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The codemeta package
provides a more minimalist approach to generating codemeta based only on
DESCRIPTION and CITATION files, while codemetar provides
additional abilities to detect metadata from README and GitHub sources,
and provide more user feedback, suggestions, and messaging.
Why codemetar? The ‘Codemeta’ Project defines a ‘JSON-LD’ format for describing software metadata, as detailed at https://codemeta.github.io. This package provides utilities to generate, parse, and modify codemeta.jsonld files automatically for R packages, as well as tools and examples for working with codemeta json-ld more generally.
It has three main goals:
Why bother creating a codemeta.json for your
package? R packages encode lots of metadata in the
DESCRIPTION file, README, and other places,
telling users and developers about the package purpose, authors,
license, dependencies, and other information that facilitates discovery,
adoption, and credit for your software. Unfortunately, because each
software language records this metadata in a different format, that
information is hard for search engines, software repositories, and other
developers to find and integrate.
By generating a codemeta.json file, you turn your
metadata into a format that can easily crosswalk between metadata in
many other software languages. CodeMeta is built on schema.org a simple structured
data format developed by major search engines like Google and Bing
to improve discoverability in search. CodeMeta is also understood by
significant software archiving efforts such as Software Heritage Project,
which seeks to permanently archive all open source software.
For more general information about the CodeMeta Project for defining software metadata, see https://codemeta.github.io. In particular, new users might want to start with the User Guide, while those looking to learn more about JSON-LD and consuming existing codemeta files should see the Developer Guide.
codemetar can take the path to the source package root
to glean as much information as possible.
codemetar::write_codemeta()… Getting CRAN metadata from RStudio CRAN mirror
✓ Got CRAN metadata!
… Asking README URL from GitHub API
✓ Got README URL!
… Asking README URL from GitHub API
✓ Got README URL!
… Getting repo topics from GitHub API
✓ Got repo topics!library("magrittr")
"../../codemeta.json" %>%
details::details(summary = "codemetar's codemeta.json",
lang = "json"){
"@context": "https://doi.org/10.5063/schema/codemeta-2.0",
"@type": "SoftwareSourceCode",
"identifier": "codemetar",
"description": "The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides utilities to generate, parse, and modify 'codemeta.json' files automatically for R packages, as well as tools and examples for working with 'codemeta.json' 'JSON-LD' more generally.",
"name": "codemetar: Generate 'CodeMeta' Metadata for R Packages",
"relatedLink": ["https://docs.ropensci.org/codemetar/", "https://CRAN.R-project.org/package=codemetar"],
"codeRepository": "https://github.com/ropensci/codemetar",
"issueTracker": "https://github.com/ropensci/codemetar/issues",
"license": "https://spdx.org/licenses/GPL-3.0",
"version": "0.3.3",
"programmingLanguage": {
"@type": "ComputerLanguage",
"name": "R",
"url": "https://r-project.org"
},
"runtimePlatform": "R version 4.1.0 (2021-05-18)",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"author": [
{
"@type": "Person",
"givenName": "Carl",
"familyName": "Boettiger",
"email": "cboettig@gmail.com",
"@id": "https://orcid.org/0000-0002-1642-628X"
},
{
"@type": "Person",
"givenName": "Maëlle",
"familyName": "Salmon",
"@id": "https://orcid.org/0000-0002-2815-0399"
}
],
"contributor": [
{
"@type": "Person",
"givenName": "Anna",
"familyName": "Krystalli",
"@id": "https://orcid.org/0000-0002-2378-4915"
},
{
"@type": "Person",
"givenName": "Maëlle",
"familyName": "Salmon",
"@id": "https://orcid.org/0000-0002-2815-0399"
},
{
"@type": "Person",
"givenName": "Katrin",
"familyName": "Leinweber",
"@id": "https://orcid.org/0000-0001-5135-5758"
},
{
"@type": "Person",
"givenName": "Noam",
"familyName": "Ross",
"@id": "https://orcid.org/0000-0002-2136-0000"
},
{
"@type": "Person",
"givenName": "Arfon",
"familyName": "Smith"
},
{
"@type": "Person",
"givenName": "Jeroen",
"familyName": "Ooms",
"@id": "https://orcid.org/0000-0002-4035-0289"
},
{
"@type": "Person",
