Expose progress bar class control

[CodyCBakerPhD]

Motivation

For @garretmflynn and the GUIDE project

How to test the behavior?

I will add a minimal test with an in-place extension of tqdm

Checklist

• Did you update CHANGELOG.md with your changes?
• Does the PR clearly describe the problem and the solution?
• Have you reviewed our Contributing Guide?
• Does the PR use "Fix #XXX" notation to tell GitHub to close the relevant issue numbered XXX when the PR is merged?

[CodyCBakerPhD]

I have no idea if docval is OK with this?

[garrettmflynn]

Nah it's giving an error.

[2024-05-13 14:06:09,926] ERROR in app: Exception on /startup/preload-imports [GET]
Traceback (most recent call last):
  File "/Users/garrettflynn/Documents/GitHub/hdmf/src/hdmf/utils.py", line 605, in dec
    a['type'] = __resolve_type(a['type'])
  File "/Users/garrettflynn/Documents/GitHub/hdmf/src/hdmf/utils.py", line 527, in __resolve_type
    raise ValueError(msg)
ValueError: argtype must be a type, a str, a list, a tuple, or None - got <class 'builtin_function_or_method'>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/garrettflynn/Documents/GitHub/nwb-guide/pyflask/apis/startup.py", line 40, in get
    import neuroconv
  File "/Users/garrettflynn/Documents/GitHub/neuroconv/src/neuroconv/__init__.py", line 1, in <module>
    from .basedatainterface import BaseDataInterface
  File "/Users/garrettflynn/Documents/GitHub/neuroconv/src/neuroconv/basedatainterface.py", line 9, in <module>
    from pynwb import NWBFile
  File "/Users/garrettflynn/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/pynwb/__init__.py", line 9, in <module>
    from hdmf.spec import NamespaceCatalog
  File "/Users/garrettflynn/Documents/GitHub/hdmf/src/hdmf/__init__.py", line 2, in <module>
    from .backends.hdf5.h5_utils import H5Dataset, H5RegionSlicer
  File "/Users/garrettflynn/Documents/GitHub/hdmf/src/hdmf/backends/__init__.py", line 1, in <module>
    from . import hdf5
  File "/Users/garrettflynn/Documents/GitHub/hdmf/src/hdmf/backends/hdf5/__init__.py", line 1, in <module>
    from . import h5_utils, h5tools
  File "/Users/garrettflynn/Documents/GitHub/hdmf/src/hdmf/backends/hdf5/h5_utils.py", line 20, in <module>
    from ...data_utils import DataIO, AbstractDataChunkIterator
  File "/Users/garrettflynn/Documents/GitHub/hdmf/src/hdmf/data_utils.py", line 140, in <module>
    class GenericDataChunkIterator(AbstractDataChunkIterator):
  File "/Users/garrettflynn/Documents/GitHub/hdmf/src/hdmf/data_utils.py", line 197, in GenericDataChunkIterator
    def __init__(self, **kwargs):
  File "/Users/garrettflynn/Documents/GitHub/hdmf/src/hdmf/utils.py", line 608, in dec
    raise Exception(msg)
Exception: docval for progress_bar_class: error parsing argument type: argtype must be a type, a str, a list, a tuple, or None - got <class 'builtin_function_or_method'>

Is there a simple way to fix this?

[CodyCBakerPhD]

@rly @oruebel I want to specify a callable in a function/class wrapped by docval

Is there any way to do that or otherwise circumvent it?

[oruebel]

The problem is that callable is not a type in Python but rather a built-in function. If you want to restrict to progress bar classes from tqdm then you could set the type to tqdm.std, which I believe is the common base class for progress bars in tqdm. Or you could make a list of all the progress bar types you want to allow. I believe docval allows this to be specified as a string tqdm.std so that you should not need to import tqdm in order to specify this for docval. Alternatively, if you want any class to pass validation, then I believe you could set type to None.

[CodyCBakerPhD]

tqdm.std is the module, not a parent class; tqdm.tqdm is the thing they recommend using as a base class when extending, but in general you could use any generic iterable wrapper if you wanted to

I'll just use the override for now

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 88.72%. Comparing base (8a2658f) to head (0753f8a).
Report is 32 commits behind head on dev.

Additional details and impacted files

@@           Coverage Diff           @@
##              dev    #1110   +/-   ##
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  Coverage   88.72%   88.72%           
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  Files          45       45           
  Lines        9765     9766    +1     
  Branches     2773     2773           
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+ Hits         8664     8665    +1     
  Misses        779      779           
  Partials      322      322           

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[CodyCBakerPhD]

@garrettmflynn Should be good to try again

[CodyCBakerPhD]

@oruebel @rly This is ready for review