Merge branch 'master' into fix/192-fix-traffic-analysis-for-nodes-att…

…ached-to-multiple-nodes

docs/user_guide/user_guide.rst

@@ -123,7 +123,7 @@ Initialization file templates
     polygon = map.geojson			# <name + file extension of the geojson polygon file in the static/network folder> / None
     network_type = drive			# drive / walk / bike / drive_service / all
     road_types = motorway,motorway_link,trunk,trunk_link,primary, primary_link,secondary,secondary_link,tertiary,tertiary_link
-    save_shp = True				# True / False
+    save_gpkg = True				# True / False
 
     [origins_destinations]
     origins = origins.shp 			# <file name> / None
@@ -159,7 +159,7 @@ Initialization file templates
   name = single link redundancy test
   analysis = single_link_redundancy
   weighing = distance
-  save_shp = True
+  save_gpkg = True
   save_csv = True
 
   [analysis2]
@@ -168,14 +168,14 @@ Initialization file templates
   aggregate_wl = max
   threshold = 0.5
   weighing = distance
-  save_shp = True
+  save_gpkg = True
   save_csv = True
 
   [analysis3]
   name = optimal origin dest test
   analysis = optimal_route_origin_destination
   weighing = distance
-  save_shp = True
+  save_gpkg = True
   save_csv = True
 
   [analysis4]
@@ -184,7 +184,7 @@ Initialization file templates
   aggregate_wl = max
   threshold = 0.5
   weighing = distance
-  save_shp = True
+  save_gpkg = True
   save_csv = False
 
   [analysis5]
@@ -193,7 +193,7 @@ Initialization file templates
   aggregate_wl = max
   threshold = 0.5
   weighing = distance
-  save_shp = True
+  save_gpkg = True
   save_csv = True
 
   [analysis6]
@@ -204,6 +204,6 @@ Initialization file templates
   weighing = length
   buffer_meters = 40
   category_field_name = category
-  save_shp = True
+  save_gpkg = True
   save_csv = True
 

examples/example_origin_destination_analysis.ipynb

@@ -4133,7 +4133,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

examples/example_ra2ce_basics.ipynb

@@ -864,7 +864,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

examples/example_single_link_redundancy.ipynb

@@ -2067,7 +2067,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

examples/pizza_course_material_DIY.ipynb

@@ -147,7 +147,7 @@
     "**polygon = ...<br>**\n",
     "network_type = drive<br>\n",
     "**road_types = ...<br>**\n",
-    "save_shp = True<br>\n",
+    "save_gpkg = True<br>\n",
     "<br>"
    ]
   },
@@ -301,7 +301,7 @@
     "name = beira_redundancy <br>\n",
     "analysis = single_link_redundancy <br>\n",
     "weighing = distance <br>\n",
-    "save_shp = True <br>\n",
+    "save_gpkg = True <br>\n",
     "save_csv = True <br>"
    ]
   },

ra2ce/analyses/direct/analyses_direct.py

@@ -75,8 +75,8 @@ def execute(self):
                 gdf = []
 
             output_path = self.config["output"] / analysis["analysis"]
-            if analysis["save_shp"]:
-                shp_path = output_path / (analysis["name"].replace(" ", "_") + ".shp")
+            if analysis["save_gpkg"]:
+                shp_path = output_path / (analysis["name"].replace(" ", "_") + ".gpkg")
                 save_gdf(gdf, shp_path)
             if analysis["save_csv"]:
                 csv_path = output_path / (analysis["name"].replace(" ", "_") + ".csv")
@@ -187,7 +187,7 @@ def effectiveness_measures(self, analysis):
         else:
             df = em.load_table(
                 self.config["input"] / "direct",
-                analysis["file_name"].replace(".shp", ".csv"),
+                analysis["file_name"].replace(".gpkg", ".csv"),
             )
 
         df = em.calculate_strategy_effectiveness(df, effectiveness_dict)

ra2ce/analyses/direct/cost_benefit_analysis.py

@@ -114,7 +114,7 @@ def create_feature_table(file_path):
 
