Moving to New NGLPy API (#30)

* Critical Bug fix: Reversing edges on negated Morse complex built for Morse-Smale construction.
* Making things compatible with the uncertain branch of NGLPy
* Adding requirements file with pinned dependencies
* Removing 2.7 build and adding more modern pythons.
* Closes #27 and uses requirements file to generate prerequisite installations
* Bumping version number
* Updating to point to new NGL API and bumping major version of topopy since it will have a breaking API change as well
* Fixing deprecation warning
* Fixing tests
* Adding requirements.txt to the Manifest file
* Cleaning documentation
* Pinning to working version of nglpy installation.
* Documenting all public functions using numpy style docstrings.
* Adding linker arg for MacOS builds
* Disabling 3.5 due to use of f-strings
* Testing staging deploy script.
* Enabling flake and mypy checks on CI

.gitignore

@@ -18,4 +18,8 @@ topopy.egg-info/*
 *.txt
 *tar.gz
 *.json
-.coverage
+.coverage
+
+.ipynb_checkpoints
+docs/_build
+

.travis.yml

@@ -2,21 +2,22 @@ language: python
 addons:
   apt_packages:
     - swig
-install: make && pip install coveralls
+install: make && pip install coveralls mypy flake8 twine
 python:
   # - "3.2" # see https://github.com/travis-ci/travis-ci/issues/4866
   # - "3.3"
   # - "3.4"
-  - "3.5"
+  # - "3.5"
   - "3.6"
   - "3.7"
   # - "3.8"
   # - "nightly"
   # PyPy versions commented out since scipy does not play well with pypy
-  # - "pypy2.7"
-  # - "pypy3.5"
-# command to install dependencies
-script: coverage run --source topopy setup.py test
+  # - "pypy3.6"
+  # - "pypy3.7"
+  # - "pypy3.8"
+script:
+  - ". travis.sh"
 after_success:
   - coveralls
 branches:

MANIFEST.in

@@ -2,4 +2,5 @@ include *.h *.cpp
 include *.md
 include *.py
 include LICENSE
-include README.rst
+include README.rst
+include requirements.txt

README.rst

@@ -82,8 +82,9 @@ Example Usage
 
 ::
 
-    import topopy
+    import nglpy as ngl
     import numpy as np
+    import topopy
 
     def hill(_x):
         _x = np.atleast_2d(_x)
@@ -93,11 +94,11 @@ Example Usage
 
     X = np.random.rand(100,2)
     Y = hill(X)
+    graph = ngl.EmptyRegionGraph(beta=1.0, relaxed=False, p=2.0)
 
-    msc = topopy.MorseSmaleComplex(graph='beta skeleton',
+    msc = topopy.MorseSmaleComplex(graph=graph,
                                    gradient='steepest',
-                                   normalization='feature',
-                                   connect=True)
+                                   normalization='feature')
     msc.build(X, Y)
     msc.get_partitions()
 

deploy/test.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+set -e
+set -x
+
+# Append the version number with this git commit hash, but hashes contain
+# letters which are not allowed in pypi versions. We can hack this to replace
+# all letters with numbers, this should still be unique enough to not collide
+# before the version number increases.
+GIT_HASH=$(git rev-parse --short HEAD | tr 'abcdefghijklmnopqrstuvwxyz' '12345678901234567890123456')
+awk -v hash=$GIT_HASH '/^__version__ = \"/{ sub(/"$/,".dev"hash"&") }1' topopy/__init__.py > tmp && mv tmp topopy/__init__.py
+TEMP_VERSION=$(grep  '__version__ = ' topopy/__init__.py | cut -d = -f 2 | sed "s/\"//g" | sed 's/^[ \t]*//;s/[ \t]*$//')
+TEMP_VERSION=$(expr $TEMP_VERSION)
+echo $TEMP_VERSION
+
+# Build the project
+make
+python setup.py sdist
+
+# Test the upload# Test the upload, temporarily disable exit on error, since there is a race 
+# condition for which build will get this out first, also, re-triggered builds
+# would never succeed in this step.
+set +e
+twine upload --repository-url https://test.pypi.org/legacy/ -u __token__ -p ${PYPI_TOKEN} --non-interactive dist/topopy-${TEMP_VERSION}.tar.gz
+set -e
+
+#Give it some time to register internally before trying to install it
+sleep 60
+
+# Now install and run it
+pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple topopy==${TEMP_VERSION}
+python -c "import topopy"

docs/api.rst

@@ -0,0 +1,6 @@
+================================================================================
+API Documentation
+================================================================================
+
+.. automodule:: topopy
+    :members:

docs/conf.py

@@ -17,11 +17,23 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
+from mock import Mock
+import os
+import subprocess
+import sys
+sys.path.insert(0, os.path.abspath('..'))
 
 
+# Mock things for readthedoc build
+class MyMock(Mock):
+    @classmethod
+    def __getattr__(cls, name):
+        return MyMock()
+
+
+MOCK_MODULES = ['_topology']
+sys.modules.update((mod_name, MyMock()) for mod_name in MOCK_MODULES)
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -31,7 +43,9 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = []
+extensions = ['sphinx.ext.autodoc',
+              'sphinx.ext.napoleon',
+              'sphinx.ext.viewcode']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
@@ -166,3 +180,6 @@
         "Miscellaneous",
     )
 ]
+
+os.chdir('..')
+subprocess.call('make')

docs/index.rst

@@ -12,6 +12,7 @@ Welcome to topopy's documentation!
 
    install.rst
    usage.rst
+   api.rst
    license.rst
 
 Indices and tables

requirements.txt

@@ -2,4 +2,4 @@ scipy>=1.3.2,<2.0
 numpy>=1.17.4,<2.0
 scikit-learn>=0.21.2,<1.0
 networkx>=2.4,<3.0
-nglpy>=0.0.2,<1.0
+nglpy>=1.0.6,<2.0

setup.cfg

@@ -1,2 +1,25 @@
 [metadata]
-description-file = README.md
+description-file = README.md
+
+[flake8]
+max-line-length = 120
+exclude = topology.py
+max-complexity = 15
+
+[mypy-topopy.topology]
+ignore_errors = True
+
+[mypy-networkx.*]
+ignore_missing_imports = True
+
+[mypy-nglpy.*]
+ignore_missing_imports = True
+
+[mypy-numpy.*]
+ignore_missing_imports = True
+
+[mypy-scipy.*]
+ignore_missing_imports = True
+
+[mypy-sklearn.*]
+ignore_missing_imports = True

setup.py

@@ -8,8 +8,11 @@
 requirements = open('requirements.txt').read().strip().split('\n')
 
 extra_compile_args = ["-O3", "-march=native", ]
+extra_link_args = []
+
 if platform.system() == 'Darwin':
     extra_compile_args.append('-stdlib=libc++')
+    extra_link_args.append('-stdlib=libc++')
 
 
 def get_property(prop, project):
@@ -80,6 +83,7 @@ def get_property(prop, project):
     ext_modules=[
         Extension("_topology",
                   FILES,
-                  extra_compile_args=extra_compile_args)
+                  extra_compile_args=extra_compile_args,
+                  extra_link_args=extra_link_args)
     ],
 )