Warn instead of error when reading values invalid per the NWB schema

[ehennestad]

Fix #776 & #827

⚠️ Depends on — merge these first:

• Add context-aware schema violation reporting #836
• Validate property values on export to prevent writing invalid files #832

Motivation

Part of #776. When reading an NWB file, a value that deviates from the schema currently causes a hard read error, which can make an otherwise-usable file completely unreadable over a minor issue (for example, a fixed attribute such as ElectricalSeries/data/unit being something other than volts).

This PR makes parsed file reads permissive: a non-conforming value produces a warning and is kept, so the data remains accessible, while constructing or assigning such a value in user code stays strict (an error). Read lenient, write strict.

Changes

A shared helper, types.util.reportSchemaViolation(id, message[, causes]), centralizes the decision: it errors in the strict (construction) context and warns in the read context, appending guidance (the value is kept; correct it and re-export if you maintain the file). The context is the one introduced in #822 (types.util.validationContext), set to read by io.createParsedType. Optional causes are attached with addCause when erroring and appended to the text when warning, so structured errors are preserved.

The following validators now route through it (warn-on-read, error-on-construct):

• Fixed/constant attribute values — new types.util.checkConstant, emitted by fillReadOnlyValidation; core type classes regenerated.
• Neurodata type — checkType.
• Shape — validateShape / checkDims.
• Soft-link target type — validateSoftLink.
• Constrained-set type — checkConstraint.

Internal invariants (for example checkType's unrecognized-expected-type assert) deliberately remain hard errors in both contexts.

Scope

This is the read-side complement to the export-side guard in #829 (writing stays strict). It does not yet cover checkDtype / correctType (the type-coercion family) — those need a careful per-assert classification and will follow in a separate PR. So this is part of #776, not a full resolution.

Notes

• nwbReadTest/readFileWithInvalidTimeSeriesTimestampsShape asserted the old "reading a bad shape fails" behavior; it now asserts the read succeeds with a warning and keeps the value.
• New unit tests: CheckConstantTest, CheckTypeTest, CheckConstraintTest, ValidateSoftLinkTest.

Checklist

• Have you ensured the PR description clearly describes the problem and solutions?
• Have you checked to ensure that there aren't other open or previously closed Pull Requests for the same change?
• If this PR fixes an issue, is the first line of the PR description fix #XX where XX is the issue number?

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR implements “read lenient, write strict” behavior for NWB schema validation: when parsing an NWB file, schema violations that previously caused hard read failures now emit warnings and keep the non-conforming values to preserve data accessibility, while construction-time validation remains strict (errors).

Changes:

• Add types.util.reportSchemaViolation(...) to centralize schema-violation reporting as warning-on-read vs error-on-construct, optionally preserving causes.
• Route multiple validators through the new helper (type checks, shape checks, soft-link target type checks, constrained-set checks), and introduce types.util.checkConstant for schema-fixed attribute validation (regenerated core type validators).
• Update and add unit tests to reflect permissive read behavior (including new validator-focused test classes).

Reviewed changes

Copilot reviewed 27 out of 27 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
+types/+util/reportSchemaViolation.m	New helper to warn-on-read / error-on-construct for schema violations (with optional causes).
+types/+util/checkConstant.m	New helper to validate schema-fixed (constant) values while keeping invalid read-time values.
+types/+util/checkType.m	Switch wrong-type reporting to reportSchemaViolation for read permissiveness.
+types/+util/validateShape.m	Convert shape failures to warn-on-read via reportSchemaViolation, preserving causes in strict mode.
+types/+util/validateSoftLink.m	Convert soft-link declared target-type mismatch to warn-on-read via reportSchemaViolation.
+types/+util/checkConstraint.m	Convert constrained-set type mismatch to warn-on-read via reportSchemaViolation.
+file/fillValidators.m	Update generator to emit constant-value validators via types.util.checkConstant.
+types/+core/*.m (multiple)	Regenerated validators to use types.util.checkConstant for fixed schema values.
+tests/+unit/nwbReadTest.m	Update read test to expect warning+successful read (instead of error) for invalid timestamps shape.
+tests/+unit/+types/+validators/CheckConstantTest.m	New unit tests for constant-value validation behavior in strict vs read contexts.
+tests/+unit/+types/+validators/CheckTypeTest.m	New unit tests for strict vs read-context type checking behavior.
+tests/+unit/+types/+validators/CheckConstraintTest.m	New unit tests for strict vs read-context constrained-set type behavior.
+tests/+unit/+types/+validators/ValidateSoftLinkTest.m	New unit tests for strict vs read-context soft-link target-type behavior.

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[codecov]

Codecov Report

❌ Patch coverage is 98.50746% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 95.30%. Comparing base (94e13bc) to head (5c1ae5a).

Files with missing lines	Patch %	Lines
+types/+util/checkConstant.m	94.73%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #830      +/-   ##
==========================================
- Coverage   95.31%   95.30%   -0.01%     
==========================================
  Files         218      220       +2     
  Lines        7634     7668      +34     
==========================================
+ Hits         7276     7308      +32     
- Misses        358      360       +2     

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