released version

.github/qgis_requirements.py

@@ -15,4 +15,7 @@ def replace_in_file(file_path, text_orig, suffix):
 replace_in_file("../requirements.txt", "pandas", "<1.2")
 replace_in_file("../pyproject.toml", "pandas", "<1.2")
 
+replace_in_file("../requirements.txt", "scipy", "<1.11")
+replace_in_file("../pyproject.toml", "scipy", "<1.11")
+
 replace_in_file("../__version__.py", "{minor_version}", ".dev0")

.github/workflows/documentation.yml

@@ -29,12 +29,13 @@ jobs:
         pip install -r docs/requirements-docs.txt
         python -m pip install sphinx-gallery --user
         sudo apt update
-        sudo apt install -y --fix-missing libsqlite3-mod-spatialite libspatialite-dev
+        sudo apt install -y --fix-missing libsqlite3-mod-spatialite libspatialite-dev pandoc
         sudo ln -s /usr/lib/x86_64-linux-gnu/mod_spatialite.so /usr/lib/x86_64-linux-gnu/mod_spatialite
 
     - name: Compile library
       run: |
         python setup.py build_ext --inplace
+        pip install .
 
     - name: Check history of versions
       run: |

README.md

@@ -15,12 +15,12 @@
 [![QAequilibraE artifacts](https://github.com/AequilibraE/aequilibrae/actions/workflows/build_artifacts_qgis.yml/badge.svg)](https://github.com/AequilibraE/aequilibrae/actions/workflows/build_artifacts_qgis.yml)
 
 
-AequilibraE is the first comprehensive Python package for transportation modeling, and it aims to provide all the
+AequilibraE is the first comprehensive Python package for transportation modeling. It aims to provide all the
 resources not available from other open-source packages in the Python (NumPy, really) ecosystem.
 
 ## Comprehensive documentation
 
-[AequilibraE documentation built with Sphinx ](http://www.aequilibrae.com>)
+[AequilibraE documentation built with Sphinx ](http://www.aequilibrae.com)
 
 ## What is available
 

__version__.py

@@ -1,5 +1,5 @@
 version = 0.9
-minor_version = "3"
+minor_version = "4"
 release_name = "Queluz"
 
 release_version = f"{version}.{minor_version}"

aequilibrae/distribution/ipf_core.pyx

@@ -56,7 +56,7 @@ cdef  _fratar(double[:, :] flows,
                    double[:] attr_factor,
                    int max_iter,
                    double toler,
-                   int cpus):
+                   int cpus) noexcept:
 
     cdef double err = 1.0
     cdef int iter = 0
@@ -99,7 +99,7 @@ cdef  _fratar(double[:, :] flows,
 cpdef void _total_attra(double[:, :] flows,
                         double[:] prod_tgt,
                         double[:] attr_tot,
-                        int cpus):
+                        int cpus) noexcept:
 
     cdef long long i, j, jk
     cdef double  *local_buf
@@ -133,7 +133,7 @@ cpdef void _total_attra(double[:, :] flows,
 cpdef void _total_prods(double[:, :] flows,
                         double[:] prod_tgt,
                         double[:] prod_tot,
-                        int cpus)nogil:
+                        int cpus) noexcept nogil:
 
     cdef long long i, j
     cdef long long I = flows.shape[0]
@@ -154,7 +154,7 @@ cpdef void _total_prods(double[:, :] flows,
 cpdef double _factors(double[:] target,
                       double[:] total,
                       double[:] factor,
-                      int cpus):
+                      int cpus) noexcept:
 
     cdef long long i, I = target.shape[0]
     cdef double err = 1.0
@@ -174,7 +174,7 @@ cpdef double _factors(double[:] target,
 @cython.embedsignature(True)
 @cython.boundscheck(False)
 cpdef double _calc_err(double[:] p_factor,
-                       double[:] a_factor):
+                       double[:] a_factor) noexcept:
 
     cdef long long i, I = p_factor.shape[0]
     cdef long long j, J = a_factor.shape[0]

aequilibrae/matrix/aequilibrae_data.py

@@ -106,6 +106,10 @@ def create_empty(
             #             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 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")
 

aequilibrae/matrix/aequilibrae_matrix.py

@@ -3,6 +3,7 @@
 import os
 import tempfile
 import uuid
+import warnings
 from functools import reduce
 from typing import List
 
