WIP: optimize reconstruction, add CLI workflow

[vivaansinghvi07]

Note: dataframe utils needs following items (to at least be planned) before merge

https://github.com/mmore500/hstrat/issues/167

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 3.55330% with 760 lines in your changes missing coverage. Please review.

Project coverage is 82.48%. Comparing base (cfb6992) to head (e860f4f).

Files with missing lines	Patch %	Lines
...ic_inference/tree/_build_tree_searchtable_debug.py	0.00%	183 Missing :warning:
...ogenetic_inference/tree/_build_tree_searchtable.py	0.00%	165 Missing :warning:
...inference/tree/_impl/_build_trie_from_artifacts.py	0.00%	154 Missing :warning:
...netic_inference/tree/_impl/_TrieSearchInnerNode.py	0.00%	121 Missing :warning:
hstrat/dataframe/_surface_unpack_reconstruct.py	0.00%	50 Missing :warning:
...hylogenetic_inference/tree/_impl/_TrieInnerNode.py	0.00%	39 Missing :warning:
hstrat/dataframe/surface_unpack_reconstruct.py	0.00%	22 Missing :warning:
...phylogenetic_inference/tree/_impl/_TrieLeafNode.py	0.00%	8 Missing :warning:
..._lib/_alifestd_try_add_ancestor_list_col_polars.py	0.00%	6 Missing :warning:
...ary_lib/_alifestd_make_ancestor_list_col_polars.py	0.00%	5 Missing :warning:
... and 4 more

:exclamation: There is a different number of reports uploaded between BASE (cfb6992) and HEAD (e860f4f). Click for more details.

HEAD has 25 uploads less than BASE

| Flag | BASE (cfb6992) | HEAD (e860f4f) | |------|------|------| |tests|48|23|

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #148 +/- ## =========================================== - Coverage 97.26% 82.48% -14.78% =========================================== Files 640 650 +10 Lines 8325 9054 +729 =========================================== - Hits 8097 7468 -629 - Misses 228 1586 +1358 ``` | [Flag](https://app.codecov.io/gh/mmore500/hstrat/pull/148/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno) | Coverage Δ | | |---|---|---| | [tests](https://app.codecov.io/gh/mmore500/hstrat/pull/148/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno) | `82.48% <3.55%> (-14.78%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno#carryforward-flags-in-the-pull-request-comment) to find out more.

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

[mmore500]

just found two bugs (not sure if the second one will reproduce):

• [x] output data file is missing ancestor_list column; this should be created by using the alifestd_try_create_ancestor_list from auxlib
• [ ] importerror

  
  >>> import hstrat
  >>> help(hstrat.dataframe.surface_unpack_reconstruct)
  Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/mmore500/2024-11-17/vivaan/hstrat/_auxiliary_lib/_GetAttrLaunderShim.py", line 36, in __call__
  attr = self._wrapped_getattr(name, *args, **kwargs)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mmore500/.local/lib/python3.12/site-packages/lazy_loader/__init__.py", line 82, in __getattr__
  submod = importlib.import_module(submod_path)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib64/python3.12/importlib/__init__.py", line 90, in import_module
  return _bootstrap._gcd_import(name[level:], package, level)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1324, in _find_and_load_unlocked
  ModuleNotFoundError: No module named 'hstrat.dataframe._surface_unpack_reconstruct'
  >>> from hstrat.dataframe import surface_unpack_reconstruct
  Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/mmore500/2024-11-17/vivaan/hstrat/_auxiliary_lib/_GetAttrLaunderShim.py", line 36, in __call__
  attr = self._wrapped_getattr(name, *args, **kwargs)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mmore500/.local/lib/python3.12/site-packages/lazy_loader/__init__.py", line 82, in __getattr__
  submod = importlib.import_module(submod_path)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib64/python3.12/importlib/__init__.py", line 90, in import_module
  return _bootstrap._gcd_import(name[level:], package, level)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  ModuleNotFoundError: No module named 'hstrat.dataframe._surface_unpack_reconstruct'