minor edit: fix the reference table formatting

[j23414]

Thanks for putting this together! Just wanted to fix the formatting in the README table.

[arendsee]

Thanks @j23414 ! Looks good!

[j23414]

Ah, might need to contact @markin-alex or @tkanderson to merge.

[tkanderson]

Thanks @j23414 and @arendsee

[j23414]

Looks like it's hitting a TypeCheck problem:

Run mypy --python-version 3.10 flutile/*py
flutile/api.py:30: error: Incompatible types in assignment (expression has type "TextIO", variable has type "TextIOWrapper")  [assignment]
flutile/api.py:35: error: Incompatible types in assignment (expression has type "TextIO", variable has type "TextIOWrapper")  [assignment]
Found 2 errors in 1 file (checked [7](https://github.com/flu-crew/flutile/actions/runs/4056720653/jobs/6981560567#step:6:8) source files)
Error: Process completed with exit code 1.

Which happens in app.py (not triggered by changes from this PR):

https://github.com/flu-crew/flutile/blob/e5b343fa0203e4d8119cad24b42b6e722d9a0be2/flutile/api.py#L27-L35

And seems related to:

• https://stackoverflow.com/questions/43910979/mypy-error-incompatible-types-in-assignment

Which means we need to explicitly define fasta_fh and outfile_fh as either type TextIO or TextIOWrapper? Assuming they auto convert to each other?

[tkanderson]

@btski when you get back to work, can you see if this will cause issues in the downstream/octofludb?

@j23414 thanks - I noticed the error :-) but then got swept into other things and didn't look further.

Which means we need to explicitly define fasta_fh and outfile_fh as either type TextIO or TextIOWrapper? Assuming they auto convert to each other?

[arendsee]

Or you could just disable the typechecking step in the git actions file. That's how I fix failing tests.

[tkanderson]

Apparently rerunning the job reuses the original yaml file? I'll give it another go later today (deleted the typechecking) - getting a crash course in git beyond my regular old commit/push/pull stuff...