@@ -399,7 +400,9 @@ def create_from_trip_list(self, path_to_file: str, from_column: str, to_column:
 
         new_mat = AequilibraeMatrix()
         nb_of_zones = len(zones_list)
-        new_mat.create_empty(file_name=path_to_file[:-4] + ".aem", zones=nb_of_zones, matrix_names=list_cores)
+        new_mat.create_empty(
+            file_name=path_to_file[:-4] + ".aem", zones=nb_of_zones, matrix_names=list_cores, memory_only=False
+        )
 
         for idx, core in enumerate(list_cores):
             m = (
@@ -677,6 +680,9 @@ def __flush(self, obj_to_flush: np.memmap):
 
     def __getattr__(self, mat_name: str):
         if mat_name in object.__dict__:
+            if mat_name == "matrix" and self.__omx:
+                warnings.warn("You can't access OMX matrix cores like that")
+                return
             return self.__dict__[mat_name]
 
         if mat_name in self.names:
@@ -748,18 +754,14 @@ def export(self, output_name: str, cores: List[str] = None):
             >>> mat2.cores
             2
         """
-
-        if self.__omx:
-            raise NotImplementedError("This operation does not make sense for OMX matrices")
-
         fname, file_extension = os.path.splitext(output_name.upper())
 
         if file_extension == ".OMX":
             if not has_omx:
                 raise ValueError("Open Matrix is not installed. Cannot continue")
 
         if file_extension not in [".AEM", ".CSV", ".OMX"]:
-            raise ValueError("File extension {} not implemented yet".format(file_extension))
+            raise NotImplementedError(f"File extension {file_extension} not implemented yet")
 
         if cores is None:
             cores = self.names
@@ -770,16 +772,21 @@ def export(self, output_name: str, cores: List[str] = None):
         elif file_extension == ".OMX":
             omx_export = omx.open_file(output_name, "w")
             for c in cores:
-                omx_export[c] = self.matrix[c]
-
+                if self.__omx:
+                    omx_export[c] = np.array(self.omx_file[c])
+                else:
+                    omx_export[c] = self.matrix[c]
             for i, idx in enumerate(self.index_names):
                 omx_export.create_mapping(idx, self.indices[:, i])
             omx_export.close()
 
         elif file_extension == ".CSV":
 
             def f(name):
-                coo = coo_matrix(self.matrix[name])
+                if self.__omx:
+                    coo = np.array(self.omx_file[name])
+                else:
+                    coo = coo_matrix(self.matrix[name])
                 data = {"row": self.index[coo.row], "column": self.index[coo.col], name: coo.data}
                 return pd.DataFrame(data).set_index(["row", "column"])
 

aequilibrae/paths/AoN.pyx

@@ -97,11 +97,10 @@ def one_to_all(origin, matrix, graph, result, aux_result, curr_thread):
         bint select_link = False
 
     if result._selected_links:
-
         has_flow_mask = aux_result.has_flow_mask[curr_thread, :]
-        sl_od_matrix_view = aux_result.temp_sl_od_matrix[:, origin_index, :, :]
-        sl_link_loading_view = aux_result.temp_sl_link_loading[:, :, :]
-        link_list = aux_result.select_links[:, :]
+        sl_od_matrix_view = aux_result.temp_sl_od_matrix[curr_thread, :, origin_index, :, :]
+        sl_link_loading_view = aux_result.temp_sl_link_loading[curr_thread, :, :, :]
+        link_list = aux_result.select_links[:, :]  # Read only, don't need to slice on curr_thread
         select_link = True
     #Now we do all procedures with NO GIL
     with nogil:

aequilibrae/paths/basic_path_finding.pyx

@@ -25,7 +25,7 @@ cpdef void network_loading(long classes,
                            long long [:] no_path,
                            long long [:] reached_first,
                            double [:, :] node_load,
-                           long found) nogil:
+                           long found) noexcept nogil:
 
     cdef long long i, j, predecessor, connector, node
     cdef long long zones = demand.shape[0]
@@ -70,7 +70,7 @@ cpdef void network_loading(long classes,
 @cython.embedsignature(True)
 @cython.boundscheck(False)
 cdef void _copy_skims(double[:,:] skim_matrix,  #Skim matrix_procedures computed from one origin to all nodes
-                      double[:,:] final_skim_matrix) nogil:  #Skim matrix_procedures computed for one origin to all other centroids only
+                      double[:,:] final_skim_matrix) noexcept nogil:  #Skim matrix_procedures computed for one origin to all other centroids only
 
     cdef long i, j
     cdef long N = final_skim_matrix.shape[0]
@@ -81,7 +81,7 @@ cdef void _copy_skims(double[:,:] skim_matrix,  #Skim matrix_procedures computed
             final_skim_matrix[i,j]=skim_matrix[i,j]
 
