Merge pull request #55 from nismod/feature/damages

Initial DamageCurve implementation plus..

.environment.yml

@@ -6,13 +6,27 @@ dependencies:
   - python=3.11
   - affine
   - black
+  - contextily
   - geopandas
+  - jupyter
+  - matplotlib
   - nbstripout
+  - networkx
   - numpy
+  - openpyxl
+  - pandera
   - pip
+  - pyarrow
+  - pyogrio
   - pytest
   - pytest-cov
   - rasterio
+  - seaborn
   - shapely
+  - scipy
   - pip:
+    - hilbertcurve
+    - irv_autopkg_client
     - python-igraph
+    - snkit
+    - tqdm

README.md

@@ -192,10 +192,10 @@ The `snail.core.intersections` module is built using `pybind11` with
 >
 > Copyright (c) 2020-23 Tom Russell and all [snail contributors](https://github.com/nismod/snail/graphs/contributors)
 
-This library is developed by researchers in the [Oxford Programme for Sustainable 
+This library is developed by researchers in the [Oxford Programme for Sustainable
 Infrastructure Systems](https://opsis.eci.ox.ac.uk/) at the University of Oxford,
 funded by multiple research projects.
 
-This research received funding from the FCDO Climate Compatible Growth Programme. 
-The views expressed here do not necessarily reflect the UK government's official 
+This research received funding from the FCDO Climate Compatible Growth Programme.
+The views expressed here do not necessarily reflect the UK government's official
 policies.

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name="nismod-snail"
-version="0.3.2"
+version="0.4.0"
 license={file = "LICENSE"}
 description="The spatial networks impact assessment library"
 readme="README.md"
@@ -24,22 +24,37 @@ keywords=[]
 requires-python=">=3.8"
 dependencies=[
     "geopandas",
+    "matplotlib",
+    "openpyxl",
+    "pandera",
     "pyarrow",
+    "pyogrio",
     "python-igraph",
     "rasterio",
     "shapely",
+    "scipy"
 ]
 
 [project.optional-dependencies]
 dev=[
     "affine",
     "black",
+    "hilbertcurve",
     "nbstripout",
     "numpy",
     "pytest-cov",
     "pytest",
 ]
 docs=["sphinx", "m2r2"]
+tutorials=[
+    "contextily",
+    "irv_autopkg_client",
+    "jupyter",
+    "networkx",
+    "seaborn",
+    "snkit",
+    "tqdm",
+]
 
 [project.urls]
 Homepage = "https://github.com/nismod/snail"

src/snail/__init__.py

@@ -1,6 +1,5 @@
 """snail - the spatial networks impact assessment library
 """
-import pkg_resources
 
 # Import things to define what is accessible directly on snail, when a client
 # writes::
@@ -10,8 +9,10 @@
 # from snail.network import Network
 
 try:
-    __version__ = pkg_resources.get_distribution(__name__).version
-except pkg_resources.DistributionNotFound:
+    from importlib.metadata import version
+
+    __version__ = version("nismod-snail")
+except:
     __version__ = "unknown"
 
 

src/snail/cli.py

@@ -8,8 +8,9 @@
 import pandas
 
 from snail.intersection import (
-    Transform,
+    GridDefinition,
     apply_indices,
+    get_raster_values_for_splits,
     prepare_linestrings,
     prepare_polygons,
     prepare_points,
@@ -19,7 +20,7 @@
     split_points,
 )
 from snail.io import (
-    associate_raster_file,
+    read_raster_band_data,
     associate_raster_files,
     read_features,
     read_raster_metadata,
@@ -171,7 +172,7 @@ def snail(args=None):
 def split(args):
     """snail split command"""
     if args.raster:
-        transform, all_bands = read_raster_metadata(args.raster)
+        grid, all_bands = read_raster_metadata(args.raster)
     else:
         crs = None
         width = args.width
@@ -181,26 +182,35 @@ def split(args):
             sys.exit(
                 "Error: Expected either a raster file or transform, width and height of splitting grid"
             )
-        transform = Transform(crs, width, height, affine_transform)
-    logging.info(f"Splitting grid {transform=}")
+        grid = GridDefinition(crs, width, height, affine_transform)
+    logging.info(f"Splitting {grid=}")
 
-    features = geopandas.read_file(args.features)
+    features = read_features(Path(args.features))
     features_crs = features.crs
     geom_type = _sample_geom_type(features)
 
     if "Point" in geom_type:
+        logging.info(f"Preparing points")
         prepared = prepare_points(features)
-        splits = split_points(prepared)
+        logging.info(f"Splitting points")
+        splits = split_features_for_rasters(prepared, [grid], split_points)
     elif "LineString" in geom_type:
+        logging.info(f"Preparing linestrings")
         prepared = prepare_linestrings(features)
-        splits = split_linestrings(prepared, transform)
+        logging.info(f"Splitting linestrings")
+        splits = split_features_for_rasters(
+            prepared, [grid], split_linestrings
+        )
     elif "Polygon" in geom_type:
+        logging.info(f"Preparing polygons")
         prepared = prepare_polygons(features)
-        splits = split_polygons(prepared, transform)
+        logging.info(f"Splitting polygons")
+        splits = split_features_for_rasters(prepared, [grid], split_polygons)
     else:
         raise ValueError("Could not process vector data of type %s", geom_type)
 
-    splits = apply_indices(splits, transform)
+    logging.info(f"Applying indices")
+    splits = apply_indices(splits, grid)
 
     if args.attribute and args.raster:
         if args.band:
@@ -225,9 +235,10 @@ def split(args):
                 args.raster,
                 band_index,
             )
-            splits[key] = associate_raster_file(
-                splits, args.raster, band_number=int(band_index)
+            band_data = read_raster_band_data(
+                args.raster, band_number=int(band_index)
             )
+            splits[key] = get_raster_values_for_splits(splits, band_data)
 
     splits.set_crs(features_crs, inplace=True)
     splits.to_file(args.output)

src/snail/core/__init__.py

@@ -1,4 +1,4 @@
-from .intersections import (get_cell_indices, split_linestring, split_polygon)
+from .intersections import get_cell_indices, split_linestring, split_polygon
 
 __all__ = [
     "get_cell_indices",