…arios

Co-authored-by: Seyed (Yahya) Shirazi <shirazi@ieee.org>

* Allowing to render JSON null type with a link

* Python style

* type: Annotate bst.utils

* type: Annotate types.namespace

* type: Annotate bst.schema

* chore: Update pre-commit hooks

Bumps [glob](https://github.com/isaacs/node-glob) from 10.4.5 to 10.5.0.
- [Changelog](https://github.com/isaacs/node-glob/blob/main/changelog.md)
- [Commits](isaacs/node-glob@v10.4.5...v10.5.0)

---
updated-dependencies:
- dependency-name: glob
  dependency-version: 10.5.0
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Add --no-warnings flag to linkchecker commands to prevent CI failures
on HTTP redirect warnings (301/302/303), which are valid links.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

[ENH] Updated HED Version to 8.4.0 in examples

chore: Add "serve" rule to Makefile and provide description to what actions available

chore: Ignore redirect warnings in link checks

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "uvx ruff check --fix",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

Bumps the node-utilities group with 2 updates: [remark-lint-no-trailing-spaces](https://github.com/Trott/remark-lint-no-trailing-spaces) and [prettier](https://github.com/prettier/prettier).


Updates `remark-lint-no-trailing-spaces` from 3.0.2 to 4.0.3
- [Release notes](https://github.com/Trott/remark-lint-no-trailing-spaces/releases)
- [Commits](Trott/remark-lint-no-trailing-spaces@v3.0.2...v4.0.3)

Updates `prettier` from 3.6.2 to 3.7.4
- [Release notes](https://github.com/prettier/prettier/releases)
- [Changelog](https://github.com/prettier/prettier/blob/main/CHANGELOG.md)
- [Commits](prettier/prettier@3.6.2...3.7.4)

---
updated-dependencies:
- dependency-name: remark-lint-no-trailing-spaces
  dependency-version: 4.0.3
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: node-utilities
- dependency-name: prettier
  dependency-version: 3.7.4
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: node-utilities
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

)

Bumps the actions-infrastructure group with 3 updates: [actions/checkout](https://github.com/actions/checkout), [actions/download-artifact](https://github.com/actions/download-artifact) and [actions/upload-artifact](https://github.com/actions/upload-artifact).


Updates `actions/checkout` from 5 to 6
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v5...v6)

Updates `actions/download-artifact` from 6 to 7
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](actions/download-artifact@v6...v7)

Updates `actions/upload-artifact` from 5 to 6
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](actions/upload-artifact@v5...v6)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-infrastructure
- dependency-name: actions/download-artifact
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-infrastructure
- dependency-name: actions/upload-artifact
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-infrastructure
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Co-authored-by: melanieganz <melanie.ganz@gmail.com>
Co-authored-by: PeerHerholz <herholz.peer@gmail.com>
Co-authored-by: Cyril Pernet <wamcyril@gmail.com>
Co-authored-by: Oscar Esteban <code@oscaresteban.es>
Co-authored-by: James Kent <jamesdkent21@gmail.com>
Co-authored-by: melanieganz <ganz@di.ku.dk>
Co-authored-by: Paul Wighton <PWIGHTON@mgh.harvard.edu>
Co-authored-by: mnoergaard <martin.noergaard@nru.dk>
Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu>
Co-authored-by: Mathieu Guay-Paquet <mathieu.guaypaquet@gmail.com>
Co-authored-by: Mark Mikkelsen <mark.mikkelsen@gmail.com>
Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

* RF: PharmaceuticalDoseAmount - shift mentioning of a "tracer" into PET use

We are to introduce use of Pharma* fields into BEP032 where it has no notion of tracers.
I am moving this extra description to become PET specific, but also PET people might want
to double check if that is what was actually intended (or it could be administered separate
from the tracer

* Fix DICOM tag for Intervention Drug Dose

Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

* fix: use 0018 not 0008 section for Drug DICOM fields and format consistently with others and hyperlink