 
-cdef return_an_int_view(input):
+cdef int[:] return_an_int_view(input) noexcept nogil:
     cdef int [:] critical_links_view = input
     return critical_links_view
 
@@ -97,7 +97,7 @@ cdef void sl_network_loading(
     double [:, :, :] sl_od_matrix,
     double [:, :, :] sl_link_loading,
     unsigned char [:] has_flow_mask,
-    long classes) nogil:
+    long classes) noexcept nogil:
 # VARIABLES:
 #   selected_links: 2d memoryview. Each row corresponds to a set of selected links specified by the user
 #   demand:         The input demand matrix for a given origin. The first index corresponds to destination,
@@ -169,7 +169,7 @@ cpdef void put_path_file_on_disk(unsigned int orig,
                                  long long [:] connectors,
                                  long long [:] all_nodes,
                                  unsigned int [:] origins_to_write,
-                                 unsigned int [:] nodes_to_write) nogil:
+                                 unsigned int [:] nodes_to_write) noexcept nogil:
     cdef long long i
     cdef long long k = pred.shape[0]
 
@@ -188,7 +188,7 @@ cdef void blocking_centroid_flows(int action,
                                   long long centroids,
                                   long long [:] fs,
                                   long long [:] temp_b_nodes,
-                                  long long [:] real_b_nodes) nogil:
+                                  long long [:] real_b_nodes) noexcept nogil:
     cdef long long i
 
     if action == 1: # We are unblocking
@@ -213,7 +213,7 @@ cdef void skim_single_path(long origin,
                            long long [:] conn,
                            double[:, :] graph_costs,
                            long long [:] reached_first,
-                           long found) nogil:
+                           long found) noexcept nogil:
     cdef long long i, node, predecessor, connector, j
 
     # sets all skims to infinity
@@ -250,7 +250,7 @@ cpdef void skim_multiple_fields(long origin,
                                 double[:, :] graph_costs,
                                 long long [:] reached_first,
                                 long found,
-                                double [:,:] final_skims) nogil:
+                                double [:,:] final_skims) noexcept nogil:
     cdef long long i, node, predecessor, connector, j
 
     # sets all skims to infinity
@@ -295,7 +295,7 @@ cpdef int path_finding(long origin,
                        long long [:] pred,
                        long long [:] ids,
                        long long [:] connectors,
-                       long long [:] reached_first) nogil:
+                       long long [:] reached_first) noexcept nogil:
 
     cdef unsigned int N = graph_costs.shape[0]
     cdef unsigned int M = pred.shape[0]

aequilibrae/paths/bpr.pyx

@@ -34,7 +34,7 @@ cpdef void bpr_cython(double[:] congested_time,
                       double [:] fftime,
                       double[:] alpha,
                       double [:] beta,
-                      int cores):
+                      int cores) noexcept:
   cdef long long i
   cdef long long l = congested_time.shape[0]
 
@@ -53,12 +53,12 @@ cpdef void dbpr_cython(double[:] deltaresult,
                        double [:] fftime,
                        double[:] alpha,
                        double [:] beta,
-                       int cores):
+                       int cores) noexcept:
   cdef long long i
   cdef long long l = deltaresult.shape[0]
 
   for i in prange(l, nogil=True, num_threads=cores):
     if link_flows[i] > 0:
         deltaresult[i] = fftime[i] * (alpha[i] * beta[i] * (pow(link_flows[i] / capacity[i], beta[i]-1)))/ capacity[i]
     else:
-        deltaresult[i] = fftime[i]
+        deltaresult[i] = fftime[i]

aequilibrae/paths/bpr2.pyx

@@ -34,7 +34,7 @@ cpdef void bpr2_cython(double[:] congested_time,
                     double [:] fftime,
                     double[:] alpha,
                     double [:] beta,
-                    int cores):
+                    int cores) noexcept:
     cdef long long i
     cdef long long l = congested_time.shape[0]
 
