Execute a document

Usage

stencila execute [OPTIONS] <INPUT>

Examples

# Execute a Stencila Markdown document
stencila execute report.smd

# Execute and cache a document
stencila execute temp.md --cache

# Force re-execution of all code
stencila execute cached.ipynb --force-all

# Execute using the shorthand alias
stencila exec script.r

Arguments

Name	Description
`<INPUT>`	The path of the document to execute.

Options

Name	Description
`--no-save`	Do not save the document after executing it. Possible values: `true`, `false`.
`--cache`	Cache the document after executing it. Possible values: `true`, `false`.
`-f, --from`	The format of the input/s.
`--fine`	Use fine decoding if available for input format. Possible values: `true`, `false`.
`--coarse`	Use coarse decoding if available for input format. Possible values: `true`, `false`.
`--pages`	Pages to include when decoding multi-page documents.
`--exclude-pages`	Pages to exclude when decoding multi-page documents.
`--ignore-artifacts`	Ignore cached artifacts and force re-processing. Possible values: `true`, `false`.
`--no-artifacts`	Prevent creating artifacts during decoding. Possible values: `true`, `false`.
`--island-wrap`	Wrap specified environments in Island nodes during decoding. Default value: `figure,table,longtable,landscape`.
`--no-island-wrap`	Disable automatic Island wrapping of environments. Possible values: `true`, `false`.
`--island-style`	Style to apply to auto-created Island nodes.
`--input-losses`	Action when there are losses decoding from input files. Default value: `debug`.
`--include-structuring`	Structuring operations to include (comma-separated).
`--exclude-structuring`	Structuring operations to exclude (comma-separated).
`--citation-style`	The citation style to assume for text-to-citation structuring.
`--ignore-errors`	Ignore any errors while executing document. Possible values: `true`, `false`.
`--force-all`	Re-execute all node types regardless of current state. Possible values: `true`, `false`.
`--skip-code`	Skip executing code. Possible values: `true`, `false`.
`--skip-instructions`	Skip executing instructions. Possible values: `true`, `false`.
`--retain-suggestions`	Retain existing suggestions for instructions. Possible values: `true`, `false`.
`--force-unreviewed`	Re-execute instructions with suggestions that have not yet been reviewed. Possible values: `true`, `false`.
`--force-accepted`	Re-execute instructions with suggestions that have been accepted. Possible values: `true`, `false`.
`--skip-rejected`	Skip re-executing instructions with suggestions that have been rejected. Possible values: `true`, `false`.
`--dry-run`	Prepare, but do not actually perform, execution tasks. Possible values: `true`, `false`.

Possible values of --citation-style

Value	Description
`author-year`	Author-year citations like (Smith, 2023)
`bracketed-numeric`	Bracketed numeric citations like [1]
`parenthetic-numeric`	Parenthetic numeric citations like (1)
`superscripted-numeric`	Superscripted numeric citations like ¹

Possible values of --include-structuring, --exclude-structuring

Value	Description
`none`	No structuring operations
`all`	All structuring operations
`sections-to-keywords`	Extract keywords from the "Keywords" section
`sections-to-abstract`	Extract abstract from the "Abstract" section
`sections-to-references`	Extract references from "References" section
`headings-to-title`	Extract document title from the first heading
`heading1-to-title`	Extract document title from the very first level 1 heading
`heading1-to-title-single`	Extract document title from a single level 1 heading (conservative)
`headings-decrement`	Decrement all heading levels by 1 (H2→H1, H3→H2, etc.)
`headings-primary-level1`	Ensure that all "primary" headings have level 1
`headings-to-sections`	Create a section for each heading
`headings-to-paragraphs`	Transform headings to paragraphs if appropriate
`paragraphs-to-keywords`	Extract keywords from paragraphs starting with "Keywords"
`paragraphs-to-headings`	Transform paragraphs to headings if appropriate
`paragraphs-to-sentences`	Split paragraphs into individual sentences
`figures-with-captions`	Combine an image with a figure caption before or after it
`tables-with-captions`	Combine a table caption with the following table or datatable
`table-images-to-rows`	Convert table images to table rows using OCR
`tables-to-datatables`	Transform tables into datatables if possible
`unwrap-media-objects`	Unwrap media objects from paragraphs to block level
`unwrap-quote-blocks`	Unwrap quote blocks containing more than two child blocks
`text-to-citations`	Convert text to structured citations
`text-to-links`	Convert URL text to structured links
`math-to-citations`	Convert math to structured citations
`math-images-to-tex`	Convert math images to TeX code using OCR
`links-to-citations`	Convert links to citations
`normalize-citations`	Normalize citation formatting and grouping
`remove-pre-primary`	Remove content before the first primary heading
`remove-frontmatter-duplicates`	Remove front matter that duplicates article metadata
`remove-empty-headings`	Remove empty headings
`remove-empty-tables`	Remove empty tables and datatables
`remove-empty-lists`	Remove empty lists
`remove-empty-paragraphs`	Remove empty paragraphs
`remove-empty-text`	Remove empty text