expand ruff rules

.github/workflows/publish.yml

@@ -7,7 +7,7 @@ jobs:
   # publish:
   #   runs-on: ubuntu-latest
   #   needs: test
-  #   # The following steps to build a Docker image and publish to the GitHub container registry on release. Alternatively, can replace with other publising steps (ie. publishing to PyPI, deploying documentation etc.)
+  #   # The following steps to build a Docker image and publish to the GitHub container registry on release. Alternatively, can replace with other publishing steps (ie. publishing to PyPI, deploying documentation etc.)
   #   steps:
   #     - name: Login to GitHub Container Registry
   #       uses: docker/login-action@v3

.pre-commit-config.yaml

@@ -20,3 +20,25 @@ repos:
     hooks:
       - id: markdownlint
         args: ["--disable", "MD013", "--"]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+    - id: codespell
+      name: Check common misspellings in text files with codespell.
+      additional_dependencies:
+      - tomli
+
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: 1.7.0
+    hooks:
+    - id: pyproject-fmt
+      name: Apply a consistent format to pyproject.toml
+
+  - repo: https://github.com/dosisod/refurb
+    rev: v1.28.0
+    hooks:
+    - id: refurb
+      name: Modernizing Python codebases using Refurb
+      additional_dependencies:
+      - numpy

README.md

@@ -71,7 +71,7 @@ To use this repository as a template for your own application:
 
 To add or remove dependencies:
 
-1. Edit the `dependencies` variables in the `pyproject.toml` file (aim to keep develpment tools separate from the project requirements).
+1. Edit the `dependencies` variables in the `pyproject.toml` file (aim to keep development tools separate from the project requirements).
 2. Update the requirements files:
    - `pip-compile` for `requirements.txt` - the project requirements.
    - `pip-compile --extra dev -o dev-requirements.txt` for `dev-requirements.txt` - the development requirements.

pyproject.toml

@@ -1,6 +1,9 @@
 [build-system]
-requires = ["setuptools", "setuptools-scm"]
 build-backend = "setuptools.build_meta"
+requires = [
+  "setuptools",
+  "setuptools-scm",
+]
 
 [tool.setuptools.packages.find]
 exclude = ["htmlcov"] # Exclude the coverage report file from setuptools package finder
@@ -13,44 +16,50 @@ authors = [
     { name = "Imperial College London RSE Team", email = "ict-rse-team@imperial.ac.uk" }
 ]
 requires-python = ">=3.10"
-dependencies = [ # TODO definitely don't need all of these
-                "cdsapi",
-                "fastparquet",
-                "fiona",
-                "geopandas",
-                "geopy",
-                "GitPython",
-                "matplotlib",
-                "netcdf4",
-                "networkx",
-                "numpy",
-                "osmnx",
-                "pandas",
-                "pyarrow",
-                "pydantic",
-                "pysheds",
-                "pyswmm",
-                "PyYAML",
-                "rasterio",
-                "rioxarray",
-                "SALib",
-                "SciPy",
-                "shapely",
-                "snkit",
-                "tqdm",
-                "xarray"
-                ]
-
+classifiers = [
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+  # TODO definitely don't need all of these
+  "cdsapi",
+  "fastparquet",
+  "fiona",
+  "geopandas",
+  "geopy",
+  "GitPython",
+  "matplotlib",
+  "netcdf4",
+  "networkx",
+  "numpy",
+  "osmnx",
+  "pandas",
+  "pyarrow",
+  "pydantic",
+  "pysheds",
+  "pyswmm",
+  "PyYAML",
+  "rasterio",
+  "rioxarray",
+  "SALib",
+  "SciPy",
+  "shapely",
+  "snkit",
+  "tqdm",
+  "xarray",
+]
 [project.optional-dependencies]
 dev = [
-    "ruff",
-    "mypy",
-    "pip-tools",
-    "pre-commit",
-    "pytest",
-    "pytest-cov",
-    "pytest-mypy",
-    "pytest-mock"
+  "mypy",
+  "pip-tools",
+  "pre-commit",
+  "pytest",
+  "pytest-cov",
+  "pytest-mock",
+  "pytest-mypy",
+  "ruff",
 ]
 
 [tool.mypy]
@@ -76,3 +85,10 @@ select = ["D", "E", "F", "I"] # pydocstyle, pycodestyle, Pyflakes, isort
 