"givenName": "Sebastian",
"familyName": "Meyer",
"@id": "https://orcid.org/0000-0002-1791-9449"
},
{
"@type": "Person",
"givenName": "Michael",
"familyName": "Rustler",
"@id": "https://orcid.org/0000-0003-0647-7726"
},
{
"@type": "Person",
"givenName": "Hauke",
"familyName": "Sonnenberg",
"@id": "https://orcid.org/0000-0001-9134-2871"
},
{
"@type": "Person",
"givenName": "Sebastian",
"familyName": "Kreutzer",
"@id": "https://orcid.org/0000-0002-0734-2199"
},
{
"@type": "Person",
"givenName": "Thierry",
"familyName": "Onkelinx",
"@id": "https://orcid.org/0000-0001-8804-4216"
}
],
"copyrightHolder": [
{
"@type": "Person",
"givenName": "Carl",
"familyName": "Boettiger",
"email": "cboettig@gmail.com",
"@id": "https://orcid.org/0000-0002-1642-628X"
}
],
"funder": [
{
"@type": "Organization",
"name": "rOpenSci"
}
],
"maintainer": [
{
"@type": "Person",
"givenName": "Carl",
"familyName": "Boettiger",
"email": "cboettig@gmail.com",
"@id": "https://orcid.org/0000-0002-1642-628X"
}
],
"softwareSuggestions": [
{
"@type": "SoftwareApplication",
"identifier": "withr",
"name": "withr",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=withr"
},
{
"@type": "SoftwareApplication",
"identifier": "covr",
"name": "covr",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=covr"
},
{
"@type": "SoftwareApplication",
"identifier": "details",
"name": "details",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=details"
},
{
"@type": "SoftwareApplication",
"identifier": "dplyr",
"name": "dplyr",
"version": ">= 0.7.0",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=dplyr"
},
{
"@type": "SoftwareApplication",
"identifier": "jsonld",
"name": "jsonld",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=jsonld"
},
{
"@type": "SoftwareApplication",
"identifier": "jsonvalidate",
"name": "jsonvalidate",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=jsonvalidate"
},
{
"@type": "SoftwareApplication",
"identifier": "knitr",
"name": "knitr",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=knitr"
},
{
"@type": "SoftwareApplication",
"identifier": "printr",
"name": "printr",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=printr"
},
{
"@type": "SoftwareApplication",
"identifier": "rmarkdown",
"name": "rmarkdown",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=rmarkdown"
},
{
"@type": "SoftwareApplication",
"identifier": "testthat",
"name": "testthat",
"version": ">= 3.0.0",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=testthat"
},
{
"@type": "SoftwareApplication",
"identifier": "usethis",
"name": "usethis",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=usethis"
}
],
"softwareRequirements": {
"1": {
"@type": "SoftwareApplication",
"identifier": "R",
"name": "R",
"version": ">= 3.2.0"
},
"2": {
"@type": "SoftwareApplication",
"identifier": "commonmark",
"name": "commonmark",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=commonmark"
},
"3": {
"@type": "SoftwareApplication",
"identifier": "crul",
"name": "crul",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=crul"
},
"4": {
"@type": "SoftwareApplication",
"identifier": "desc",
"name": "desc",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=desc"
},
"5": {
"@type": "SoftwareApplication",
"identifier": "gert",
"name": "gert",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=gert"
},
"6": {
"@type": "SoftwareApplication",
"identifier": "gh",
"name": "gh",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=gh"
},
"7": {
"@type": "SoftwareApplication",
"identifier": "jsonlite",
"name": "jsonlite",
"version": ">= 1.6",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=jsonlite"
},
"8": {
"@type": "SoftwareApplication",
"identifier": "magrittr",
"name": "magrittr",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=magrittr"
},
"9": {
"@type": "SoftwareApplication",
"identifier": "memoise",
"name": "memoise",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=memoise"
},
"10": {
"@type": "SoftwareApplication",
"identifier": "methods",
"name": "methods"
},
"11": {
"@type": "SoftwareApplication",
"identifier": "pingr",
"name": "pingr",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=pingr"
},
"12": {
"@type": "SoftwareApplication",
"identifier": "purrr",
"name": "purrr",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=purrr"
},
"13": {
"@type": "SoftwareApplication",
"identifier": "remotes",
