From d568801d39651419287eb2b3d268c22b8514acd3 Mon Sep 17 00:00:00 2001 From: Diego H Date: Tue, 13 Feb 2024 12:28:21 +0100 Subject: [PATCH] Overhaul of cff-bibtex conversion system (#63) * Start review of article * Update bibtex to cff * Prepare crosswalk * Update vignette * Finish tables * Finish article * Try new test suite * Full results * New testing process in GHA * Finish test new * Ready to merge * Roll back action * Go! --- .github/workflows/test-ci.yaml | 23 +- CITATION.cff | 12 +- DESCRIPTION | 3 +- NAMESPACE | 1 + NEWS.md | 14 + R/assertions.R | 14 +- R/cff-class.R | 12 + R/cff_create.R | 6 +- R/cff_gha_update.R | 3 +- R/cff_git_hook.R | 3 +- R/cff_parse_citation.R | 239 ++- R/cff_parse_person.R | 16 +- R/cff_read.R | 4 +- R/{cff_to_bibtex.R => cff_to_bibentry.R} | 70 +- R/cff_validate.R | 2 +- R/cff_write.R | 4 +- R/deprecated.R | 32 + R/parse_citation.R | 2 +- R/parse_description.R | 8 +- R/utils.R | 6 +- R/write_bib.R | 2 +- R/write_citation.R | 8 +- README.Rmd | 5 +- README.md | 51 +- codemeta.json | 8 +- data-raw/crosswalk_tables.R | 17 + data-raw/crosswalk_tables.xlsx | Bin 0 -> 16689 bytes data/cran_to_spdx.rda | Bin 916 -> 916 bytes inst/WORDLIST | 15 +- .../DESCRIPTION_posit_package_manager | 31 + inst/examples/DESCRIPTION_r_universe | 19 +- inst/extdata/bibtex_field_entry.csv | 26 - inst/extdata/crosswalk_tables.csv | 248 +++ inst/schemaorg.json | 4 +- man/cff-class.Rd | 9 + man/cff_from_bibtex.Rd | 2 +- man/{cff_to_bibtex.Rd => cff_to_bibentry.Rd} | 25 +- man/encoded_utf_to_latex.Rd | 2 +- man/figures/lifecycle-archived.svg | 21 + man/figures/lifecycle-defunct.svg | 21 + man/figures/lifecycle-deprecated.svg | 21 + man/figures/lifecycle-experimental.svg | 22 +- man/figures/lifecycle-maturing.svg | 21 + man/figures/lifecycle-questioning.svg | 21 + man/figures/lifecycle-soft-deprecated.svg | 21 + man/figures/lifecycle-stable.svg | 29 + man/figures/lifecycle-superseded.svg | 21 + man/figures/logo.png | Bin 44443 -> 16971 bytes man/previous_cff_to_bib.Rd | 48 + man/write_bib.Rd | 4 +- man/write_citation.Rd | 8 +- pkgdown/favicon/apple-touch-icon-180x180.png | Bin 9124 -> 9121 bytes pkgdown/favicon/apple-touch-icon-60x60.png | Bin 2528 -> 2504 bytes pkgdown/favicon/apple-touch-icon-76x76.png | Bin 3154 -> 3123 bytes pkgdown/favicon/apple-touch-icon.png | Bin 9124 -> 9121 bytes pkgdown/favicon/favicon-32x32.png | Bin 1581 -> 1578 bytes tests/testthat.R | 4 +- tests/testthat/_snaps/bibtex-check-ruby.md | 3 - tests/testthat/_snaps/bibtex2cff.md | 81 +- tests/testthat/_snaps/cff_description.md | 35 +- tests/testthat/_snaps/cff_parse_citation.md | 2 +- .../{cff_to_bibtex.md => cff_to_bibentry.md} | 3 +- tests/testthat/_snaps/deprecated.md | 9 + tests/testthat/_snaps/merge_desc_cit.md | 66 +- tests/testthat/test-assertions.R | 46 +- tests/testthat/test-bibtex-check-ruby.R | 33 +- tests/testthat/test-bibtex2cff.R | 153 +- tests/testthat/test-cff_description.R | 20 + tests/testthat/test-cff_parse_person.R | 5 + tests/testthat/test-cff_read.R | 10 +- ...cff_to_bibtex.R => test-cff_to_bibentry.R} | 66 +- tests/testthat/test-deprecated.R | 8 + tests/testthat/test-utils.R | 17 + tests/testthat/test_ci/.gitignore | 1 + tests/testthat/test_ci/README.md | 16 +- tests/testthat/test_ci/test-full_cff.R | 186 +- tests/testthat/test_ci/test-new.R | 149 ++ vignettes/REFERENCES.bib | 21 + vignettes/bibtex_cff.Rmd | 1531 +++++++++-------- vignettes/cffr.Rmd | 2 +- vignettes/crosswalk.Rmd | 2 +- 81 files changed, 2419 insertions(+), 1254 deletions(-) create mode 100644 R/cff-class.R rename R/{cff_to_bibtex.R => cff_to_bibentry.R} (89%) create mode 100644 R/deprecated.R create mode 100644 data-raw/crosswalk_tables.R create mode 100644 data-raw/crosswalk_tables.xlsx create mode 100644 inst/examples/DESCRIPTION_posit_package_manager delete mode 100644 inst/extdata/bibtex_field_entry.csv create mode 100644 inst/extdata/crosswalk_tables.csv create mode 100644 man/cff-class.Rd rename man/{cff_to_bibtex.Rd => cff_to_bibentry.Rd} (78%) create mode 100644 man/figures/lifecycle-archived.svg create mode 100644 man/figures/lifecycle-defunct.svg create mode 100644 man/figures/lifecycle-deprecated.svg create mode 100644 man/figures/lifecycle-maturing.svg create mode 100644 man/figures/lifecycle-questioning.svg create mode 100644 man/figures/lifecycle-soft-deprecated.svg create mode 100644 man/figures/lifecycle-stable.svg create mode 100644 man/figures/lifecycle-superseded.svg create mode 100644 man/previous_cff_to_bib.Rd rename tests/testthat/_snaps/{cff_to_bibtex.md => cff_to_bibentry.md} (99%) create mode 100644 tests/testthat/_snaps/deprecated.md rename tests/testthat/{test-cff_to_bibtex.R => test-cff_to_bibentry.R} (88%) create mode 100644 tests/testthat/test-deprecated.R create mode 100644 tests/testthat/test_ci/test-new.R diff --git a/.github/workflows/test-ci.yaml b/.github/workflows/test-ci.yaml index 7ec4d6a1..881ef265 100644 --- a/.github/workflows/test-ci.yaml +++ b/.github/workflows/test-ci.yaml @@ -92,37 +92,34 @@ jobs: # Check packages not installed yet instpack <- as.character(installed.packages()[, "Package"]) - toinstall <- setdiff(all, instpack) + toinstall_init <- setdiff(all, instpack) # Install options(repos = c( ropensci = "https://ropensci.r-universe.dev", ropenscireviewtools = "https://ropensci-review-tools.r-universe.dev", - RSPM = "https://packagemanager.rstudio.com/all/latest", + RSPM = "https://packagemanager.posit.co/cran/latest", CRAN = "https://cloud.r-project.org" )) - message("Installing ", length(toinstall)," packages: ", paste0(toinstall, collapse = ",")) + # Check packages available + pakav <- as.data.frame(available.packages(repos = getOption("repos"))) + toinstall <- toinstall_init[toinstall_init %in% pakav$Package] + message("Installing ", length(toinstall)," packages") install.packages(toinstall, - dependencies = TRUE, - verbose = TRUE, quiet = TRUE + dependencies = TRUE, verbose = TRUE, + quiet = TRUE, type = "binary" ) - # Update binary - # update.packages(type = "binary") - shell: Rscript {0} - name: Test GHA run: | - # Load package - devtools::load_all() - # Run the tests - testthat::test_dir("tests/testthat/test_ci") + source("tests/testthat/test_ci/test-new.R") shell: Rscript {0} @@ -131,5 +128,5 @@ jobs: shell: bash run: | # OK :) - cat ./tests/testthat/test_ci/_snaps/full_cff.md >$GITHUB_STEP_SUMMARY + cat ./tests/testthat/test_ci/results.md >$GITHUB_STEP_SUMMARY diff --git a/CITATION.cff b/CITATION.cff index c7d66878..ae2c7213 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,5 +1,5 @@ # ----------------------------------------------------------- -# CITATION file created with {cffr} R package, v0.5.0 +# CITATION file created with {cffr} R package, v0.5.0.9000 # See also: https://docs.ropensci.org/cffr/ # ----------------------------------------------------------- @@ -8,7 +8,7 @@ message: 'To cite package "cffr" in publications use:' type: software license: GPL-3.0-or-later title: 'cffr: Generate Citation File Format (''cff'') Metadata for R Packages' -version: 0.5.0 +version: 0.5.0.9000 doi: 10.21105/joss.03900 abstract: The Citation File Format version 1.2.0 is a human and machine readable file format which provides citation metadata for software. @@ -92,11 +92,10 @@ references: url: https://www.R-project.org/ authors: - name: R Core Team - location: - name: Vienna, Austria - year: '2024' institution: name: R Foundation for Statistical Computing + address: Vienna, Austria + year: '2024' version: '>= 3.6.0' - type: software title: cli @@ -139,9 +138,6 @@ references: email: jeroen@berkeley.edu orcid: https://orcid.org/0000-0002-4035-0289 year: '2024' - identifiers: - - type: url - value: https://arxiv.org/abs/1403.2805 version: '>= 1.7.2' - type: software title: jsonvalidate diff --git a/DESCRIPTION b/DESCRIPTION index a1337671..b3eae1d3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: cffr Title: Generate Citation File Format ('cff') Metadata for R Packages -Version: 0.5.0 +Version: 0.5.0.9000 Authors@R: c( person("Diego", "Hernangómez", , "diego.hernangomezherrero@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0001-8457-4658")), @@ -34,6 +34,7 @@ Suggests: VignetteBuilder: knitr Config/testthat/edition: 3 +Config/testthat/parallel: true Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) diff --git a/NAMESPACE b/NAMESPACE index d370f864..16d8f1c6 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -19,6 +19,7 @@ export(cff_schema_definitions_person) export(cff_schema_definitions_refs) export(cff_schema_keys) export(cff_schema_keys_license) +export(cff_to_bibentry) export(cff_to_bibtex) export(cff_validate) export(cff_write) diff --git a/NEWS.md b/NEWS.md index 21bb148f..fe67541a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,17 @@ +# cffr (development version) + +## Major changes in the API + +- The conversion from `cff` to `bibentry` is performed now by a new function + `cff_to_bibentry()`. Previous names of this function were `cff_to_bibtex()` + and `cff_extract_to_bibtex()` that are now superseded. + +## Changes on bibtex crosswalk + +- **\@inbook** and **\@book** gains a new value on [CFF]{.underline} when + **series** is provided: [collection-type: book-series.]{.underline} +- Review and update `vignette("bibtex_cff", package = "cffr")`. + # cffr 0.5.0 ## Lifecycle diff --git a/R/assertions.R b/R/assertions.R index 17ac7038..d703d6f5 100644 --- a/R/assertions.R +++ b/R/assertions.R @@ -1,7 +1,7 @@ #' Check if a string is an email #' @param email The string to be evaluated #' @noRd -is.email <- function(email) { +is_email <- function(email) { if (is.null(email)) { return(FALSE) } @@ -17,7 +17,7 @@ is.email <- function(email) { #' Check if a string is an url #' @param url The url to be evaluated #' @noRd -is.url <- function(url) { +is_url <- function(url) { if (is.null(url)) { return(FALSE) } @@ -31,7 +31,7 @@ is.url <- function(url) { #' @param x string #' @param sub subtring to be evaluated #' @noRd -is.substring <- function(x, sub) { +is_substring <- function(x, sub) { if (is.null(x)) { return(FALSE) } @@ -46,7 +46,7 @@ is.substring <- function(x, sub) { #' Check if a object is cff #' @param x object to be evaluated #' @noRd -is.cff <- function(x) { +is_cff <- function(x) { if (inherits(x, "cff")) { return(TRUE) } else { @@ -57,7 +57,7 @@ is.cff <- function(x) { #' Check if a object is cff file #' @param x object to be evaluated #' @noRd -is.cff_file <- function(x) { +is_cff_file <- function(x) { if (!inherits(x, "character")) { return(FALSE) } @@ -73,7 +73,7 @@ is.cff_file <- function(x) { #' Check if a object is cff #' @param x object to be evaluated #' @noRd -is.github <- function(x) { +is_github <- function(x) { res <- isTRUE(grep( "^http[a-z]://github.com/", x["repository-code"] @@ -86,7 +86,7 @@ is.github <- function(x) { #' @param x file to be evaluated #' @noRd stopifnotcff <- function(x) { - if (is.cff(x)) { + if (is_cff(x)) { return(invisible()) } diff --git a/R/cff-class.R b/R/cff-class.R new file mode 100644 index 00000000..87b0d599 --- /dev/null +++ b/R/cff-class.R @@ -0,0 +1,12 @@ +#' The `cff` class +#' +#' @name cff-class +#' +#' @description +#' TODO +#' +#' @keywords internal +#' +#' +#' +NULL diff --git a/R/cff_create.R b/R/cff_create.R index b11bd6f3..ddb05320 100644 --- a/R/cff_create.R +++ b/R/cff_create.R @@ -117,7 +117,7 @@ cff_create <- function(x, # On missing use package root if (missing(x)) x <- getwd() - if (!is.cff(x) && !is.character(x)) { + if (!is_cff(x) && !is.character(x)) { msg <- "{.arg x} should be a {.cls cff} or {.cls character} object." cli::cli_abort(msg) } @@ -129,7 +129,7 @@ cff_create <- function(x, desc_path <- NULL # Paths - if (is.cff(x)) { + if (is_cff(x)) { # It is already an object cffobj <- x cffobj["cff-version"] <- cff_version @@ -163,7 +163,7 @@ cff_create <- function(x, msg <- paste0( "{.arg x} ({x}) not valid. If it is a package ", "you may need to install it with ", - "{.fun install.packages}" + "{.fn install.packages}" ) cli::cli_abort(msg) } diff --git a/R/cff_gha_update.R b/R/cff_gha_update.R index 00b33f76..5a066074 100644 --- a/R/cff_gha_update.R +++ b/R/cff_gha_update.R @@ -16,7 +16,8 @@ #' @details #' #' Triggers on your action can be modified, see -#' [Events that trigger workflows](https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows). +#' [Events that trigger +#' workflows](https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows). #' #' @examples #' \dontrun{ diff --git a/R/cff_git_hook.R b/R/cff_git_hook.R index 3b675cb4..0c54797b 100644 --- a/R/cff_git_hook.R +++ b/R/cff_git_hook.R @@ -3,7 +3,8 @@ #' @description #' #' Install a -#' [pre-commit hook](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks#_committing_workflow_hooks) +#' [pre-commit +#' hook](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks#_committing_workflow_hooks) #' that remembers you to update your `CITATION.cff` file. #' #' @name cff_git_hook diff --git a/R/cff_parse_citation.R b/R/cff_parse_citation.R index 9001c63f..c7fccc55 100644 --- a/R/cff_parse_citation.R +++ b/R/cff_parse_citation.R @@ -86,11 +86,9 @@ cff_parse_citation <- function(bib) { } # Parse BibTeX entry ---- - parse_cit <- parse_bibtex_entry(bib) ## If no title (case of some Misc) then return null - if (!