nearneighbor.py | 3 +- pygmt/tests/test_surface.py | 3 +- pygmt/tests/test_triangulate.py | 3 +- pygmt/tests/test_x2sys_cross.py | 6 +-- 10 files changed, 89 insertions(+), 48 deletions(-) diff --git a/pygmt/helpers/utils.py b/pygmt/helpers/utils.py index 6585bb7566b..24a938df518 100644 --- a/pygmt/helpers/utils.py +++ b/pygmt/helpers/utils.py @@ -207,13 +207,11 @@ def data_kind( Parameters ---------- - data : str, pathlib.PurePath, None, bool, xarray.DataArray or {table-like} - Pass in either a file name or :class:`pathlib.Path` to an ASCII data - table, an :class:`xarray.DataArray`, a 1-D/2-D - {table-classes} or an option argument. + data + The data to be passed to a GMT module. required - Set to True when 'data' is required, or False when dealing with - optional virtual files. [Default is True]. + Whether 'data' is required. Set to ``False`` when dealing with optional virtual + files. Returns ------- @@ -222,30 +220,72 @@ def data_kind( Examples -------- + >>> import io + >>> from pathlib import Path >>> import numpy as np + >>> import pandas as pd >>> import xarray as xr - >>> import pathlib - >>> import io - >>> data_kind(data=None) - 'vectors' - >>> data_kind(data=np.arange(10).reshape((5, 2))) - 'matrix' - >>> data_kind(data="my-data-file.txt") - 'file' - >>> data_kind(data=pathlib.Path("my-data-file.txt")) - 'file' + + The "arg" kind: + + >>> [data_kind(data=data, required=False) for data in (2, 2.0, True, False)] + ['arg', 'arg', 'arg', 'arg'] >>> data_kind(data=None, required=False) 'arg' - >>> data_kind(data=2.0, required=False) - 'arg' - >>> data_kind(data=True, required=False) - 'arg' - >>> data_kind(data=xr.DataArray(np.random.rand(4, 3))) + + The "file" kind: + + >>> [data_kind(data=data) for data in ("file.txt", ("file1.txt", "file2.txt"))] + ['file', 'file'] + >>> data_kind(data=Path("file.txt")) + 'file' + >>> data_kind(data=(Path("file1.txt"), Path("file2.txt"))) + 'file' + + The "grid" kind: + + >>> data_kind(data=xr.DataArray(np.random.rand(4, 3))) # 2-D xarray.DataArray + 'grid' + >>> data_kind(data=xr.DataArray(np.arange(12))) # 1-D xarray.DataArray + 'grid' + >>> data_kind(data=xr.DataArray(np.random.rand(2, 3, 4, 5))) # 4-D xarray.DataArray 'grid' - >>> data_kind(data=xr.DataArray(np.random.rand(3, 4, 5))) + + The "image" kind: + + >>> data_kind(data=xr.DataArray(np.random.rand(3, 4, 5))) # 3-D xarray.DataArray 'image' + + The "stringio"`` kind: + >>> data_kind(data=io.StringIO("TEXT1\nTEXT23\n")) 'stringio' + + The "matrix"`` kind: + + >>> data_kind(data=np.arange(10)) # 1-D numpy.ndarray + 'matrix' + >>> data_kind(data=np.arange(10).reshape((5, 2))) # 2-D numpy.ndarray + 'matrix' + >>> data_kind(data=np.arange(60).reshape((3, 4, 5))) # 3-D numpy.ndarray + 'matrix' + >>> data_kind(xr.DataArray(np.arange(12), name="x").to_dataset()) # xarray.Dataset + 'matrix' + >>> data_kind(data=[1, 2, 3]) # 1-D sequence + 'matrix' + >>> data_kind(data=[[1, 2, 3], [4, 5, 6]]) # sequence of sequences + 'matrix' + >>> data_kind(data={"x": [1, 2, 3], "y": [4, 5, 6]}) # dictionary + 'matrix' + >>> data_kind(data=pd.DataFrame({"x": [1, 2, 3], "y": [4, 5, 6]})) # pd.DataFrame + 'matrix' + >>> data_kind(data=pd.Series([1, 2, 3], name="x")) # pd.Series + 'matrix' + + The "vectors" kind: + + >>> data_kind(data=None) + 'vectors' """ kind: Literal[ "arg", "file", "geojson", "grid", "image", "matrix", "stringio", "vectors" diff --git a/pygmt/tests/test_blockm.py b/pygmt/tests/test_blockm.py index b9f656e99ea..a0e2ee49d4e 100644 --- a/pygmt/tests/test_blockm.py +++ b/pygmt/tests/test_blockm.py @@ -12,7 +12,7 @@ from pygmt import blockmean, blockmode from pygmt.datasets import load_sample_data from pygmt.exceptions import GMTInvalidInput -from pygmt.helpers import GMTTempFile, data_kind +from pygmt.helpers import GMTTempFile @pytest.fixture(scope="module", name="dataframe") @@ -68,7 +68,6 @@ def test_blockmean_wrong_kind_of_input_table_grid(dataframe): Run blockmean using table input that is not a pandas.DataFrame or file