"name": "remotes",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=remotes"
},
"14": {
"@type": "SoftwareApplication",
"identifier": "sessioninfo",
"name": "sessioninfo",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=sessioninfo"
},
"15": {
"@type": "SoftwareApplication",
"identifier": "stats",
"name": "stats"
},
"16": {
"@type": "SoftwareApplication",
"identifier": "urltools",
"name": "urltools",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=urltools"
},
"17": {
"@type": "SoftwareApplication",
"identifier": "xml2",
"name": "xml2",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=xml2"
},
"18": {
"@type": "SoftwareApplication",
"identifier": "cli",
"name": "cli",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=cli"
},
"19": {
"@type": "SoftwareApplication",
"identifier": "codemeta",
"name": "codemeta",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=codemeta"
},
"SystemRequirements": null
},
"isPartOf": "https://ropensci.org",
"keywords": ["metadata", "codemeta", "ropensci", "citation", "credit", "linked-data", "json-ld", "r", "rstats", "r-package", "peer-reviewed"],
"fileSize": "NAKB",
"releaseNotes": "https://github.com/ropensci/codemetar/blob/master/NEWS.md",
"readme": "https://github.com/ropensci/codemetar/blob/master/README.md",
"contIntegration": ["https://github.com/ropensci/codemetar/actions", "https://codecov.io/github/ropensci/codemetar?branch=master"],
"developmentStatus": "https://www.repostatus.org/",
"review": {
"@type": "Review",
"url": "https://github.com/ropensci/software-review/issues/130",
"provider": "https://ropensci.org"
}
}By default most often from within your package folder you’ll simply
run codemetar::write_codemeta().
How to keep codemeta.json up-to-date? In particular,
how to keep it up to date with DESCRIPTION?
codemetar itself no longer supports automatic sync, but
there are quite a few methods available out there. Choose one that fits
well into your workflow!
You could rely on devtools::release() since it will
ask you whether you updated codemeta.json when such a file
exists.
You could use a git pre-commit hook that prevents a commit from being done if DESCRIPTION is newer than codemeta.json.
You can use the precommit package in which there’s a “codemeta-description-updated” hook.
If that’s your only pre-commit hook (i.e. you don’t have one
created by e.g. usethis::use_readme_rmd()), then you can
create it using
script = readLines(system.file("templates", "description-codemetajson-pre-commit.sh", package = "codemetar"))
usethis::use_git_hook("pre-commit",
script = script)system.file("templates", "codemeta-github-actions.yml", package = "codemetar")).
You can use the cm-skip keyword in your commit message if
you don’t want this to run on a specific commit. The example workflow
provided is setup to only run when a push is made to the master branch.
This setup is designed for if you’re using a git
flow setup where the master branch is only committed and pushed to
via pull requests. After each PR merge (and the completion of this
GitHub action), your master branch will always be up to date and so long
as you don’t make manual changes to the codemeta.json file, you won’t
have merge conflicts.Alternatively, you can have GitHub actions route run
codemetar on each commit. If you do this you should try to
remember to run git pull before making any new changes on
your local project. However, if you forgot to pull and already committed
new changes, fret not, you can use (git pull --rebase)
to rewind you local changes on top of the current upstream
HEAD.
on:
push:
branches: master
paths:
- DESCRIPTION
- .github/workflows/main.yml
name: Render codemeta
jobs:
render:
name: Render codemeta
runs-on: macOS-latest
if: "!contains(github.event.head_commit.message, 'cm-skip')"
steps:
- uses: actions/checkout@v1
- uses: r-lib/actions/setup-r@v1
- name: Install codemetar
run: Rscript -e 'install.packages("codemetar")'
- name: Render codemeta
run: Rscript -e 'codemetar::write_codemeta()'
- name: Commit results
run: |
git commit codemeta.json -m 'Re-build codemeta.json' || echo "No changes to commit"
git push https://${{github.actor}}:${{secrets.GITHUB_TOKEN}}@github.com/${{github.repository}}.git HEAD:${{ github.ref }} || echo "No changes to commit"The best way to ensure codemeta.json is as complete as
possible is to set metadata in all the usual places, and then if needed
add more metadata.
