MRG: LineageTree class to help with LINGroup ordering

[bluegenes]

Note: based off of #2469

• Rewrites build_tree, find_lca functions as LineageTree class. Using same tests, we produce same results
• Adds ordered_paths method to produce ~ordered lineages from tree for LINgroup ordered output.
• Removes num_bp_assigned column because it was artificial anyway (our counts are all assigned at the genome level) and we're not trying to replicate a format exactly, as we are with kreport output, where we have this column.

Note that LINgroups will not be ordered absolutely, as there will be some stochasticity as we descend the dictionary. Instead, related subpaths will be grouped.

e.g. two potential outputs:

LINgroup_name	LINgroup_prefix	percent_containment	num_bp_contained	num_bp_assigned
lg3	2;0;0	1.56	192000	0
lg1	0;0;0	5.82	714000	0
lg2	1;0;0	5.05	620000	0
lg3	1;0;1	0.65	80000	0
lg4	1;0;1;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	0.65	80000	80000

LINgroup_name	LINgroup_prefix	percent_containment	num_bp_contained	num_bp_assigned
lg2	1;0;0	5.05	620000	0
lg3	1;0;1	0.65	80000	0
lg4	1;0;1;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0	0.65	80000	80000
lg1	0;0;0	5.82	714000	0
lg3	2;0;0	1.56	192000	0

In these examples, the 1;0.. paths are always grouped together, but may come before or after the 0;0 and 2;0 groups

[codecov]

Codecov Report

Merging #2496 (e35db91) into lins-v2 (caa42f6) will increase coverage by 7.69%.
The diff coverage is 98.59%.

@@             Coverage Diff             @@
##           lins-v2    #2496      +/-   ##
===========================================
+ Coverage    85.06%   92.75%   +7.69%     
===========================================
  Files          133      104      -29     
  Lines        15036    12260    -2776     
  Branches      2575     2582       +7     
===========================================
- Hits         12790    11372    -1418     
+ Misses        1944      586    -1358     
  Partials       302      302              

Flag	Coverage Δ
python	92.75% <98.59%> (+0.01%)	⬆️
rust	?

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Impacted Files	Coverage Δ
src/sourmash/tax/tax_utils.py	98.29% <98.59%> (+0.02%)	⬆️
src/core/src/ffi/hyperloglog.rs
src/core/src/index/revindex.rs
src/core/src/ffi/utils.rs
src/core/src/index/bigsi.rs
src/core/src/encodings.rs
src/core/src/signature.rs
src/core/src/ffi/nodegraph.rs
src/core/src/sketch/hyperloglog/mod.rs
src/core/src/cmd.rs
... and 20 more

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[bluegenes]

@ctb sub-PR ready for review.

In main LINS PR, I copied over the build_tree and find_lca functions and tests from lca_utils.py so I could use them. Here, I rewrite those in the LineageTree class so I can add the ordered_paths method for LINgroup ordering.

The diff here ~clearly shows the code reorganization and that the same tests pass for LineageTree as for build_tree and find_lca (will not be so clear when diff is with latest).

[bluegenes]

upd: decided to remove the num_bp_assigned column here, since it doesn't actually provide any useful or meaningful information. Back to "ready for review" status :).