Remove unnecessary calls to deepcopy(get_type_map)

[rly]

Motivation

Fix #1958. Closes #2075. Similar approach as in #2075. Adds a copy argument to get_type_map that is default True but can be set to False. The False setting is used when creating a setter for each attribute in each NWB container class. Previously, a deepcopy was performed when creating every setter, which significantly hurt performance.

This PR deprecates calling get_type_map with any 'extensions' arguments, a use case I have never seen. IMO it's easy for the rare user to just call load_namespaces on the type map than us maintain all this extra convenience logic that even we don't use. See similar PR for hdmf-common in hdmf-dev/hdmf#1302.

It is possible that deepcopying of typemaps in get_type_map can be removed entirely. That will be investigated separately as part of #2120.

How to test the behavior?

Profile performance, run pytest

Checklist

• Did you update CHANGELOG.md with your changes?
• Have you checked our Contributing document?
• Have you ensured the PR clearly describes the problem and the solution?
• Is your contribution compliant with our coding style? This can be checked running ruff check . && codespell from the source directory.
• Have you checked to ensure that there aren't other open Pull Requests for the same change?
• Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.

[codecov]

Codecov Report

❌ Patch coverage is 90.90909% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 95.19%. Comparing base (f9cd2a2) to head (a6bf5bf).
⚠️ Report is 11 commits behind head on dev.

Files with missing lines	Patch %	Lines
src/pynwb/__init__.py	90.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #2121      +/-   ##
==========================================
- Coverage   95.32%   95.19%   -0.14%     
==========================================
  Files          28       28              
  Lines        2846     2849       +3     
  Branches      735      736       +1     
==========================================
- Hits         2713     2712       -1     
- Misses         77       83       +6     
+ Partials       56       54       -2     

Flag	Coverage Δ
integration	74.16% <63.63%> (-0.12%)	⬇️
unit	85.08% <81.81%> (-0.13%)	⬇️

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[Copilot]

Pull Request Overview

Optimizes performance by reducing unnecessary deep copying of type maps when creating NWB container setters. The PR adds a copy parameter to get_type_map() (defaulting to True for backward compatibility) and deprecates the extensions argument in favor of calling load_namespaces() directly on the returned TypeMap.

• Add copy parameter to get_type_map() to control whether a deep copy is returned
• Deprecate the extensions argument in get_type_map() with a warning message
• Update all test files to use the new pattern of calling load_namespaces() on the TypeMap

Reviewed Changes

Copilot reviewed 5 out of 6 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/pynwb/init.py	Adds copy parameter to get_type_map(), deprecates extensions argument, and updates utility functions to use global TypeMap directly
src/pynwb/core.py	Updates _get_type_map() to use copy=False for performance optimization
tests/unit/test_extension.py	Refactors test calls to use new pattern of get_type_map() followed by load_namespaces()
tests/integration/helpers/utils.py	Updates test helper to use new TypeMap loading pattern
CHANGELOG.md	Documents the performance fix, API changes, and deprecation

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[stephprince]

LGTM!