* Also move "tracer" mentioning into addendum for PharmaceuticalName

---------

Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

* type: Avoid breaking third-party autodoc generation

* chore: ruff check --fix

* chore: Recognize _laztypes as typing, for linting purposes

updates:
- [github.com/python-jsonschema/check-jsonschema: 0.35.0 → 0.36.0](python-jsonschema/check-jsonschema@0.35.0...0.36.0)
- [github.com/pre-commit/mirrors-mypy: v1.19.0 → v1.19.1](pre-commit/mirrors-mypy@v1.19.0...v1.19.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* minor update md

* final changes and working version with mkdocs

* add forgotten example

* final changes

* latest changes

* Update 10-eye-tracking.md

correction of text

* Apply suggestions from code review

* fix bad latin

* md lint

* fix yml

* md lint

* lint yml

* add semantic line breaks

* move suffix

* rm CogPOID and CogAtlas yml

* move some metadata

* move more metadata

* move more metadata

* rely on task.yml for events

* change extension to tsv

* fix schema

* fix links

* fix typos

* fix link

* most of the change but mkserve not working yet

* some more change still not working

* change in mkdocs.yml based on commments

* run pre-commit and fix yml

* add eyetrack modality object

* format markdown

* format markdown

* space missing in tabular_data/eyetrack.yaml

* fixing conflict for real

* automatic changes by pre-commit

* instru

* pre-commit stuff

* correct error of manipulation of logo.eps

* some test

* some test

* some test

* some test

* changes of columns names

* Update src/modality-specific-files/eye-tracking.md

Co-authored-by: Taylor Salo <tsalo90@gmail.com>

* change in metadata

* test new changes with pre-commit

* correct error in eyetrack.md

* add RecordTimeStart and RecordTimeEnd

* cahnge eye_sample to eye_timestamp

* correct error example json

* error in datasets links

* last round of review on main doc

* slight modif of SAOI

* slight modif of main md

* correction of space

* try without modality

* Update src/modality-specific-files/eye-tracking.md

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

* put back mkdocs.yaml with unsorted modality specific files

* Update src/modality-specific-files/eye-tracking.md

Co-authored-by: Taylor Salo <tsalo90@gmail.com>

* Update src/schema/objects/metadata.yaml

Co-authored-by: Taylor Salo <tsalo90@gmail.com>

* Update src/schema/objects/metadata.yaml

Co-authored-by: Taylor Salo <tsalo90@gmail.com>

* Update src/schema/objects/metadata.yaml

Co-authored-by: Taylor Salo <tsalo90@gmail.com>

* change after review of tsalo

* put back /tool/filetree_exampl.ipynb

* instru

* change on metadata based on tsalo comments

* change to desambiguate the columns in case of two eyes recording

* change to account for the BEP020

* change of json example in reply to https://github.com/bids-standard/bids-specification/pull/1128/files/9f223a1488ed1ac844f1bfd63ffd93af696102fd#r1047302456

* change RecordTimeStart and RecordTimeEnd to StartTime_eyetrack (with same name as StartTime physio) and StopTime_eyetrack

* take out Scree settings from metadata as they were put in the main branch of bids specification

* insist on calibration in the text

* add eyetrack suffix to timeseries suffixes in task.yaml in order to add eyetrack files to other modality automatically by macros

* point 2 on suggestion #1128 (comment)

* fix markdown

* fix markdown

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* codespell fixes

* schema fix

* change to follow recommandations of https://doi.org/10.3758/s13428-021-01762-8

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* split metadata

* fix metadata

* format

* fix typo

* update example

* make gunzip optional

* add required events.json metadata

* fix list

* fix list

* Update eye-tracking.md

Change link to new version of resting state dataset on openneuro

* Changes for metadata

- change DataType from number to array of arrays for AverageCalibrationError and MaximalCalibrationError
- delete CalibrationList from metadata.yaml and eyetrack.yaml as it only contains dublicates of other metadata and thus not needed
- fix typo in metadata.yaml: CalibrationCount was wrongly named "CalibrationType" so CalibrationType was listed twice