         # save as csv
         path, file = os.path.split(file_path)
-        df.to_csv(os.path.join(path, file.replace(".shp", ".csv")), index=False)
+        df.to_csv(os.path.join(path, file.replace(".gpkg", ".csv")), index=False)
         return df
 
     @staticmethod

ra2ce/analyses/indirect/analyses_indirect.py

@@ -779,10 +779,8 @@ def multi_link_origin_destination_regional_impact(self, gdf_ori):
         gdf_ori_ = gdf_ori.copy()
 
         # read origin points
-        origin_fn = (
-            Path(self.config["static"])
-            / "output_graph"
-            / "origin_destination_table.gpkg"
+        origin_fn = Path(self.config["static"]).joinpath(
+            "output_graph", "origin_destination_table.gpkg"
         )
         origin = gpd.read_file(origin_fn)
         index = [type(x) == str for x in origin["o_id"]]
@@ -917,7 +915,7 @@ def multi_link_isolated_locations(
             results_hz_roads.to_file(
                 self.config["output"]
                 / analysis["analysis"]
-                / f"flooded_and_isolated_roads_{hazard_name}.shp"
+                / f"flooded_and_isolated_roads_{hazard_name}.gpkg"
             )
 
             # relate the locations to network disruption due to hazard by spatial overlay
@@ -1036,7 +1034,7 @@ def execute(self):
             opt_routes = None
             output_path = self.config["output"] / analysis["analysis"]
 
-            def _save_shp_analysis(
+            def _save_gpkg_analysis(
                 base_graph,
                 to_save_gdf: List[gpd.GeoDataFrame],
                 to_save_gdf_names: List[str],
@@ -1165,11 +1163,11 @@ def _save_shp_analysis(
                     opt_routes,
                     destinations,
                 ) = analyzer.optimal_route_origin_closest_destination()
-                if analysis["save_shp"]:
+                if analysis["save_gpkg"]:
                     # Save the GeoDataFrames
                     to_save_gdf = [destinations, opt_routes]
                     to_save_gdf_names = ["destinations", "optimal_routes"]
-                    _save_shp_analysis(base_graph, to_save_gdf, to_save_gdf_names)
+                    _save_gpkg_analysis(base_graph, to_save_gdf, to_save_gdf_names)
 
                 if analysis["save_csv"]:
                     csv_path = output_path / (
@@ -1219,7 +1217,7 @@ def _save_shp_analysis(
                     ) = analyzer.multi_link_origin_closest_destination()
                     opt_routes_without_hazard = gpd.GeoDataFrame()
 
-                if analysis["save_shp"]:
+                if analysis["save_gpkg"]:
                     # Save the GeoDataFrames
                     to_save_gdf = [
                         origins,
@@ -1233,7 +1231,7 @@ def _save_shp_analysis(
                         "optimal_routes_without_hazard",
                         "optimal_routes_with_hazard",
                     ]
-                    _save_shp_analysis(base_graph, to_save_gdf, to_save_gdf_names)
+                    _save_gpkg_analysis(base_graph, to_save_gdf, to_save_gdf_names)
                 if analysis["save_csv"]:
                     csv_path = output_path / (
                         analysis["name"].replace(" ", "_") + "_destinations.csv"
@@ -1281,7 +1279,7 @@ def _save_shp_analysis(
 
             if not gdf.empty:
                 # Not for all analyses a gdf is created as output.
-                if analysis["save_shp"]:
+                if analysis["save_gpkg"]:
                     gpkg_path = output_path.joinpath(
                         analysis["name"].replace(" ", "_") + ".gpkg"
                     )
@@ -1308,13 +1306,12 @@ def _save_shp_analysis(
             )
 
 
-def save_gdf(gdf, save_path):
+def save_gdf(gdf: gpd.GeoDataFrame, save_path: Path):
     """Takes in a geodataframe object and outputs shapefiles at the paths indicated by edge_shp and node_shp
 
