Reserve the DOI of the data deposit on Zenodo

Uploads the data and code compendium – data_and_code.zip, which make_submission() and make_preprint() build – to a new Zenodo deposit, fills in its description from the project, and reserves its DOI, so the manuscript can cite the data before they are published. It never publishes: the deposit stays a draft until you review it on Zenodo and press Publish there, which cannot be undone. Nothing in the package needs it; it runs only when you call it.

Usage

deposit_zenodo(file = NULL, sandbox = FALSE, token = NULL, path = NULL)

Arguments

file

The compendium to upload. NULL, the default, takes the newest data_and_code.zip in submission/.

sandbox

TRUE deposits on https://sandbox.zenodo.org, to try it.

token

The personal access token. NULL, the default, reads ZENODO_TOKEN, or ZENODO_SANDBOX_TOKEN with sandbox = TRUE.

path

The project, or any folder inside it. Left out, the one set_paper() named; with none named, this stops before writing: it writes into the project, and easypaper never takes the working directory for it.

Value

A list with the deposit's id, the reserved doi and the url of the draft, invisibly.

Details

The description comes from the manuscript: the title (the short title, short-title:, when there is one; the title otherwise), the authors with their affiliations and ORCID (orcid: on an author), the keywords, and the licence of the data, from the project's LICENSE.txt (CC BY 4.0 in a new project). Zenodo refuses a whole deposit over one ORCID it cannot read, so one that is not four groups of four digits – 0000-0000-0000-000X, the last may be an X – is left out of it, with a warning naming the author: add it on the draft, or correct it in manuscript.qmd and call again. The deposit and its DOI are recorded in the easypaper: block of _quarto.yml, so a second call – after the data changed – replaces the file of the same draft instead of opening another. A deposit already published is left alone: a new version of it is made on Zenodo.

The DOI is written into the text wherever it says 10.5281/zenodo.XXXXXXX – the placeholder of the data availability statement –, into the cover letters of submission/ where they say [repository DOI], and into the project's README.md, as a badge and in its citation; and it is printed, to cite it wherever else it belongs. A cover letter written after it carries the DOI from the start.

It needs a personal access token of Zenodo, with the scopes deposit:write and deposit:actions: create one at https://zenodo.org/account/settings/applications/tokens/new/ and put it in your .Renviron as ZENODO_TOKEN=... (usethis::edit_r_environ() opens it). To try it first, use Zenodo's sandbox, a copy of the site for tests: a token from https://sandbox.zenodo.org as ZENODO_SANDBOX_TOKEN, and sandbox = TRUE. A sandbox DOI does not resolve, so it is never written into the text.

Examples

# It needs a Zenodo token (see Details), Quarto for the compendium, and a
# connection, so it does not run here.
if (FALSE) { # \dontrun{
make_submission(path = "my_paper")
deposit_zenodo(sandbox = TRUE, path = "my_paper")
deposit_zenodo(path = "my_paper")
} # }