Import error

Start with the imports shown in versalign/scoring.py and versalign/aligner.py, then reproduce the failure by importing from versalign.scoring before the aligner, msa, or pairwise modules. The issue is done when scoring imports successfully without requiring another module to be imported first, and the documented import order is no longer needed.

When importing any method from versalign.scoring before importing a method from either the aligner, msa, or pairwise modules will results in an ImportError:

Traceback (most recent call last):
  File "/Users/davidmeijer/repos/CLM/./harvest/scripts/parse_retromol_results.py", line 14, in <module>
    from versalign.scoring import create_substituion_matrix_dynamically
  File "/Users/davidmeijer/miniforge3/envs/clm/lib/python3.10/site-packages/versalign/scoring.py", line 9, in <module>
    from versalign.aligner import substitution_matrices
  File "/Users/davidmeijer/miniforge3/envs/clm/lib/python3.10/site-packages/versalign/aligner.py", line 8, in <module>
    from versalign.scoring import T
ImportError: cannot import name 'T' from partially initialized module 'versalign.scoring' (most likely due to a circular import) (/Users/davidmeijer/miniforge3/envs/clm/lib/python3.10/site-packages/versalign/scoring.py)

The issue can be mitigated by importing the scoring module after importing either aligner, msa, or pairwise module first. This will work, for example:

from versalign.aligner import setup_aligner
from versalign.scoring import create_substituion_matrix_dynamically