CODEX reader: TypeError: SpatialData.__init__() got an unexpected keyword argument 'table'

[nilchia]

same as this issue for CosMX, codex rises error: unexpected keyword argument 'table'.

script:

from spatialdata_io import codex
spdata = codex(path="./",
               fcs=False,
               )


print(spdata)

error:

/usr/local/lib/python3.12/functools.py:912: ImplicitModificationWarning: Transforming to str index.
  return dispatch(args[0].__class__)(*args, **kw)
/usr/local/lib/python3.12/functools.py:912: ImplicitModificationWarning: Transforming to str index.
  return dispatch(args[0].__class__)(*args, **kw)
Traceback (most recent call last):
  File "/tmp/tmpu8rew9nt/job_working_directory/000/3/working/spdata_io.py", line 3, in <module>
    spdata = codex(path="./",
             ^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/spatialdata_io/readers/codex.py", line 87, in codex
    sdata = SpatialData(images=images, shapes={str(region): shapes}, table=table)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: SpatialData.__init__() got an unexpected keyword argument 'table'

xref: galaxyproject/tools-iuc#7455

[LucaMarconato]

Thanks for reporting, if you could make a quick PR I'll review and merge.

[nilchia]

sure #377