Release candidate (#361)

* Upgrades Numpy version (#353)

* Limits pyarrow version

* Makes PyArrow an optional dependency (#356)

Co-authored-by: pveigadecamargo <pveigadecamargo@anl.gov>

* Update setup.py (#357)

* Bumps up version

* Updates setup

* Sets version for AequilibraE

* Fixes packaging (#362)


Co-authored-by: pveigadecamargo <pveigadecamargo@anl.gov>
Co-authored-by: djfrancesco <pacullfrancois@gmail.com>

* Fix: #365 Use specified number of cores (#366)

* Fix skim cost calculation on compact graph (#367)

When skimming the network using the compact graph the last link (within
the dataframe) was being ignored.
Co-authored-by: chrisobi02 <chrisgobrien02@gmail.com>
Co-authored-by: Jamie Cook <jamie.cook@veitchlister.com.au>
Co-authored-by: djfrancesco <pacullfrancois@gmail.com>
Co-authored-by: Jake Moss <jake.moss@uqconnect.edu.au>

.github/tests_linux.yml

@@ -32,7 +32,7 @@ jobs:
     - name: Compile library
       run: |
         cd aequilibrae/paths
-        python3 setup_Assignment.py build_ext --inplace
+        python3 setup_assignment.py build_ext --inplace
         cd ..
         cd ..
 

.github/workflows/build_windows.yml

@@ -34,7 +34,7 @@ jobs:
     - name: Compile library
       run: |
         cd aequilibrae/paths
-        python setup_Assignment.py build_ext --inplace
+        python setup_assignment.py build_ext --inplace
         cd ..
         cd ..
 

.github/workflows/documentation.yml

@@ -38,7 +38,7 @@ jobs:
     - name: Compile library
       run: |
         cd aequilibrae/paths
-        python3 setup_Assignment.py build_ext --inplace
+        python3 setup_assignment.py build_ext --inplace
         cd ..
         cd ..
 

.github/workflows/test_linux_with_coverage.yml

@@ -28,7 +28,7 @@ jobs:
     - name: Compile library
       run: |
         cd aequilibrae/paths
-        python3 setup_Assignment.py build_ext --inplace
+        python3 setup_assignment.py build_ext --inplace
         cd ..
         cd ..
     - name: Generate coverage report

.github/workflows/unit_tests.yml

@@ -63,7 +63,7 @@ jobs:
     - name: Compile library
       run: |
         cd aequilibrae/paths
-        python setup_Assignment.py build_ext --inplace
+        python setup_assignment.py build_ext --inplace
         cd ../..
 
     - name: Build

MANIFEST.in

@@ -0,0 +1,2 @@
+global-include *.pyx
+global-include *.pxd

aequilibrae/distribution/gravity_application.py

@@ -15,8 +15,6 @@
 from aequilibrae.distribution.synthetic_gravity_model import SyntheticGravityModel
 from aequilibrae.matrix import AequilibraeMatrix, AequilibraeData
 
-sys.dont_write_bytecode = True
-
 spec = iutil.find_spec("openmatrix")
 has_omx = spec is not None
 

aequilibrae/paths/graph.py

@@ -441,9 +441,9 @@ def set_graph(self, cost_field) -> None:
         """
         if cost_field in self.graph.columns:
             self.cost_field = cost_field
-            self.compact_cost = np.zeros(self.compact_graph.id.max() + 1, self.__float_type)
+            self.compact_cost = np.zeros(self.compact_graph.id.max() + 2, self.__float_type)
             df = self.__graph_groupby.sum()[[cost_field]].reset_index()
-            self.compact_cost[df.index.values[:-1]] = df[cost_field].values[:-1]
+            self.compact_cost[df.index.values] = df[cost_field].values
             if self.graph[cost_field].dtype == self.__float_type:
                 self.cost = np.array(self.graph[cost_field].values, copy=True)
             else:
@@ -475,10 +475,10 @@ def set_skimming(self, skim_fields: list) -> None:
         if k:
             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, len(skim_fields) + 1), self.__float_type)
+        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()
         for i, skm in enumerate(skim_fields):
-            self.compact_skims[df.index.values[:-1], i] = df[skm].values[:-1].astype(self.__float_type)
+            self.compact_skims[df.index.values, i] = df[skm].values.astype(self.__float_type)
 
         self.skims = np.zeros((self.num_links, len(skim_fields) + 1), self.__float_type)
         t = [x for x in skim_fields if self.graph[x].dtype != self.__float_type]

aequilibrae/paths/parameters.pxi

@@ -16,5 +16,5 @@ cdef double INFINITE = 1.79769313e+308
 
 VERSION = 0.7
 MINOR_VRSN = 6
-binary_version = "0.7.6"
+binary_version = "0.7.7"
 release_name = "Queluz"

aequilibrae/paths/results/skim_results.py

@@ -89,7 +89,7 @@ def set_cores(self, cores: int) -> None:
             if cores == 0:
                 self.cores = mp.cpu_count()
             elif cores > 0:
-                cores = max(mp.cpu_count(), cores)
+                cores = min(mp.cpu_count(), cores)
                 if self.cores != cores:
                     self.cores = cores
         else:

aequilibrae/paths/setup_Assignment.py → aequilibrae/paths/setup_assignment.py

@@ -1,13 +1,8 @@
-import sys
 import platform
+
 import numpy as np
 import pyarrow as pa
-import Cython.Compiler.Options
-from Cython.Distutils import build_ext
 from Cython.Build import cythonize
-import shutil
-
-# Cython.Compiler.Options.annotate = True
 
 try:
     from setuptools import setup
@@ -16,15 +11,14 @@
     from distutils.core import setup
     from distutils.extension import Extension
 
