We should provide an example dataset on string data.

Cluster should have both bft and dft methods to make traversing over all clusters an easier task

The manifold class should have an optional parameter (ex: mode), which can be set to strict or auto. In strict mode, functions should fail anytime there is an issue in the flow. In auto mode, anytime we can automatically resolve an issue we should do so.

Great example is to consider random walks, if a user passes in a cluster which is subsumed. We can promote the cluster to one which is not subsumed without much trouble, but the user may want to know they've erred.

2021-08-09 17:44:15,940:INFO:root:manifold.build_tree:depth: 20, 213 clusters
2021-08-09 17:44:15,943:WARNING:root:manifold.build:No Selection Criterion was provided. Using leaves for building graph.
2021-08-09 17:44:15,944:INFO:root:manifold.build_edges:building edges for graph with 213 clusters in [2, 20] depth range.
2021-08-09 17:44:16,246:INFO:root:manifold.build_edges:building edges for graph with 1 clusters in [0, 0] depth range.
Traceback (most recent call last):
File "main.py", line 21, in
_dot_string = _manifold[_depth].build_edges().as_dot_string(DATA_NAME)
File "/home/joey/Documents/Research/dot_files/venv/lib/python3.8/site-packages/pyclam/manifold.py", line 675, in as_dot_string
for cluster, lfd in zip(self.clusters, normalized_lfds)
TypeError: iteration over a 0-d array

From the example code-snippets in README:

rnn_results = search.rnn(query, radius)

The output rnn_results prints the following;

{1923: 0.1594879931018627,
 593: 0.2600480386352904,
 0: 0.0,
 23: 0.08578112997186696,
 60: 0.09579264266309048,
...
 1982: 0.4878119826728968,
 1021: 0.4956229780631022}

What does the above output mean?

Similarly printing manifold from

manifold = Manifold(data, 'euclidean')

gives

euclidean-0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223 ....

what does this mean?
Also, can we avoid having everything printed when we run the following code snippet:

manifold.build(
    criterion.MaxDepth(20),  # build the tree to a maximum depth of 20
    criterion.MinRadius(0.25),  # clusters with radius less than 0.25 cannot be partitioned.
    criterion.Layer(6),  # use the clusters ad depth 6 to build a Graph.
    criterion.Leaves(),  # use the leaves of the tree to build another Graph.
)

The output is just really too large.

The links are old, from the archived CHESS repo. Can we update these?

This is an atrocity.

Let's look into https://github.com/cross-rs/cross as an alternative to Earthly.