To ensure you have metadata in the usual places, you can run
codemetar::give_opinions().
Fill BugReports and URL.
Using the Authors@R notation allows a much richer
specification of author roles, correct parsing of given vs family names,
and email addresses.
In the current implementation, developers may specify an ORCID url
for an author in the optional comment field of
Authors@R, e.g.
Authors@R: c(person(given = "Carl",
family = "Boettiger",
role = c("aut", "cre", "cph"),
email = "cboettig@gmail.com",
comment = c(ORCID = "0000-0002-1642-628X")))which will allow codemetar to associate an identifier
with the person. This is clearly something of a hack since R’s
person object lacks an explicit notion of id,
and may be frowned upon.
In the README, you can use badges for continuous integration, repo development status (repostatus.org or lifecycle.org), provider (e.g. for CRAN).
If your package source is hosted on GitHub and there’s a way for codemetar to determine that (URL in DESCRIPTION, or git remote URL) codemetar will use GitHub repo topics as keywords in codemeta.json. If you also set keywords in DESCRIPTION (see next section), codemetar will merge the two lists.
In general, setting metadata via the places stated earlier is the best solution because that metadata is used by other tools (e.g. the URLs in DESCRIPTION can help the package users, not only codemetar).
The DESCRIPTION file is the natural place to specify any metadata for
an R package. The codemetar package can detect certain
additional terms in the CodeMeta context. Almost
any additional codemeta field can be added to and read from the
DESCRIPTION into a codemeta.json file (see
codemetar:::additional_codemeta_terms for a list).
CRAN requires that you prefix any additional such terms to indicate
the use of schema.org explicitly,
e.g. keywords would be specified in a DESCRIPTION file
as:
X-schema.org-keywords: metadata, codemeta, ropensci, citation, credit, linked-dataWhere applicable, these will override values otherwise guessed from the source repository. Use comma-separated lists to separate multiple values to a property, e.g. keywords.
See the DESCRIPTION
file of the codemetar package for an example.
There are a number of places that codemetar will reference a github
branch if your code is hosted on github (e.g. for release notes, readme,
etc.). By default, codemetar will use the name “master” but you can
change that to whatever your default branch is by setting the option
“codemeta_branch” (e.g. options(codemeta_branch = "main")
before calling write_codemeta() to use the branch named
“main” as the default branch).
You can install the latest version from CRAN using:
install.packages("codemetar")You can also install the development version of
codemetar from GitHub with:
# install.packages("devtools")
devtools::install_github("ropensci/codemetar")For optimal results you need a good internet connection.
The package queries
utils::available.packages() for CRAN and
Bioconductor packages;
GitHub API via the gh package, if it
finds a GitHub repo URL in DESCRIPTION or as git remote. GitHub API is
queried to find the preferred
README, and the repo
topics. If you use codemetar for many packages having a GITHUB_PAT
is better;
R-hub sysreqs API to parse SystemRequirements.
If your machine is offline, a more minimal codemeta.json will be created. If your internet connection is poor or there are firewalls, the codemeta creation might indefinitely hang.
Check out all the codemetar man for tutorials on other cool stuff you can do with codemeta and json-ld.
A new feature is the creation of a minimal schemaorg.json for
insertion on your website’s webpage for Search Engine Optimization, when
the write_minimeta argument of
write_codemeta() is TRUE.
You could e.g. use the code below in a chunk in README.Rmd with
results="asis".
glue::glue('<script type="application/ld+json">
{glue::glue_collapse(readLines("schemaorg.json"), sep = "\n")}
</script>')Refer to Google documentation for more guidance.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.