-sys.dont_write_bytecode = True
-
 if "WINDOWS" in platform.platform().upper():
     ext_modules = [
         Extension(
             "AoN",
             ["AoN.pyx"],
             extra_compile_args=["/openmp"],
             extra_link_args=["/openmp"],
+            define_macros=[("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")],
             include_dirs=[np.get_include(), pa.get_include()],
         )
     ]

docs/source/index.rst

@@ -83,6 +83,7 @@ documentation for all versions since 0.5.3.
 * `0.7.4 <https://aequilibrae.com/python/V.0.7.4/>`_
 * `0.7.5 <https://aequilibrae.com/python/V.0.7.5/>`_
 * `0.7.6 <https://aequilibrae.com/python/V.0.7.6/>`_
+* `0.7.7 <https://aequilibrae.com/python/V.0.7.7/>`_
 
 * `Develop Branch (upcoming version) <https://aequilibrae.com/python/develop/>`_
 This documentation correspond to software version:

pyproject.toml

@@ -4,4 +4,4 @@ target-version = ['py36', 'py37', 'py38']
 include = '\.pyi?$'
 
 [build-system]
-requires = ["setuptools", "numpy<1.22", "cython", "pyaml", "pyqt5", "requests", "scipy", "shapely", "pandas", "pyarrow<10.0.0", "pyproj"]
+requires = ["setuptools", "numpy<1.22", "cython", "pyaml", "pyqt5", "requests", "scipy", "shapely", "pandas", "pyarrow<10.0.0", "pyproj", "wheel"]

setup.py

@@ -1,7 +1,7 @@
 import importlib.util as iutil
 import os
 import platform
-from os.path import dirname, join
+from os.path import dirname, join, isfile
 
 import numpy as np
 from Cython.Distutils import build_ext
@@ -19,21 +19,32 @@
     include_dirs.append(pa.get_include())
 
 whole_path = join(dirname(os.path.realpath(__file__)), "aequilibrae/paths", "AoN.pyx")
-ext_module = Extension("aequilibrae.paths.AoN", [whole_path], include_dirs=include_dirs, language="c++")
+ext_module = Extension(
+    "aequilibrae.paths.AoN",
+    [whole_path],
+    define_macros=[("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")],
+    include_dirs=include_dirs,
+    language="c++",
+)
 
 # this is for building pyarrow on platforms w/o wheel, like our one of our macos/python combos
 if "WINDOWS" not in platform.platform().upper():
     ext_module.extra_compile_args.append("-std=c++17")
 
-with open("requirements.txt", "r") as fl:
-    install_requirements = [x.strip() for x in fl.readlines()]
+reqs = ["numpy>=1.18.0,<1.22", "scipy", "pyaml", "cython", "pyshp", "requests", "shapely >= 1.7.0", "pandas", "pyproj"]
+
+if isfile("requirements.txt"):
+    # We just make sure to keep the requirements sync'ed with the setup file
+    with open("requirements.txt", "r") as fl:
+        install_requirements = [x.strip() for x in fl.readlines()]
+    assert sorted(install_requirements) == sorted(reqs)
 
 pkgs = [pkg for pkg in find_packages()]
 
 pkg_data = {
     "aequilibrae.reference_files": ["spatialite.sqlite", "nauru.zip", "sioux_falls.zip"],
-    "aequilibrae.paths": ["parameters.pxi"],
-    "aequilibrae": ["parameters.yml"],
+    "aequilibrae.paths": ["parameters.pxi", "*.pyx"],
+    "aequilibrae": ["./parameters.yml"],
     "aequilibrae.project": ["database_specification/tables/*.*", "database_specification/triggers/*.*"],
 }
 loose_modules = ["__version__", "parameters"]
@@ -43,7 +54,7 @@
         name="aequilibrae",
         version=release_version,
         # TODO: Fix the requirements and optional requirements to bring directly from the requirements file
-        install_requires=install_requirements,
+        install_requires=reqs,
         packages=pkgs,
         package_dir={"": "."},
         py_modules=loose_modules,

tests/compile.py

@@ -7,5 +7,5 @@
 
 os.chdir(pth)
 subprocess.Popen(
-    f"{sys.executable} setup_Assignment.py build_ext --inplace", shell=True, stdout=subprocess.PIPE
+    f"{sys.executable} setup_assignment.py build_ext --inplace", shell=True, stdout=subprocess.PIPE
 ).stdout.read()