Merge pull request #81 from ai4er-cdt/feature/unit-tests

Feature/unit tests

.github/workflows/ci.yml

@@ -4,10 +4,10 @@
 name: Continuous integration loop
 
 # Triggers the workflow on pull request
-# events but only for the master branch
+# events but only for the main branch
 on:
   pull_request:
-    branches: [master]
+    branches: [main]
 
 jobs:
   build:

.github/workflows/python-package.yml

@@ -0,0 +1,35 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ "main", "feature/unit-tests" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ${{matrix.os}}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.8", "3.9", "3.10"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install pytest
+        pip install -e .
+    - name: Test with pytest
+      run: |
+        pytest geograph

docs/utils.py

@@ -3,6 +3,7 @@
 
 import glob
 
+
 def create_notebook_links():
     """Create links and entries for notebook in sphinx docs.
 
@@ -13,7 +14,7 @@ def create_notebook_links():
     notebooks = glob.glob("./notebooks/*.ipynb")
     notebooks.sort()
 
-    file_name_tmp = 'docs/notebooks/{}.nblink'
+    file_name_tmp = "docs/notebooks/{}.nblink"
     file_content_tmp = """
 {{
 "path": "../../notebooks/{}.ipynb"
@@ -32,12 +33,13 @@ def create_notebook_links():
         nb_name = path.split("/")[-1].split(".")[0]
         file_name = file_name_tmp.format(nb_name)
         file_content = file_content_tmp.format(nb_name)
-        with open(file_name,'w') as f:
-                f.write(file_content)
-                rst_index += "\n   notebooks/{}".format(nb_name)
+        with open(file_name, "w") as f:
+            f.write(file_content)
+            rst_index += "\n   notebooks/{}".format(nb_name)
 
-    with open("docs/tutorials.rst",'w') as f:
+    with open("docs/tutorials.rst", "w") as f:
         f.write(rst_index)
 
+
 if __name__ == "__main__":
-    create_notebook_links()
+    create_notebook_links()

geograph/binary_graph_operations.py

@@ -1,12 +1,9 @@
 """Contains tools for binary operations between GeoGraph objects."""
 from __future__ import annotations
-
 from typing import TYPE_CHECKING, Dict, List, Tuple
-
 import geopandas as gpd
 from shapely.geometry.base import BaseGeometry
 from shapely.geometry.polygon import Polygon
-
 import geograph.utils.geopandas_utils as gpd_utils
 from geograph.utils.polygon_utils import EMPTY_POLYGON, collapse_empty_polygon
 

geograph/demo/binder_constants.py

@@ -1,7 +1,7 @@
 """This file is for constants relevant to the binder demo."""
-
 from geograph.constants import PROJECT_PATH
 
+
 # Data directory on GWS
 DATA_DIR = PROJECT_PATH / "data"
 # Polygon data of Chernobyl Exclusion Zone (CEZ)

geograph/demo/plot_settings.py

@@ -42,7 +42,6 @@
 import itertools
 from distutils.spawn import find_executable
 from typing import Sequence, Tuple
-
 import matplotlib
 import matplotlib.style
 import numpy as np
@@ -57,6 +56,10 @@ def ps_defaults(use_tex: bool = True) -> None:
     Args:
         use_tex (bool, optional): Whether or not to use latex matplotlib backend.
             Defaults to True.
+
+    Example::
+        >>> from geograph.demo.plot_settings import ps_defaults
+        >>> ps_defaults(use_tex=False)
     """
     # matplotlib.use('agg') this used to be required for jasmin
     p_general = {
@@ -142,7 +145,7 @@ def label_subplots(
 def get_dim(
     width: float = 600,
     fraction_of_line_width: float = 1,
-    ratio: float = (5 ** 0.5 - 1) / 2,
+    ratio: float = (5**0.5 - 1) / 2,
 ) -> Tuple[float, float]:
     """Return figure height, width in inches to avoid scaling in latex.
 