("title" %in% names(parse_cit))) { entry <- capture.output(print(bib, bibtex = FALSE)) entry <- as.character(entry) @@ -100,29 +98,34 @@ cff_parse_citation <- function(bib) { return(NULL) } - # Parse BibTeX fields ---- parsed_fields <- parse_bibtex_fields(parse_cit) + ## Handle collection types ---- + parsed_fields <- add_bibtex_coltype(parsed_fields) + + ## Add conference + parsed_fields <- add_conference(parsed_fields) + + # Create BibTeX to CFF institution logic ---- + parsed_fields <- parse_bibtex_to_inst(parsed_fields) - # Create BibTeX person models ---- - parsed_fields <- parse_bibtex_person_models(parsed_fields) # Parse persons ---- # Special case: authors # Some keys does not strictly require authors, so we create one for cff - # https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#how-to-deal-with-unknown-individual-authors + # https://github.com/citation-file-format/citation-file-format/blob/main/ + # (cont) schema-guide.md#how-to-deal-with-unknown-individual-authors + if (is.null(parsed_fields$authors)) { parsed_fields$authors <- person(family = "anonymous") } - ## authors ---- parse_all_authors <- drop_null( lapply(parsed_fields$authors, cff_parse_person) ) parsed_fields$authors <- unique(parse_all_authors) - ## other persons---- parse_other_persons <- building_other_persons(parsed_fields) @@ -136,19 +139,8 @@ cff_parse_citation <- function(bib) { # Building blocks---- - # Fallback for year and month: use date-published - - if (is.null(parse_cit$month) && !is.null(parse_cit$`date-published`)) { - parse_cit$month <- format(as.Date(parse_cit$`date-published`), "%m") - } - - - if (is.null(parse_cit$year) && !is.null(parse_cit$`date-published`)) { - parse_cit$year <- format(as.Date(parse_cit$`date-published`), "%Y") - } - - ## month ---- - parse_cit$month <- building_month(parse_cit) + # Fallback for year and month: use date-published ---- + parse_cit <- fallback_dates(parse_cit) ## doi---- bb_doi <- building_doi(parse_cit) @@ -171,8 +163,14 @@ cff_parse_citation <- function(bib) { ) } + ## Add thesis type ---- + parse_cit <- add_thesis(parse_cit) - # Last step: Field models---- + ## Handle location ---- + parse_cit <- add_address(parse_cit) + + + # Last step---- # Initial order but starting with type, title, authors final_order <- unique(c( @@ -183,9 +181,6 @@ cff_parse_citation <- function(bib) { parse_cit <- parse_cit[final_order] - parse_cit <- parse_bibtex_fields_models(parse_cit) - - # Remove non-valid names validnames <- cff_schema_definitions_refs() parse_cit <- parse_cit[names(parse_cit) %in% validnames] @@ -231,6 +226,14 @@ parse_bibtex_entry <- function(bib) { ) + # Check if it an inbook with booktitle (BibLaTeX style) + if (all(init_type == "inbook", "booktitle" %in% names(parse_cit))) { + # Make it incollection + parse_cit$bibtex_entry <- "incollection" + parse_cit$type <- "generic" + } + + return(parse_cit) } @@ -239,7 +242,6 @@ parse_bibtex_entry <- function(bib) { parse_bibtex_fields <- function(parse_cit) { # to lowercase names(parse_cit) <- tolower(names(parse_cit)) - nm <- names(parse_cit) # Standard BibTeX fields: # address annote author booktitle chapter crossref edition editor @@ -250,10 +252,15 @@ parse_bibtex_fields <- function(parse_cit) { # edition journal month publisher title volume year # Mapped: - # author booktitle chapter editor howpublished note number + # author booktitle series chapter editor howpublished note number nm[nm == "author"] <- "authors" + # Make collection title + # booktitle takes precedence over series nm[nm == "booktitle"] <- "collection-title" + if (!"collection-title" %in% nm) { + nm[nm == "series"] <- "collection-title" + } nm[nm == "chapter"] <- "section" nm[nm == "editor"] <- "editors" nm[nm == "howpublished"] <- "medium" @@ -274,8 +281,6 @@ parse_bibtex_fields <- function(parse_cit) { # abstract, doi, isbn, issn, url, version - cff_schema_definitions_refs() - # Keywords may be duplicated, unify if ("keywords" %in% nm) { kwords <- unlist(parse_cit["keywords" == nm]) @@ -284,12 +289,11 @@ parse_bibtex_fields <- function(parse_cit) { parse_cit$keywords <- unique(kwords) } - # Not mapped: # annote crossref key organization series type # - # Fields address, organization, series and type already treated on - # parse_bibtex_for_cff()/main function + # Fields address, organization, series and type are treated on + # main function # key is a special field, treated apart # Fields ignored: annote, crossref @@ -354,76 +358,139 @@ parse_bibtex_fields <- function(parse_cit) { #' Modify mapping of some org. fields on BibTeX to CFF #' @noRd -parse_bibtex_person_models <- function(parsed_fields) { - # Manual - if (parsed_fields$bibtex_entry == "manual") { - parsed_fields$institution <- parsed_fields$organization - } else if (parsed_fields$bibtex_entry %in% c( - "conference", "inproceedings", - "proceedings" - )) { - # Conference, InProceedings, Proceedings - if (!is.null(parsed_fields$series)) { - parsed_fields$conference <- person(family = parsed_fields$series) - } - if (!is.null(parsed_fields$organization)) { - parsed_fields$institution <- person(family = parsed_fields$organization) - } - } else if (parsed_fields$bibtex_entry %in% c("mastersthesis", "phdthesis")) { - # Mastersthesis, PhdThesis - parsed_fields$institution <- person(family = parsed_fields$school) +parse_bibtex_to_inst <- function(parsed_fields) { + # Initial values + bibtex_entry <- parsed_fields$bibtex_entry + to_replace <- switch(bibtex_entry, + "mastersthesis" = "school", + "phdthesis" = "school", + "conference" = "organization", + "inproceedings" = "organization", + "manual" = "organization", + "proceedings" = "organization", + "institution" + ) + + if (to_replace == "institution") { + return(parsed_fields) } + # Rest of cases remove bibtex institution and rename + nms <- names(parsed_fields) + + parsed_fields <- parsed_fields["institution" != nms] + + # Rename + nms2 <- names(parsed_fields) + nms2[nms2 == to_replace] <- "institution" + names(parsed_fields) <- nms2 + + parsed_fields +} + +add_conference <- function(parsed_fields) { + bibtex_entry <- parsed_fields$bibtex_entry + + if (bibtex_entry %in% c("conference", "inproceedings", "proceedings")) { + parsed_fields$conference <- parsed_fields$`collection-title` + } return(parsed_fields) } + + #' Adapt cff keys to bibtex entries #' @noRd -parse_bibtex_fields_models <- function(parse_cit) { - # thesis type ---- - if (parse_cit$bibtex_entry %in% c("phdthesis", "mastersthesis")) { - parse_cit$`thesis-type` <- switch(parse_cit$bibtex_entry, - phdthesis = "PhD Thesis", - "Master's Thesis" - ) +add_thesis <- function(parse_cit) { + bibtex_entry <- parse_cit$bibtex_entry + if (!bibtex_entry %in% c("phdthesis", "mastersthesis")) { + return(parse_cit) } - # address---- - - if (!is.null(parse_cit$location)) { - # Usually the address of the publisher as per BibTeX - if (!is.null(parse_cit$publisher) && - !(parse_cit$bibtex_entry %in% c( - "conference", "inproceedings", - "proceedings" - ))) { - parse_cit$publisher$address <- parse_cit$location$name - parse_cit$location <- NULL - } + parse_cit$`thesis-type` <- switch(bibtex_entry, + phdthesis = "PhD Thesis", + "Master's Thesis" + ) - parse_cit$conference + parse_cit +} - # If this is a conference then add to conference - if (!is.null(parse_cit$conference)) { - parse_cit$conference$address <- parse_cit$location$name - } +add_address <- function(parse_cit) { + loc <- parse_cit$location$name + # If available + if (is.null(loc)) { + return(parse_cit) + } - # If is a report or a thesis, add to institution - if (parse_cit$bibtex_entry %in% c( - "techreport", - "phdthesis", "mastersthesis" - ) && - !is.null(parse_cit$institution)) { - parse_cit$institution$address <- parse_cit$location$name - parse_cit$location <- NULL - } + # At this point is in location, see to move + + # Logic order. + # 1. To conference + # 2. To institution + # 3. To publisher + # Otherwise leave on location + + nms <- names(parse_cit) + has_conf <- "conference" %in% nms + has_inst <- "institution" %in% nms + has_publish <- "publisher" %in% nms + + if (!any(has_conf, has_inst, has_publish)) { + return(parse_cit) + } + + if (has_conf) { + parse_cit$conference$address <- loc + parse_cit$location <- NULL + } else if (has_inst) { + parse_cit$institution$address <- loc + parse_cit$location <- NULL + } else { + parse_cit$publisher$address <- loc + parse_cit$location <- NULL + } + + return(parse_cit) +} + +add_bibtex_coltype <- function(parsed_fields) { + # Add collection-type if applicable and rearrange fields + nms <- names(parsed_fields) + + if (!"collection-title" %in% nms) { + return(parsed_fields) + } + + # Made collection-type if we create collection-title + bibtex_type <- parsed_fields$bibtex_entry + + # Remove `in` at init: inbook, incollection affected + coltype <- clean_str(gsub("^in", "", bibtex_type)) + parsed_fields$`collection-type` <- coltype + + # Rearrange to make both collection keys together + nm_first <- nms[seq(1, match("collection-title", nms))] + + nms_end <- unique(c(nm_first, "collection-type", nms)) + + parsed_fields <- parsed_fields[nms_end] + + return(parsed_fields) +} + +fallback_dates <- function(parse_cit) { + # Fallback for year and month: use date-published + if (is.null(parse_cit$month) && !is.null(parse_cit$`date-published`)) { + parse_cit$month <- format(as.Date(parse_cit$`date-published`), "%m") } - # Book, InBook: collection-title. Use series field - if (parse_cit$bibtex_entry %in% c("book", "inbook")) { - parse_cit$`collection-title` <- clean_str(parse_cit$series) + if (is.null(parse_cit$year) && !is.null(parse_cit$`date-published`)) { + parse_cit$year <- format(as.Date(parse_cit$`date-published`), "%Y") } + ## month ---- + parse_cit$month <- building_month(parse_cit) + return(parse_cit) } diff --git a/R/cff_parse_person.R b/R/cff_parse_person.R index 74b7ba92..a19d87e2 100644 --- a/R/cff_parse_person.R +++ b/R/cff_parse_person.R @@ -60,6 +60,10 @@ cff_parse_person <- function(person) { person <- as.person(person) + if (length(person) == 0) { + return(NULL) + } + if (length(person) > 1) { person <- lapply(person, cff_parse_person) class(person) <- "cff" @@ -68,7 +72,7 @@ cff_parse_person <- function(person) { # Special case for Bioconductor - if (is.substring(person$given, "Bioconductor")) { + if (is_substring(person$given, "Bioconductor")) { person <- person( given = paste( clean_str(person$given), @@ -81,11 +85,9 @@ cff_parse_person <- function(person) { } # Special case for R Core Team - - if (all( - is.substring(clean_str(person$given), "R Core"), - is.substring(person$family, "Team") + is_substring(clean_str(person$given), "R Core"), + is_substring(person$family, "Team") )) { person <- person( given = paste( @@ -112,7 +114,7 @@ cff_parse_person <- function(person) { } # Check if several mails (MomTrunc 6.0) - valid_emails <- unlist(lapply(person$email, is.email)) + valid_emails <- unlist(lapply(person$email, is_email)) email <- person$email[valid_emails][1] parsed_person$email <- clean_str(email) @@ -145,7 +147,7 @@ cff_parse_person <- function(person) { web <- parsed_comments$website if (!is.null(web)) { - parsed_comments$website <- clean_str(web[is.url(web)]) + parsed_comments$website <- clean_str(web[is_url(web)]) } # Add comments diff --git a/R/cff_read.R b/R/cff_read.R index 38ad7880..d2c8433f 100644 --- a/R/cff_read.R +++ b/R/cff_read.R @@ -79,7 +79,7 @@ cff_read <- function(path) { #' @rdname cff_read #' @export cff <- function(path, ...) { - if (!missing(path) && is.cff(path)) { + if (!missing(path) && is_cff(path)) { return(path) } @@ -131,7 +131,7 @@ cff <- function(path, ...) { #' # Nice display thanks to yaml package #' cffobj as.cff <- function(x) { - if (is.cff(x)) { + if (is_cff(x)) { return(x) } diff --git a/R/cff_to_bibtex.R b/R/cff_to_bibentry.R similarity index 89% rename from R/cff_to_bibtex.R rename to R/cff_to_bibentry.R index d4555872..c44fe704 100644 --- a/R/cff_to_bibtex.R +++ b/R/cff_to_bibentry.R @@ -2,12 +2,15 @@ #' #' @description #' -#' This function creates BibTeX entries (in the form of [bibentry()] objects +#' This function creates [bibentry()] objects #' from different metadata sources (`cff` objects, `DESCRIPTION` files, etc.). -#' The function tries to parse the information of the source `x` into a `cff` +#' The function tries to map the information of the source `x` into a `cff` #' object and performs a mapping of the metadata to BibTeX, according to #' `vignette("bibtex_cff", "cffr")`. #' +#' Note that a **R** [bibentry()] object is the representation of a BibTeX +#' entry, see **Examples**. +#' #' #' @references #' - Patashnik, Oren. "BIBTEXTING" February 1988. @@ -18,7 +21,7 @@ #' \doi{10.5281/zenodo.1184077}. #' #' - Hernangómez D (2022). "BibTeX and CFF, a potential crosswalk." -#' *The cffr package, Vignettes* +#' *The cffr package, Vignettes*. \doi{10.21105/joss.03900}, #' . #' #' @param x The source that would be used for generating @@ -42,8 +45,8 @@ #' be parsed to BibTeX using [toBibtex()] #' #' @export -#' @name cff_to_bibtex -#' @rdname cff_to_bibtex +#' @name cff_to_bibentry +#' @rdname cff_to_bibentry #' #' @examples #' \donttest{ @@ -53,7 +56,7 @@ #' cff_object #' #' # bibentry object -#' bib <- cff_to_bibtex(cff_object) +#' bib <- cff_to_bibentry(cff_object) #' #' class(bib) #' @@ -66,13 +69,13 @@ #' # From a CITATION.cff file with options #' #' path <- system.file("examples/CITATION_complete.cff", package = "cffr") -#' cff_file <- cff_to_bibtex(path, what = "all") +#' cff_file <- cff_to_bibentry(path, what = "all") #' #' toBibtex(cff_file) #' #' # For an installed package #' -#' installed_package <- cff_to_bibtex("jsonvalidate") +#' installed_package <- cff_to_bibentry("jsonvalidate") #' #' toBibtex(installed_package) #' @@ -80,22 +83,22 @@ #' # Use a DESCRIPTION file #' #' path2 <- system.file("examples/DESCRIPTION_gitlab", package = "cffr") -#' desc_file <- cff_to_bibtex(path2) +#' desc_file <- cff_to_bibentry(path2) #' #' toBibtex(desc_file) #' } -cff_to_bibtex <- function(x, - what = c("preferred", "references", "all")) { +cff_to_bibentry <- function(x, + what = c("preferred", "references", "all")) { what <- match.arg(what) if (is.null(x)) { return(NULL) } - if (is.cff_file(x)) { + if (is_cff_file(x)) { x <- cff_read(x) } - if (is.cff(x)) { + if (is_cff(x)) { obj <- x } else { obj <- cff_create(x) @@ -125,9 +128,9 @@ cff_to_bibtex <- function(x, } #' @export -#' @rdname cff_to_bibtex +#' @rdname cff_to_bibentry #' @usage NULL -cff_extract_to_bibtex <- cff_to_bibtex +cff_to_bibtex <- cff_to_bibentry cff_bibtex_parser <- function(x) { if (is.null(x)) { @@ -137,11 +140,10 @@ cff_bibtex_parser <- function(x) { stopifnotcff(x) # Read cff of CITATION.cff file - if (!is.cff(x)) { + if (!is_cff(x)) { x <- cff(x) } - # Try to generate preferred if not present if (!("preferred-citation" %in% names(x))) { origtype <- clean_str(x$type) @@ -197,7 +199,7 @@ cff_bibtex_parser <- function(x) { if (all( tobibentry$bibtype == "misc", !is.null(x$`collection-title`), - !is.null(x$publisher) + !is.null(x$publisher), !is.null(x$year) )) { tobibentry$bibtype <- "incollection" } @@ -206,10 +208,10 @@ cff_bibtex_parser <- function(x) { # address---- # BibTeX 'address' is taken from the publisher (book, others) or the # conference (inproceedings). - - if (tobibentry$bibtype %in% c("proceedings", "inproceedings")) { + # Set logic: conference > institution > publisher + if (!is.null(x$conference)) { addr_search <- x$conference - } else if (tobibentry$bibtype == "techreport") { + } else if (!is.null(x$institution)) { addr_search <- x$institution } else { addr_search <- x$publisher @@ -380,6 +382,11 @@ cff_bibtex_parser <- function(x) { # note ---- tobibentry$note <- x$notes + # unpublished needs a note + if (all(is.null(x$notes), tobibentry$bibtype == "unpublished")) { + tobibentry$note <- "Extracted with cffr R package" + } + # number---- @@ -403,18 +410,10 @@ cff_bibtex_parser <- function(x) { # series---- - if (tobibentry$bibtype %in% c( - "book", "inbook" - )) { + if (is.null(tobibentry$booktitle)) { tobibentry$series <- x$`collection-title` } - if (tobibentry$bibtype %in% c( - "proceedings", "inproceedings" - )) { - tobibentry$series <- x$conference$name - } - # title ---- tobibentry$title <- x$title @@ -520,8 +519,17 @@ cff_bibtex_parser <- function(x) { sorted <- unique[unique %in% names(tobibentry)] tobibentry <- tobibentry[sorted] - bib <- do.call(bibentry, tobibentry) + # Shouldn't happen but just in case + # nocov start + if (inherits(bib, "try-error")) { + message <- attributes(bib)$condition$message + cli::cli_alert_danger(paste("Can't convert to {.fn bibentry}: ", message)) + cli::cli_alert_info("Returning {.val NULL}") + return(NULL) + } + # nocov end + return(bib) } diff --git a/R/cff_validate.R b/R/cff_validate.R index 75d9dd9c..ceaa3110 100644 --- a/R/cff_validate.R +++ b/R/cff_validate.R @@ -58,7 +58,7 @@ #' try(cff_validate(system.file("CITATION", package = "cffr"))) cff_validate <- function(x = "CITATION.cff", verbose = TRUE) { # If is a cff create the object - if (is.cff(x)) { + if (is_cff(x)) { tmpfile <- tempfile(fileext = ".cff") suppressMessages(yaml::write_yaml(x, tmpfile)) path <- tmpfile diff --git a/R/cff_write.R b/R/cff_write.R index 031f2580..31865a61 100644 --- a/R/cff_write.R +++ b/R/cff_write.R @@ -84,7 +84,7 @@ cff_write <- function(x, # Fix string if it is not cff - if (!is.substring(outfile, ".cff$")) outfile <- paste0(outfile, ".cff") + if (!is_substring(outfile, ".cff$")) outfile <- paste0(outfile, ".cff") # Check if dir exist and if not create outdir <- dirname(outfile) @@ -122,7 +122,7 @@ cff_write <- function(x, } # Add CITATION.cff to .Rbuildignore - if (!is.cff(x) && x == getwd() && file.exists(".Rbuildignore")) { + if (!is_cff(x) && x == getwd() && file.exists(".Rbuildignore")) { ignore <- readLines(".Rbuildignore") # If not already diff --git a/R/deprecated.R b/R/deprecated.R new file mode 100644 index 00000000..07b26ba9 --- /dev/null +++ b/R/deprecated.R @@ -0,0 +1,32 @@ +#' Previous API: Create BibTeX entries from several sources +#' +#' @description +#' `r lifecycle::badge('superseded')` +#' Please use [cff_to_bibentry()] instead. +#' +#' @rdname previous_cff_to_bib +#' @inheritParams cff_to_bibentry +#' @export +#' @keywords internal +#' +#' @return See [cff_to_bibentry()] +#' @examples +#' \donttest{ +#' # From a cff object +#' cff_object <- cff() +#' +#' cff_object +#' +#' # bibentry object +#' bib <- cff_to_bibentry(cff_object) +#' } +cff_extract_to_bibtex <- function(x, + what = c("preferred", "references", "all")) { + if (requireNamespace("lifecycle", quietly = TRUE)) { + lifecycle::deprecate_soft( + "0.5.0", "cff_extract_to_bibtex()", + "cff_to_bibentry()" + ) + } + cff_to_bibentry(x, what) +} diff --git a/R/parse_citation.R b/R/parse_citation.R index 02bfc071..87d0d65b 100644 --- a/R/parse_citation.R +++ b/R/parse_citation.R @@ -132,7 +132,7 @@ building_url <- function(parse_cit) { allurls <- parse_cit$url } - allurls <- allurls[is.url(allurls)] + allurls <- allurls[is_url(allurls)] # The first url goes to url key url <- unlist(allurls[1]) diff --git a/R/parse_description.R b/R/parse_description.R index 7997e4ae..d26b4e51 100644 --- a/R/parse_description.R +++ b/R/parse_description.R @@ -146,7 +146,7 @@ parse_desc_repository <- function(pkg) { repo <- clean_str(pkg$get("Repository")) # Repo is url - if (is.url(repo)) { + if (is_url(repo)) { return(repo) } @@ -160,7 +160,7 @@ parse_desc_repository <- function(pkg) { # Repo is CRAN # Canonic url to CRAN - if (is.substring(repo, "^CRAN$")) { + if (is_substring(repo, "^CRAN$")) { return( paste0("https://CRAN.R-project.org/package=", name) ) @@ -206,7 +206,7 @@ parse_desc_urls <- function(pkg) { # Join issues and urls allurls <- unique(c(issues, url)) - allurls <- allurls[is.url(allurls)] + allurls <- allurls[is_url(allurls)] @@ -279,7 +279,7 @@ parse_desc_version <- function(pkg) { #' @noRd parse_ghtopics <- function(x) { # Only for GitHub repos - if (!is.github(x)) { + if (!is_github(x)) { return(NULL) } diff --git a/R/utils.R b/R/utils.R index 225a6c6d..2b6e07e4 100644 --- a/R/utils.R +++ b/R/utils.R @@ -91,10 +91,12 @@ search_on_repos <- function(name, detect_repos <- function(repos = getOption("repos")) { # Not use RSPM repos <- repos[names(repos) != "RSPM"] - repos <- repos[!grepl("//rspm", repos)] + repos <- repos[!grepl("rspm", repos)] + repos <- repos[!grepl("posit", repos)] + repos <- repos[!grepl("rstudio", repos)] # If not set use 0-Cloud - if (!is.url(repos["CRAN"])) { + if (!is_url(repos["CRAN"])) { repos["CRAN"] <- "https://cloud.r-project.org/" } diff --git a/R/write_bib.R b/R/write_bib.R index 983d586c..7623cfde 100644 --- a/R/write_bib.R +++ b/R/write_bib.R @@ -3,7 +3,7 @@ #' Creates `a .bib` file from a `bibentry` object(s) #' #' @param x A `bibentry` object created with: -#' - [cff_to_bibtex()] +#' - [cff_to_bibentry()] #' - [citation()] or [bibentry()] #' #' @param file Name of the file. If `NULL` it would display the lines to be diff --git a/R/write_citation.R b/R/write_citation.R index 2ba3239d..36f3f0a4 100644 --- a/R/write_citation.R +++ b/R/write_citation.R @@ -6,9 +6,9 @@ #' CITATION.cff file or `cff` object. #' #' @param x It could be -#' - A `bibentry` object created with [cff_to_bibtex()], [citation()] or +#' - A `bibentry` object created with [cff_to_bibentry()], [citation()] or #' [bibentry()] -#' - Any of the valid inputs of [cff_to_bibtex()]: +#' - Any of the valid inputs of [cff_to_bibentry()]: #' * A missing value. That would retrieve the DESCRIPTION file on your #' in-development package. #' * An existing [`cff`] object, @@ -17,7 +17,7 @@ #' * Path to a DESCRIPTION file (`"*/DESCRIPTION*"`). #' @param file Name of the file to write. #' @inheritParams write_bib -#' @inheritDotParams cff_to_bibtex +#' @inheritDotParams cff_to_bibentry #' #' @export #' @family BibTeX helpers @@ -66,7 +66,7 @@ write_citation <- function(x, verbose = TRUE, ...) { if (!inherits(x, "bibentry")) { - x <- cff_to_bibtex(x, ...) + x <- cff_to_bibentry(x, ...) } bentr <- format(x, style = "R") diff --git a/README.Rmd b/README.Rmd index f6cf504d..09167f48 100644 --- a/README.Rmd +++ b/README.Rmd @@ -15,8 +15,7 @@ knitr::opts_chunk$set( ) ``` -# cffr - +# cffr cffr website [![CRAN-status](https://www.r-pkg.org/badges/version/cffr)](https://CRAN.R-project.org/package=cffr) @@ -197,7 +196,7 @@ We can validate the result using `cff_validate()`: cff_validate(test) ``` -Check the [docs](https://docs.ropensci.org/cffr/reference/index.html) and +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 diff --git a/README.md b/README.md index 7102a86a..b87bcf35 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ -# cffr +# cffr cffr website @@ -72,7 +72,7 @@ file and the `CITATION` file (if present) of your package. Note that **cffr** works best if your package pass `R CMD check/devtools::check()`. -As per 2024-02-06 there are at least 235 repos on GitHub using **cffr**. +As per 2024-02-13 there are at least 235 repos on GitHub using **cffr**. [Check them out here](https://github.com/search?q=cffr%20path%3A**%2FCITATION.cff&type=code). @@ -276,11 +276,10 @@ test <- cff_create("rmarkdown") url: https://www.R-project.org/ authors: - name: R Core Team - location: - name: Vienna, Austria - year: '2024' institution: name: R Foundation for Statistical Computing + address: Vienna, Austria + year: '2024' version: '>= 3.0' - type: software title: bslib @@ -386,9 +385,6 @@ test <- cff_create("rmarkdown") email: jeroen@berkeley.edu orcid: https://orcid.org/0000-0002-4035-0289 year: '2024' - identifiers: - - type: url - value: https://arxiv.org/abs/1403.2805 - type: software title: knitr abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R' @@ -408,11 +404,10 @@ test <- cff_create("rmarkdown") notes: Imports authors: - name: R Core Team - location: - name: Vienna, Austria - year: '2024' institution: name: R Foundation for Statistical Computing + address: Vienna, Austria + year: '2024' - type: software title: stringr abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations' @@ -445,22 +440,20 @@ test <- cff_create("rmarkdown") notes: Imports authors: - name: R Core Team - location: - name: Vienna, Austria - year: '2024' institution: name: R Foundation for Statistical Computing + address: Vienna, Austria + year: '2024' - type: software title: utils abstract: 'R: A Language and Environment for Statistical Computing' notes: Imports authors: - name: R Core Team - location: - name: Vienna, Austria - year: '2024' institution: name: R Foundation for Statistical Computing + address: Vienna, Austria + year: '2024' - type: software title: xfun abstract: 'xfun: Supporting Functions for Packages Maintained by ''Yihui Xie''' @@ -757,18 +750,6 @@ test <- cff_create("rmarkdown") given-names: Davis email: davis@posit.co year: '2024' - - type: software - title: cleanrmd - abstract: 'cleanrmd: Clean Class-Less ''R Markdown'' HTML Documents' - notes: Suggests - url: https://pkg.garrickadenbuie.com/cleanrmd/ - repository: https://CRAN.R-project.org/package=cleanrmd - authors: - - family-names: Aden-Buie - given-names: Garrick - email: garrick@adenbuie.com - orcid: https://orcid.org/0000-0002-7111-0077 - year: '2024' - type: software title: withr abstract: 'withr: Run Code ''With'' Temporarily Modified Global State' @@ -806,7 +787,7 @@ cff_validate(test) #> ✔ Congratulations! This is valid ``` -Check the [docs](https://docs.ropensci.org/cffr/reference/index.html) +Check the [docs](https://docs.ropensci.org/cffr//reference/index.html) and `vignette("cffr", package = "cffr")` to learn how to work with `cff` objects. @@ -907,9 +888,9 @@ for more info.
