Github actions and horizon OSX fix (#10)

* gh action template yml

* fix flake8 call

* install topocalc to build C code

* try with tox

* install tox

* tox env

* run setup.py test

* os matrix

* cleanup

* coverage

* coverage try 2

* coverage try 3

* cibuildwheel for linux osx

* seperate build wheels workflow

* wrong directory

* fixing build-wheels

* fixing build-wheels

* wheel dependancy on unittest

* cap numpy

* cc env

* cython capy

* cython 0.28.X doesn't work

* gcc version print

* specify gcc alias

* testing with ubuntu

* cc testing

* updating setup.py for cc overwrite

* full test

* moved all actions to one file

* moved all actions to one file

* restructuring

* fixing

* removing O3 flag

* gcc version

* removed slopef/b functions and was more explicit

* updated setup.py for cython language directive and simplified topo_core.pyx

* dist in slope int to double more explicit

* viewf test more verbose

* up nangles for viewf test

* viewf test for osx

* upping osx tolerance

* updating setup.py to be like smrf's

* move cython to dev requirement and see if osx will use c code instead

* pyx bool to bint

* viewf test assert all close

* double declaration

* wrong c type

* debugging and cleanupy

* c typingy

* relaxed osx viewf test

* hypot

* zeros

* gcc

* refactor c code a bit

* add linux

* more print

* just horizon

* hor1f was going 1 index too far

* remove debug

* cleanup

* delete travis.yml

* action on

* updated action on

* updating README

.github/workflows/python-package.yml

@@ -0,0 +1,153 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Unittest, flake8, coverage
+
+# Run action on pull requests
+# Run on a published release and push to Pypi
+on:
+  pull_request:
+    branches: [ main ]
+  release: 
+    types: [published]
+
+jobs:
+
+  flake8:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.7'
+
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install flake8
+
+      - name: Lint with flake8
+        run: |
+          flake8 topocalc
+
+  coverage:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.7'
+
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install coverage coveralls PyYAML
+          python3 -m pip install -r requirements.txt
+
+      - name: Run coverage
+        run: |
+          make coveralls
+
+
+  unittest:
+    needs: [flake8, coverage]
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: [3.6, 3.7, 3.8, 3.9]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install -r requirements.txt
+
+      - name: Run unittests
+        run: |
+           python3 setup.py test
+
+  build_wheels:
+    needs: unittest
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macos-10.15]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: '3.8'
+
+      - name: Build wheels
+        uses: joerick/[email protected]
+        env:
+          CIBW_SOME_OPTION: value
+          CIBW_TEST_REQUIRES: nose
+          CIBW_TEST_COMMAND: "nosetests -vv --exe topocalc"
+          CIBW_BUILD: "cp3*-manylinux_x86_64 cp3*-macosx_x86_64"
+          CIBW_SKIP: "?p27* pp* ?p35"
+          CIBW_BUILD_VERBOSITY: 3
+          CIBW_BEFORE_BUILD: "pip install -r requirements.txt"
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    needs: unittest
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: '3.8'
+
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install -r requirements.txt
+
+      - name: Build sdist
+        run: python setup.py sdist --formats=gztar
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    # upload to PyPI on every tag starting with 'v'
+    # if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
+    # alternatively, to publish when a GitHub Release is created, use the following rule:
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: artifact
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}
+          # To test: repository_url: https://test.pypi.org/legacy/

README.md

@@ -1,7 +1,6 @@
 # topocalc
 
 [![Pypi version](https://img.shields.io/pypi/v/topocalc.svg)](https://pypi.python.org/pypi/topocalc)
-[![Build Status](https://travis-ci.com/USDA-ARS-NWRC/topocalc.svg?branch=main)](https://travis-ci.com/USDA-ARS-NWRC/topocalc)
 [![Coverage Status](https://coveralls.io/repos/github/USDA-ARS-NWRC/topocalc/badge.svg?branch=main)](https://coveralls.io/github/USDA-ARS-NWRC/topocalc?branch=main)
 [![Maintainability](https://api.codeclimate.com/v1/badges/20930fef2e7b7fe91dd3/maintainability)](https://codeclimate.com/github/USDA-ARS-NWRC/topocalc/maintainability)
 
