Merge pull request #492 from Jake-Moss/route_choice

Route choice

.flake8

@@ -3,4 +3,4 @@ max-line-length = 120
 ignore = E203, E266, E501, W503, F403, F401, C901, W605
 max-complexity = 20
 select = B,C,E,F,W,T4,B9
-exclude = .idea,.git,__pycache__,sphinx,.venv*,.venv,venv,docs/*,benchmarks/*
+exclude = .idea,.git,__pycache__,sphinx,.venv*,.venv,venv,docs/*,benchmarks/*,*.pyx,*pxd,*.pxi

.github/build_artifacts_qgis.yml

@@ -19,7 +19,7 @@ jobs:
         architecture: ['x64']
         os: [windows-latest, macos-latest]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set Python environment
       uses: actions/setup-python@v4
       with:

.github/workflows/build_linux.yml

@@ -9,7 +9,7 @@ jobs:
       HAS_SECRETS: ${{ secrets.AWS_SECRET_ACCESS_KEY != '' }}
     continue-on-error: true
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python 3.9
       uses: actions/setup-python@v4
       with:

.github/workflows/build_mac.yml

@@ -16,7 +16,7 @@ jobs:
       matrix:
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set Python environment
       uses: actions/setup-python@v4
       with:

.github/workflows/build_windows.yml

@@ -13,7 +13,7 @@ jobs:
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         architecture: ['x64']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set Python environment
       uses: actions/setup-python@v4
       with:

.github/workflows/debug_tests.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     container: python:3.9
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/documentation.yml

@@ -15,7 +15,7 @@ jobs:
     env:
       HAS_SECRETS: ${{ secrets.AWS_SECRET_ACCESS_KEY != '' }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python 3.9
       uses: actions/setup-python@v4
       with:

.github/workflows/test_linux_with_coverage.yml

@@ -11,7 +11,7 @@ jobs:
       matrix:
         python-version: [3.10]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Install dependencies
       run: |
         sudo apt update

.github/workflows/unit_tests.yml

@@ -6,7 +6,7 @@ jobs:
   linting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set Python environment
         uses: actions/setup-python@v4
         with:
@@ -20,8 +20,8 @@ jobs:
           pip install -r requirements_additional.txt
           pip install -r tests/requirements_tests.txt
 
-      - name: Lint with flake8
-        run: flake8
+      - name: Lint with ruff
+        run: ruff .
 
       - name: Check code format with Black
         run: black --check .
@@ -36,7 +36,7 @@ jobs:
 
       max-parallel: 20
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set Python environment
       uses: actions/setup-python@v4
       with:

aequilibrae/distribution/gravity_calibration.py

@@ -4,6 +4,7 @@
 The procedures implemented in this code are some of those suggested in
 Modelling Transport, 4th Edition, Ortuzar and Willumsen, Wiley 2011
 """
+
 from time import perf_counter
 
 import numpy as np

aequilibrae/distribution/synthetic_gravity_model.py

@@ -57,7 +57,7 @@ def load(self, file_name):
                     else:
                         raise ValueError("Model has unknown parameters: " + str(key))
         except ValueError as err:
-            raise ValueError("File provided is not a valid Synthetic Gravity Model - {}".format(err.__str__()))
+            raise ValueError("File provided is not a valid Synthetic Gravity Model - {}".format(err.__str__())) from err
 
     def save(self, file_name):
         R"""Saves model to disk in yaml format. Extension is \*.mod"""

aequilibrae/matrix/aequilibrae_data.py

@@ -99,23 +99,18 @@ def create_empty(
 
             if not isinstance(self.data_types, list):
                 raise ValueError('Data types, "data_types", needs to be a list')
-            # The check below is not working properly with the QGIS importer
-            # else:
-            #     for dt in self.data_types:
-            #         if not isinstance(dt, type):
-            #             raise ValueError('Data types need to be Python or Numpy data types')
 
             for field in self.fields:
-                if not type(field) is str:
-                    raise TypeError(field + " is not a string. You cannot use it as a field name")
+                if not isinstance(field, str):
+                    raise TypeError(f"{field} is not a string. You cannot use it as a field name")
                 if not field.isidentifier():
                     raise Exception(field + " is a not a valid identifier name. You cannot use it as a field name")
                 if field in object.__dict__:
                     raise Exception(field + " is a reserved name. You cannot use it as a field name")
 
             self.num_fields = len(self.fields)
 
-            dtype = [("index", self.aeq_index_type)] + [(f, dt) for f, dt in zip(self.fields, self.data_types)]
+            dtype = [("index", self.aeq_index_type)] + list(zip(self.fields, self.data_types))
 
             # the file
             if self.memory_mode:

aequilibrae/matrix/aequilibrae_matrix.py

@@ -4,7 +4,9 @@
 import tempfile
 import uuid
 import warnings
+from copy import copy
 from functools import reduce
+from pathlib import Path
 from typing import List
 
 import numpy as np
@@ -90,14 +92,18 @@ def __init__(self):
         self.omx_file = None  # type: omx.File
         self.__version__ = VERSION  # Writes file version
 
-    def save(self, names=()) -> None:
+    def save(self, names=(), file_name=None) -> None:
         """Saves matrix data back to file.
 
