maljovec / topopy / 63

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Morse complex (#23)

* Removing License preamble from all source files.
* Blacking code (https://github.com/ambv/black)
* Renaming testFunctions.py to test_functions.py
* Removing C++ code for Morse-Smale complex
* Adding C++ code for Morse Complex
* Creating Python wrapper for Morse Complex
* Creating test class for Morse Complex
* Updating swig and setup files to reflect new Morse Complex
* Removing unused "names" parameter floating throughout code.
* Adding separate class for testing the Merge tree.
* Renaming variables to be pythonic
* Capturing output of debug print statements in test assertions
* Changing debug to stdout
* Correcting gold file to represent json output of the MorseComplex
* After careful analysis, the new merge sequence is an equally valid representation:

You will merge 0 into 1599 at 0.500192, it doesn't matter if it goes through 39 or 1560 to get there. This shows this is a poor test function and I should consider using the gerber version where the maxima have different heights, but again being able to consistently handle this degenerate case is also valuable. This highlights that the assertions should be more robust and test the actual result not the internal representation.

* Testing warning message and suppressing it in other cases of TO testing
* Updating manifest file to associate with proper file extensions.
* Reducing hard-coded data in lieu of a gold file that can be maintained separately.
* More robust testing of the Morse-Smale Complex that won't report as many false negatives
* Incrementing the version number

67 of 68 branches covered (98.53%)

Branch coverage included in aggregate %.

152 of 153 relevant lines covered (99.35%)

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