Make Subject required by default in NWBFile::initialize()

[Copilot]

Fixes #290

nwb-inspector upgraded check_subject_exists to a warning/error for DANDI compliance. AqNWB did not yet support Subject and was silently ignoring this check in CI via --ignore=check_subject_exists.

Changes

• Added Subject class to represent the /general/subject group in NWB files.
• Added Subject::SubjectSpec to configure a Subject and facilitate initialization also via NWBFile.
• Updated nwbinspector tests to remove --ignore=check_subject_exists option to require subject.
• Updated NWBFile::initialize to accept a SubjectSpec argument for subject metadata initialization

[codecov-commenter]

Codecov Report

❌ Patch coverage is 80.37383% with 21 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.52%. Comparing base (c092a77) to head (76be639).

Files with missing lines	Patch %	Lines
src/nwb/file/Subject.cpp	74.07%	21 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #320      +/-   ##
==========================================
- Coverage   84.69%   84.52%   -0.18%     
==========================================
  Files          57       59       +2     
  Lines        2699     2805     +106     
  Branches      347      371      +24     
==========================================
+ Hits         2286     2371      +85     
- Misses        413      434      +21     

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[Copilot]

Pull request overview

This PR adds first-class support for the NWB /general/subject group and wires it into NWBFile::initialize() so CI nwbinspector validation no longer needs to ignore the subject-exists check, improving DANDI compliance.

Changes:

• Added a new NWB::Subject container with a SubjectSpec for initializing subject metadata.
• Extended NWBFile::initialize() to accept (optional) subject metadata and create /general/subject accordingly.
• Updated tests, examples, and CI workflows to stop ignoring the subject-exists inspector check.

Reviewed changes

Copilot reviewed 17 out of 17 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
tests/testUtils.hpp	Adds a shared helper to generate consistent SubjectSpec test metadata.
tests/testSubject.cpp	New unit tests covering Subject registration, read/write of fields, and integration with NWBFile::initialize().
tests/testRegisteredType.cpp	Adds Subject to the registered type path/name expectations.
tests/testRecordingWorkflow.cpp	Updates workflow test to initialize NWBFile with Subject metadata.
tests/testProcessingModule.cpp	Updates processing module tests to initialize NWBFile with Subject metadata.
tests/testNWBFile.cpp	Updates NWBFile tests for the new initialize signature and Subject default creation expectations.
tests/examples/testWorkflowExamples.cpp	Updates example workflow to initialize NWBFile with Subject metadata.
tests/examples/test_link_timeseries_example.cpp	Updates link-timeseries example to initialize NWBFile with Subject metadata.
tests/CMakeLists.txt	Adds the new testSubject.cpp to the test build.
src/nwb/NWBFile.hpp	Extends initialize() API to accept SubjectSpec (via std::optional).
src/nwb/NWBFile.cpp	Implements Subject creation during NWBFile initialization.
src/nwb/file/Subject.hpp	Introduces the Subject container and SubjectSpec definition and read accessors.
src/nwb/file/Subject.cpp	Implements Subject initialization/writing of provided metadata.
CMakeLists.txt	Adds Subject.cpp to the library build.
CHANGELOG.md	Documents addition of Subject and nwbinspector/initialize updates.
.github/workflows/upgrade_schema.yml	Removes ignore of subject-exists; keeps ignore for Allen CCF electrodes location check.
.github/workflows/tests.yml	Removes ignore of subject-exists; keeps ignore for Allen CCF electrodes location check.

Suppressed comments (2)

src/nwb/NWBFile.hpp:113

• The PR title/issue says Subject should be created by default (with an explicit opt-out), but initialize() currently defaults subjectSpec to std::nullopt, so callers who omit the argument still get no /general/subject and will fail nwbinspector unless they remember to pass metadata.

                    const std::string& timestampsReferenceTime = "",
                    const std::optional<AQNWB::NWB::Subject::SubjectSpec>&
                        subjectSpec = std::nullopt);

src/nwb/file/Subject.hpp:78

• Leftover TODO suggests the initialize method is incomplete, but initialize() is already implemented in Subject.cpp. This looks like generated boilerplate that should be removed to avoid confusion.

  // TODO: Update the initialize method as appropriate.
  /**

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[oruebel]

Constructor for the Subject class must be made protected