Replace the internal Fibonacci heap with a 4-ary priority queue (Aequ…

…ilibraE#374)

* Default to using memory-only mode for matrices
* Enable Numpy API version macro and language level 3
* Replace Fibonacci heap with 4-ary heap written by François Pacull.

Change the Dijkstra's implementation to make use of this new heap.
Originally written by François Pacull.

Co-authored-by: djfrancesco <pacullfrancois@gmail.com>
Co-authored-by: chrisobi02 <chrisgobrien02@gmail.com>
Co-authored-by: Jamie Cook <jimi.cook@gmail.com>
Co-authored-by: Pedro Camargo <c@margo.co>

.github/workflows/documentation.yml

@@ -22,13 +22,13 @@ jobs:
         python-version: 3.9
     - name: Install dependencies
       run: |
-        sudo apt update
         python -m pip install --upgrade pip
         pip install wheel openmatrix
         pip install -r requirements.txt
         pip install -r requirements_additional.txt
         pip install -r docs/requirements-docs.txt
         python -m pip install sphinx-gallery --user
+        sudo apt update
         sudo apt install libsqlite3-mod-spatialite
         sudo apt install -y libspatialite-dev
         sudo ln -s /usr/lib/x86_64-linux-gnu/mod_spatialite.so /usr/lib/x86_64-linux-gnu/mod_spatialite

aequilibrae/matrix/aequilibrae_matrix.py

@@ -85,7 +85,7 @@ def __init__(self):
         self.description = ""
         self.current_index = None
         self.__omx = False
-        self.__memory_only = False
+        self.__memory_only = True
         self.omx_file = None  # type: omx.File
         self.__version__ = VERSION  # Writes file version
 
@@ -128,7 +128,7 @@ def create_empty(
         data_type: np.dtype = np.float64,
         index_names: List[str] = None,
         compressed: bool = False,
-        memory_only: bool = False,
+        memory_only: bool = True,
     ):
         """
         Creates an empty matrix in the AequilibraE format
@@ -257,7 +257,7 @@ def create_from_omx(
         mappings: List[str] = None,
         robust: bool = True,
         compressed: bool = False,
-        memory_only: bool = False,
+        memory_only: bool = True,
     ) -> None:
         """
         Creates an AequilibraeMatrix from an original OpenMatrix
@@ -759,7 +759,7 @@ def export(self, output_name: str, cores: List[str] = None):
             cores = self.names
 
         if file_extension == ".AEM":
-            self.copy(output_name=output_name, cores=cores)
+            self.copy(output_name=output_name, cores=cores, memory_only=False)
 
         elif file_extension == ".OMX":
             omx_export = omx.open_file(output_name, "w")
@@ -880,7 +880,7 @@ def copy(
         cores: List[str] = None,
         names: List[str] = None,
         compress: bool = None,
-        memory_only: bool = False,
+        memory_only: bool = True,
     ):
         """
         Copies a list of cores (or all cores) from one matrix file to another one

aequilibrae/paths/AoN.pyx

@@ -1,6 +1,6 @@
+# cython: language_level=3
 import os
 
-# cython: language_level=3
 cimport numpy as np
 from libcpp cimport bool