     Arguments:
         gdf [geodataframe]: geodataframe object to be converted
-        edge_shp [str]: output path including extension for edges shapefile
-        node_shp [str]: output path including extension for nodes shapefile
+        save_path [str]: output path including extension for edges shapefile
     Returns:
         None
     """

ra2ce/graph/exporters/geodataframe_network_exporter.py

@@ -29,8 +29,8 @@
 
 
 class GeoDataFrameNetworkExporter(NetworkExporterBase):
-    def export_to_shp(self, output_dir: Path, export_data: gpd.GeoDataFrame) -> None:
-        _output_shp_path = output_dir / (self._basename + ".shp")
+    def export_to_gpkg(self, output_dir: Path, export_data: gpd.GeoDataFrame) -> None:
+        _output_shp_path = output_dir / (self._basename + ".gpkg")
         export_data.to_file(
             _output_shp_path, index=False
         )  # , encoding='utf-8' -Removed the encoding type because this causes some shapefiles not to save.

ra2ce/graph/exporters/multi_graph_network_exporter.py

@@ -35,7 +35,7 @@
 class MultiGraphNetworkExporter(NetworkExporterBase):
     pickle_path: Optional[Path]
 
-    def export_to_shp(self, output_dir: Path, export_data: MULTIGRAPH_TYPE) -> None:
+    def export_to_gpkg(self, output_dir: Path, export_data: MULTIGRAPH_TYPE) -> None:
         if not output_dir.is_dir():
             output_dir.mkdir(parents=True)
 
@@ -46,7 +46,7 @@ def export_to_shp(self, output_dir: Path, export_data: MULTIGRAPH_TYPE) -> None:
             output_dir / (self._basename + "_nodes.gpkg"),
         )
         logging.info(
-            f"Saved {self._basename + '_edges.shp'} and {self._basename + '_nodes.shp'} in {output_dir}."
+            f"Saved {self._basename + '_edges.gpkg'} and {self._basename + '_nodes.gpkg'} in {output_dir}."
         )
 
     def export_to_pickle(self, output_dir: Path, export_data: MULTIGRAPH_TYPE) -> None:

ra2ce/graph/exporters/network_exporter_base.py

@@ -42,9 +42,9 @@ def __init__(self, basename: str, export_types: List[str]) -> None:
         self._export_types = export_types
         self.pickle_path = None
 
-    def export_to_shp(self, output_dir: Path, export_data: NETWORK_TYPE) -> None:
+    def export_to_gpkg(self, output_dir: Path, export_data: NETWORK_TYPE) -> None:
         """
-        Exports the given data into a `*.shp` file.
+        Exports the given data into a `*.gpkg` file.
 
         Args:
             output_dir (Path): Output directory where the save the exported data.
@@ -75,4 +75,4 @@ def export(self, export_path: Path, export_data: Any) -> None:
             self.export_to_pickle(export_path, export_data)
 
         if "shp" in self._export_types:
-            self.export_to_shp(export_path, export_data)
+            self.export_to_gpkg(export_path, export_data)

ra2ce/graph/hazard/hazard_overlay.py

@@ -66,7 +66,7 @@ def __init__(self, config: NetworkConfigData, graphs: dict, files: dict):
         self._output_dir = config.output_path
         self._origins = config.origins_destinations.origins
         self._destinations = config.origins_destinations.destinations
-        self._save_shp = config.network.save_shp
+        self._save_gpkg = config.network.save_gpkg
         self._isolation_locations = config.static_path.joinpath(
             "network", config.isolation.locations
         )
@@ -427,7 +427,7 @@ def get_filtered_files(*suffix) -> list[Path]:
 
         _hazard_files = {}
         _hazard_files["tif"] = get_filtered_files(".tif")
-        _hazard_files["shp"] = get_filtered_files(".shp")
+        _hazard_files["shp"] = get_filtered_files(".gpkg")
         _hazard_files["table"] = get_filtered_files(".csv", ".json")
         return _hazard_files
 
@@ -552,7 +552,7 @@ def create(self):
             write all the objects
 
         """
-        types_to_export = ["pickle"] if not self._save_shp else ["pickle", "shp"]
+        types_to_export = ["pickle"] if not self._save_gpkg else ["pickle", "shp"]
 
         if (
             not self.files["base_graph"]
@@ -712,9 +712,9 @@ def create(self):
             )
 
