improve test coverage (#159)

ecoscope/mapping/map.py

@@ -1,6 +1,5 @@
 import base64
 import os
-import tempfile
 import time
 import typing
 import urllib
@@ -306,19 +305,19 @@ def to_png(self, outfile, sleep_time=5, **kwargs):
             fully loaded but can also be decreased in most cases.
 
         """
-
-        with tempfile.NamedTemporaryFile(mode="w", suffix=".html") as tmp:
-            super().to_html(tmp.name, **kwargs)
-            chrome_options = selenium.webdriver.chrome.options.Options()
-            chrome_options.add_argument("--headless")
-            chrome_options.add_argument("--no-sandbox")
-            chrome_options.add_argument("--disable-dev-shm-usage")
-            driver = selenium.webdriver.Chrome(options=chrome_options)
-            if self.px_width and self.px_height:
-                driver.set_window_size(width=self.px_width, height=self.px_height)
-            driver.get(f"file://{os.path.abspath(tmp.name)}")
-            time.sleep(sleep_time)
-            driver.save_screenshot(outfile)
+        tempfile = "tmp_to_png.html"
+        super().to_html(tempfile, **kwargs)
+        chrome_options = selenium.webdriver.chrome.options.Options()
+        chrome_options.add_argument("--headless")
+        chrome_options.add_argument("--no-sandbox")
+        chrome_options.add_argument("--disable-dev-shm-usage")
+        driver = selenium.webdriver.Chrome(options=chrome_options)
+        if self.px_width and self.px_height:
+            driver.set_window_size(width=self.px_width, height=self.px_height)
+        driver.get(f"file://{os.path.abspath(tempfile)}")
+        time.sleep(sleep_time)
+        driver.save_screenshot(outfile)
+        os.remove(tempfile)
 
     def add_ee_layer(self, ee_object, visualization_params, name) -> None:
         """

ecoscope/plotting/plot.py

@@ -188,7 +188,7 @@ def nsd(relocations):
     relocations = relocations.to_crs(relocations.estimate_utm_crs())
 
     times = relocations["fixtime"]
-    distances = relocations.distance(relocations.geometry[0]) ** 2
+    distances = relocations.distance(relocations.geometry.iat[0]) ** 2
 
     fig = go.FigureWidget()
 

environment.yml

@@ -8,6 +8,7 @@ dependencies:
   - jupyterlab
   - geopandas<=0.14.2
   - beautifulsoup4
+  - ipywidgets
   - pip:
       - kaleido
       - pre-commit>=3

setup.py

@@ -21,6 +21,7 @@
     "folium",
     "geopandas<=0.14.2",
     "igraph",
+    "ipywidgets",
     "kaleido",
     "mapclassify",
     "matplotlib",

tests/test_astronomy.py

@@ -0,0 +1,30 @@
+import pyproj
+from ecoscope.analysis import astronomy
+
+
+def test_to_EarthLocation(movebank_relocations):
+    geometry = movebank_relocations["geometry"]
+    test_point = geometry.iloc[0]
+
+    transformed = astronomy.to_EarthLocation(geometry)
+
+    assert len(geometry) == len(transformed)
+
+    transform = pyproj.Transformer.from_proj(
+        proj_from="+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs",
+        proj_to="+proj=geocent +ellps=WGS84 +datum=WGS84 +units=m +no_defs",
+    )
+
+    # Check the projected values in the returned EarthLocation are what we expect
+    test_val = transform.transform(xx=test_point.x, yy=test_point.y, zz=0)
+    assert test_val[0] == transformed[0].x.value
+    assert test_val[1] == transformed[0].y.value
+    assert test_val[2] == transformed[0].z.value
+
+
+def test_is_night(movebank_relocations):
+    subset = movebank_relocations.iloc[12:15].copy()
+
+    subset["is_night"] = astronomy.is_night(subset.geometry, subset.fixtime)
+
+    assert subset["is_night"].values.tolist() == [True, True, False]

