Merge pull request #57 from nismod/feature/damages

Experimental flag

.github/workflows/build.yml

@@ -13,7 +13,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Checkout submodules
         run: git submodule update --init --recursive
@@ -31,7 +31,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Checkout submodules
         run: git submodule update --init --recursive
@@ -55,7 +55,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4

.github/workflows/docs.yml

@@ -21,7 +21,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Setup Pages
         id: pages
         uses: actions/configure-pages@v3
@@ -44,7 +44,7 @@ jobs:
           popd
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v2
         with:
           path: docs/build/html
 

.github/workflows/package.yml

@@ -9,7 +9,7 @@ jobs:
     name: Build SDist
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Build SDist
         run: pipx run build --sdist
@@ -30,7 +30,7 @@ jobs:
         os: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: pypa/[email protected]
         env:

pyproject.toml

@@ -1,17 +1,17 @@
 [project]
-name="nismod-snail"
-version="0.4.1"
-license={file = "LICENSE"}
-description="The spatial networks impact assessment library"
-readme="README.md"
-authors=[
-    {name="Tom Russell", email="[email protected]"},
-    {name="Thibault Lestang"},
-    {name="Raghav Pant"},
-    {name="Lena Fuldauer"},
+name = "nismod-snail"
+version = "0.5.0"
+license = { file = "LICENSE" }
+description = "The spatial networks impact assessment library"
+readme = "README.md"
+authors = [
+    { name = "Tom Russell", email = "[email protected]" },
+    { name = "Thibault Lestang" },
+    { name = "Raghav Pant" },
+    { name = "Lena Fuldauer" },
 ]
-maintainers=[{name="Tom Russell", email="[email protected]"}]
-classifiers=[
+maintainers = [{ name = "Tom Russell", email = "[email protected]" }]
+classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: MIT License",
@@ -20,9 +20,9 @@ classifiers=[
     "Topic :: Scientific/Engineering :: GIS",
     "Topic :: Utilities"
 ]
-keywords=[]
-requires-python=">=3.8"
-dependencies=[
+keywords = []
+requires-python = ">=3.8"
+dependencies = [
     "geopandas",
     "matplotlib",
     "openpyxl",
@@ -36,7 +36,7 @@ dependencies=[
 ]
 
 [project.optional-dependencies]
-dev=[
+dev = [
     "affine",
     "black",
     "hilbertcurve",
@@ -45,8 +45,8 @@ dev=[
     "pytest-cov",
     "pytest",
 ]
-docs=["sphinx", "m2r2"]
-tutorials=[
+docs = ["sphinx", "m2r2"]
+tutorials = [
     "contextily",
     "irv_autopkg_client",
     "jupyter",
@@ -62,7 +62,7 @@ Documentation = "https://nismod.github.io/snail/"
 Repository = "https://github.com/nismod/snail.git"
 
 [project.scripts]
-snail="snail.cli:snail"
+snail = "snail.cli:snail"
 
 [build-system]
 requires = ["scikit-build-core>=0.3.3", "pybind11"]

src/snail/__init__.py

@@ -12,7 +12,7 @@
     from importlib.metadata import version
 
     __version__ = version("nismod-snail")
-except:
+except Exception:
     __version__ = "unknown"
 
 

src/snail/cli.py

@@ -18,6 +18,7 @@
     split_linestrings,
     split_polygons,
     split_points,
+    split_polygons_experimental,
 )
 from snail.io import (
     read_raster_band_data,
@@ -32,6 +33,7 @@ def snail(args=None):
     """snail command"""
     parser = argparse.ArgumentParser(prog="snail")
     parser.add_argument("--verbose", "-v", action="count", default=0)
+    parser.add_argument("-x", "--experimental", action="store_true")
     subparsers = parser.add_subparsers(help="Run a command")
 
     parser_split = subparsers.add_parser(
@@ -190,26 +192,34 @@ def split(args):
     geom_type = _sample_geom_type(features)
 