-Boettiger, Carl, and Maëlle Salmon. 2021a. *codemeta: A Smaller codemetar Package*. +Boettiger, Carl, and Maëlle Salmon. 2021a. +*codemeta: A Smaller +codemetar Package*. .
@@ -930,8 +911,8 @@ Among Citation Formats*.
-Dietrich, Jan Philipp, and Waldir Leoncio. 2022. *citation: Software Citation Tools*. +Dietrich, Jan Philipp, and Waldir Leoncio. 2022. +*citation: Software Citation Tools*.
diff --git a/codemeta.json b/codemeta.json index be76fce2..1551c39b 100644 --- a/codemeta.json +++ b/codemeta.json @@ -8,13 +8,13 @@ "codeRepository": "https://github.com/ropensci/cffr", "issueTracker": "https://github.com/ropensci/cffr/issues", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "0.5.0", + "version": "0.5.0.9000", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", "url": "https://r-project.org" }, - "runtimePlatform": "R version 4.3.2 (2023-10-31)", + "runtimePlatform": "R version 4.3.2 (2023-10-31 ucrt)", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -200,7 +200,7 @@ }, "isPartOf": "https://ropensci.org", "keywords": ["attribution", "citation", "credit", "citation-files", "cff", "metadata", "r", "r-package", "citation-file-format", "rstats", "ropensci", "cran"], - "fileSize": "906.703KB", + "fileSize": "911.371KB", "citation": [ { "@type": "ScholarlyArticle", @@ -286,7 +286,7 @@ "sameAs": "https://doi.org/10.5281/zenodo.5171937" } ], - "releaseNotes": "https://github.com/ropensci/cffr/blob/master/NEWS.md", + "releaseNotes": "https://github.com/ropensci/cffr/blob/main/NEWS.md", "readme": "https://github.com/ropensci/cffr/blob/main/README.md", "contIntegration": ["https://github.com/ropensci/cffr/actions/workflows/check-full.yaml", "https://app.codecov.io/gh/ropensci/cffr", "https://github.com/ropensci/cffr/actions/workflows/cff-validator.yml"], "developmentStatus": ["https://www.repostatus.org/#active", "https://lifecycle.r-lib.org/articles/stages.html#experimental"], diff --git a/data-raw/crosswalk_tables.R b/data-raw/crosswalk_tables.R new file mode 100644 index 00000000..b2199230 --- /dev/null +++ b/data-raw/crosswalk_tables.R @@ -0,0 +1,17 @@ +## code to prepare `crosswalk_tables.csv` +library(tidyverse) +df <- openxlsx::read.xlsx("data-raw/crosswalk_tables.xlsx") + +unlink("/inst/extdata/crosswalk_tables.csv") +lapply(df, trimws) %>% + bind_rows() %>% + setNames(names(df)) %>% + write.csv("./inst/extdata/crosswalk_tables.csv", row.names = FALSE) + +cli::cli_alert_success("Excel updated") + +# +# lapply(df, trimws) %>% +# bind_rows() %>% +# setNames(names(df)) %>% +# openxlsx::write.xlsx("data-raw/crosswalk_tables.xlsx", overwrite = TRUE) diff --git a/data-raw/crosswalk_tables.xlsx b/data-raw/crosswalk_tables.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..4421650879e2ebcc37c4ab5b4098e665c146cd2a GIT binary patch literal 16689 zcmeIZ1$QMmvIcm~%*@PGW@ct)W@eX}xy;N=WtW+m*{(7(Gc!}!>+YV}ndvvXf8f2m z=iE#w^@T!GghDArC`f~Vq5{AHkN^OH2w-%PZJ`GQ0K|a;04M-RU~OT0I~P+s7kw2E z2UBNVdUsnJ!U9lW$~*w@XZioT{ulQ^Mbfxj{})8jM~OG#JvyniIsr)5^T1(bYDK=D zfyAL7#@acSmLECaUJ-@z(X7~Oktf%@n67_W)Y;iK1%?l`E5SwvjP$7L;jl9d4xf>A zV_+pXX=z^Oq2dTIV(IHgn`Hvh9Gm-6)O;FC{r0JwK~0|N_RO^wlL2d z7z1y7361N7U!T|nZ|`Eqmu11OD~q`Mp*0j|P1EhI_Nm z4)py#GTOq?BY$p;>upyu4Y3C*`t*VNfOOn;+arWH+CxO@6L!8ea?I^@Hnp!Eba9<> 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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. +Description: The 'Codemeta' Project defines a 'JSON-LD' format for + describing software metadata, as detailed at + . 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. License: GPL-3 URL: https://github.com/ropensci/codemetar, https://docs.ropensci.org/codemetar/ @@ -85,10 +85,10 @@ Roxygen: list(markdown = TRUE) Config/testthat/edition: 3 Repository: https://ropensci.r-universe.dev RemoteUrl: https://github.com/ropensci/codemetar -RemoteRef: master -RemoteSha: 4cd7ccc51455f4fad762da8d3cca3f46c368e299 +RemoteRef: main +RemoteSha: bdd9a29d7eabcc43c3195fe461f884932eba763c NeedsCompilation: no -Packaged: 2023-04-05 06:11:53 UTC; root +Packaged: 2024-02-09 05:55:58 UTC; root Author: Carl Boettiger [aut, cre, cph] (), Anna Krystalli [rev, ctb] (), @@ -105,3 +105,4 @@ Author: Carl Boettiger [aut, cre, cph] Sebastian Kreutzer [ctb] (), Thierry Onkelinx [ctb] () Maintainer: Carl Boettiger +Built: R 4.3.2; ; 2024-02-09 05:58:05 UTC; windows diff --git a/inst/extdata/bibtex_field_entry.csv b/inst/extdata/bibtex_field_entry.csv deleted file mode 100644 index 74a7f182..00000000 --- a/inst/extdata/bibtex_field_entry.csv +++ /dev/null @@ -1,26 +0,0 @@ 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**\@phdthesis**","Using [thesis-type]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"entry_cff2bib","[unpublished]{.underline}","**\@unpublished**",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"entry_cff2bib","[generic]{.underline}","**\@misc**, **\@incollection**","**\@incollection** is a [generic]{.underline} with [year,publisher,collection-title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"entry_cff2bib","\<[any other value]{.underline}\>","**\@misc**",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**address**","Several possibilities","In **BibTeX** it may be the address of a **publisher, conference, organization, institution** or **school**.",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","***annote***","Not clear, won't be mapped",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**author**","[authors]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**booktitle**","[collection-title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**chapter**","[section]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","***crossref***","Not clear, won't be mapped",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**edition**","[edition]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**editor**","[editors]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**howpublished**","[medium]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**institution, school, organization**","[institution]{.underline}","No overlapping on **BibteX** requirements",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**journal**","[journal]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","***key***","Not clear, won't be mapped",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**month**","[month]{.underline}","Fallback: information in [date-published]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**note**","[notes]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**number**","[issue]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**pages**","[start]{.underline} & [end]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**publisher**","[publisher]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**series**","[collection-title]{.underline} if no **booktitle**",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**title**","[title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","***type***","Won't be mapped","This is a special key in [CFF]{.underline} resembling the **BibteX** entry.",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**volume**","[volume]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_bib2cff","**year**","[year]{.underline}","Fallback: information in [date-published]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_biblatex2cff","**abstract**","[abstract]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_biblatex2cff","**date**","[date-published]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_biblatex2cff","**doi**","[doi]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_biblatex2cff","**file**","[filename]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_biblatex2cff","**isbn**","[isbn]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_biblatex2cff","**issn**","[issn]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_biblatex2cff","**issuetitle**","[issue-title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_biblatex2cff","**pagetotal**","[pages]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_biblatex2cff","**translator**","[translators]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_biblatex2cff","**url**","[url]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_biblatex2cff","**urldate**","[date-accessed]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"fields_biblatex2cff","**version**","[version]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_article","**\@article**","[type: article, magazine-article, newspaper-article]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_article","**author** (required)","[authors]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_article","**title** (required)","[title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_article","**journal** (required)","[journal]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_article","**year** (required)","[year]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_article","**volume**","[volume]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_article","**number**","[issue]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_article","**pages**","[start]{.underline} and [end]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_article","**month**","[month]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_article","**note**","[notes]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**\@book, \@inbook**","[type: book]{.underline}","If [section]{.underline} or [start-end]{.underline} informed, it would be treated as **\@inbook**",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**author** (required)","[authors]{.underline}","At least one of **author,editor** required",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**editor** (required)","[editors]{.underline}","At least one of **author,editor** required",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**title** (required)","[title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**publisher** (required)","[publisher]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**year** (required)","[year]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**chapter** (required in **\@inbook** only)","[section]{.underline}","Not even optional in **\@book**",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**pages** (required in **\@inbook** only)","[start]{.underline} and [end]{.underline}","Not even optional in **\@book**",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**volume**","[volume]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**number**","[issue]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**series**","[collection-title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**address**","[address]{.underline} property of [publisher]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**edition**","[edition]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**month**","[month]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**note**","[notes]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_book","**type**","Ignored","Only optional in **\@inbook**",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_booklet","**\@booklet**","[type: pamphlet]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_booklet","**title** (required)","[title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_booklet","**author**","[authors]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_booklet","**howpublished**","[medium]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_booklet","**address**","[location]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_booklet","**month**","[month]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_booklet","**year**","[year]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_booklet","**note**","[notes]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**\@conference / \@inproceedings**","[type: conference-paper, conference]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**author** (required)","[authors]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**title** (required)","[title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**booktitle** (required)","[collection-title]{.underline} and [conference]{.underline}","Additionally [collection-type]{.underline} would be populated as ""proceedings""",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**year** (required)","[year]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**editor**","[editors]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**volume**","[volume]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**number**","[issue]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**series**","Ignored",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**pages**","[start]{.underline} and [end]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**address**","[address]{.underline} property of [conference]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**month**","[month]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**organization**","[institution]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**publisher**","[publisher]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_inproceedings","**note**","[notes]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**\@incollection**","[type: generic]{.underline}","Including a [collection-title]{.underline} value",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**author** (required)","[authors]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**title** (required)","[title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**booktitle** (required)","[collection-title]{.underline}","Additionally [collection-type]{.underline} would be populated as ""collection""",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**publisher** (required)","[publisher]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**year** (required)","[year]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**editor**","[editors]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**volume**","[volume]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**number**","[issue]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**series**","Ignored",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**type**","Ignored",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**chapter**","[section]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**pages**","[start]{.underline} and [end]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**address**","[address]{.underline} property of [publisher]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**edition**","[edition]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**month**","[month]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_incollection","**note**","[notes]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_manual","**\@manual**","[type: manual]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_manual","**title** (required)","[title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_manual","**author**","[authors]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_manual","**organization**","[institution]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_manual","**address**","[address]{.underline} property