@@ -180,7 +183,7 @@ def set_dim(
     fig: matplotlib.pyplot.figure,
     width: float = 600,
     fraction_of_line_width: float = 1,
-    ratio: float = (5 ** 0.5 - 1) / 2,
+    ratio: float = (5**0.5 - 1) / 2,
 ) -> None:
     """Set aesthetic figure dimensions to avoid scaling in latex.
 

geograph/geograph.py

@@ -4,7 +4,6 @@
 See https://networkx.org/documentation/stable/index.html for graph operations.
 """
 from __future__ import annotations
-
 import bz2
 import gzip
 import inspect
@@ -14,7 +13,6 @@
 from copy import deepcopy
 from itertools import zip_longest
 from typing import Any, Callable, Dict, Iterable, List, Optional, Sequence, Union
-
 import geopandas as gpd
 import networkx as nx
 import numpy as np
@@ -24,7 +22,6 @@
 import shapely
 from shapely.prepared import prep
 from tqdm import tqdm
-
 from geograph import binary_graph_operations, metrics
 from geograph.metrics import CLASS_METRICS_DICT, Metric
 from geograph.utils import rasterio_utils
@@ -677,12 +674,12 @@ def add_habitat(
                         # barrier polygon. If this results in multiple polygons,
                         # then the barrier polygon fully cuts the buffered polygon.
                         #
-                        # We find the resulting buffered polygon fragment that contains 
-                        # the original node polygon, by selecting the polygon that 
-                        # contains a representative point sampled from the original 
-                        # polygon. 
-                        # We then check if that polygon fragment intersects the 
-                        # neighbour polygon we're trying to reach. 
+                        # We find the resulting buffered polygon fragment that contains
+                        # the original node polygon, by selecting the polygon that
+                        # contains a representative point sampled from the original
+                        # polygon.
+                        # We then check if that polygon fragment intersects the
+                        # neighbour polygon we're trying to reach.
                         # If it does not, there is no path.
                         # If it does, there may be a path or there may not - it
                         # would require complex pathfinding code to discover, but

geograph/geotimeline.py

@@ -1,14 +1,11 @@
 """Module for analysing multiple GeoGraph objects."""
 from __future__ import annotations
-
 import datetime
 from bisect import bisect_left
 from typing import Callable, Dict, Iterable, List, Optional, Tuple, Union
-
 import numpy as np
 import pandas as pd
 import xarray as xr
-
 from geograph import GeoGraph
 from geograph.binary_graph_operations import NodeMap, identify_graphs
 
@@ -121,7 +118,7 @@ def _sort_by_time(self, reverse: bool = False) -> None:
         }
 
     def _load_from_sequence(self, graph_list: List[TimedGeoGraph]) -> None:
-        """Loads the sorted list of timed geographs into the timeline. """
+        """Loads the sorted list of timed geographs into the timeline."""
 
         # Make sure list is sorted in ascending time order (earliest = left)
         by_time = lambda item: item.time
@@ -186,7 +183,7 @@ def node_map_cache(self, time1: TimeStamp, time2: TimeStamp) -> NodeMap:
             raise NotCachedError
 
     def _empty_node_map_cache(self) -> None:
-        """ Empties the node map cache."""
+        """Empties the node map cache."""
         self._node_map_cache = dict()
 
     def timestack(self, use_cached: bool = True) -> List[NodeMap]:

geograph/metrics.py

@@ -1,9 +1,7 @@
 """Functions for calculating metrics from a GeoGraph."""
 from __future__ import annotations
-
 from dataclasses import dataclass
 from typing import TYPE_CHECKING, Any, Optional, Union
-
 import networkx as nx
 import numpy as np
 
@@ -164,7 +162,7 @@ def _simpson_diversity_index(geo_graph: geograph.GeoGraph) -> Metric:
     )
 
     return Metric(
-        value=1 - np.sum(class_prop_of_landscape ** 2),
+        value=1 - np.sum(class_prop_of_landscape**2),
         name="simpson_diversity_index",
         description=description,
         variant="conventional",
@@ -391,7 +389,7 @@ def _class_effective_mesh_size(
     )
 
     return Metric(
-        value=np.sum(class_areas ** 2) / total_area,
+        value=np.sum(class_areas**2) / total_area,
         name=f"effective_mesh_size_class={class_value}",
         description=description,
         variant="conventional",

geograph/tests/create_test_data.py → geograph/tests/create_data_test.py

@@ -2,10 +2,10 @@
 
 Note: We may want to delete this at some point.
 """
+import numpy as np
 from typing import Dict, Iterable, Tuple
-
 import geopandas as gpd
-import numpy as np
+import pytest
 from geograph.constants import SRC_PATH
 from geograph.tests.utils import get_array_transform, polygonise_sub_array
 from geograph.utils.rasterio_utils import polygonise
@@ -41,7 +41,9 @@ def _polygonise_splits(
     return result
 
