Fix for #25: CellDiff2Vec doesn't terminate

[jarpri]

The issue appears to be from complexes that are too small. The _run_diffusion_process method runs a while loop, comparing the number of nodes to diffusion_cover (which defaults to 80). For graphs with fewer than 80 nodes, this loop never terminates:

def _run_diffusion_process(self, node):
    """
    Generating a diffusion tree from a given source node and linearizing it
    with a directed Eulerian tour.

    Args:
        node (int): The source node of the diffusion.

    Returns:
        list of str: The list of nodes in the walk.
    """
    infected = [node]
    sub_graph = nx.DiGraph()
    sub_graph.add_node(node)
    infected_counter = 1
    while infected_counter < self.diffusion_cover:
        end_point = random.sample(infected, 1)[0]
        nebs = [node for node in self.graph.neighbors(end_point)]
        sample = random.choice(nebs)
        if sample not in infected:
            infected_counter += 1
            infected.append(sample)
            sub_graph.add_edges_from([(end_point, sample), (sample, end_point)])
            if infected_counter == self.diffusion_cover:
                break

To solve this I added an exception to CellDiff2Vec inside the fit method:

if self.diffusion_cover > g.number_of_nodes():
        raise ValueError(
            "The diffusion_cover is too large for the size of the graph.")

I didn't find any more issues with graphs meeting this requirement.

edit: Thank you Florian for spotting the issue with PathComplex! I reverted this change with rebase now.

[ffl096]

Note I have deleted all the references to PathComplex as I couldn't find this in the current version of TopoNetX. Please suggest otherwise if my steps weren't correct and I'm happy to edit this!

PathComplex is here. Looking at your fork of TopoNetX, you are quite behind on commits to the upstream repository. You should sync your fork to have the latest version: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork

Please revert your changes regarding PathComplex afterwards. Thanks!

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (85638fd) 94.63% compared to head (05b2320) 95.18%.
Report is 4 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #36      +/-   ##
==========================================
+ Coverage   94.63%   95.18%   +0.54%     
==========================================
  Files           8        8              
  Lines         149      166      +17     
==========================================
+ Hits          141      158      +17     
  Misses          8        8              

Files	Coverage Δ
topoembedx/classes/cell_diff2vec.py	75.00% <ø> (+16.17%)	⬆️

... and 6 files with indirect coverage changes

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[mhajij]

@jarpri can you please fix the lint before we merge ? Thanks!