of [organization]{.underline}","On missing [organization]{.underline} mapped to [location]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_manual","**edition**","[edition]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_manual","**month**","[month]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_manual","**year**","[year]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_manual","**note**","[notes]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_thesis","**\@mastersthesis, \@phdthesis**","[type: thesis]{.underline}","Use also [thesis-type]{.underline} for identifying the thesis type.",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_thesis","**author** (required)","[authors]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_thesis","**title** (required)","[title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_thesis","**school** (required)","[institution]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_thesis","**year** (required)","[year]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_thesis","**type**","Ignored",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_thesis","**address**","[address]{.underline} property of [institution]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_thesis","**month**","[month]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_thesis","**note**","[notes]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_misc","**\@misc**","[type: generic]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_misc","**author**","[authors]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_misc","**title**","[title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_misc","**howpublished**","[medium]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_misc","**month**","[month]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_misc","**year**","[year]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_misc","**note**","[notes]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_proceedings","**\@proceedings**","[type: proceedings]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_proceedings","**title** (required)","[title]{.underline} and [conference]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_proceedings","**year** (required)","[year]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_proceedings","**editor**","[editors]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_proceedings","**volume**","[volume]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_proceedings","**number**","[issue]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_proceedings","**series**","[collection-title]{.underline}","Additionally [collection-type]{.underline} would be populated as ""proceedings""",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_proceedings","**address**","[address]{.underline} property of [conference]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_proceedings","**month**","[month]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_proceedings","**organization**","[institution]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_proceedings","**publisher**","[publisher]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_proceedings","**note**","[notes]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_techreport","**\@techreport**","[type: report]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_techreport","**author** (required)","[authors]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_techreport","**title** (required)","[title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_techreport","**institution** (required)","[institution]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_techreport","**year** (required)","[year]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_techreport","**type**","Ignored",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_techreport","**number**","[issue]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_techreport","**address**","[address]{.underline} property of [institution]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_techreport","**month**","[month]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_techreport","**note**","[notes]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_unpublished","**\@unpublished**","[type: unpublished]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_unpublished","**author** (required)","[authors]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_unpublished","**title** (required)","[title]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_unpublished","**note** (required)","[notes]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_unpublished","**month**","[month]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"model_unpublished","**year**","[year]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[art]{.underline}","A work of art, e.g., a painting",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[article]{.underline}",NA,"[[article]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[audiovisual]{.underline}",NA,"[[audiovisual]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[bill]{.underline}","A legal bill","[[bill]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[blog]{.underline}","A blog post","[[blog]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[book]{.underline}","A book or e-book","[[book]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[catalogue]{.underline}",NA,"[[catalogue]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[conference]{.underline}",NA,"[[conference]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[conference-paper]{.underline}",NA,"[[conference-paper]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[data]{.underline}","A data set","[[data]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[database]{.underline}","An aggregated or online database","[[database]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[dictionary]{.underline}",NA,"[[dictionary]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[edited-work]{.underline}","An edited work, e.g., a book","[[edited-work]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[encyclopedia]{.underline}",NA,"[[encyclopedia]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[film-broadcast]{.underline}","A film or broadcast","[[film-broadcast]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[generic]{.underline}","The fallback type","[[generic]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[government-document]{.underline}",NA,"[[government-document]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[grant]{.underline}","A research or other grant","[[grant]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[hearing]{.underline}",NA,"[[hearing]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[historical-work]{.underline}","A historical work, e.g., a medieval manuscript","[[historical-work]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[legal-case]{.underline}",NA,"[[legal-case]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[legal-rule]{.underline}",NA,"[[legal-rule]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[magazine-article]{.underline}",NA,"[[magazine-article]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[manual]{.underline}","A manual","[[manual]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[map]{.underline}","A geographical map","[[map]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[multimedia]{.underline}","A multimedia file","[[multimedia]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[music]{.underline}","A music file or sheet music","[[music]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[newspaper-article]{.underline}",NA,"[[newspaper-article]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[pamphlet]{.underline}",NA,"[[pamphlet]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[patent]{.underline}",NA,"[[patent]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[personal-communication]{.underline}",NA,"[[personal-communication]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[proceedings]{.underline}","Conference proceedings","[[proceedings]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[report]{.underline}",NA,"[[report]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[serial]{.underline}",NA,"[[serial]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[slides]{.underline}","Slides, i.e., a published slide deck","[[slides]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[software]{.underline}","Software","[[software]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[software-code]{.underline}","Software source code","[[software-code]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[software-container]{.underline}","A software container (e.g., a docker container)","[[software-container]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[software-executable]{.underline}","An executable software, i.e., a binary/artifact","[[software-executable]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[software-virtual-machine]{.underline}","A virtual machine/vm image","[[software-virtual-machine]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[sound-recording]{.underline}",NA,"[[sound-recording]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[standard]{.underline}",NA,"[[standard]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[statute]{.underline}",NA,"[[statute]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[thesis]{.underline}","An academic thesis","[[thesis]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[unpublished]{.underline}",NA,"[[unpublished]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[video]{.underline}","A video recording","[[video]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +"cff_types","[website]{.underline}",NA,"[[website]{.underline}]{.underline}",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA diff --git a/inst/schemaorg.json b/inst/schemaorg.json index 71cc4348..dec7a9c6 100644 --- a/inst/schemaorg.json +++ b/inst/schemaorg.json @@ -26,6 +26,6 @@ "name": "Comprehensive R Archive Network (CRAN)", "url": "https://cran.r-project.org" }, - "runtimePlatform": "R version 4.3.2 (2023-10-31)", - "version": "0.5.0" + "runtimePlatform": "R version 4.3.2 (2023-10-31 ucrt)", + "version": "0.5.0.9000" } diff --git a/man/cff-class.Rd b/man/cff-class.Rd new file mode 100644 index 00000000..79127b37 --- /dev/null +++ b/man/cff-class.Rd @@ -0,0 +1,9 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/cff-class.R +\name{cff-class} +\alias{cff-class} +\title{The \code{cff} class} +\description{ +TODO +} +\keyword{internal} diff --git a/man/cff_from_bibtex.Rd b/man/cff_from_bibtex.Rd index b6adf32f..d87fc3b4 100644 --- a/man/cff_from_bibtex.Rd +++ b/man/cff_from_bibtex.Rd @@ -63,7 +63,7 @@ if (requireNamespace("bibtex", quietly = TRUE)) { information between BibTeX and CITATION.cff. Other BibTeX helpers: -\code{\link{cff_to_bibtex}()}, +\code{\link{cff_to_bibentry}()}, \code{\link{encoded_utf_to_latex}()}, \code{\link{write_bib}()}, \code{\link{write_citation}()} diff --git a/man/cff_to_bibtex.Rd b/man/cff_to_bibentry.Rd similarity index 78% rename from man/cff_to_bibtex.Rd rename to man/cff_to_bibentry.Rd index 709b0224..338a14e4 100644 --- a/man/cff_to_bibtex.Rd +++ b/man/cff_to_bibentry.Rd @@ -1,11 +1,11 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/cff_to_bibtex.R -\name{cff_to_bibtex} +% Please edit documentation in R/cff_to_bibentry.R +\name{cff_to_bibentry} +\alias{cff_to_bibentry} \alias{cff_to_bibtex} -\alias{cff_extract_to_bibtex} \title{Create BibTeX entries from several sources} \usage{ -cff_to_bibtex(x, what = c("preferred", "references", "all")) +cff_to_bibentry(x, what = c("preferred", "references", "all")) } \arguments{ \item{x}{The source that would be used for generating @@ -33,11 +33,14 @@ A \code{bibentry} object or a list of \code{bibentry} objects. This could be parsed to BibTeX using \code{\link[=toBibtex]{toBibtex()}} } \description{ -This function creates BibTeX entries (in the form of \code{\link[=bibentry]{bibentry()}} objects +This function creates \code{\link[=bibentry]{bibentry()}} objects from different metadata sources (\code{cff} objects, \code{DESCRIPTION} files, etc.). -The function tries to parse the information of the source \code{x} into a \code{cff} +The function tries to map the information of the source \code{x} into a \code{cff} object and performs a mapping of the metadata to BibTeX, according to \code{vignette("bibtex_cff", "cffr")}. + +Note that a \strong{R} \code{\link[=bibentry]{bibentry()}} object is the representation of a BibTeX +entry, see \strong{Examples}. } \examples{ \donttest{ @@ -47,7 +50,7 @@ cff_object <- cff() cff_object # bibentry object -bib <- cff_to_bibtex(cff_object) +bib <- cff_to_bibentry(cff_object) class(bib) @@ -60,13 +63,13 @@ toBibtex(bib) # From a CITATION.cff file with options path <- system.file("examples/CITATION_complete.cff", package = "cffr") -cff_file <- cff_to_bibtex(path, what = "all") +cff_file <- cff_to_bibentry(path, what = "all") toBibtex(cff_file) # For an installed package -installed_package <- cff_to_bibtex("jsonvalidate") +installed_package <- cff_to_bibentry("jsonvalidate") toBibtex(installed_package) @@ -74,7 +77,7 @@ toBibtex(installed_package) # Use a DESCRIPTION file path2 <- system.file("examples/DESCRIPTION_gitlab", package = "cffr") -desc_file <- cff_to_bibtex(path2) +desc_file <- cff_to_bibentry(path2) toBibtex(desc_file) } @@ -87,7 +90,7 @@ toBibtex(desc_file) \emph{Ruby CFF Library (Version 0.9.0)} (Computer software). \doi{10.5281/zenodo.1184077}. \item Hernangómez D (2022). "BibTeX and CFF, a potential crosswalk." -\emph{The cffr package, Vignettes} +\emph{The cffr package, Vignettes}. \doi{10.21105/joss.03900}, \url{https://docs.ropensci.org/cffr/articles/bibtex_cff.html}. } } diff --git a/man/encoded_utf_to_latex.Rd b/man/encoded_utf_to_latex.Rd index 3a44a611..43cd3d1d 100644 --- a/man/encoded_utf_to_latex.Rd +++ b/man/encoded_utf_to_latex.Rd @@ -47,7 +47,7 @@ ascii_table Other BibTeX helpers: \code{\link{cff_from_bibtex}()}, -\code{\link{cff_to_bibtex}()}, +\code{\link{cff_to_bibentry}()}, \code{\link{write_bib}()}, \code{\link{write_citation}()} } diff --git a/man/figures/lifecycle-archived.svg b/man/figures/lifecycle-archived.svg new file mode 100644 index 00000000..745ab0c7 --- /dev/null +++ b/man/figures/lifecycle-archived.svg @@ -0,0 +1,21 @@ + + lifecycle: archived + + + + + + + + + + + + + + + lifecycle + + archived + + diff --git a/man/figures/lifecycle-defunct.svg b/man/figures/lifecycle-defunct.svg new file mode 100644 index 00000000..d5c9559e --- /dev/null +++ b/man/figures/lifecycle-defunct.svg @@ -0,0 +1,21 @@ + + lifecycle: defunct + + + + + + + + + + + + + + + lifecycle + + defunct + + diff --git a/man/figures/lifecycle-deprecated.svg b/man/figures/lifecycle-deprecated.svg new file mode 100644 index 00000000..b61c57c3 --- /dev/null +++ b/man/figures/lifecycle-deprecated.svg @@ -0,0 +1,21 @@ + + lifecycle: deprecated + + + + + + + + + + + + + + + lifecycle + + deprecated + + diff --git a/man/figures/lifecycle-experimental.svg