 
-if __name__ == "__main__":
+@pytest.mark.unit
+def test_create_data() -> None:
+    """Create the test data."""
     print("Creating test data ... ")
     TEST_DATA_FOLDER = SRC_PATH / "tests" / "testdata"
     TEST_DATA_FOLDER.mkdir(parents=True, exist_ok=True)
@@ -96,3 +98,7 @@ def _polygonise_splits(
         polygons_t = polygonise(arr_t, transform=get_array_transform(arr_t))
         save_path = TEST_DATA_FOLDER / "timestack" / f"time_{i}.gpkg"
         polygons_t.to_file(save_path, driver="GPKG")
+
+
+if __name__ == "__main__":
+    test_create_data()

geograph/tests/utils.py

@@ -1,6 +1,5 @@
 """Convenience functions for creating and analysing test data for GeoGraph"""
 from typing import Iterable, Tuple
-
 import affine
 import geograph
 import geopandas as gpd
@@ -9,6 +8,7 @@
 import seaborn as sns
 from geograph.utils.rasterio_utils import polygonise
 
+
 # Mirror the x axis
 AFFINE_MIRROR_X = affine.Affine(-1, 0, 0, 0, 1, 0)
 # Mirror the y axis
@@ -86,7 +86,6 @@ def polygonise_sub_array(
     Args:
         arr (np.ndarray): The numpy array from which to select the sub-array
         x_lims (Tuple[int, int]): The x-limits of the sub-array. Must be >=0 or None.
-
         y_lims (Tuple[int, int]): The y-limits of the sub-array. Must be >=0 or None.
 
     Returns:

geograph/utils/geopandas_utils.py

@@ -1,6 +1,5 @@
 """Helper functions for operating with geopandas objects."""
 from typing import Dict, List
-
 import geopandas as gpd
 import networkx as nx
 import tqdm
@@ -11,6 +10,7 @@
 )
 from shapely.geometry import MultiPolygon
 
+
 # For switching identifiction mode in `identify_node`
 _BULK_SPATIAL_IDENTIFICATION_FUNCTION = {
     "corner": connect_with_interior_or_edge_or_corner_bulk,

geograph/utils/polygon_utils.py

@@ -1,10 +1,10 @@
 """Helper functions for overlap computations with polygons in shapely."""
 from typing import List
-
 from geopandas.array import GeometryArray
 from numpy import ndarray
 from shapely.geometry.polygon import Polygon
 
+
 # Note: All DE-9IM patterns below are streamlined to work well with polygons.
 #  They are not guaranteed to work on lower dimensional objects (points/lines)
 CORNER_ONLY_PATTERN = "FF*F0****"

geograph/utils/rasterio_utils.py

@@ -1,7 +1,5 @@
 """A collection of utility functions for data loading with rasterio."""
-
 from typing import Iterable, Optional, Tuple, Union
-
 import affine
 import geograph.utils.geopandas_utils as gpd_utils
 import geopandas as gpd

geograph/visualisation/control_widgets.py

@@ -1,10 +1,7 @@
 """Module with widgets to control GeoGraphViewer."""
-
 from __future__ import annotations
-
 import logging
 from typing import Dict, Optional
-
 import ipywidgets as widgets
 import traitlets
 from geograph.visualisation import geoviewer, widget_utils
@@ -807,20 +804,21 @@ def _hover_callback(self, feature, **kwargs):  # pylint: disable=unused-argument
         """Callback function on hover on graph polygon patch"""
         try:
             # self.logger.debug("HoverWidget callback called.")
-            new_value = widget_utils.create_html_header(
-                "Current Patch"
-            ).value + """</br>
+            new_value = (
+                widget_utils.create_html_header("Current Patch").value
+                + """</br>
                 <b>Class label:</b> {}</br>
                 <b>Area:</b> {:.2f} ha</br>
                 <b>Perimeter:</b> {:.2f} km</br>
                 <b>Shape index:</b> {:.2f}</br>
                 <b>Fractal dim.:</b> {:.2f}
             """.format(
-                feature["properties"]["class_label"],
-                feature["properties"]["area"] / 1e4,
-                feature["properties"]["perimeter"] / 1e3,
-                feature["properties"]["shape_index"],
-                feature["properties"]["fractal_dimension"],
+                    feature["properties"]["class_label"],
+                    feature["properties"]["area"] / 1e4,
+                    feature["properties"]["perimeter"] / 1e3,
+                    feature["properties"]["shape_index"],
+                    feature["properties"]["fractal_dimension"],
+                )
             )
             if "node_dynamic" in feature["properties"].keys():
                 new_value += "</br><b>Node dyanmic:</b> {}".format(

geograph/visualisation/folium_utils.py

@@ -1,9 +1,6 @@
 """Module with utility functions to plot graphs in folium."""
-
 from __future__ import annotations
-
 from typing import Callable, List, Optional, Tuple
-
 import folium
 import geograph
 import geopandas as gpd