     if "Point" in geom_type:
-        logging.info(f"Preparing points")
+        logging.info("Preparing points")
         prepared = prepare_points(features)
-        logging.info(f"Splitting points")
+        logging.info("Splitting points")
         splits = split_features_for_rasters(prepared, [grid], split_points)
     elif "LineString" in geom_type:
-        logging.info(f"Preparing linestrings")
+        logging.info("Preparing linestrings")
         prepared = prepare_linestrings(features)
-        logging.info(f"Splitting linestrings")
+        logging.info("Splitting linestrings")
         splits = split_features_for_rasters(
             prepared, [grid], split_linestrings
         )
     elif "Polygon" in geom_type:
-        logging.info(f"Preparing polygons")
+        logging.info("Preparing polygons")
         prepared = prepare_polygons(features)
-        logging.info(f"Splitting polygons")
-        splits = split_features_for_rasters(prepared, [grid], split_polygons)
+        if args.experimental:
+            logging.info("Splitting polygons (experimental)")
+            splits = split_features_for_rasters(
+                prepared, [grid], split_polygons_experimental
+            )
+        else:
+            logging.info("Splitting polygons")
+            splits = split_features_for_rasters(
+                prepared, [grid], split_polygons
+            )
     else:
         raise ValueError("Could not process vector data of type %s", geom_type)
 
-    logging.info(f"Applying indices")
+    logging.info("Applying indices")
     splits = apply_indices(splits, grid)
 
     if args.attribute and args.raster:
@@ -280,10 +290,10 @@ def process(args):
         )
 
     for vector_layer in vector_layers.itertuples():
-        _process_layer(vector_layer, transforms, rasters)
+        _process_layer(vector_layer, transforms, rasters, args.experimental)
 
 
-def _process_layer(vector_layer, transforms, rasters):
+def _process_layer(vector_layer, transforms, rasters, experimental=False):
     vector_path = Path(vector_layer.path)
     layer = getattr(vector_layer, "layer", None)
     logging.info("Processing %s", vector_path.name)
@@ -304,9 +314,15 @@ def _process_layer(vector_layer, transforms, rasters):
         with_data = associate_raster_files(split, rasters)
     elif "Polygon" in geom_type:
         prepared = prepare_polygons(features)
-        split = split_features_for_rasters(
-            prepared, transforms, split_polygons
-        )
+        if experimental:
+            logging.info("Split polygons (experimental)")
+            split = split_features_for_rasters(
+                prepared, transforms, split_polygons_experimental
+            )
+        else:
+            split = split_features_for_rasters(
+                prepared, transforms, split_polygons
+            )
         with_data = associate_raster_files(split, rasters)
     else:
         raise ValueError(f"Could not process vector data of type {geom_type}")

src/snail/intersection.py

@@ -12,7 +12,7 @@
 from shapely.geometry import mapping, shape
 from shapely.ops import linemerge, polygonize
 
-from snail.core.intersections import (
+from snail.core.intersections import (  # type: ignore
     get_cell_indices,
     split_linestring,
     split_polygon,
@@ -96,7 +96,7 @@ def from_extent(
             crs=crs,
             width=math.ceil((xmax - xmin) / cell_width),
             height=math.ceil((ymax - ymin) / cell_height),
-            transform=(cell_width, 0, xmin, 0, cell_height, ymin),
+            transform=(cell_width, 0.0, xmin, 0.0, cell_height, ymin),
         )
 
 

src/snail/io.py

@@ -1,3 +1,4 @@
+import importlib.util
 import logging
 from typing import List, Tuple
 
@@ -106,12 +107,11 @@ def read_features(path, layer=None):
     if path.suffix in (".parquet", ".geoparquet"):
         features = geopandas.read_parquet(path)
     else:
-        try:
-            import pyogrio
-
+        if importlib.util.find_spec("pyogrio"):
             engine = "pyogrio"
-        except ImportError:
+        else:
             engine = "fiona"
+
         if layer:
             features = geopandas.read_file(path, layer=layer, engine=engine)
         else:

tests/test_intersection.py

@@ -177,11 +177,11 @@ def test_split_linestrings(self, grid, linestrings, linestrings_split):
         # Ideally we'd like to use geopandas.assert_geodataframe_equal to
         # to compare both expected and actual geodfs, but this function offers
         # little control over tolerance. When using option "check_less_precise",
-        # it used GeoSeries.geom_almost_equals under the hood, which has an kwarg
-        # "decimal". But assert_geodataframe_equal does not recognise kwarg "decimal".
+        # it uses GeoSeries.geom_equals_exact under the hood, which has an kwarg
+        # "tolerance". But assert_geodataframe_equal does not recognise kwarg "tolerance".
         assert (
             actual["geometry"]
-            .geom_almost_equals(expected_gdf["geometry"], decimal=3)
+            .geom_equals_exact(expected_gdf["geometry"], tolerance=1e-3)
             .values.all()
         )
         assert_array_equal(actual["col1"].values, expected_gdf["col1"].values)