         If working with AEM file, it flushes data to disk. If working with OMX, requires new names.
 
         :Arguments:
             **names** (:obj:`tuple(str)`, `Optional`): New names for the matrices. Required if working with OMX files
         """
+        if file_name is not None:
+            cores = names if len(names) else self.names
+            self.__save_as(file_name, cores)
+            return
 
         if not self.__omx:
             self.__flush(self.matrices)
@@ -122,6 +128,37 @@ def save(self, names=()) -> None:
         self.names = self.omx_file.list_matrices()
         self.computational_view(names)
 
+    def __save_as(self, file_name: str, cores: List[str]):
+        if Path(file_name).suffix.lower() == ".aem":
+            mat = AequilibraeMatrix()
+            args = {
+                "zones": self.zones,
+                "matrix_names": cores,
+                "index_names": self.index_names,
+                "memory_only": False,
+                "file_name": file_name,
+            }
+            mat.create_empty(**args)
+            mat.indices[:, :] = self.indices[:, :]
+            for core in cores:
+                mat.matrix[core][:, :] = self.matrix[core][:, :]
+            mat.name = self.name
+            mat.description = self.description
+            mat.close()
+            del mat
+
+        elif Path(file_name).suffix.lower() == ".omx":
+            omx_mat = omx.open_file(file_name, "w")
+            for core in cores:
+                omx_mat[core] = self.matrix[core]
+
+            for index in self.index_names:
+                omx_mat.create_mapping(index, self.indices[index])
+
+            omx_mat.attrs.name = self.name
+            omx_mat.attrs.description = self.description
+            omx_mat.close()
+
     def create_empty(
         self,
         file_name: str = None,
@@ -212,16 +249,13 @@ def create_empty(
                         if mat_name in object.__dict__:
                             raise ValueError(mat_name + " is a reserved name")
                         if len(mat_name) > CORE_NAME_MAX_LENGTH:
-                            raise ValueError(
-                                "Matrix names need to be be shorter "
-                                "than {}: {}".format(CORE_NAME_MAX_LENGTH, mat_name)
-                            )
+                            raise ValueError(f"Matrix names need to be shorter than {CORE_NAME_MAX_LENGTH}: {mat_name}")
                     else:
                         raise ValueError("Matrix core names need to be strings: " + str(mat_name))
             else:
                 raise Exception("Matrix names need to be provided as a list")
 
-        self.names = [x for x in matrix_names]
+        self.names = copy(matrix_names)
         self.cores = len(self.names)
         if self.zones is None:
             return
@@ -344,8 +378,8 @@ def robust_name(input_name: str, max_length: int, forbiden_names: List[str]) ->
             )
             idx_names = functools.reduce(lambda acc, n: acc + [robust_name(n, INDEX_NAME_MAX_LENGTH, acc)], do_idx, [])
         else:
-            core_names = [x for x in do_cores]
-            idx_names = [x for x in do_idx]
+            core_names = list(do_cores)
+            idx_names = list(do_idx)
 
         self.create_empty(
             file_name=file_path,
@@ -391,7 +425,7 @@ def create_from_trip_list(self, path_to_file: str, from_column: str, to_column:
         trip_df = pd.read_csv(path_to_file)
 
         # Creating zone indices
-        zones_list = sorted(list(set(list(trip_df[from_column].unique()) + list(trip_df[to_column].unique()))))
+        zones_list = sorted(set(list(trip_df[from_column].unique()) + list(trip_df[to_column].unique())))
         zones_df = pd.DataFrame({"zone": zones_list, "idx": list(np.arange(len(zones_list)))})
 
         trip_df = trip_df.merge(
@@ -570,9 +604,7 @@ def __write__(self):
             np.memmap(self.file_path, dtype="uint8", offset=17, mode="r+", shape=1)[0] = data_size
 
             # matrix name
-            np.memmap(self.file_path, dtype="S" + str(MATRIX_NAME_MAX_LENGTH), offset=18, mode="r+", shape=1)[
-                0
-            ] = self.name
+            np.memmap(self.file_path, dtype=f"S{MATRIX_NAME_MAX_LENGTH}", offset=18, mode="r+", shape=1)[0] = self.name
 