b/man/figures/lifecycle-experimental.svg index d1d060e9..5d88fc2c 100644 --- a/man/figures/lifecycle-experimental.svg +++ b/man/figures/lifecycle-experimental.svg @@ -1 +1,21 @@ -lifecyclelifecycleexperimentalexperimental \ No newline at end of file + + lifecycle: experimental + + + + + + + + + + + + + + + lifecycle + + experimental + + diff --git a/man/figures/lifecycle-maturing.svg b/man/figures/lifecycle-maturing.svg new file mode 100644 index 00000000..897370ec --- /dev/null +++ b/man/figures/lifecycle-maturing.svg @@ -0,0 +1,21 @@ + + lifecycle: maturing + + + + + + + + + + + + + + + lifecycle + + maturing + + diff --git a/man/figures/lifecycle-questioning.svg b/man/figures/lifecycle-questioning.svg new file mode 100644 index 00000000..7c1721d0 --- /dev/null +++ b/man/figures/lifecycle-questioning.svg @@ -0,0 +1,21 @@ + + lifecycle: questioning + + + + + + + + + + + + + + + lifecycle + + questioning + + diff --git a/man/figures/lifecycle-soft-deprecated.svg b/man/figures/lifecycle-soft-deprecated.svg new file mode 100644 index 00000000..9c166ff3 --- /dev/null +++ b/man/figures/lifecycle-soft-deprecated.svg @@ -0,0 +1,21 @@ + + lifecycle: soft-deprecated + + + + + + + + + + + + + + + lifecycle + + soft-deprecated + + diff --git a/man/figures/lifecycle-stable.svg b/man/figures/lifecycle-stable.svg new file mode 100644 index 00000000..9bf21e76 --- /dev/null +++ b/man/figures/lifecycle-stable.svg @@ -0,0 +1,29 @@ + + lifecycle: stable + + + + + + + + + + + + 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+\alias{cff_extract_to_bibtex} +\title{Previous API: Create BibTeX entries from several sources} +\usage{ +cff_extract_to_bibtex(x, what = c("preferred", "references", "all")) +} +\arguments{ +\item{x}{The source that would be used for generating +the \code{\link[=bibentry]{bibentry()}} object via \code{cff}. It could be: +\itemize{ +\item A missing value. That would retrieve the DESCRIPTION +file on your in-development package. +\item An existing \code{\link{cff}} object, +\item Path to a CITATION.cff file (\code{"*/CITATION.cff*"}), +\item The name of an installed package (\code{"jsonlite"}), or +\item Path to a DESCRIPTION file (\code{"*/DESCRIPTION*"}). +}} + +\item{what}{Fields to extract. The value could be: +\itemize{ +\item \code{preferred}: This would create a single entry with the main citation +info of the package. +\item \code{references}: Extract all the entries on \code{references}. +\item \code{all}: A combination of the previous two options. This would extract +both the preferred citation info and the references. +}} +} +\value{ +See \code{\link[=cff_to_bibentry]{cff_to_bibentry()}} +} +\description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}} +Please use \code{\link[=cff_to_bibentry]{cff_to_bibentry()}} instead. +} +\examples{ +\donttest{ +# From a cff object +cff_object <- cff() + +cff_object + +# bibentry object +bib <- cff_to_bibentry(cff_object) +} +} +\keyword{internal} diff --git a/man/write_bib.Rd b/man/write_bib.Rd index 07904f8d..5240e5a0 100644 --- a/man/write_bib.Rd +++ b/man/write_bib.Rd @@ -9,7 +9,7 @@ write_bib(x, file = NULL, append = FALSE, verbose = TRUE, ascii = FALSE) \arguments{ \item{x}{A \code{bibentry} object created with: \itemize{ -\item \code{\link[=cff_to_bibtex]{cff_to_bibtex()}} +\item \code{\link[=cff_to_bibentry]{cff_to_bibentry()}} \item \code{\link[=citation]{citation()}} or \code{\link[=bibentry]{bibentry()}} }} @@ -56,7 +56,7 @@ following packages: Other BibTeX helpers: \code{\link{cff_from_bibtex}()}, -\code{\link{cff_to_bibtex}()}, +\code{\link{cff_to_bibentry}()}, \code{\link{encoded_utf_to_latex}()}, \code{\link{write_citation}()} } diff --git a/man/write_citation.Rd b/man/write_citation.Rd index 09aa9e7b..55d8d8fe 100644 --- a/man/write_citation.Rd +++ b/man/write_citation.Rd @@ -15,9 +15,9 @@ write_citation( \arguments{ \item{x}{It could be \itemize{ -\item A \code{bibentry} object created with \code{\link[=cff_to_bibtex]{cff_to_bibtex()}}, \code{\link[=citation]{citation()}} or +\item A \code{bibentry} object created with \code{\link[=cff_to_bibentry]{cff_to_bibentry()}}, \code{\link[=citation]{citation()}} or \code{\link[=bibentry]{bibentry()}} -\item Any of the valid inputs of \code{\link[=cff_to_bibtex]{cff_to_bibtex()}}: +\item Any of the valid inputs of \code{\link[=cff_to_bibentry]{cff_to_bibentry()}}: \itemize{ \item A missing value. That would retrieve the DESCRIPTION file on your in-development package. @@ -35,7 +35,7 @@ in-development package. \item{verbose}{Display informative messages} \item{...}{ - Arguments passed on to \code{\link[=cff_to_bibtex]{cff_to_bibtex}} + Arguments passed on to \code{\link[=cff_to_bibentry]{cff_to_bibentry}} \describe{ \item{\code{what}}{Fields to extract. The value could be: \itemize{ @@ -91,7 +91,7 @@ R version 4.3.0 (2023-04-21) edition. 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Beaver}, year = {1995}, + address = {Edinburgh}, school = {Centre for Cognitive Science, University of Edinburgh}, } diff --git a/tests/testthat/_snaps/deprecated.md b/tests/testthat/_snaps/deprecated.md new file mode 100644 index 00000000..ac22bc72 --- /dev/null +++ b/tests/testthat/_snaps/deprecated.md @@ -0,0 +1,9 @@ +# cff_extract_to_bibtex + + Code + old1 <- cff_extract_to_bibtex(a_cff) + Condition + Warning: + `cff_extract_to_bibtex()` was deprecated in cffr 0.5.0. + i Please use `cff_to_bibentry()` instead. + diff --git a/tests/testthat/_snaps/merge_desc_cit.md b/tests/testthat/_snaps/merge_desc_cit.md index 50bd133f..4476fa32 100644 --- a/tests/testthat/_snaps/merge_desc_cit.md +++ b/tests/testthat/_snaps/merge_desc_cit.md @@ -562,6 +562,70 @@ isbn: 978-3-319-24277-4 url: https://ggplot2.tidyverse.org +--- + + Code + merged + Output + cff-version: 1.2.0 + message: 'To cite package "resmush" in publications use:' + type: software + title: 'resmush: Optimize and Compress Image Files with ''reSmush.it''' + version: 0.1.0 + authors: + - family-names: Hernangómez + given-names: Diego + email: diego.hernangomezherrero@gmail.com + orcid: https://orcid.org/0000-0001-8457-4658 + abstract: Compress local and online images using the 'reSmush.it' API service . + repository: https://CRAN.R-project.org/package=resmush + repository-code: https://github.com/dieghernan/resmush + url: https://dieghernan.github.io/resmush/ + date-released: '2024-02-02' + contact: + - family-names: Hernangómez + given-names: Diego + email: diego.hernangomezherrero@gmail.com + orcid: https://orcid.org/0000-0001-8457-4658 + keywords: + - r + - compress-images + - optimize-images + - resmushit + - api + license: MIT + doi: 10.1111/2041-210X.12469 + preferred-citation: + type: article + title: 'RNeXML: A Package for Reading and Writing Richly Annotated Phylogenetic, + Character, and Trait Data in R' + authors: + - family-names: Boettiger + given-names: Carl + - family-names: Chamberlain + given-names: Scott + - family-names: Vos + given-names: Rutger + - family-names: Lapp + given-names: Hilmar + journal: Methods in Ecology and Evolution + year: '2016' + volume: '7' + doi: 10.1111/2041-210X.12469 + start: '352' + end: '357' + references: + - type: book + title: 'ggplot2: Elegant Graphics for Data Analysis' + authors: + - family-names: Wickham + given-names: Hadley + publisher: + name: Springer-Verlag New York + year: '2016' + isbn: 978-3-319-24277-4 + url: https://ggplot2.tidyverse.org + --- Code @@ -587,7 +651,7 @@ repository: https://ropensci.r-universe.dev repository-code: https://github.com/ropensci/codemetar url: https://docs.ropensci.org/codemetar/ - date-released: '2023-04-05' + date-released: '2024-02-09' contact: - family-names: Boettiger given-names: Carl diff --git a/tests/testthat/test-assertions.R b/tests/testthat/test-assertions.R index 920d6027..aaebfdb9 100644 --- a/tests/testthat/test-assertions.R +++ b/tests/testthat/test-assertions.R @@ -1,49 +1,49 @@ -test_that("Check is.email", { +test_that("Check is_email", { # Examples from https://www.nicebread.de/validating-email-adresses-in-r/ # Valid addresses expect_true( all( - is.email("felix@nicebread.de"), - is.email("felix.123.honeyBunny@nicebread.lmu.de"), - is.email("felix@nicebread.de "), - is.email(" felix@nicebread.de"), - is.email("felix+batman@nicebread.de"), - is.email("felix@nicebread.office") + is_email("felix@nicebread.de"), + is_email("felix.123.honeyBunny@nicebread.lmu.de"), + is_email("felix@nicebread.de "), + is_email(" felix@nicebread.de"), + is_email("felix+batman@nicebread.de"), + is_email("felix@nicebread.office") ) ) # invalid addresses expect_false( any( - is.email("felix@nicebread"), - is.email("felix@nicebread@de"), - is.email("felixnicebread.de"), - is.email("@felixnicebread"), - is.email(NULL), - is.email(NA) + is_email("felix@nicebread"), + is_email("felix@nicebread@de"), + is_email("felixnicebread.de"), + is_email("@felixnicebread"), + is_email(NULL), + is_email(NA) ) ) }) -test_that("Check is.url", { +test_that("Check is_url", { # Valid urls expect_true( all( - is.url("https://github.com/dieghernan"), - is.url("http://github.com/dieghernan"), - is.url("ftp://github.com/dieghernan"), - is.url("sftp://github.com/dieghernan") + is_url("https://github.com/dieghernan"), + is_url("http://github.com/dieghernan"), + is_url("ftp://github.com/dieghernan"), + is_url("sftp://github.com/dieghernan") ) ) # invalid addresses expect_false( any( - is.url("https:/github.com/dieghernan"), - is.url("http:/github.com/dieghernan"), - is.url("ftp:/github.com/dieghernan"), - is.url("sftp:/github.com/dieghernan"), - is.url("www.github.com/dieghernan") + is_url("https:/github.com/dieghernan"), + is_url("http:/github.com/dieghernan"), + is_url("ftp:/github.com/dieghernan"), + is_url("sftp:/github.com/dieghernan"), + is_url("www.github.com/dieghernan") ) ) }) diff --git a/tests/testthat/test-bibtex-check-ruby.R b/tests/testthat/test-bibtex-check-ruby.R index c6347475..6dd4f780 100644 --- a/tests/testthat/test-bibtex-check-ruby.R +++ b/tests/testthat/test-bibtex-check-ruby.R @@ -1,4 +1,5 @@ -# See https://github.com/citation-file-format/ruby-cff/tree/main/test/files/formatted +# See ´ +# https://github.com/citation-file-format/ruby-cff/tree/main/test/files/formatted test_that("preferred-citation-book-missing", { @@ -6,7 +7,7 @@ test_that("preferred-citation-book-missing", { package = "cffr" ) - expect_warning(expect_error(cff_to_bibtex(x))) + expect_warning(expect_error(cff_to_bibentry(x))) }) test_that("preferred-citation-book", { @@ -14,7 +15,7 @@ test_that("preferred-citation-book", { package = "cffr" ) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) @@ -23,7 +24,7 @@ test_that("preferred-citation-conference-paper-2", { package = "cffr" ) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) @@ -32,7 +33,7 @@ test_that("preferred-citation-conference-paper-missing", { package = "cffr" ) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) @@ -41,7 +42,7 @@ test_that("preferred-citation-conference-paper", { package = "cffr" ) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) @@ -50,7 +51,7 @@ test_that("preferred-citation-manual", { package = "cffr" ) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) @@ -59,7 +60,7 @@ test_that("preferred-citation-no-month", { package = "cffr" ) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) @@ -68,7 +69,7 @@ test_that("preferred-citation-no-vol", { package = "cffr" ) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) @@ -78,7 +79,7 @@ test_that("preferred-citation-pamphlet", { package = "cffr" ) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) @@ -87,7 +88,7 @@ test_that("preferred-citation-report-no-institution", { package = "cffr" ) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) @@ -96,7 +97,7 @@ test_that("preferred-citation-report", { package = "cffr" ) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) @@ -106,7 +107,7 @@ test_that("preferred-citation-unpublished", { package = "cffr" ) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) @@ -115,7 +116,7 @@ test_that("reprozip", { package = "cffr" ) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) @@ -125,7 +126,7 @@ test_that("smith-et-al", { package = "cffr" ) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) @@ -134,6 +135,6 @@ test_that("tidyverse-joss-paper", { package = "cffr" ) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) diff --git a/tests/testthat/test-bibtex2cff.R b/tests/testthat/test-bibtex2cff.R index 4af1feb7..29a49e4b 100644 --- a/tests/testthat/test-bibtex2cff.R +++ b/tests/testthat/test-bibtex2cff.R @@ -21,6 +21,13 @@ test_that("Article", { ) expect_true(cff_validate(cffobj, verbose = FALSE)) + + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- sort(names(unclass(bib)[[1]])) + fld2 <- sort(names(unclass(tobib)[[1]])) + expect_identical(fld1, fld2) }) @@ -53,6 +60,13 @@ test_that("Book", { ) expect_true(cff_validate(cffobj, verbose = FALSE)) + + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- sort(names(unclass(bib)[[1]])) + fld2 <- sort(names(unclass(tobib)[[1]])) + expect_identical(fld1, fld2) }) @@ -78,6 +92,15 @@ test_that("Booklet", { ) expect_true(cff_validate(cffobj, verbose = FALSE)) + + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- sort(names(unclass(bib)[[1]])) + fld2 <- sort(names(unclass(tobib)[[1]])) + + # Keyword is not parsed + expect_identical(setdiff(fld1, fld2), "keywords") }) test_that("Conference", { @@ -108,8 +131,6 @@ test_that("Conference", { bib <- list(bib_un) class(bib) <- "bibentry" - - bibparsed <- cff_parse_citation(bib) expect_snapshot(bibparsed) @@ -119,6 +140,14 @@ test_that("Conference", { ) expect_true(cff_validate(cffobj, verbose = FALSE)) + + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- unique(sort(names(unclass(bib)[[1]]))) + fld2 <- unique(sort(names(unclass(tobib)[[1]]))) + + expect_identical(setdiff(fld1, fld2), "series") }) test_that("InBook", { @@ -150,6 +179,13 @@ test_that("InBook", { ) expect_true(cff_validate(cffobj, verbose = FALSE)) + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- unique(sort(names(unclass(bib)[[1]]))) + fld2 <- unique(sort(names(unclass(tobib)[[1]]))) + + expect_identical(setdiff(fld1, fld2), "type") }) test_that("InCollection", { @@ -183,8 +219,15 @@ test_that("InCollection", { ) expect_true(cff_validate(cffobj, verbose = FALSE)) -}) + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- unique(sort(names(unclass(bib)[[1]]))) + fld2 <- unique(sort(names(unclass(tobib)[[1]]))) + + expect_identical(setdiff(fld1, fld2), c("series", "type")) +}) test_that("InProceedings", { bib <- bibentry("InProceedings", @@ -214,8 +257,15 @@ test_that("InProceedings", { ) expect_true(cff_validate(cffobj, verbose = FALSE)) -}) + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- unique(sort(names(unclass(bib)[[1]]))) + fld2 <- unique(sort(names(unclass(tobib)[[1]]))) + + expect_identical(setdiff(fld1, fld2), "series") +}) test_that("Manual", { bib <- bibentry("Manual", @@ -238,8 +288,15 @@ test_that("Manual", { ) expect_true(cff_validate(cffobj, verbose = FALSE)) -}) + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- unique(sort(names(unclass(bib)[[1]]))) + fld2 <- unique(sort(names(unclass(tobib)[[1]]))) + + expect_identical(fld1, fld2) +}) test_that("MastersThesis", { bib <- bibentry("MastersThesis", @@ -255,7 +312,6 @@ test_that("MastersThesis", { month = "August", note = "Example modified for testing purposes" ) - bibparsed <- cff_parse_citation(bib) expect_snapshot(bibparsed) @@ -264,8 +320,15 @@ test_that("MastersThesis", { ) expect_true(cff_validate(cffobj, verbose = FALSE)) -}) + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- unique(sort(names(unclass(bib)[[1]]))) + fld2 <- unique(sort(names(unclass(tobib)[[1]]))) + + expect_identical(setdiff(fld1, fld2), "type") +}) test_that("Misc", { bib <- bibentry("Misc", @@ -286,6 +349,14 @@ test_that("Misc", { ) expect_true(cff_validate(cffobj, verbose = FALSE)) + + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- unique(sort(names(unclass(bib)[[1]]))) + fld2 <- unique(sort(names(unclass(tobib)[[1]]))) + + expect_identical(fld1, fld2) }) @@ -311,6 +382,14 @@ test_that("PhdThesis", { ) expect_true(cff_validate(cffobj, verbose = FALSE)) + + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- unique(sort(names(unclass(bib)[[1]]))) + fld2 <- unique(sort(names(unclass(tobib)[[1]]))) + + expect_identical(setdiff(fld1, fld2), "type") }) @@ -338,6 +417,14 @@ test_that("Proceedings", { ) expect_true(cff_validate(cffobj, verbose = FALSE)) + + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- unique(sort(names(unclass(bib)[[1]]))) + fld2 <- unique(sort(names(unclass(tobib)[[1]]))) + + expect_identical(fld1, fld2) }) test_that("TechReport", { @@ -362,6 +449,14 @@ test_that("TechReport", { ) expect_true(cff_validate(cffobj, verbose = FALSE)) + + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- unique(sort(names(unclass(bib)[[1]]))) + fld2 <- unique(sort(names(unclass(tobib)[[1]]))) + + expect_identical(setdiff(fld1, fld2), "type") }) test_that("Unpublished", { @@ -382,8 +477,52 @@ test_that("Unpublished", { ) expect_true(cff_validate(cffobj, verbose = FALSE)) + + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- unique(sort(names(unclass(bib)[[1]]))) + fld2 <- unique(sort(names(unclass(tobib)[[1]]))) + + expect_identical(fld1, fld2) }) +test_that("InBook with booktitle", { + bib <- bibentry("InBook", + title = "Bibliographies and citations", + year = "2020", + author = "Yihui Xie and Christophe Dervieux and Emily Riederer", + booktitle = "{R} Markdown Cookbook", + publisher = "Chapman and Hall/CRC", + address = "Boca Raton, Florida", + series = "The {R} Series", + isbn = "9780367563837", + url = "https://bookdown.org/yihui/rmarkdown-cookbook", + chapter = "4.5" + ) + + bibparsed <- cff_parse_citation(bib) + expect_snapshot(bibparsed) + + cffobj <- cff_create(cff(), + keys = list(references = list(bibparsed)) + ) + + expect_true(cff_validate(cffobj, verbose = FALSE)) + + # Should be an incollection now + res <- cff_to_bibentry(bibparsed) + init_type <- attr(unclass(res)[[1]], "bibtype") + expect_identical(tolower(init_type), "incollection") + + # Back to bibtex and check names + tobib <- cff_to_bibentry(bibparsed) + + fld1 <- unique(sort(names(unclass(bib)[[1]]))) + fld2 <- unique(sort(names(unclass(tobib)[[1]]))) + + expect_identical(setdiff(fld1, fld2), "series") +}) test_that("Test entry without author", { bib <- bibentry("Proceedings", diff --git a/tests/testthat/test-cff_description.R b/tests/testthat/test-cff_description.R index b096a052..2a6f8f1d 100644 --- a/tests/testthat/test-cff_description.R +++ b/tests/testthat/test-cff_description.R @@ -172,6 +172,26 @@ test_that("Parsing Bioconductor", { expect_true(cff_validate(parsed, verbose = FALSE)) }) +test_that("Parsing Posit Package Manager", { + desc_path <- system.file("examples/DESCRIPTION_posit_package_manager", + package = "cffr" + ) + + parsed <- cff_create(desc_path, + gh_keywords = FALSE, + keys = list(references = NULL) + ) + + expect_length(parsed$repository, 1) + expect_identical( + parsed$repository, + "https://CRAN.R-project.org/package=resmush" + ) + expect_s3_class(parsed, "cff") + expect_snapshot(parsed) + expect_true(cff_validate(parsed, verbose = FALSE)) +}) + test_that("Search package on CRAN", { basic_path <- system.file("examples/DESCRIPTION_basic", package = "cffr" diff --git a/tests/testthat/test-cff_parse_person.R b/tests/testthat/test-cff_parse_person.R index 952809f5..2e169564 100644 --- a/tests/testthat/test-cff_parse_person.R +++ b/tests/testthat/test-cff_parse_person.R @@ -1,3 +1,8 @@ +test_that("NULL gives NULL", { + expect_null(cff_parse_person(NULL)) + expect_null(cff_parse_person(NA)) +}) + test_that("Parse one person", { p <- person("one", "person") expect_snapshot(cff_parse_person(p)) diff --git a/tests/testthat/test-cff_read.R b/tests/testthat/test-cff_read.R index 2fd047d1..0c437b26 100644 --- a/tests/testthat/test-cff_read.R +++ b/tests/testthat/test-cff_read.R @@ -58,13 +58,13 @@ test_that("Other convertes", { a <- cff(a) expect_s3_class(a, "cff") a <- as.cff(a) - expect_true(is.cff(a)) + expect_true(is_cff(a)) expect_s3_class(a, "cff") expect_message(noadd <- cff(address = "New York", version = 5)) - expect_true(is.cff(noadd)) - expect_false(is.cff(list(a = 1, b = 2))) - expect_true(is.cff(as.cff(list(a = 1, b = 2)))) + expect_true(is_cff(noadd)) + expect_false(is_cff(list(a = 1, b = 2))) + expect_true(is_cff(as.cff(list(a = 1, b = 2)))) }) @@ -107,7 +107,7 @@ test_that("Fuzzy matching of keys on cff", { ) ) - expect_true(is.cff(cffobj)) + expect_true(is_cff(cffobj)) expect_true(cff_validate(cffobj, verbose = FALSE)) expect_snapshot(print_snapshot("Fuzzy keys", cffobj)) diff --git a/tests/testthat/test-cff_to_bibtex.R b/tests/testthat/test-cff_to_bibentry.R similarity index 88% rename from tests/testthat/test-cff_to_bibtex.R rename to tests/testthat/test-cff_to_bibentry.R index 04e804f6..d5438428 100644 --- a/tests/testthat/test-cff_to_bibtex.R +++ b/tests/testthat/test-cff_to_bibentry.R @@ -14,7 +14,7 @@ test_that("Article to bibtex", { ) expect_snapshot(toBibtex(bib)) x <- cff_parse_citation(bib) - bib <- cff_to_bibtex(x) + bib <- cff_to_bibentry(x) expect_snapshot(toBibtex(bib)) }) @@ -42,7 +42,7 @@ test_that("Book to bibtex", { expect_snapshot(toBibtex(bib)) bibparsed <- cff_parse_citation(bib) - bib <- cff_to_bibtex(bibparsed) + bib <- cff_to_bibentry(bibparsed) expect_snapshot(toBibtex(bib)) }) @@ -63,7 +63,7 @@ test_that("Booklet to bibtex", { expect_snapshot(toBibtex(bib)) bibparsed <- cff_parse_citation(bib) - bib <- cff_to_bibtex(bibparsed) + bib <- cff_to_bibentry(bibparsed) expect_snapshot(toBibtex(bib)) }) @@ -91,7 +91,7 @@ test_that("InBook to bibtex with pages", { expect_snapshot(toBibtex(bib)) bibparsed <- cff_parse_citation(bib) - bib <- cff_to_bibtex(bibparsed) + bib <- cff_to_bibentry(bibparsed) expect_snapshot(toBibtex(bib)) }) @@ -110,7 +110,7 @@ test_that("InCollection to bibtex", { expect_snapshot(toBibtex(bib)) bibparsed <- cff_parse_citation(bib) - bib <- cff_to_bibtex(bibparsed) + bib <- cff_to_bibentry(bibparsed) expect_snapshot(toBibtex(bib)) }) @@ -135,7 +135,7 @@ test_that("InProceedings to bibtex", { expect_snapshot(toBibtex(bib)) bibparsed <- cff_parse_citation(bib) - bib <- cff_to_bibtex(bibparsed) + bib <- cff_to_bibentry(bibparsed) expect_snapshot(toBibtex(bib)) }) @@ -153,7 +153,7 @@ test_that("Manual to bibtex", { expect_snapshot(toBibtex(bib)) bibparsed <- cff_parse_citation(bib) - bib <- cff_to_bibtex(bibparsed) + bib <- cff_to_bibentry(bibparsed) expect_snapshot(toBibtex(bib)) }) @@ -172,7 +172,7 @@ test_that("MastersThesis to bibtex", { expect_snapshot(toBibtex(bib)) bibparsed <- cff_parse_citation(bib) - bib <- cff_to_bibtex(bibparsed) + bib <- cff_to_bibentry(bibparsed) expect_snapshot(toBibtex(bib)) }) @@ -189,7 +189,7 @@ test_that("PhdThesis to bibtex", { expect_snapshot(toBibtex(bib)) bibparsed <- cff_parse_citation(bib) - bib <- cff_to_bibtex(bibparsed) + bib <- cff_to_bibentry(bibparsed) expect_snapshot(toBibtex(bib)) }) @@ -208,7 +208,7 @@ test_that("Proceedings to bibtex", { expect_snapshot(toBibtex(bib)) bibparsed <- cff_parse_citation(bib) - bib <- cff_to_bibtex(bibparsed) + bib <- cff_to_bibentry(bibparsed) expect_snapshot(toBibtex(bib)) }) @@ -224,7 +224,7 @@ test_that("TechReport to bibtex", { expect_snapshot(toBibtex(bib)) bibparsed <- cff_parse_citation(bib) - bib <- cff_to_bibtex(bibparsed) + bib <- cff_to_bibentry(bibparsed) expect_snapshot(toBibtex(bib)) }) @@ -239,7 +239,7 @@ test_that("Unpublished to bibtex", { expect_snapshot(toBibtex(bib)) bibparsed <- cff_parse_citation(bib) - bib <- cff_to_bibtex(bibparsed) + bib <- cff_to_bibentry(bibparsed) expect_snapshot(toBibtex(bib)) }) @@ -264,7 +264,7 @@ test_that("particle names", { expect_snapshot(bibparsed) - bib <- cff_to_bibtex(bibparsed) + bib <- cff_to_bibentry(bibparsed) expect_snapshot(toBibtex(bib)) }) @@ -281,12 +281,12 @@ test_that("From plain cff with a citation", { s$`preferred-citation` <- cff_parse_citation(acit) s$`preferred-citation`$editors <- list(cff_parse_person("A name")) - bib <- cff_to_bibtex(s) + bib <- cff_to_bibentry(s) expect_snapshot(toBibtex(bib)) }) test_that("From plain cff", { - expect_message(bib <- cff_to_bibtex(cff())) + expect_message(bib <- cff_to_bibentry(cff())) expect_snapshot(toBibtex(bib)) }) @@ -295,13 +295,13 @@ test_that("From file", { package = "cffr" ) - bib <- cff_to_bibtex(file) + bib <- cff_to_bibentry(file) expect_snapshot(toBibtex(bib)) }) test_that("NULL", { s <- NULL - expect_null(cff_to_bibtex(s)) + expect_null(cff_to_bibentry(s)) }) @@ -311,7 +311,7 @@ test_that("Test anonymous", { ) - expect_message(back <- cff_to_bibtex(cff_parse_citation(bib))) + expect_message(back <- cff_to_bibentry(cff_parse_citation(bib))) expect_snapshot(toBibtex(back)) @@ -320,7 +320,7 @@ test_that("Test anonymous", { ) - expect_message(back <- cff_to_bibtex(cff_parse_citation(bib))) + expect_message(back <- cff_to_bibentry(cff_parse_citation(bib))) expect_snapshot(toBibtex(back)) bib <- bibentry("misc", @@ -328,7 +328,7 @@ test_that("Test anonymous", { ) - expect_message(back <- cff_to_bibtex(cff_parse_citation(bib))) + expect_message(back <- cff_to_bibentry(cff_parse_citation(bib))) expect_snapshot(toBibtex(back)) bib <- bibentry("proceedings", @@ -337,7 +337,7 @@ test_that("Test anonymous", { ) - expect_silent(back <- cff_to_bibtex(cff_parse_citation(bib))) + expect_silent(back <- cff_to_bibentry(cff_parse_citation(bib))) expect_snapshot(toBibtex(back)) }) @@ -356,7 +356,7 @@ test_that("Fallback month", { # Delete here the month x$month <- NULL - bibback <- cff_to_bibtex(x) + bibback <- cff_to_bibentry(x) expect_snapshot(toBibtex(bibback)) }) @@ -390,7 +390,7 @@ test_that("Test BibLateX entry", { x <- cff_parse_citation(bib) - parsed <- cff_to_bibtex(x) + parsed <- cff_to_bibentry(x) expect_snapshot(toBibtex(parsed)) }) @@ -398,7 +398,7 @@ test_that("Test BibLateX entry", { test_that("Test Fallback year", { x <- cff() - expect_message(msg <- cff_to_bibtex(x)) + expect_message(msg <- cff_to_bibentry(x)) expect_snapshot(toBibtex(msg)) @@ -407,32 +407,32 @@ test_that("Test Fallback year", { expect_true(cff_validate(x, verbose = FALSE)) - parsed <- cff_to_bibtex(x) + parsed <- cff_to_bibentry(x) expect_snapshot(toBibtex(parsed)) }) test_that("Errors", { - expect_silent(b <- cff_to_bibtex("testthat")) + expect_silent(b <- cff_to_bibentry("testthat")) expect_s3_class(b, "bibentry") - expect_error(cff_to_bibtex("testthat", what = "aa")) + expect_error(cff_to_bibentry("testthat", what = "aa")) }) test_that("From package", { skip_if_not_installed("rmarkdown") - base <- cff_to_bibtex("rmarkdown") + base <- cff_to_bibentry("rmarkdown") expect_s3_class(base, "bibentry") expect_length(base, 1) - refs <- cff_to_bibtex("rmarkdown", "references") + refs <- cff_to_bibentry("rmarkdown", "references") expect_s3_class(refs, "bibentry") expect_gte(length(refs), 1) - all <- cff_to_bibtex("rmarkdown", "all") + all <- cff_to_bibentry("rmarkdown", "all") expect_s3_class(all, "bibentry") expect_length(all, length(base) + length(refs)) @@ -441,10 +441,10 @@ test_that("From package", { test_that("NULL references", { basic <- cff() - expect_null(cff_to_bibtex(basic, "references")) + expect_null(cff_to_bibentry(basic, "references")) # Test all - expect_message(l <- cff_to_bibtex(basic, "all")) + expect_message(l <- cff_to_bibentry(basic, "all")) expect_length(l, 1) }) @@ -452,7 +452,7 @@ test_that("NULL references", { test_that("From CITATION.cff", { p <- system.file("examples/smith-et-al.cff", package = "cffr") - base <- cff_to_bibtex(p) + base <- cff_to_bibentry(p) expect_s3_class(base, "bibentry") diff --git a/tests/testthat/test-deprecated.R b/tests/testthat/test-deprecated.R new file mode 100644 index 00000000..7097e013 --- /dev/null +++ b/tests/testthat/test-deprecated.R @@ -0,0 +1,8 @@ +test_that("cff_extract_to_bibtex", { + a_cff <- cff_create("cffr") + + current <- cff_to_bibentry(a_cff) + expect_snapshot(old1 <- cff_extract_to_bibtex(a_cff)) + + expect_identical(current, old1) +}) diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R index 800df3c4..a77bfd96 100644 --- a/tests/testthat/test-utils.R +++ b/tests/testthat/test-utils.R @@ -24,3 +24,20 @@ test_that("Try cleaning string", { expect_null(clean_str(logical(0))) expect_null(clean_str(list())) }) + +test_that("Use right repo", { + # Use some other repos + repos <- c("https://ropensci.r-universe.dev", "https://cloud.r-project.org") + + final <- detect_repos(repos) + expect_identical(final, c(CRAN = "https://cloud.r-project.org/")) + + # With posit package manager + repos <- c( + CRAN = "https://packagemanager.posit.co/cran/latest", + RPSM = "https://packagemanager.rstudio.com/", + ANOTHER = "https://packagemanager.rspm.com/" + ) + final <- detect_repos(repos) + expect_identical(final, c(CRAN = "https://cloud.r-project.org/")) +}) diff --git a/tests/testthat/test_ci/.gitignore b/tests/testthat/test_ci/.gitignore index a7cc310b..84cb1ec8 100644 --- a/tests/testthat/test_ci/.gitignore +++ b/tests/testthat/test_ci/.gitignore @@ -1,3 +1,4 @@ _snaps CITATION allpackages.csv +results.