tests/test_base.py

@@ -165,3 +165,66 @@ def test_daynight_ratio(movebank_relocations):
         ),
         expected,
     )
+
+
+def test_edf_filter(movebank_relocations):
+    movebank_relocations["junk_status"] = True
+
+    empty = movebank_relocations.remove_filtered()
+    assert len(empty) == 0
+
+    reset = movebank_relocations.reset_filter().remove_filtered()
+    assert len(reset) > 0
+
+
+def test_relocs_from_gdf_with_warnings():
+    df = pd.read_feather("tests/sample_data/vector/movebank_data.feather")
+    geometry = gpd.points_from_xy(df.pop("location-long"), df.pop("location-lat"))
+
+    gdf = gpd.GeoDataFrame(df, geometry=geometry)
+
+    with pytest.warns(UserWarning, match="CRS was not set"):
+        ecoscope.base.Relocations.from_gdf(gdf, time_col="timestamp")
+
+    gdf = gpd.GeoDataFrame(df, geometry=geometry, crs=4326)
+    gdf["timestamp"] = pd.to_datetime(gdf["timestamp"])
+
+    with pytest.warns(UserWarning, match="timestamp is not timezone aware"):
+        ecoscope.base.Relocations.from_gdf(gdf, time_col="timestamp")
+
+    gdf["timestamp"] = "1/1/2000"
+
+    with pytest.warns(UserWarning, match="timestamp is not of type datetime64"):
+        ecoscope.base.Relocations.from_gdf(gdf, time_col="timestamp")
+
+
+def test_apply_traj_filter(movebank_relocations):
+    trajectory = ecoscope.base.Trajectory.from_relocations(movebank_relocations)
+
+    min_length = 0.2
+    max_length = 6000
+    min_time = 100
+    max_time = 300000
+    min_speed = 0.1
+    max_speed = 5
+
+    traj_seg_filter = ecoscope.base.TrajSegFilter(
+        min_length_meters=min_length,
+        max_length_meters=max_length,
+        min_time_secs=min_time,
+        max_time_secs=max_time,
+        min_speed_kmhr=min_speed,
+        max_speed_kmhr=max_speed,
+    )
+
+    filtered = trajectory.apply_traj_filter(traj_seg_filter)
+    filtered.remove_filtered(inplace=True)
+
+    assert filtered["dist_meters"].min() >= min_length
+    assert filtered["dist_meters"].max() <= max_length
+
+    assert filtered["timespan_seconds"].min() >= min_time
+    assert filtered["timespan_seconds"].max() <= max_time
+
+    assert filtered["speed_kmhr"].min() >= min_speed
+    assert filtered["speed_kmhr"].max() <= max_speed

tests/test_ecomap.py

@@ -6,6 +6,7 @@
     GeoTIFFElement,
     PrintControl,
 )
+import os
 import ee
 import geopandas
 import pytest
@@ -35,6 +36,18 @@ def test_repr_html():
     assert m._parent.width == 800 and m._parent.height == 600
 
 
+def test_static_map():
+    m = EcoMap(width=800, height=600, static=True)
+    assert len(m._children) == 2
+
+
+def test_to_png():
+    output_path = "tests/outputs/ecomap.png"
+    m = EcoMap(width=800, height=600)
+    m.to_png(output_path)
+    assert os.path.exists(output_path)
+
+
 def test_add_legend():
     m = EcoMap()
     # Test that we can assign hex colors with or without #
@@ -157,11 +170,11 @@ def test_add_print_control():
 @pytest.mark.parametrize(
     "file, geom_type",
     [
-        ("tests/sample_data/vector/maec_4zones_UTM36S.gpkg", "tests/sample_data/vector/observations.geojson"),
-        ("polygon", "point"),
+        ("tests/sample_data/vector/maec_4zones_UTM36S.gpkg", "polygon"),
+        ("tests/sample_data/vector/observations.geojson", "point"),
     ],
 )
-def add_datashader_gdf(file, geom_type):
+def test_add_datashader_gdf(file, geom_type):
     m = EcoMap()
     gdf = geopandas.GeoDataFrame.from_file(file)
     m.add_datashader_gdf(gdf, geom_type, zoom=False)
@@ -170,7 +183,7 @@ def add_datashader_gdf(file, geom_type):
     assert "L.imageOverlay(" in m._repr_html_()
 