but a grid. """ invalid_table = dataframe.bathymetry.to_xarray() - assert data_kind(invalid_table) == "grid" with pytest.raises(GMTInvalidInput): blockmean(data=invalid_table, spacing="5m", region=[245, 255, 20, 30]) diff --git a/pygmt/tests/test_blockmedian.py b/pygmt/tests/test_blockmedian.py index 6f3f24b3c77..64d642f424d 100644 --- a/pygmt/tests/test_blockmedian.py +++ b/pygmt/tests/test_blockmedian.py @@ -10,7 +10,7 @@ from pygmt import blockmedian from pygmt.datasets import load_sample_data from pygmt.exceptions import GMTInvalidInput -from pygmt.helpers import GMTTempFile, data_kind +from pygmt.helpers import GMTTempFile @pytest.fixture(scope="module", name="dataframe") @@ -65,7 +65,6 @@ def test_blockmedian_wrong_kind_of_input_table_grid(dataframe): Run blockmedian using table input that is not a pandas.DataFrame or file but a grid. """ invalid_table = dataframe.bathymetry.to_xarray() - assert data_kind(invalid_table) == "grid" with pytest.raises(GMTInvalidInput): blockmedian(data=invalid_table, spacing="5m", region=[245, 255, 20, 30]) diff --git a/pygmt/tests/test_geopandas.py b/pygmt/tests/test_geopandas.py index 77fa7a9f9d5..336a076d64c 100644 --- a/pygmt/tests/test_geopandas.py +++ b/pygmt/tests/test_geopandas.py @@ -6,6 +6,7 @@ import pandas as pd import pytest from pygmt import Figure, info, makecpt, which +from pygmt.helpers import data_kind from pygmt.helpers.testing import skip_if_no gpd = pytest.importorskip("geopandas") @@ -243,3 +244,18 @@ def test_geopandas_plot_int64_as_float(gdf_ridge): makecpt(cmap="lisbon", series=[10, 60, 10], continuous=True) fig.colorbar() return fig + + +def test_geopandas_data_kind_geopandas(gdf): + """ + Check if geopandas.GeoDataFrame object is recognized as a "geojson" kind. + """ + assert data_kind(data=gdf) == "geojson" + + +def test_geopandas_data_kind_shapely(): + """ + Check if shapely.geometry object is recognized as a "geojson" kind. + """ + polygon = shapely.geometry.Polygon([(20, 10), (23, 10), (23, 14), (20, 14)]) + assert data_kind(data=polygon) == "geojson" diff --git a/pygmt/tests/test_grdtrack.py b/pygmt/tests/test_grdtrack.py index f3862adeae0..8bfb6cf98fb 100644 --- a/pygmt/tests/test_grdtrack.py +++ b/pygmt/tests/test_grdtrack.py @@ -10,7 +10,7 @@ import pytest from pygmt import grdtrack from pygmt.exceptions import GMTInvalidInput -from pygmt.helpers import GMTTempFile, data_kind +from pygmt.helpers import GMTTempFile from pygmt.helpers.testing import load_static_earth_relief POINTS_DATA = Path(__file__).parent / "data" / "track.txt" @@ -126,22 +126,18 @@ def test_grdtrack_profile(dataarray): def test_grdtrack_wrong_kind_of_points_input(dataarray, dataframe): """ - Run grdtrack using points input that is not a pandas.DataFrame (matrix) or file. + Run grdtrack using points input that is not a pandas.DataFrame or file. """ invalid_points = dataframe.longitude.to_xarray() - - assert data_kind(invalid_points) == "grid" with pytest.raises(GMTInvalidInput): grdtrack(points=invalid_points, grid=dataarray, newcolname="bathymetry") def test_grdtrack_wrong_kind_of_grid_input(dataarray, dataframe): """ - Run grdtrack using grid input that is not as xarray.DataArray (grid) or file. + Run grdtrack using grid input that is not an xarray.DataArray or file. """ invalid_grid = dataarray.to_dataset() - - assert data_kind(invalid_grid) == "matrix" with pytest.raises(GMTInvalidInput): grdtrack(points=dataframe, grid=invalid_grid, newcolname="bathymetry") diff --git a/pygmt/tests/test_grdview.py b/pygmt/tests/test_grdview.py index b8f597b2bf0..f73b1150e54 100644 --- a/pygmt/tests/test_grdview.py +++ b/pygmt/tests/test_grdview.py @@ -5,7 +5,7 @@ import pytest from pygmt import Figure, grdcut from pygmt.exceptions import GMTInvalidInput -from pygmt.helpers import GMTTempFile, data_kind +from pygmt.helpers import GMTTempFile from pygmt.helpers.testing import load_static_earth_relief @@ -58,8 +58,6 @@ def test_grdview_wrong_kind_of_grid(xrgrid): Run grdview using grid input that