study

cli.study

tvbo study — scaffold and inspect a study dataset.

Two subcommands, both reading the one layout record (schema/study_layout.yaml, see :mod:tvbo.utils.study_layout):

tvbo study init <Name> creates a BIDS study dataset: the directories, the two ignore files derived from the record, dataset_description.json for the study and its derivative, and a seed for every file the record gives a template. -t <variant> adds the entries that variant declares, and swaps in any seed it names in place of the general one, so a replication gets a report about reproducing a paper and every other study does not.
tvbo study layout prints the tree or either ignore file, and --sync rewrites the layout region of a document in place so no document retypes the tree.

Attributes

Name	Description
SLIM_ROLES	What `--slim` writes, at the study root only: the one specification a run is given, the rules that keep the run’s products out of version control, and the file that makes the directory identifiable as a study.
TEMPLATE_DIR	Seeds for the files the record gives a `template`.
app

Functions

Name	Description
init	Scaffold a BIDS study dataset from the layout record.
show_layout	Print part of the layout record, or splice the tree into a document.

init

cli.study.init(
    name=typer.Argument(..., help="Study name; also the dataset name and the entry recipe's stem."),
    parent=typer.Option(Path(), '--in', '-C', help='Directory to create the study in.'),
    template=typer.Option([], '--template', '-t', help='Study kind to include, one the layout record declares. Repeatable; omit for the general study.'),
    force=typer.Option(False, '--force', help='Overwrite files that already exist.'),
    slim=typer.Option(False, '--slim/--full', help='`--slim` writes the entry recipe, a `.gitignore` and `dataset_description.json`, and stops. The result is a runnable study, NOT a complete BIDS dataset: `tvbo validate study` will report the documentation a study of record needs and a demonstration does not. For a docs page, a notebook, or anything driven from the Python API. `--full` (default) scaffolds the whole BIDS study dataset.'),
)

Scaffold a BIDS study dataset from the layout record.

Every directory, both ignore files and every dataset_description.json are derived from the record, so a study’s shape is never typed out a second time. An empty directory gets a .gitkeep only when it is tracked; an untracked one is left for the run to create.

--template selects a study kind the record declares. A kind both adds entries of its own and may supersede the seed of one every study has, since the same file needs different starting text once the kind is known: with no template the study reports its own results, -t replication adds the scorecard and the copyright-safe figure split a reproduction needs, and -t collection gives a study that nests other studies the document and the results manifest in place of a single report. A name the record does not declare is rejected rather than quietly selecting nothing.

--slim writes only what a human authors (:data:SLIM_ROLES), for a study that demonstrates something rather than being archived.

show_layout

cli.study.show_layout(
    what=typer.Argument('tree', help='tree | gitignore | bidsignore'),
    study=typer.Option('<Study>', '--study', '-s', help='Study name to interpolate into the layout.'),
    template=typer.Option([], '--template', '-t', help='Layout variant to include. Repeatable.'),
    sync=typer.Option([], '--sync', help="Rewrite each file's marker-delimited layout region in place instead of printing."),
)

Print part of the layout record, or splice the tree into a document.

--sync is how documentation stops restating the layout: a file carrying the layout markers gets the current tree written into them, so a tree in prose can no longer fall behind the record.