@@ -55,7 +54,7 @@ The sky view factor (`svf`) is the amount of the sky that is visible to a partic
 
 ## Installation
 
-> **NOTE**: `topocalc` has only been tested for Python 3.5 to 3.8 on Linux and MacOSX environments.
+> **NOTE**: `topocalc` has only been tested for Python 3.6 to 3.9 on Linux and MacOSX environments. If building from source, topocalc must be compiled with `gcc`, `clang` will not work if on MacOS.
 
 To install:
 

requirements.txt

@@ -1,5 +1,4 @@
 numpy>=1.15
 Click>=7.0
-Cython>=0.28.4
 spatialnc>=0.2.12
 setuptools_scm<4.2

requirements_dev.txt

@@ -1,9 +1,9 @@
 -r requirements.txt
+Cython>=0.29
 netCDF4>=1.2.9
 wheel==0.33.6
 watchdog==0.9.0
 flake8==3.7.8
-tox==3.14.0
 coverage
 Sphinx==1.8.5
 twine==1.14.0

setup.py

@@ -3,24 +3,39 @@
 import os
 
 import numpy
-from Cython.Distutils import build_ext
 from setuptools import Extension, find_packages, setup
+from setuptools.command.build_ext import build_ext as _build_ext
+
+# Test if compiling with cython or using the C source
+try:
+    from Cython.Distutils import build_ext as _build_ext
+except ImportError:
+    USE_CYTHON = False
+else:
+    USE_CYTHON = True
+
+print('Using Cython {}'.format(USE_CYTHON))
+ext = '.pyx' if USE_CYTHON else '.c'
+
+
+class build_ext(_build_ext):
+    def finalize_options(self):
+        _build_ext.finalize_options(self)
+
 
 with open('README.md') as readme_file:
     readme = readme_file.read()
 
-# with open('HISTORY.md') as history_file:
-#     history = history_file.read()
-
 with open('requirements.txt') as requirements_file:
     requirements = requirements_file.read()
 
 setup_requirements = ['setuptools_scm']
 
 test_requirements = []
 
-# force the compiler to use gcc
-os.environ["CC"] = "gcc"
+# Give user option to specify their local compiler name
+if "CC" not in os.environ:
+    os.environ["CC"] = "gcc"
 
 cmdclass = {'build_ext': build_ext}
 ext_modules = []
@@ -36,25 +51,23 @@
                   "hor1d.c",
               ]],
               include_dirs=[numpy.get_include()],
-              extra_compile_args=['-O3'],
-              extra_link_args=['-O3'],
               ),
 ]
 
 setup(
-    author="Scott Havens",
-    author_email='scott.havens@ars.usda.gov',
-    python_requires='>=3.5',
+    author="USDA ARS NWRC",
+    author_email='snow@ars.usda.gov',
+    python_requires='>=3.6',
     classifiers=[
         'Development Status :: 2 - Pre-Alpha',
         'Intended Audience :: Developers',
         'License :: OSI Approved :: MIT License',
         'Natural Language :: English',
         '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'
     ],
     description="Topo calculations like gradient and sky view",
     entry_points={
@@ -67,9 +80,6 @@
     long_description=readme,
     long_description_content_type="text/markdown",
     include_package_data=True,
-    # package_data={
-    #     'topocalc': ['*.pyx', '*.pxd', '*.c', '*.h'],
-    # },
     keywords='topocalc',
     name='topocalc',
     packages=find_packages(include=['topocalc', 'topocalc.*']),
@@ -79,7 +89,6 @@
     cmdclass=cmdclass,
     ext_modules=ext_modules,
     url='https://github.com/USDA-ARS-NWRC/topocalc',
-    # version='0.1.0',
     use_scm_version={
         "local_scheme": "no-local-version"
     },