README.Rmd

---
output: github_document
bibliography: inst/REFERENCES.bib
link-citations: yes
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# cffr <a href='https://docs.ropensci.org/cffr/'><img src="man/figures/logo.png" align="right" height="139"/></a>

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**cffr** provides utilities to generate, parse, modify and validate
`CITATION.cff` files automatically for **R** packages, as well as tools and
examples for working with .cff more generally.

## What is a `CITATION.cff` file?

[Citation File Format (CFF](https://citation-file-format.github.io/))
[@druskat_citation_2021] (v1.2.0) are plain text files with human- and
machine-readable citation information for software (and datasets). Code
developers can include them in their repositories to let others know how to
correctly cite their software.

This format is becoming popular within the software citation ecosystem. Recently
[GitHub](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files),
[Zenodo](https://twitter.com/ZENODO_ORG/status/1420357001490706442) and
[Zotero](https://twitter.com/zotero/status/1420515377390530560) have included
full support of this citation format [@druskat_stephan_making_2021]. GitHub
support is of special interest:

```{r echo=FALSE, out.width="400", fig.align='center', fig.alt="GitHub-link"}
knitr::include_graphics("vignettes/tweet-1.png")
```

*--- Nat Friedman (\@natfriedman) [July 27,
2021](https://twitter.com/natfriedman/status/1420122675813441540?ref_src=twsrc%5Etfw)*

See [Enhanced support for citations on
GitHub](https://github.blog/2021-08-19-enhanced-support-citations-github/)
[@smith2021] for more info.

### Related projects

[The CodeMeta Project](https://codemeta.github.io/) [@jones2017] creates a
concept vocabulary that can be used to standardize the exchange of software
metadata across repositories and organizations. One of the many uses of a
`codemeta.json` file (created following the standards defined on The CodeMeta
Project) is to provide citation metadata such as title, authors, publication
year, and venue [@fenner2021]. The packages
[**codemeta**](https://github.com/cboettig/codemeta)/
[**codemetar**](https://github.com/ropensci/codemetar) allows to generate
`codemeta.json` files from R packages metadata.

## The cffr package

**cffr** maximizes the data extraction by using both the `DESCRIPTION` file and
the `CITATION` file (if present) of your package. Note that **cffr** works best
if your package pass 
`R CMD check/devtools::check()`.

```{r count_cffr, echo=FALSE, results='asis'}
cat("\n")
today <- Sys.Date()
# Try get the count of GitHub repos here
token <- (Sys.getenv(c("GITHUB_PAT", "GITHUB_TOKEN")))
token <- token[!token %in% c(NA, NULL, "")][1]
ghtoken <- paste("token", token)
tmpfile <- tempfile(fileext = ".json")
# Get numbers of repos
api_url <- "https://api.github.com/search/code?q=cffr+extension:cff+filename:CITATION"
res <- tryCatch(download.file(api_url,
  tmpfile,
  quiet = TRUE,
  headers = c(Authorization = ghtoken)
),
warning = function(e) {
  return(TRUE)
},
error = function(e) {
  return(TRUE)
}
)
# If not successful
if (isTRUE(res)) {
  cat(paste0(
    "\n", "See [some projects already using **cffr**]",
    "(https://github.com/search?l=&o=desc&q=cffr+extension%3Acff+filename%3ACITATION&s=indexed&type=Code)",
    "."
  ))
} else {
  nreps <- as.integer(jsonlite::read_json(tmpfile)$total_count)
  cat(paste0(
    "As per ", today, " there are at least ", nreps, " repos on GitHub using **cffr**. ",
    "[Check them out here]",
    "(https://github.com/search?l=&o=desc&q=cffr+extension%3Acff+filename%3ACITATION&s=indexed&type=Code)."
  ))
}
cat("\n")
```

### Installation

Install **cffr** from [CRAN](https://CRAN.R-project.org/package=cffr):

```{r, eval=FALSE}
install.packages("cffr")
```

You can install the developing version of **cffr** with:

```{r, eval=FALSE}
devtools::install_github("ropensci/cffr")
```

Alternatively, you can install **cffr** using the
[r-universe](https://ropensci.r-universe.dev/ui#builds):

```{r, eval=FALSE}

# Enable this universe
options(repos = c(
  ropensci = "https://ropensci.r-universe.dev",
  CRAN = "https://cloud.r-project.org"
))

# Install some packages
install.packages("cffr")
```

### Example

By default most often from within your package folder you'll simply run
`cff_write()`, that creates a `cff` object, write it on a `CITATION.cff` file
and validates it on a single command:

```{r, eval=FALSE}

library(cffr)

# For in-development packages
cff_write()
#>
#> CITATION.cff generated
#>
#> cff_validate results-----
#> Congratulations! This .cff file is valid
```

However, **cffr** provides also custom print methods and mechanisms that allows
you to customize the `CITATION.cff` and integrate them in your workflows.