 [tool.ruff.pydocstyle]
 convention = "google"
+
+[tool.codespell]
+skip = "swmmanywhere/defs/iso_converter.yml,*.inp"
+ignore-words-list = "gage,gages"
+
+[tool.refurb]
+ignore = [184]

swmmanywhere/geospatial_utilities.py

@@ -6,8 +6,10 @@
 
 @author: Barnaby Dobson
 """
+import itertools
 import json
 import math
+import operator
 from copy import deepcopy
 from functools import lru_cache
 from pathlib import Path
@@ -248,8 +250,9 @@ def reproject_graph(G: nx.Graph,
     # Convert and add edges with 'geometry' property
     for u, v, data in G_new.edges(data=True):
         if 'geometry' in data.keys():
-            data['geometry'] = sgeom.LineString(transformer.transform(x, y) 
-                                      for x, y in data['geometry'].coords)
+            data['geometry'] = sgeom.LineString(
+                itertools.starmap(transformer.transform,
+                                  data['geometry'].coords))
         else:
             data['geometry'] = sgeom.LineString([[G_new.nodes[u]['x'],
                                         G_new.nodes[u]['y']],
@@ -440,7 +443,7 @@ def delineate_catchment(grid: pysheds.sgrid.sGrid,
         polys.append({'id': id, 
                       'geometry': catchment_polygon,
                       'area': catchment_polygon.area})
-    polys = sorted(polys, key=lambda d: d['area'], reverse=True)
+    polys.sort(key=operator.itemgetter("area"), reverse=True)
     return gpd.GeoDataFrame(polys, crs = grid.crs)
 
 def remove_intersections(polys: gpd.GeoDataFrame) -> gpd.GeoDataFrame:
@@ -461,9 +464,11 @@ def remove_intersections(polys: gpd.GeoDataFrame) -> gpd.GeoDataFrame:
     result_polygons = polys.copy()
 
     # Sort the polygons by area (smallest first)
-    result_polygons['area'] = result_polygons.geometry.area
-    result_polygons = result_polygons.sort_values('area', ascending=True)
-    result_polygons = result_polygons.reset_index(drop=True)
+    result_polygons = (
+        result_polygons.assign(area=result_polygons.geometry.area)
+        .sort_values('area', ascending=True)
+        .reset_index(drop=True)
+    )
 
     # Store the area of 'trimmed' polygons into a combined geometry, starting
     # with the smallest area polygon
@@ -480,8 +485,10 @@ def remove_intersections(polys: gpd.GeoDataFrame) -> gpd.GeoDataFrame:
 
     # Sort the polygons by area (largest first) - this is just to conform to
     # the unit test and is not strictly essential
-    result_polygons = result_polygons.sort_values('area', ascending=False)
-    result_polygons = result_polygons.drop('area', axis=1)
+    result_polygons = (
+        result_polygons.sort_values('area', ascending=False)
+        .drop('area', axis=1)
+    )
 
     return result_polygons
 
@@ -592,7 +599,7 @@ def derive_subcatchments(G: nx.Graph, fid: Path) -> gpd.GeoDataFrame:
     polys_gdf = polys_gdf[~polys_gdf['geometry'].is_empty]
 
     # Remove zero area subareas and attach to nearest polygon
-    removed_subareas: List[sgeom.Polygon] = list() # needed for mypy
+    removed_subareas: List[sgeom.Polygon] = [] # needed for mypy
     def remove_(mp): return remove_zero_area_subareas(mp, removed_subareas)
     polys_gdf['geometry'] = polys_gdf['geometry'].apply(remove_)
     polys_gdf = attach_unconnected_subareas(polys_gdf, removed_subareas)
@@ -614,7 +621,7 @@ def derive_rc(polys_gdf: gpd.GeoDataFrame,
     impervious area is calculated by overlaying the subcatchments with building
     footprints and all edges in G buffered by their width parameter (i.e., to
     calculate road area).
-    
+
     Args:
         polys_gdf (gpd.GeoDataFrame): A GeoDataFrame containing polygons that
             represent subcatchments with columns: 'geometry', 'area', and 'id'. 
@@ -632,12 +639,15 @@ def derive_rc(polys_gdf: gpd.GeoDataFrame,
     ## Format as swmm type catchments 
 