is not an xarray.DataArray or file. """ dataset = xrgrid.to_dataset() # convert xarray.DataArray to xarray.Dataset - assert data_kind(dataset) == "matrix" - fig = Figure() with pytest.raises(GMTInvalidInput): fig.grdview(grid=dataset) @@ -238,8 +236,6 @@ def test_grdview_wrong_kind_of_drapegrid(xrgrid): Run grdview using drapegrid input that is not an xarray.DataArray or file. """ dataset = xrgrid.to_dataset() # convert xarray.DataArray to xarray.Dataset - assert data_kind(dataset) == "matrix" - fig = Figure() with pytest.raises(GMTInvalidInput): fig.grdview(grid=xrgrid, drapegrid=dataset) diff --git a/pygmt/tests/test_nearneighbor.py b/pygmt/tests/test_nearneighbor.py index f37365fbdb4..9d08aa0e8d1 100644 --- a/pygmt/tests/test_nearneighbor.py +++ b/pygmt/tests/test_nearneighbor.py @@ -11,7 +11,7 @@ from pygmt import nearneighbor from pygmt.datasets import load_sample_data from pygmt.exceptions import GMTInvalidInput -from pygmt.helpers import GMTTempFile, data_kind +from pygmt.helpers import GMTTempFile @pytest.fixture(scope="module", name="ship_data") @@ -61,7 +61,6 @@ def test_nearneighbor_wrong_kind_of_input(ship_data): Run nearneighbor using grid input that is not file/matrix/vectors. """ data = ship_data.bathymetry.to_xarray() # convert pandas.Series to xarray.DataArray - assert data_kind(data) == "grid" with pytest.raises(GMTInvalidInput): nearneighbor( data=data, spacing="5m", region=[245, 255, 20, 30], search_radius="10m" diff --git a/pygmt/tests/test_surface.py b/pygmt/tests/test_surface.py index 39860dd2069..e8ec0cf3445 100644 --- a/pygmt/tests/test_surface.py +++ b/pygmt/tests/test_surface.py @@ -9,7 +9,7 @@ import xarray as xr from pygmt import surface, which from pygmt.exceptions import GMTInvalidInput -from pygmt.helpers import GMTTempFile, data_kind +from pygmt.helpers import GMTTempFile @pytest.fixture(scope="module", name="data") @@ -125,7 +125,6 @@ def test_surface_wrong_kind_of_input(data, region, spacing): Run surface using grid input that is not file/matrix/vectors. """ data = data.z.to_xarray() # convert pandas.Series to xarray.DataArray - assert data_kind(data) == "grid" with pytest.raises(GMTInvalidInput): surface(data=data, spacing=spacing, region=region) diff --git a/pygmt/tests/test_triangulate.py b/pygmt/tests/test_triangulate.py index 75cccbf17ab..97c29a273e6 100644 --- a/pygmt/tests/test_triangulate.py +++ b/pygmt/tests/test_triangulate.py @@ -10,7 +10,7 @@ import xarray as xr from pygmt import triangulate, which from pygmt.exceptions import GMTInvalidInput -from pygmt.helpers import GMTTempFile, data_kind +from pygmt.helpers import GMTTempFile @pytest.fixture(scope="module", name="dataframe") @@ -93,7 +93,6 @@ def test_delaunay_triples_wrong_kind_of_input(dataframe): Run triangulate.delaunay_triples using grid input that is not file/matrix/vectors. """ data = dataframe.z.to_xarray() # convert pandas.Series to xarray.DataArray - assert data_kind(data) == "grid" with pytest.raises(GMTInvalidInput): triangulate.delaunay_triples(data=data) diff --git a/pygmt/tests/test_x2sys_cross.py b/pygmt/tests/test_x2sys_cross.py index eba29aa6242..c72cca04420 100644 --- a/pygmt/tests/test_x2sys_cross.py +++ b/pygmt/tests/test_x2sys_cross.py @@ -16,7 +16,6 @@ from pygmt.clib import __gmt_version__ from pygmt.datasets import load_sample_data from pygmt.exceptions import GMTInvalidInput -from pygmt.helpers import data_kind @pytest.fixture(name="mock_x2sys_home") @@ -237,11 +236,10 @@ def test_x2sys_cross_input_two_filenames(): def test_x2sys_cross_invalid_tracks_input_type(tracks): """ - Run x2sys_cross using tracks input that is not a pandas.DataFrame (matrix) or str - (file) type, which would raise a GMTInvalidInput error. + Run x2sys_cross using tracks input that is not a pandas.DataFrame or str type, + which would raise a GMTInvalidInput error. """ invalid_tracks = tracks[0].to_xarray().z - assert data_kind(invalid_tracks) == "grid" with pytest.raises(GMTInvalidInput): x2sys_cross(tracks=[invalid_tracks])