Merge the update for re-publish 2.0.0

[chtsai0105]

No description provided.

[codecov]

Codecov Report

Attention: Patch coverage is 82.26913% with 336 lines in your changes missing coverage. Please review.

Project coverage is 81.93%. Comparing base (885f950) to head (95a40d0).
Report is 44 commits behind head on main.

Files with missing lines	Patch %	Lines
src/phyling/libphyling/tree.py	82.00%	77 Missing ⚠️
src/phyling/libphyling/_abc.py	78.91%	66 Missing ⚠️
src/phyling/pipeline/_outputprecheck.py	41.81%	64 Missing ⚠️
src/phyling/libphyling/align.py	86.96%	61 Missing ⚠️
src/phyling/libphyling/_utils.py	73.41%	46 Missing ⚠️
src/phyling/pipeline/align.py	90.52%	9 Missing ⚠️
src/phyling/pipeline/tree.py	95.34%	4 Missing ⚠️
src/phyling/pipeline/filter.py	96.00%	3 Missing ⚠️
src/phyling/__main__.py	94.28%	2 Missing ⚠️
src/phyling/libphyling/download.py	93.10%	2 Missing ⚠️
... and 2 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #31      +/-   ##
==========================================
- Coverage   85.20%   81.93%   -3.27%     
==========================================
  Files          10       15       +5     
  Lines        1717     2032     +315     
==========================================
+ Hits         1463     1665     +202     
- Misses        254      367     +113     

Flag	Coverage Δ
3.10	81.93% <82.26%> (-3.27%)	⬇️
3.11	81.93% <82.26%> (-3.27%)	⬇️
3.12	81.93% <82.26%> (-3.27%)	⬇️
3.9	81.92% <82.25%> (-3.29%)	⬇️

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