     # TODO think harder about lane widths (am I double counting here?)
-    lines = []
-    for u, v, x in G.edges(data=True):
-        lines.append({'geometry' : x['geometry'].buffer(x['width'], 
-                                                                cap_style = 2, 
-                                                                join_style=2),
-                            'id' : x['id']})
+    lines = [
+        {
+            'geometry': x['geometry'].buffer(x['width'], 
+                                             cap_style=2, 
+                                             join_style=2),
+            'id': x['id']
+        }
+        for u, v, x in G.edges(data=True)
+    ]
     lines_df = pd.DataFrame(lines)
     lines_gdf = gpd.GeoDataFrame(lines_df, 
                                 geometry=lines_df.geometry,

swmmanywhere/graph_utilities.py

@@ -45,8 +45,7 @@ def load_graph(fid: Path) -> nx.Graph:
 def _serialize_line_string(obj):
     if isinstance(obj, shapely.LineString):
         return obj.wkt
-    else:
-        return obj
+    return obj
 def save_graph(G: nx.Graph, 
                fid: Path) -> None:
     """Save a graph to a file.
@@ -57,7 +56,7 @@ def save_graph(G: nx.Graph,
     """
     json_data = nx.node_link_data(G)
 
-    with open(fid, 'w') as file:
+    with fid.open('w') as file:
         json.dump(json_data, 
                   file,
                   default = _serialize_line_string)
@@ -73,25 +72,21 @@ class BaseGraphFunction(ABC):
     their requirements and additions a-priori when the list is provided.
     """
 
-    required_edge_attributes: List[str] = list()
-    adds_edge_attributes: List[str] = list()
-    required_node_attributes: List[str] = list()
-    adds_node_attributes: List[str] = list()
+    required_edge_attributes: List[str] = []
+    adds_edge_attributes: List[str] = []
+    required_node_attributes: List[str] = []
+    adds_node_attributes: List[str] = []
     def __init_subclass__(cls, 
                           required_edge_attributes: Optional[List[str]] = None,
                           adds_edge_attributes: Optional[List[str]] = None,
                           required_node_attributes : Optional[List[str]] = None,
                           adds_node_attributes : Optional[List[str]] = None
                           ):
         """Set the required and added attributes for the subclass."""
-        cls.required_edge_attributes = required_edge_attributes if \
-            required_edge_attributes else []
-        cls.adds_edge_attributes = adds_edge_attributes if \
-            adds_edge_attributes  else []
-        cls.required_node_attributes = required_node_attributes if \
-            required_node_attributes else []
-        cls.adds_node_attributes = adds_node_attributes if \
-            adds_node_attributes  else []
+        cls.required_edge_attributes = required_edge_attributes or []
+        cls.adds_edge_attributes = adds_edge_attributes or []
+        cls.required_node_attributes = required_node_attributes or []
+        cls.adds_node_attributes = adds_node_attributes or []
 
     @abstractmethod
     def __call__(self, 
@@ -243,7 +238,7 @@ def __call__(self, G: nx.Graph, **kwargs) -> nx.Graph:
         Returns:
             G (nx.Graph): A graph
         """
-        #TODO the geometry is left as is currently - should be reveresed, however
+        #TODO the geometry is left as is currently - should be reversed, however
         # in original osmnx geometry there are some incorrectly directed ones
         # someone with more patience might check start and end Points to check
         # which direction the line should be going in...
@@ -734,8 +729,7 @@ def __call__(self, G: nx.Graph,
                 if d['edge_type'] == 'outlet':
                     nodes_to_remove.append(v)
                 else:
-                    nodes_to_remove.append(u)
-                    nodes_to_remove.append(v)
+                    nodes_to_remove.extend((u,v))
 
         isolated_nodes = list(nx.isolates(G))
 
@@ -779,7 +773,7 @@ def __call__(self, G: nx.Graph,
                 # Push the neighbor to the heap
                 heappush(heap, (alt_dist, neighbor))
 
-        edges_to_keep = set()
+        edges_to_keep: set = set() # no clue why mypy wants me to do this..
         for path in paths.values():
             # Assign outlet
             outlet = path[0]
@@ -788,10 +782,9 @@ def __call__(self, G: nx.Graph,
                 G.nodes[node]['shortest_path'] = shortest_paths[node]
 
             # Store path
-            for i in range(len(path) - 1):
-                edges_to_keep.add((path[i+1], path[i]))
-
-        # Remvoe edges not on paths
+            edges_to_keep.update(zip(path[1:], path[:-1]))
+
+        # Remove edges not on paths
         new_graph = G.copy()
         for u,v in G.edges():
             if (u,v) not in edges_to_keep:

swmmanywhere/parameters.py

@@ -229,10 +229,10 @@ def _generate_property(self,
         """
         if property_name in self.__dict__.keys():
              return self.__dict__[property_name]
-        else:
-            return self._generate_path(self.project_name, 
-                                       getattr(self, location),
-                                       property_name)
+
+        return self._generate_path(self.project_name, 
+                                    getattr(self, location),
+                                    property_name)
 
     def _generate_project(self):
         return self._generate_path(self.project_name)