* change unit of ScreenSize in example events.json

* Update src/modality-specific-files/eye-tracking.md

Co-authored-by: Arshitha Basavaraj <arsh2794@proton.me>

* Apply suggestions from code review

Co-authored-by: Oscar Esteban <code@oscaresteban.es>

* Update src/schema/objects/columns.yaml

Co-authored-by: Oscar Esteban <code@oscaresteban.es>

* Update src/schema/objects/columns.yaml

Co-authored-by: Oscar Esteban <code@oscaresteban.es>

* Update metadata.yaml

Attempt to fix the type of AverageCalibrationError and MaximalCalibrationError, leaving empty the number of maxItems as it is possible to have as many calibration as desired

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update src/schema/objects/metadata.yaml

* fix issues in mkdocs.yml

* hasty copy paste

* fix time stamp

* add placeholder for eventual publication

* Update metadata.yaml

Add description for two eyes.

* Update src/modality-specific-files/eye-tracking.md

Co-authored-by: Oscar Esteban <code@oscaresteban.es>

* Update src/modality-specific-files/eye-tracking.md

Co-authored-by: Oscar Esteban <code@oscaresteban.es>

* Update src/modality-specific-files/near-infrared-spectroscopy.md

Co-authored-by: Oscar Esteban <code@oscaresteban.es>

* enh: a proposal for the new ``RecordingType`` (-> ``PhysioType``) idea

* enh: add eyetracking examples

* enh: revise metadata specifications

* fix: remove duplicated metadata entry

* restore eyetrack sidecars

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix: pacify codespell

* fix: pacify markdown linter

* fix: attempt to get line numbers on tsv files

* fix: attempt 2 to get line numbers on tsv files

* Update src/modality-specific-files/eye-tracking.md

* fix: address several issues, add example datasets, pacify remark

* enh: better ordering, clearer definitions

* sty: pacify remark

* enh: change zero-based to one-base indexes, more consistent with BIDS

* fix: remove redirected URL

* enh: add columns definition for physioevents and improve eyetracker examples

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix: length of new message column description

* fix: improved definition of ForeignIndexColumn

* enh: clearly state specific physio types at the outset

* enh: improving and adding example file trees

* fix: normalize file tree macros and repare syntax of some

* fix: typos and readability improvements

* review and slight text modification

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix: revert boilerplate about publication

* enh: drop "old" eyetrack

* fix: ``"cyclopean"`` value for ``RecordedEye`` metadata

* fix: deduplicate example datasets, and move eyetrack's ones into an admonition at the beginning of its section

* fix: missing setting eyetrack tabular data allowed to add columns

* enh: deep reorganization of the section

* fix: pacify linter

* Update src/modality-specific-files/physiological-and-other-continuous-recordings.md

Co-authored-by: Remi Gau <remi_gau@hotmail.com>

* enh: move escalating events' metadata to REQUIRED into task data section

* fix unit

* use levels to describe metadata

* fix typo

* minor schema fix

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix

* enh: add @Sourav-Kulkarni's suggestions about eye-tracker/screen distance

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* enh: address @qian-chu's review comment about documenting timestamp

* enh: address @Remi-Gau's comment on column order

* Update src/modality-specific-files/physiological-recordings.md

* Update src/modality-specific-files/physiological-recordings.md

Co-authored-by: Scott Huberty <52462026+scott-huberty@users.noreply.github.com>

* Update src/modality-specific-files/physiological-recordings.md

Co-authored-by: Scott Huberty <52462026+scott-huberty@users.noreply.github.com>

* fix: address issue of ``EnvironmentCoordinates``

* enh: add note about the type of pupil size being recorded

Reference: https://github.com/bids-standard/bids-specification/pull/1128/files#r1916646141

* enh: document all four columns of physio.json file

* Update src/schema/objects/metadata.yaml

* fix: remove backtick breaking yaml file

* Update physiological-recordings.md to change the BIDS example

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update metadata.yaml 

Changing AverageCalibrationError and MaximalCalibrationError to use the term "degrees of visual angle" rather than "degrees" and "visual degrees".