 
-def add_datashader_gdf_with_zoom():
+def test_add_datashader_gdf_with_zoom():
     m = EcoMap()
     gdf = geopandas.GeoDataFrame.from_file("tests/sample_data/vector/maec_4zones_UTM36S.gpkg")
     m.add_datashader_gdf(gdf, "polygon", zoom=True)

tests/test_ecoplot.py

@@ -0,0 +1,47 @@
+import numpy as np
+from ecoscope.plotting.plot import EcoPlotData, ecoplot, mcp, nsd, speed
+from ecoscope.base import Trajectory
+
+
+def test_ecoplot(movebank_relocations):
+    traj = Trajectory.from_relocations(movebank_relocations)
+    epd = EcoPlotData(traj.groupby("groupby_col"), "segment_start", "speed_kmhr", line=dict(color="blue"))
+    figure = ecoplot([epd], "EcoPlot")
+
+    habiba = traj.loc[traj["groupby_col"] == "Habiba"]
+    salif = traj.loc[traj["groupby_col"] == "Salif Keita"]
+
+    assert len(figure.data) == 2
+
+    assert figure.data[0].name == "Habiba"
+    assert np.equal(figure.data[0].x, habiba["segment_start"].array).all()
+    assert np.equal(figure.data[0].y, habiba["speed_kmhr"].array).all()
+
+    assert figure.data[1].name == "Salif Keita"
+    assert np.equal(figure.data[1].x, salif["segment_start"].array).all()
+    assert np.equal(figure.data[1].y, salif["speed_kmhr"].array).all()
+
+
+def test_mcp(movebank_relocations):
+    figure = mcp(movebank_relocations)
+
+    assert len(figure.data) == 1
+    assert movebank_relocations["fixtime"].iat[0] == figure.data[0].x[0]
+    assert movebank_relocations["fixtime"].iat[-1] == figure.data[0].x[-1]
+
+
+def test_nsd(movebank_relocations):
+    figure = nsd(movebank_relocations)
+
+    assert len(figure.data) == 1
+    assert len(figure.data[0].x) == len(movebank_relocations)
+    assert len(figure.data[0].y) == len(movebank_relocations)
+
+
+def test_speed(movebank_relocations):
+    traj = Trajectory.from_relocations(movebank_relocations)
+    figure = speed(traj)
+
+    assert len(figure.data) == 1
+    len(figure.data[0].x) == len(traj) * 4
+    len(figure.data[0].y) == len(traj) * 4

tests/test_proiximity.py

@@ -0,0 +1,20 @@
+import pytest
+from ecoscope.analysis.proximity import SpatialFeature, Proximity, ProximityProfile
+from ecoscope.base import Trajectory
+
+
+@pytest.mark.skipif(not pytest.earthranger, reason="No connection to EarthRanger")
+def test_proximity(er_io):
+    er_features = er_io.get_spatial_features_group(spatial_features_group_id="15698426-7e0f-41df-9bc3-495d87e2e097")
+
+    prox_profile = ProximityProfile([])
+
+    for row in er_features.iterrows():
+        prox_profile.spatial_features.append(SpatialFeature(row[1]["name"], row[1]["pk"], row[1]["geometry"]))
+
+    relocations = er_io.get_subjectgroup_observations(group_name=er_io.GROUP_NAME)
+    trajectory = Trajectory.from_relocations(relocations)
+
+    proximity_events = Proximity.calculate_proximity(proximity_profile=prox_profile, trajectory=trajectory)
+
+    assert len(proximity_events["spatialfeature_id"].unique()) == len(prox_profile.spatial_features)