Replace networkx by proprietary data structure and algorithms

[janezd]

Issue

This add-on uses networkx for

• its basic data structure (which is inefficient because it is based on dictionaries),
• reading files (which is so buggy that it works, basically, for Pajek, and even for this we need to pre-process the file before passing it to networkx),
• computing some statistics (which is way too slow, because it's implemented in pure Python).

Networkx needs to be replaced with something better and more efficient. A few months ago I looked around and found nothing useful.

Also fixes #24, fixes #104.

Description of changes

This PR implements a new (and quite simple) data structure, based on sparse matrices, and ports the widgets to it.

Includes

• Code changes
• Tests
• Documentation

[pavlin-policar]

This looks great - networkx is pretty terrible. However, we should make sure removing networkx doesn't break the Louvain clustering widget.

The widget outputs an Orange graph if the addon is available and relies on networkx to compute the clustering. As far as I am aware, that is the only widget in core orange that works like that.

[janezd]

I will remove networkx only in the addon. Core widgets can still use it. I believe that some widgets in bioinformatics or single cell use networkx, too.

As for outputting data to add-on widgets, I can provide a function to transform networkx graph to the new graph.

I guess I will pack the new graph into a separate package. This will allow core and other add-ons to include it as dependency instead of checking (like Louvain) whether the add-on is installed. The package will also be useful when we/I also implement some algorithms on graphs.

[codecov-io]

Codecov Report

Merging #115 into master will decrease coverage by 1.41%.
The diff coverage is 58.49%.

@@            Coverage Diff             @@
##           master     #115      +/-   ##
==========================================
- Coverage   63.56%   62.14%   -1.42%     
==========================================
  Files          25       29       +4     
  Lines        2835     2800      -35     
==========================================
- Hits         1802     1740      -62     
- Misses       1033     1060      +27

Impacted Files	Coverage Δ
...contrib/network/widgets/tests/test_OWNxExplorer.py	100% <ø> (ø)	⬆️
setup.py	96.96% <ø> (ø)	⬆️
orangecontrib/network/network/twomode.py	100% <100%> (ø)
orangecontrib/network/network/__init__.py	100% <100%> (ø)
orangecontrib/network/__init__.py	80% <100%> (-5.72%)	⬇️
...gecontrib/network/widgets/tests/test_OWNxGroups.py	98.79% <100%> (-0.07%)	⬇️
orangecontrib/network/widgets/ownxsinglemode.py	100% <100%> (ø)	⬆️
...ntrib/network/widgets/tests/test_OWNxClustering.py	100% <100%> (ø)	⬆️
orangecontrib/network/tests/test_twomode.py	94.44% <100%> (-3.71%)	⬇️
...ontrib/network/widgets/tests/test_OWNxGenerator.py	100% <100%> (ø)	⬆️
... and 24 more

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[janezd]

I'm merging this. I'd like to have the bulk porting done, and now separately improve individual parts.

• It passes existing tests. It is probably still buggy, so we won't release a new version of add-on before new tests are added and widgets are tested manually.
• Some functionality is missing - compared with the previous version. It doesn't generate a myriad of different graphs, and, more importantly, network analysis widget is rather poor. This will be fixed in subsequent pull requests.
• Some functionality that couldn't be supported earlier (directed graphs, multimodal graph) is not supported yet. This will be improved on in future PRs, too.