chore: update build system to py39 and drop pbr

Author: william-silversmith

.dockerignore

@@ -0,0 +1,9 @@
+build
+*.egg-info
+benchmarks
+__pycache__
+manual_testing
+.eggs
+.git
+.tox
+.pytest_cache

ChangeLog

@@ -1,6 +1,15 @@
 CHANGES
 =======
 
+1.6.0
+-----
+
+* release(1.6.0): faster 6 and 18-way dijkstra
+* fix: CC -> CXX
+* chore: add py39 to build
+* perf: improve speed for dijkstra 6-way and 18-way
+* chore(build): add infrastructure for building manylinux2010 & 2014
+
 1.5.1
 -----
 

build_linux.sh

@@ -1,7 +1,7 @@
 #!/usr/local/bin/bash
 # docker build . -f manylinux1.Dockerfile --tag seunglab/dijkstra3d:manylinux1
-# docker build . -f manylinux2010.Dockerfile --tag seunglab/dijkstra3d:manylinux2010
+docker build . -f manylinux2010.Dockerfile --tag seunglab/dijkstra3d:manylinux2010
 docker build . -f manylinux2014.Dockerfile --tag seunglab/dijkstra3d:manylinux2014
-# docker run -v $PWD/dist:/output seunglab/dijkstra3d:manylinux1 /bin/bash -c "cp -r wheelhouse/* /output"
-# docker run -v $PWD/dist:/output seunglab/dijkstra3d:manylinux2010 /bin/bash -c "cp -r wheelhouse/* /output"
+docker run -v $PWD/dist:/output seunglab/dijkstra3d:manylinux1 /bin/bash -c "cp -r wheelhouse/* /output"
+docker run -v $PWD/dist:/output seunglab/dijkstra3d:manylinux2010 /bin/bash -c "cp -r wheelhouse/* /output"
 docker run -v $PWD/dist:/output seunglab/dijkstra3d:manylinux2014 /bin/bash -c "cp -r wheelhouse/* /output"

manylinux2010.Dockerfile

@@ -1,4 +1,4 @@
-FROM quay.io/pypa/manylinux1_x86_64
+FROM quay.io/pypa/manylinux2010_x86_64
 MAINTAINER William Silversmith
 
 ADD . /dijkstra3d
@@ -13,30 +13,30 @@ RUN /opt/python/cp27-cp27m/bin/pip2.7 install pip --upgrade
 RUN /opt/python/cp35-cp35m/bin/pip3.5 install pip --upgrade
 RUN /opt/python/cp36-cp36m/bin/pip3.6 install pip --upgrade
 RUN /opt/python/cp37-cp37m/bin/pip3.7 install pip --upgrade
-# RUN /opt/python/cp38-cp38/bin/pip3.8 install pip --upgrade
+RUN /opt/python/cp38-cp38/bin/pip3.8 install pip --upgrade
 
 RUN /opt/python/cp27-cp27m/bin/pip2.7 install -r requirements.txt pytest 
 RUN /opt/python/cp35-cp35m/bin/pip3.5 install -r requirements.txt pytest
 RUN /opt/python/cp36-cp36m/bin/pip3.6 install -r requirements.txt pytest
 RUN /opt/python/cp37-cp37m/bin/pip3.7 install -r requirements.txt pytest
-# RUN /opt/python/cp38-cp38/bin/pip3.8 install -r requirements.txt pytest
+RUN /opt/python/cp38-cp38/bin/pip3.8 install -r requirements.txt pytest
 
 RUN /opt/python/cp27-cp27m/bin/python2.7 setup.py develop
 RUN /opt/python/cp35-cp35m/bin/python3.5 setup.py develop
 RUN /opt/python/cp36-cp36m/bin/python3.6 setup.py develop
 RUN /opt/python/cp37-cp37m/bin/python3.7 setup.py develop
-# RUN /opt/python/cp38-cp38/bin/python3.8 setup.py develop
+RUN /opt/python/cp38-cp38/bin/python3.8 setup.py develop
 
 RUN /opt/python/cp27-cp27m/bin/python2.7 -m pytest -v -x automated_test.py
 RUN /opt/python/cp35-cp35m/bin/python3.5 -m pytest -v -x automated_test.py
 RUN /opt/python/cp36-cp36m/bin/python3.6 -m pytest -v -x automated_test.py
 RUN /opt/python/cp37-cp37m/bin/python3.7 -m pytest -v -x automated_test.py
-# RUN /opt/python/cp38-cp38/bin/python3.8 -m pytest -v -x automated_test.py
+RUN /opt/python/cp38-cp38/bin/python3.8 -m pytest -v -x automated_test.py
 
 RUN /opt/python/cp27-cp27m/bin/python2.7 setup.py bdist_wheel
 RUN /opt/python/cp35-cp35m/bin/python3.5 setup.py bdist_wheel
 RUN /opt/python/cp36-cp36m/bin/python3.6 setup.py bdist_wheel
 RUN /opt/python/cp37-cp37m/bin/python3.7 setup.py bdist_wheel
-# RUN /opt/python/cp38-cp38/bin/python3.8 setup.py bdist_wheel
+RUN /opt/python/cp38-cp38/bin/python3.8 setup.py bdist_wheel
 
 RUN for whl in `ls dist/*.whl`; do auditwheel repair $whl --plat manylinux2010_x86_64; done

manylinux2014.Dockerfile

@@ -1,4 +1,4 @@
-FROM quay.io/pypa/manylinux1_x86_64
+FROM quay.io/pypa/manylinux2014_x86_64
 MAINTAINER William Silversmith
 
 ADD . /dijkstra3d

setup.cfg

@@ -7,6 +7,10 @@
 
 import numpy as np
 
+def read(fname):
+  with open(os.path.join(os.path.dirname(__file__), fname), 'rt') as f:
+    return f.read()
+
 extra_compile_args = [
   '-std=c++11', '-O3', '-ffast-math', 
 ]
@@ -15,10 +19,11 @@
   extra_compile_args += [ '-stdlib=libc++', '-mmacosx-version-min=10.9' ]
 
 setuptools.setup(
-  setup_requires=['pbr', 'numpy'],
+  name="dijkstra3d",
+  version="1.6.0",
+  setup_requires=['numpy'],
   extras_require={
     ':python_version == "2.7"': ['futures'],
-    ':python_version == "2.6"': ['futures'],
   },
   ext_modules=[
     setuptools.Extension(
@@ -29,7 +34,39 @@
       extra_compile_args=extra_compile_args,
     )
   ],
-  pbr=True)
+  url="https://github.com/seung-lab/dijkstra3d/",
+  author="William Silversmith",
+  author_email="[email protected]",
+  packages=setuptools.find_packages(),
+  package_data={
+    'dijkstra3d': [
+      'LICENSE',
+    ],
+  },
+  description="Implementation of Dijkstra's Shortest Path algorithm on 3D images.",
+  long_description=read('README.md'),
+  long_description_content_type="text/markdown",
+  license = "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+  classifiers=[
+    "Intended Audience :: Developers",
+    "Development Status :: 5 - Production/Stable",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 2",
+    "Programming Language :: Python :: 2.7",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.5",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Topic :: Scientific/Engineering",
+    "Intended Audience :: Science/Research",
+    "Operating System :: POSIX",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows :: Windows 10",
+  ]
+)
 
 
 

setup.py

@@ -1,5 +1,5 @@
 [tox]
-envlist = py27,py36,py37,py38
+envlist = py27,py36,py37,py38,py39
 
 [testenv]
 platform = darwin