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update metadata.yaml

Change EyeTrackingMethod to get rid of the citation of a retracted paper.

* fix: implement association for StimulusPresentation mutation

* fix: bad merge from upstream/master

* fix: potential conflict created by `SampleCoordinatesUnits`

Resolves: https://github.com/bids-standard/bids-specification/pull/1128/files#r1712953676

cc: @Remi-Gau

* fix: onset definition of physioevents should allow units other than s

Resolves: https://github.com/bids-standard/bids-specification/pull/1128/files#r1693909512

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix: convert `SampleCoordinateSystem` into an enum

* fix: remove old leftover in AverageCalibrationError

* Update src/modality-specific-files/physiological-recordings.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Apply suggestions from code review

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* fix(schema): Make StimulusPresentation__eyetrack

* Apply suggestions from code review

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* fix: onset__physioevents; make timestamp required

* fix: Remove ForeignIndexColumn

* Revert "fix: Remove ForeignIndexColumn"

This reverts commit f5b123d.

* fix: tables

* Update src/modality-specific-files/physiological-recordings.md

* fix: Broken link

* fix(schema): Quote valid YAML expression, expect strings in selectors

* fix: Physio files do not inherit

* Make ForeignIndexColumn required, simplify section by placing timestamp first

* Fix style complaint

* chore: Add associations.events.sidecar, remove task selector

* feat(schema): Make assertions on physio, not events

* Remove associations.physio

* Revert "Remove associations.physio"

This reverts commit 8c97ae1.

* fix(schema): Extension is a string

* feat: Add ForeignIndexColumn consistency check

* fix: Remove bad selector

* Apply suggestions from code review

* Apply suggestions from code review

Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com>

* Limit screen requirements to gaze-on-screen

* Update src/schema/objects/metadata.yaml

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

* Account for n/a values in StimulusPresentation

* fix: Clarify pupil size can be diameter, add check for description

* test: Allow sidecar expressions to include known column names

* fix: Restrict eye-tracking column requirements to physio files

* Update src/schema/objects/metadata.yaml

Co-authored-by: Oscar Esteban <code@oscaresteban.es>

* Update src/schema/objects/metadata.yaml

* Apply suggestions from code review

* Update src/modality-specific-files/physiological-recordings.md

* Remove ScreenAOIDefinition field in agreement with getting rid with these parameters

Removed ScreenAOIDefinition from physiological recordings.

* Demote non-essential fields to optional

* Fix invalid JSON in eye-tracking physioevents example (#13)

Remove trailing commas before closing braces/brackets which are
invalid in JSON (valid in JavaScript but not JSON).

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

---------

Co-authored-by: Klara Gregorova <49999446+greckla@users.noreply.github.com>
Co-authored-by: mszinte <mszinte@invibe.nohost.me>
Co-authored-by: Remi Gau <remi_gau@hotmail.com>
Co-authored-by: mszinte <mail@martinszinte.net>
Co-authored-by: Taylor Salo <tsalo90@gmail.com>
Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: julia-pfarr <pfarr@staff.uni-marburg.de>
Co-authored-by: julia-pfarr <111446107+julia-pfarr@users.noreply.github.com>
Co-authored-by: Arshitha Basavaraj <arsh2794@proton.me>
Co-authored-by: Oscar Esteban <code@oscaresteban.es>
Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Co-authored-by: Scott Huberty <52462026+scott-huberty@users.noreply.github.com>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
Co-authored-by: Ross Blair <rosswilsonblair@gmail.com>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

updates:
- [github.com/adrienverge/yamllint: v1.37.1 → v1.38.0](adrienverge/yamllint@v1.37.1...v1.38.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…2316)

The comment incorrectly referenced eyetrack.yaml when the actual
schema file is physio.yaml (as correctly used in the macro call).

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>

* add checks for multiple frame consistency issues

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* keeping me honest yamllint

* remove redundant selector ||

* remove redundant check

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>