             # matrix description
             offset = 18 + MATRIX_NAME_MAX_LENGTH
@@ -1095,9 +1127,7 @@ def setName(self, matrix_name: str):
             if len(str(matrix_name)) > MATRIX_NAME_MAX_LENGTH:
                 matrix_name = str(matrix_name)[0:MATRIX_NAME_MAX_LENGTH]
 
-            np.memmap(self.file_path, dtype="S" + str(MATRIX_NAME_MAX_LENGTH), offset=18, mode="r+", shape=1)[
-                0
-            ] = matrix_name
+            np.memmap(self.file_path, dtype=f"S{MATRIX_NAME_MAX_LENGTH}", offset=18, shape=1)[0] = matrix_name
 
     def setDescription(self, matrix_description: str):
         """

aequilibrae/paths/AoN.pyx

@@ -11,7 +11,6 @@ include 'conical.pyx'
 include 'inrets.pyx'
 include 'parallel_numpy.pyx'
 include 'path_file_saving.pyx'
-include 'graph_building.pyx'
 
 def one_to_all(origin, matrix, graph, result, aux_result, curr_thread):
     # type: (int, AequilibraeMatrix, Graph, AssignmentResults, MultiThreadedAoN, int) -> int
@@ -242,19 +241,20 @@ def path_computation(origin, destination, graph, results):
                                     original_b_nodes_view)
 
         if a_star_bint:
-            w = path_finding_a_star(origin_index,
-                                    dest_index,
-                                    g_view,
-                                    b_nodes_view,
-                                    graph_fs_view,
-                                    nodes_to_indices_view,
-                                    lat_view,
-                                    lon_view,
-                                    predecessors_view,
-                                    ids_graph_view,
-                                    conn_view,
-                                    reached_first_view,
-                                    heuristic)
+            path_finding_a_star(
+                origin_index,
+                dest_index,
+                g_view,
+                b_nodes_view,
+                graph_fs_view,
+                nodes_to_indices_view,
+                lat_view,
+                lon_view,
+                predecessors_view,
+                ids_graph_view,
+                conn_view,
+                heuristic
+            )
         else:
             w = path_finding(origin_index,
                              dest_index if early_exit_bint else -1,
@@ -267,7 +267,7 @@ def path_computation(origin, destination, graph, results):
                              reached_first_view)
 
 
-        if skims > 0:
+        if skims > 0 and not a_star_bint:
             skim_single_path(origin_index,
                              nodes,
                              skims,

aequilibrae/paths/all_or_nothing.py

@@ -36,8 +36,6 @@ def __init__(self, matrix, graph, results):
         self.graph = graph
         self.results = results
         self.aux_res = MultiThreadedAoN()
-        self.report = []
-        self.cumulative = 0
 
         if results._graph_id != graph._id:
             raise ValueError("Results object not prepared. Use --> results.prepare(graph)")
@@ -55,6 +53,9 @@ def doWork(self):
         self.execute()
 
     def execute(self):
+        self.report = []
+        self.cumulative = 0
+
         if pyqt:
             self.assignment.emit(["zones finalized", 0])
 

aequilibrae/paths/assignment_paths.py

@@ -94,15 +94,12 @@ def _read_compressed_graph_correspondence(self) -> Dict:
 
     def read_path_file(self, origin: int, iteration: int, traffic_class_id: str) -> (pd.DataFrame, pd.DataFrame):
         possible_traffic_classes = list(filter(lambda x: x.id == traffic_class_id, self.classes))
-        assert (
-            len(possible_traffic_classes) == 1
-        ), f"traffic class id not unique, please choose one of {list(map(lambda x: x.id, self.classes))}"
+        class_ids = [x.id for x in self.classes]
+        assert len(possible_traffic_classes) == 1, f"traffic class id not unique, please choose one of {class_ids}"
         traffic_class = possible_traffic_classes[0]
-        base_dir = os.path.join(
-            self.path_base_dir, f"iter{iteration}", f"path_c{traffic_class.id}_{traffic_class.name}"
-        )
-        path_o_f = os.path.join(base_dir, f"o{origin}.feather")
-        path_o_index_f = os.path.join(base_dir, f"o{origin}_indexdata.feather")
+        b_dir = os.path.join(self.path_base_dir, f"iter{iteration}", f"path_c{traffic_class.id}_{traffic_class.name}")
+        path_o_f = os.path.join(b_dir, f"o{origin}.feather")
+        path_o_index_f = os.path.join(b_dir, f"o{origin}_indexdata.feather")
         path_o = pd.read_feather(path_o_f)
         path_o_index = pd.read_feather(path_o_index_f)
         return path_o, path_o_index