Add context-aware schema violation reporting

[ehennestad]

Motivation

MatNWB needs to report schema validation violations differently depending on when validation runs (PR #830, PR #832). Values read from existing files should remain readable, so read-time schema violations should warn. Values being written should not produce invalid NWB output, so write-time schema violations should always error. During normal in-memory editing, validation should error by default, while specific backwards-compatible validators can opt into warning instead of error (This requirement was added during review in PR #837).

This PR adds matnwb.common.validation.reportSchemaViolation as the shared reporting helper for schema validation failures. It gates warning and error through a validation context with READ, EDIT, and WRITE modes:

• READ always warns.
• EDIT errors by default.
• EDIT can warn when a validator passes WarnInsteadOfError=true.
• WRITE always errors.

The read context is set while deserializing parsed types, and the write context is set during NwbFile.export. Existing DynamicTable validation paths now use the shared reporter.

How to test the behavior?

runtests('tests.unit.common.validation.ReportSchemaViolationTest')
runtests('tests.unit.io.testCreateParsedType')
runtests('tests.unit.dynamicTableTest')

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 Codex

[Copilot]

Pull request overview

This PR introduces a centralized, context-aware mechanism for reporting schema validation violations so MatNWB can be lenient when reading existing files (warn + keep value) while remaining strict during editing (error by default, optionally warn for backwards-compatible validators) and writing (always error to prevent invalid NWB output).

Changes:

• Added matnwb.common.validation.reportSchemaViolation plus a new internal validation context (READ/EDIT/WRITE) to gate warning vs. error behavior.
• Set the validation context during deserialization (io.createParsedType => READ) and export (NwbFile.export => WRITE).
• Routed DynamicTable schema-violation reporting through the new shared reporter and added unit tests for the new behavior.

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
NwbFile.m	Sets schema validation context to WRITE during export and restores it afterward.
+io/createParsedType.m	Sets schema validation context to READ during parsed type construction and restores it afterward.
+types/+util/+dynamictable/validateUniqueColnames.m	Uses the shared reporter for duplicate colname violations.
+types/+util/+dynamictable/syncNamedColumn.m	Skips syncing on read using the new read-context helper.
+types/+util/+dynamictable/checkConfig.m	Uses the shared reporter for colnames mismatch and references new read-context helper.
+types/+util/validationContext.m	Removes the old strict/read context helper.
+tests/+unit/+io/testCreateParsedType.m	Updates tests to use the new validation context setter.
+tests/+unit/+common/+validation/ReportSchemaViolationTest.m	Adds focused tests for context-aware schema violation reporting behavior.
+matnwb/+common/+validation/reportSchemaViolation.m	Implements the shared error/warn reporting helper with optional causes and WarnInsteadOfError.
+matnwb/+common/+validation/isReadContext.m	Adds a helper for checking read context.
+matnwb/+common/+validation/+internal/ValidationContext.m	Adds the READ/EDIT/WRITE enum.
+matnwb/+common/+validation/+internal/context.m	Adds process-local get/set for the validation context.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.32%. Comparing base (40b87bc) to head (c606f8c).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #836      +/-   ##
==========================================
+ Coverage   95.31%   95.32%   +0.01%     
==========================================
  Files         219      221       +2     
  Lines        7667     7686      +19     
==========================================
+ Hits         7308     7327      +19     
  Misses        359      359              

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