@@ -58,7 +58,7 @@ cpdef void dbpr2_cython(double[:] deltaresult,
                     double [:] fftime,
                     double[:] alpha,
                     double [:] beta,
-                    int cores):
+                    int cores) noexcept:
     cdef long long i
     cdef long long l = deltaresult.shape[0]
 

aequilibrae/paths/conical.pyx

@@ -34,7 +34,7 @@ cpdef void conical_cython(double[:] congested_time,
                         double [:] fftime,
                         double[:] alpha,
                         double [:] beta,
-                        int cores):
+                        int cores) noexcept:
     cdef long long i
     cdef long long l = congested_time.shape[0]
 
@@ -57,7 +57,7 @@ cpdef void dconical_cython(double[:] deltaresult,
                        double [:] fftime,
                        double[:] alpha,
                        double [:] beta,
-                       int cores):
+                       int cores) noexcept:
     cdef long long i
     cdef long long l = deltaresult.shape[0]
 

aequilibrae/paths/graph.py

@@ -192,8 +192,8 @@ def __build_directed_graph(self, network: pd.DataFrame, centroids: np.ndarray):
         nlist = np.arange(num_nodes)
         nodes_to_indices[all_nodes] = nlist
 
-        df.loc[:, "a_node"] = nodes_to_indices[df.a_node.values][:]
-        df.loc[:, "b_node"] = nodes_to_indices[df.b_node.values][:]
+        df.a_node = nodes_to_indices[df.a_node.values]
+        df.b_node = nodes_to_indices[df.b_node.values]
         df = df.sort_values(by=["a_node", "b_node"])
         df.index = np.arange(df.shape[0])
         df["id"] = np.arange(df.shape[0])
@@ -321,7 +321,7 @@ def set_skimming(self, skim_fields: list) -> None:
             raise ValueError("At least one of the skim fields does not exist in the graph: {}".format(",".join(k)))
 
         self.compact_skims = np.zeros((self.compact_num_links + 1, len(skim_fields) + 1), self.__float_type)
-        df = self.__graph_groupby.sum()[skim_fields].reset_index()
+        df = self.__graph_groupby.sum(numeric_only=True)[skim_fields].reset_index()
         for i, skm in enumerate(skim_fields):
             self.compact_skims[df.index.values, i] = df[skm].values.astype(self.__float_type)
 

aequilibrae/paths/graph_building.pyx

@@ -19,7 +19,7 @@ cdef long long _build_compressed_graph(long long[:] link_idx,
                                   long long[:] all_links,
                                   long long[:] compressed_dir,
                                   long long[:] compressed_a_node,
-                                  long long[:] compressed_b_node) nogil:
+                                  long long[:] compressed_b_node) noexcept nogil:
     cdef:
         long long slink = 0
         long long pre_link, n, first_node, lnk, lidx, a_node, b_node
@@ -93,7 +93,7 @@ cdef long long _build_compressed_graph(long long[:] link_idx,
 @cython.wraparound(False)
 @cython.embedsignature(True)
 @cython.boundscheck(False)
-cdef void _back_fill(long long[:] links_index, long long max_node):
+cdef void _back_fill(long long[:] links_index, long long max_node) noexcept:
     cdef Py_ssize_t i
 
     for i in range(max_node + 1, 0, -1):
@@ -172,7 +172,7 @@ def build_compressed_graph(graph):
         }
     )
     max_link_id = link_id_max * 10
-    comp_lnk.loc[:, "link_id"] += max_link_id
+    comp_lnk.link_id += max_link_id
 
     df = pd.concat([df, comp_lnk])
     df = df[["id", "link_id", "a_node", "b_node", "direction"]]
@@ -193,11 +193,11 @@ def build_compressed_graph(graph):
     )
 
     crosswalk = crosswalk[crosswalk.compressed_link >= 0]
-    crosswalk.loc[:, "compressed_link"] += max_link_id
+    crosswalk.compressed_link += max_link_id
 
     cw2 = pd.DataFrame(crosswalk, copy=True)
-    cw2.loc[:, "link_direction"] *= -1
-    cw2.loc[:, "compressed_direction"] = -1
+    cw2.link_direction *= -1
+    cw2.compressed_direction = -1
 
     crosswalk = pd.concat([crosswalk, cw2])
     crosswalk = crosswalk.assign(key=crosswalk.compressed_link * crosswalk.compressed_direction)