             # Save the OD pairs (GeoDataFrame) as shapefile
-            if self._save_shp:
+            if self._save_gpkg:
                 ods_path = self._output_graph_dir.joinpath(
-                    "origin_destination_table.shp"
+                    "origin_destination_table.gpkg"
                 )
                 ods.to_file(ods_path, index=False)
                 logging.info(f"Saved {ods_path.stem} in {ods_path.resolve().parent}.")

ra2ce/graph/network_config_data/network_config_data.py

@@ -45,7 +45,7 @@ class NetworkSection:
     polygon: Optional[Path] = None
     network_type: str = ""  # Should be enum
     road_types: list[str] = field(default_factory=list)
-    save_shp: bool = False
+    save_gpkg: bool = False
 
 
 @dataclass

ra2ce/graph/network_config_data/network_config_data_reader.py

@@ -149,8 +149,8 @@ def get_network_section(self) -> NetworkSection:
         _network_section.directed = self._parser.getboolean(
             _section, "directed", fallback=_network_section.directed
         )
-        _network_section.save_shp = self._parser.getboolean(
-            _section, "save_shp", fallback=_network_section.save_shp
+        _network_section.save_gpkg = self._parser.getboolean(
+            _section, "save_gpkg", fallback=_network_section.save_gpkg
         )
         _network_section.road_types = self._parser.getlist(
             _section, "road_types", fallback=_network_section.road_types

ra2ce/graph/network_config_data/network_config_data_validator.py

@@ -53,7 +53,7 @@
     ],
     "origins": ["file", None],
     "destinations": ["file", None],
-    "save_shp": [True, False, None],
+    "save_gpkg": [True, False, None],
     "save_csv": [True, False, None],
     "hazard_map": ["file", None],
     "aggregate_wl": ["max", "min", "mean", None],

ra2ce/graph/network_wrappers/shp_network_wrapper.py

@@ -179,7 +179,7 @@ def get_network(
                 col="geometry", inplace=True
             )  # To ensure the object is a GeoDataFrame and not a Series
             _emerged_lines_file = self.output_graph_dir.joinpath(
-                f"{self.project_name}_lines_that_merged.shp"
+                f"{self.project_name}_lines_that_merged.gpkg"
             )
             lines_merged.to_file(_emerged_lines_file)
             logging.info(

ra2ce/graph/networks.py

@@ -117,8 +117,8 @@ def add_od_nodes(
         logging.info(f"Saved {name + '.feather'} in {self.output_graph_dir}.")
 
         # Save the OD pairs (GeoDataFrame) as shapefile
-        if self._network_config.save_shp:
-            ods_path = self.output_graph_dir.joinpath(name + ".shp")
+        if self._network_config.save_gpkg:
+            ods_path = self.output_graph_dir.joinpath(name + ".gpkg")
             ods.to_file(ods_path, index=False)
             logging.info(f"Saved {ods_path.stem} in {ods_path.resolve().parent}.")
 
@@ -209,7 +209,7 @@ def create(self) -> dict:
             (dict): A dict of a network (GeoDataFrame) and 1 (base NetworkX graph) or 2 graphs (base NetworkX and OD graph)
         """
         # Save the 'base' network as gpickle and if the user requested, also as shapefile.
-        to_save = ["pickle"] if not self._network_config.save_shp else ["pickle", "shp"]
+        to_save = ["pickle"] if not self._network_config.save_gpkg else ["pickle", "shp"]
         od_graph = None
         base_graph = None
         network_gdf = None

ra2ce/graph/origins_destinations.py

@@ -585,7 +585,7 @@ def origins_from_raster(output_folder: Path, mask_fn, raster_fn) -> Path:
         + " origin points."
     )
 
-    out_fn = output_folder / "origins_points.shp"
+    out_fn = output_folder / "origins_points.gpkg"
     out_fn = generate_points_from_raster(outputfile, out_fn)
 
     return out_fn

tests/analyses/direct/test_analyses_direct.py

@@ -15,7 +15,7 @@ def test_execute(self):
                 {
                     "name": "DummyExecute",
                     "analysis": "",
-                    "save_shp": False,
+                    "save_gpkg": False,
                     "save_csv": False,
                 }
             ],