This is a basic example which shows you how to create a `cff` object (see `?cff`
for more info). In this case, we are creating a `cff` object from the metadata
of the **rmarkdown** package:

```{r }
library(cffr)

# Example with an installed package
test <- cff_create("rmarkdown")
```

<details>
<summary><code>CITATION.cff</code> for <strong>rmarkdown</strong>
</summary>

```{r, echo=FALSE, comment=""}

test
```

</details>

<p>

We can validate the result using `cff_validate()`:

```{r }

cff_validate(test)
```

Check the [docs](https://docs.ropensci.org/cffr/reference/index.html) and
`vignette("cffr", package = "cffr")` to learn how to work with `cff` objects.

### Keep your `CITATION.cff` file up-to-date

#### GitHub Actions

The easiest way for keeping you `CITATION.cff` file up-to-date is using GitHub
Actions. Use `cff_gha_update()`function to install a GitHub Action that would
update your `CITATION.cff` file on the following events:

-   When you publish a new release of the package on your GitHub repo.
-   Each time that you modify your DESCRIPTION or inst/CITATION files.
-   The action can be run also manually.

```{r, eval=FALSE}
cff_gha_update()

#> Installing update-citation-cff.yaml on './.github/workflows'
#> Adding .github to .Rbuildignore
```

See the example workflow file
[here](https://github.com/ropensci/cffr/blob/main/.github/workflows/update-citation-cff.yaml).

#### Git pre-commit hook [![Experimental](https://lifecycle.r-lib.org/articles/figures/lifecycle-experimental.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)

You can also use a [git pre-commit
hook](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks#_committing_workflow_hooks):

> The `pre-commit` hook is run first, before you even type in a commit message.
> It's used to inspect the snapshot that's about to be committed, to see if
> you've forgotten something, to make sure tests run, or to examine whatever you
> need to inspect in the code. Exiting non-zero from this hook aborts the
> commit, although you can bypass it with `git commit --no-verify`.

A specific pre-commit hook can be installed with `cff_git_hook_install()`. If
you want to use a pre-commit hook, please make sure you have the **testthat**
package installed.

### Learn more

Check the following articles to learn more about **cffr**:

-   [cffr: Create a CITATION.cff File for your R
    Package](https://ropensci.org/blog/2021/11/23/cffr/)
-   [How I Test cffr on (about) 2,000 Packages using GitHub Actions and
    R-universe](https://ropensci.org/blog/2021/11/23/how-i-test-cffr/)

## Related packages

-   [**citation**](https://github.com/pik-piam/citation/): The development
    version (at the time of this writing) includes a new function `r2cff` that
    creates a `CITATION.cff` file (v1.1.0) using the information of your
    `DESCRIPTION` file. It also provide minimal validity checks.
-   [**handlr**](https://github.com/ropensci/handlr): Tool for converting among
    citation formats, including `*.cff` files. At the time of this writing only
    CFF v1.1.0 was supported (see
    [#24](https://github.com/ropensci/handlr/issues/24)).
-   [**codemeta**](https://github.com/cboettig/codemeta)/
    [**codemetar**](https://github.com/ropensci/codemetar) provides similar
    solutions for creating `codemeta.json` file, another format for storing and
    sharing software metadata.

## Citation

```{r echo=FALSE, results='asis'}
print(citation("cffr")[1], bibtex = FALSE)
```

A BibTeX entry for LaTeX users is

```{r echo=FALSE, comment=''}
toBibtex(citation("cffr")[1])
```

You can also use the [citation provided by
GitHub](https://github.com/ropensci/cffr), that is generated from the
information of a `CITATION.cff` created with **cffr**. See [About CITATION
files](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files)
for more info.

## References

::: {#refs}
:::

[![rofooter](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)