Enhance get_type_map to support deepcopy option and improve extensions handling

[bendichter]

Cline-assisted

fix #1958

I have addressed the performance issue in PoseEstimationSeries creation by making two key changes:

1. Modified pynwb.get_type_map() (in src/pynwb/__init__.py):

   • Added a copy parameter (boolean, defaults to True).
   • If copy=False is passed, this function now returns a direct reference to the TypeMap instead of a deepcopy. This is crucial for performance-sensitive internal calls.
   • Corrected the rtype in the @docval decorator from tuple to TypeMap.

2. Modified NWBMixin._get_type_map() (in src/pynwb/core.py):

   • This method, which is called by HDMF during object instantiation and attribute setting, now calls pynwb.get_type_map(copy=False).
   • This ensures that the expensive deepcopy operation on the TypeMap is avoided in these frequent, performance-critical operations, directly resolving the slowdown.

These changes prevent the unnecessary and costly duplication of the TypeMap object, particularly when creating complex objects like PoseEstimationSeries with many attributes, thus restoring the expected performance.

[codecov]

Codecov Report

Attention: Patch coverage is 47.05882% with 9 lines in your changes missing coverage. Please review.

Project coverage is 94.86%. Comparing base (f956fbb) to head (1c7f24c).

Files with missing lines	Patch %	Lines
src/pynwb/__init__.py	43.75%	8 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #2075      +/-   ##
==========================================
+ Coverage   94.83%   94.86%   +0.03%     
==========================================
  Files          28       28              
  Lines        2749     2748       -1     
  Branches      708      707       -1     
==========================================
  Hits         2607     2607              
+ Misses         82       81       -1     
  Partials       60       60              

Flag	Coverage Δ
integration	74.19% <47.05%> (+0.02%)	⬆️
unit	84.86% <47.05%> (+0.03%)	⬆️

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