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…ids-standard#2409) PR bids-standard#2191 added rawbids/ to the study DatasetType but not to derivative, even though the same convention -- "rawbids/ holds the raw BIDS dataset" -- is equally applicable when a standalone derivative dataset includes its raw source. - Add rawbids as an optional opaque subdirectory of the derivative DatasetType in src/schema/rules/directories.yaml. - Update the derivative example in common-principles.md to use rawbids/ instead of sourcedata/raw/. - Clarify that rawbids/ is reserved for raw BIDS datasets in both study and derivative cases, and that derivatives of derivatives MUST place their source derivative under sourcedata/ (not rawbids/). Co-authored-by: Claude Code 2.1.116 / Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…can be overloaded (bids-standard#2400) * Clarify that age Units could be overriden and refer to Units in common principles * Add ISO 8601-based duration units for age and validate in schema Document in common-principles.md that age Units MAY be overridden to one of: year, month, week, day, hour, minute, or second (based on ISO 8601 duration designators). Add AgeUnits schema check rule that validates participants.json age Units against the allowed set. Co-Authored-By: Claude Code 2.1.110 / Claude Opus 4.6 <noreply@anthropic.com> * Keep compatible (warning, not error) + simplify check Co-authored-by: Chris Markiewicz <effigies@gmail.com> * Remove duplicate specification of units in the Description Co-authored-by: Yaroslav Halchenko <debian@onerussian.com> * Make check operate on participants.tsv not .json Co-authored-by: Chris Markiewicz <effigies@gmail.com> --------- Co-authored-by: Claude Code 2.1.110 / Claude Opus 4.6 <noreply@anthropic.com> Co-authored-by: Chris Markiewicz <effigies@gmail.com>
) * Allow for institutions to be listed as Authors It is not uncommon to have datasets which are a truly an institutional effort -- from data collection planing, acquisition, curation, harmonization etc, where it is a pipeline to deliver high quality datasets. For instance we have a number of such contributions from Allen Institute(s) in DANDI archive. In DANDI schema we allow for both Person and Organization entries, and e.g. in https://github.com/dandisets/000020 we have ```yaml contributor: - affiliation: - identifier: https://ror.org/00dcv1019 name: Allen Institute for Brain Science schemaKey: Affiliation email: nathang@alleninstitute.org identifier: 0000-0001-8429-4090 includeInCitation: false name: Gouwens, Nathan roleName: - dcite:ContactPerson schemaKey: Person - contactPoint: [] identifier: https://ror.org/00dcv1019 includeInCitation: true name: Allen Institute for Brain Science roleName: [] schemaKey: Organization url: https://alleninstitute.org ``` so there is an Organization, which is actually the one to cite, although we do not list any particular roleName, and then responsible ContactPerson (who is not even listed as an Author) who could be contacted ATM (but might be a different person later) about this dandiset. I have tried to make wording a bit more explicit than just listing Organizations as a possible entry here, rather to keep it for large efforts. * Shorten and generalize statement about Authors Co-authored-by: Chris Markiewicz <effigies@gmail.com> --------- Co-authored-by: Chris Markiewicz <effigies@gmail.com> Co-authored-by: Mark Mikkelsen <mark.mikkelsen@gmail.com>
…ering (bids-standard#2438) * [FIX] Bump pymdown-extensions to >=10.21.2 to restore code-block rendering (bids-standard#2421) Pygments 2.20.0 made `html.escape()` on the formatter's `filename` option strict, raising `AttributeError` when the value is `None`. pymdownx.highlight 10.21 (and earlier) passed `filename=title` where `title` defaults to `None` for code blocks without a title, which triggered the crash. pymdownx.superfences catches that exception and silently falls back to inline-`<code>` rendering, so fenced code blocks inside list items (e.g. the "Plain" examples in common-principles.md) lost their `<pre>` formatting and showed the language tag as literal text. pymdown-extensions 10.21.2 fixes the upstream defect, so require it (or newer) in both the docs build and bidsschematools[render]. Closes: bids-standard#2421 Co-Authored-By: Claude Code 2.1.160 / Claude Opus 4.7 (1M context) <noreply@anthropic.com> * [FIX] Regenerate tools/schemacode/uv.lock for pymdown-extensions bump The previous commit updated tools/schemacode/pyproject.toml but forgot to refresh its sibling uv.lock. The `latest` tox envs use the `uv-venv-lock-runner` with `--locked`, so they failed `Setup test suite` with the pyproject/lockfile mismatch. Co-Authored-By: Claude Code 2.1.160 / Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Code 2.1.160 / Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Merge @effigies fixes