[BEP032] Review and clean-up suggestions

[ree-gupta]

Units & Dimensions

• 3fece84: Removed dimension_unit column and instead explicitly mentioned unit in the height, width and depth columns for probes. Based on discussions in the meeting, changes in the doc and this comment. Rationale: fits BIDS TSV concept better and default unit was agreed upon.
• be82cb9, 923349a, 3a86a52: Fixed electrode size unit to um² and removed remaining dimension_unit references per ProbeInterface conventions.

Schema Refactoring (Column Unification)

• 938e9f9: Refactored x__electrodes, y__electrodes, z__electrodes to use base x, y, z columns with description_addendum for microephys-specific context (matching iEEG pattern).
• 866aced: Refactored units__channels to use base units column (matching iEEG, EEG, MEG, EMG pattern).

Resolved TODOs

• 4e28f8e: Removed gain TODO - no objections and comment favoring current implementation.
• 80d70dd: Removed MicroephysCoordinateSystem TODOs - enums already added in 6284d36, unified system preferred over ecephys/icephys split.
• 06a3c6e: Removed duplicate RequiredCoordsystem check from checks/microephys.yaml

Future Unification Comments

• e8b1268, 65b5289, 9444263: Added TODO comments marking hemisphere__probes, manufacturer__probes, and material__probes for future unification with base columns (requires generalizing base descriptions from "electrode" to be context-agnostic).

Documentation Fixes

• 89ed1f5: Added proper markdown link to 2D coordinate systems section in MicroephysCoordinateSystem description.
• 57b0292, 5112f4f: Fixed events.yaml to include microephys in channel column addendum, fixed typo.
• Unused Code Removal
• add8b6f: Removed unused surgery_date column (moved to PR [ENH] Additional age related columns for participants.tsv file to cover animal data #1839).
• 7a23830, 5e91f38: Removed unused contact_count column and old probe suffix.

[ree-gupta]

Hi @bendichter, could you please review this? these are not major changes but already discussed decisions and refactoring/comment cleanups.

I will continue refactoring the schema to follow BIDS best practices but these were the only ones I had noticed so far.

Thanks!

[bendichter]

4e28f8e: Removed gain TODO - no objections and comment favoring current implementation.

why was this removed? My comment you reference was in support of keeping this.

[ree-gupta]

4e28f8e: Removed gain TODO - no objections and comment favoring current implementation.

why was this removed? My comment you reference was in support of keeping this.

Sorry the commit message is a bit confusing. I just removed the TODO comment, the column is still in there.

[bendichter]

ah! haha sorry I understand now.