* diff --git a/tests/testthat/test_ci/README.md b/tests/testthat/test_ci/README.md index 0500a79b..983fc683 100644 --- a/tests/testthat/test_ci/README.md +++ b/tests/testthat/test_ci/README.md @@ -13,21 +13,15 @@ This test validates the `cff` parsing for \>1500 packages: This test is deployed in [GitHub Actions](https://github.com/ropensci/cffr/actions/workflows/test-ci.yaml) and -the results are uploaded as an artifact. We use here Windows and MacOS binaries -for speeding up the process. +the results are uploaded as an report on the action itself. We use here Windows +and MacOS. -As the installations differs across users and machines, the snapshot testing is -expected to fail on a normal run. However, the snapshots are quite useful for -extensive tests and debugging, as well as for capturing corner cases. For that -reason, these tests are no run in **CRAN** or in the regular package development -workflow. - -However, the test can be run locally with +The test can be run locally with ``` r # Load package devtools::load_all() -# Run the tests -testthat::test_dir("tests/testthat/test_ci") +# Run the report +source("tests/testthat/test_ci/test-new.R") ``` diff --git a/tests/testthat/test_ci/test-full_cff.R b/tests/testthat/test_ci/test-full_cff.R index f86a598f..453fe002 100644 --- a/tests/testthat/test_ci/test-full_cff.R +++ b/tests/testthat/test_ci/test-full_cff.R @@ -1,89 +1,97 @@ -test_that("Test ALL installed packages", { - expect_snapshot_output(print_snapshot("Sessioninfo", sessionInfo())) - - installed <- as.data.frame(installed.packages()[, c("Package", "Version")]) - installed <- installed[order(installed$Package), ] - - rownames(installed) <- seq_len(nrow(installed)) - - l <- nrow(installed) - - # Initial set of packages - write.csv(installed, "allpackages.csv", row.names = FALSE) - expect_snapshot_output(print_snapshot("Summary", paste( - "testing a sample of", - nrow(installed), "installed packages" - ))) - message("Sample of ", nrow(installed)) - - res <- c() - withcit <- c() - - for (i in seq_len(nrow(installed))) { - pkg <- installed[i, ]$Package - # Display some advances - message( - "Testing ", i, "/", nrow(installed), - " (", sprintf("%05.02f", i / nrow(installed) * 100), "%)" - ) - cit_path <- file.path(find.package(installed[i, ]$Package), "CITATION") - - - if (file.exists(cit_path)) { - withcit <- c(withcit, TRUE) - } else { - withcit <- c(withcit, FALSE) - } - - # Add cffobj - cffobj <- suppressMessages( - cff_create(pkg, gh_keywords = FALSE, dependencies = FALSE) - ) - - s <- suppressMessages(cff_validate(cffobj)) - - - res <- c(res, s) - } - - - expect_snapshot_output({ - installed$with_citation <- withcit - installed$is_ok <- res - - errors <- installed[installed$is_ok == FALSE, ] - - okrate <- 1 - nrow(errors) / nrow(installed) - - expect_snapshot_output(print_snapshot( - "OK rate", - sprintf("%1.2f%%", 100 * okrate) - )) - - - if (nrow(errors) > 0) { - print_snapshot( - "Errors", - errors - ) - - print_snapshot( - "Error reports for ", - paste(errors$Package, collapse = ", ") - ) - - for (j in seq_len(nrow(errors))) { - pkg <- errors[j, ]$Package - cff <- cff_create(pkg, gh_keywords = FALSE, dependencies = FALSE) - - print_snapshot(paste0(pkg, ": cffr object"), cff) - - print_snapshot("Validation results", cff_validate(cff)) - } - } else { - print_snapshot(obj = "No errors, hooray!") - } - }) - - write.csv(installed, "allpackages.csv", row.names = FALSE) -}) +# ---------------------------------------------------------------- +# DEPRECATED: SEE ./tests/testthat/test_ci/test-new.R file instead +# ---------------------------------------------------------------- + + +# test_that("Test ALL installed packages", { +# expect_snapshot_output(print_snapshot("Sessioninfo", sessionInfo())) +# +# installed <- as.data.frame(installed.packages()[, c("Package", "Version")]) +# installed <- installed[order(installed$Package), ] +# +# end <- match("ctv", installed$Package) + 10 +# installed <- installed[seq_len(end), ] +# +# rownames(installed) <- seq_len(nrow(installed)) +# +# l <- nrow(installed) +# +# # Initial set of packages +# write.csv(installed, "allpackages.csv", row.names = FALSE) +# expect_snapshot_output(print_snapshot("Summary", paste( +# "testing a sample of", +# nrow(installed), "installed packages" +# ))) +# message("Sample of ", nrow(installed)) +# +# res <- c() +# withcit <- c() +# +# for (i in seq_len(nrow(installed))) { +# pkg <- installed[i, ]$Package +# # Display some advances +# message( +# "Testing ", i, "/", nrow(installed), +# " (", sprintf("%05.02f", i / nrow(installed) * 100), "%)" +# ) +# cit_path <- file.path(find.package(installed[i, ]$Package), "CITATION") +# +# +# if (file.exists(cit_path)) { +# withcit <- c(withcit, TRUE) +# } else { +# withcit <- c(withcit, FALSE) +# } +# +# # Add cffobj +# cffobj <- suppressMessages( +# cff_create(pkg, gh_keywords = FALSE, dependencies = FALSE) +# ) +# +# s <- suppressMessages(cff_validate(cffobj)) +# +# +# res <- c(res, s) +# } +# +# +# expect_snapshot_output({ +# installed$with_citation <- withcit +# installed$is_ok <- res +# +# errors <- installed[installed$is_ok == FALSE, ] +# +# okrate <- 1 - nrow(errors) / nrow(installed) +# +# expect_snapshot_output(print_snapshot( +# "OK rate", +# sprintf("%1.2f%%", 100 * okrate) +# )) +# +# +# if (nrow(errors) > 0) { +# print_snapshot( +# "Errors", +# errors +# ) +# +# print_snapshot( +# "Error reports for ", +# paste(errors$Package, collapse = ", ") +# ) +# +# for (j in seq_len(nrow(errors))) { +# pkg <- errors[j, ]$Package +# cff <- cff_create(pkg, gh_keywords = FALSE, dependencies = FALSE) +# +# print_snapshot(paste0(pkg, ": cffr object"), cff) +# +# print_snapshot("Validation results", cff_validate(cff)) +# } +# } else { +# print_snapshot(obj = "No errors, hooray!") +# } +# }) +# +# write.csv(installed, "allpackages.csv", row.names = FALSE) +# }) diff --git a/tests/testthat/test_ci/test-new.R b/tests/testthat/test_ci/test-new.R new file mode 100644 index 00000000..5ea2c93e --- /dev/null +++ b/tests/testthat/test_ci/test-new.R @@ -0,0 +1,149 @@ +library(cffr) +installed <- as.data.frame(installed.packages()[, c("Package", "Version")]) +installed <- installed[order(installed$Package), ] + + +rownames(installed) <- seq_len(nrow(installed)) + +l <- nrow(installed) + +dir_path <- "./tests/testthat/test_ci/" + +message("Testing a sample of ", nrow(installed), " packages") + +res <- c() +withcit <- c() +note <- c() +for (i in seq_len(nrow(installed))) { + pkg <- installed[i, ]$Package + # Display some advances + message( + "Testing ", i, "/", nrow(installed), + " (", sprintf("%05.02f", i / nrow(installed) * 100), "%) [", + installed[i, ]$Package, "]" + ) + cit_path <- file.path(find.package(installed[i, ]$Package), "CITATION") + + + if (file.exists(cit_path)) { + withcit <- c(withcit, TRUE) + } else { + withcit <- c(withcit, FALSE) + } + + # Add cffobj + cffobj <- try( + cff_create(pkg, gh_keywords = FALSE, dependencies = FALSE), + silent = TRUE + ) + + if (inherits(cffobj, "cff")) { + s <- try(cff_validate(cffobj, verbose = FALSE), silent = TRUE) + if (!is.logical(s)) s <- FALSE + + res <- c(res, s) + note <- c(note, "") + } else { + res <- c(res, FALSE) + note <- c(note, "Other errors") + } +} + +installed$with_citation <- withcit +installed$is_ok <- res +installed$note <- note + +# Create report + +options(cli.width = 60) +outmd <- file.path(dir_path, "results.md") +unlink(outmd) + +cat("# Test all files\n\n", file = outmd) +write("## Session info\n", outmd, append = TRUE) +write("

", outmd, append = TRUE) +write("\n```r", outmd, append = TRUE) +conn <- file(outmd, "a") +capture.output(sessioninfo::session_info(), file = conn) +close(conn) +write("```\n", outmd, append = TRUE) +write("
", outmd, append = TRUE) + +errors <- installed[installed$is_ok == FALSE, ] +errother <- errors$Package[errors$note == "Other errors"] +errcff <- setdiff(errors$Package, errother) +errother_df <- installed[installed$Package %in% errother, c(1, 2)] + + + +write("\n## High level summary", outmd, append = TRUE) +write(paste0("\n- I checked ", nrow(installed), " packages"), + outmd, + append = TRUE +) +write(paste0("- Invalid cff in ", length(errcff), " packages"), + outmd, + append = TRUE +) +write(paste0("- I failed to generate cff in ", length(errother), " packages"), + outmd, + append = TRUE +) + +okrate <- 100 * (1 - length(errcff) / (nrow(installed) - length(errother))) +write(paste0("- OK Rate: ", round(okrate, 2), "%"), outmd, append = TRUE) + + +if (nrow(errors) == 0) { + write("\nNo errors, hooray!", outmd, append = TRUE) +} else { + write("\nPackages with errors:", outmd, append = TRUE) + conn <- file(outmd, "a") + capture.output(knitr::kable(errors, row.names = FALSE), + file = conn + ) + close(conn) + + + if (length(errother) > 0) { + pk <- paste0(errother, collapse = ", ") + line <- paste0("\n## Packages with errors not coming from cff") + write(line, outmd, append = TRUE) + conn <- file(outmd, "a") + capture.output(knitr::kable(errother_df, row.names = FALSE), + file = conn + ) + close(conn) + } + + if (length(errcff) > 0) { + write("\n## cff errors reported", outmd, append = TRUE) + # Prepare links + cfflist <- paste0("- [", errcff, "](#", tolower(errcff), ")", + collapse = "\n" + ) + write(cfflist, outmd, append = TRUE) + + for (j in errcff) { + write(paste0("\n### ", j, ""), outmd, append = TRUE) + write("\n#### cff object\n", outmd, append = TRUE) + write("
", outmd, append = TRUE) + write("\n```r", outmd, append = TRUE) + cff <- cff_create(j, gh_keywords = FALSE, dependencies = FALSE) + conn <- file(outmd, "a") + capture.output(print(cff), file = conn) + close(conn) + write("```\n", outmd, append = TRUE) + write("
", outmd, append = TRUE) + + + write("\n#### Validation results", outmd, append = TRUE) + + s <- cff_validate(cff, verbose = FALSE) + df <- attr(s, "errors") + conn <- file(outmd, "a") + capture.output(knitr::kable(df, row.names = FALSE), file = conn) + close(conn) + } + } +} diff --git a/vignettes/REFERENCES.bib b/vignettes/REFERENCES.bib index 6bbbf02a..78eb0a53 100644 --- a/vignettes/REFERENCES.bib +++ b/vignettes/REFERENCES.bib @@ -8,6 +8,16 @@ @misc{biblatexcheatsheet note = {Version Number: 2017-06-24}, date = {2017-06-24} } +@misc{biblatexpack, + title = {The {biblatex} package}, + author = {Philip Kime and Moritz Wemheuer and Philipp Lehman}, + year = 2023, + month = {mar}, + url = {https://osl.ugr.es/CTAN/macros/latex/contrib/biblatex/doc/biblatex.pdf}, + urldate = {2024-02-07}, + note = {Version Number: 3.19}, + date = {2023-03-05} +} @manual{codemetar2021, title = {{codemetar}: Generate '{CodeMeta}' Metadata for {R} Packages}, author = {Carl Boettiger and Maëlle Salmon}, @@ -212,3 +222,14 @@ @manual{codemeta url = {https://CRAN.R-project.org/package=codemeta}, note = {R package version 0.1.1} } +@misc{druskat2019, + title = {{Citation File Format (CFF)} - Specifications}, + author = {Druskat, Stephan and Spaaks, Jurriaan H. and Chue Hong, Neil and Haines, Robert and Baker, James}, + year = 2019, + month = 11, + doi = {10.5281/ZENODO.3515946}, + url = {https://zenodo.org/record/3515946}, + note = {Version 1.0.3-4}, + date = {2019-11-04}, + langid = {en} +} diff --git a/vignettes/bibtex_cff.Rmd b/vignettes/bibtex_cff.Rmd index 05e76077..c86fdeb6 100644 --- a/vignettes/bibtex_cff.Rmd +++ b/vignettes/bibtex_cff.Rmd @@ -2,23 +2,25 @@ title: "BibTeX and CFF" subtitle: A potential crosswalk bibliography: REFERENCES.bib -author: Diego Hernangómez ORCID logo +author: Diego Hernangómez description: >- This article presents a crosswalk between BibTeX and Citation File Format [@druskat_citation_2021], as it is performed by the cffr package [@hernangomez2021]. abstract: >- - This article presents a crosswalk between BibTeX and Citation File Format - [@druskat_citation_2021], as it is performed by the cffr package - [@hernangomez2021]. Several crosswalk models specific for each BibTeX entry - type [@patashnik1988] are proposed. The article also provide examples using real - BibTeX entries and tips for developers that would like to implement the crosswalk - on different programming languages. + This article introduces a crosswalk between **BibTeX** and the Citation File + Format (CFF) [@druskat_citation_2021], as implemented by the **cffr** package + [@hernangomez2021]. The crosswalk aims to facilitate seamless translation + between these two reference formats. Specifically, it proposes various + crosswalk models tailored to different **BibTeX** entry types + [@patashnik1988]. Additionally, the article includes practical examples using + real **BibTeX** entries and offers tips for developers interested in + implementing this crosswalk across various programming languages. link-citations: yes documentclass: article editor_options: markdown: - wrap: 120 + wrap: 80 output: rmarkdown::html_vignette: toc: true @@ -34,9 +36,18 @@ knitr::opts_chunk$set( comment = "" ) -options(width = 60) +# Load the table of tables + +p2file <- system.file("extdata/crosswalk_tables.csv", package = "cffr") + +table_master <- read.csv(p2file) ``` +## Disclaimer + +*This article was reviewed and updated in 2024, along with the release of +**cffr** v0.6.0.* + ## Citation Please cite this article as: @@ -49,12 +60,14 @@ thisart <- bibentry("article", journal = "The {cffr} package", year = 2022, volume = "Vignettes", + doi = "10.21105/joss.03900", + url = "https://docs.ropensci.org/cffr/articles/bibtex_cff.html" ) cat(" \n") thisart ``` -A BibTeX entry for LaTeX users: +A **BibTeX** entry for LaTeX users: ``` bibtex @article{hernangomez2022, @@ -62,17 +75,21 @@ A BibTeX entry for LaTeX users: author = {Diego Hernangómez}, year = 2022, journal = {The {cffr} package}, - volume = {Vignettes} + volume = {Vignettes}, + doi = {10.21105/joss.03900}, + url = {https://docs.ropensci.org/cffr/articles/bibtex_cff.html} } ``` ## BibTeX and R -[BibTeX](https://en.wikipedia.org/wiki/BibTeX) is a well-known format for storing references created by [Oren -Patashnik](https://en.wikipedia.org/wiki/Oren_Patashnik "Oren Patashnik") and [Leslie -Lamport](https://en.wikipedia.org/wiki/Leslie_Lamport "Leslie Lamport") back in 1985. BibTeX that may be reused by -another software, like [LaTeX](https://en.wikipedia.org/wiki/LaTeX), for adding references to a work. An example -structure of a BibTeX entry would be: +[**BibTeX**](https://en.wikipedia.org/wiki/BibTeX) is a well-known format for +storing references created by [Oren +Patashnik](https://en.wikipedia.org/wiki/Oren_Patashnik "Oren Patashnik") and +[Leslie Lamport](https://en.wikipedia.org/wiki/Leslie_Lamport "Leslie Lamport") +back in 1985. **BibTeX** can be reused by other software, such as +[LaTeX](https://en.wikipedia.org/wiki/LaTeX), to add references to scholarly +works. An example structure of a **BibTeX** entry would be: ``` bibtex @book{einstein1921, @@ -85,10 +102,10 @@ structure of a BibTeX entry would be: } ``` -On this case, the entry (identified as `einstein1921`) would refer to a book. This entry then can be used on a document -and include references to it. - -On **R** [@R_2021], we can replicate this structure using the `bibentry()` and `toBibtex()` functions: +In this case, the entry (identified as `einstein1921`) refers to a book. This +entry can then be used in a document to include references to it. In **R** +[@R_2021], we can replicate this structure using the `bibentry()` and +`toBibtex()` functions: ```{r bibentry, comment="#>"} entry <- bibentry("book", @@ -106,14 +123,16 @@ toBibtex(entry) The final results of the entry as a text string would be parsed as[^1]: -[^1]: By default R Pandoc would generate the cite on the Chicago author-date format [@rmarkdowncookbook2020] +[^1]: By default **R** Pandoc would generate the cite on the Chicago author-date + format [@rmarkdowncookbook2020] ```{r echo=FALSE, results='asis'} entry ``` -Additionally, **cffr** [@hernangomez2021] incorporates a function `cff_from_bibtex()` than can be used to read and -transform BibTeX strings into different formats: +Additionally, the **cffr** package [@hernangomez2021] incorporates a function +`cff_from_bibtex()` that can be used to read and transform **BibTeX** strings +into different formats: ```{r cffbibread,comment="#>"} string <- "@book{einstein1921, @@ -131,362 +150,398 @@ cff_format <- cff_from_bibtex(string) cff_format # To citation R format and bibtex -citation_format <- cff_to_bibtex(cff_format) +citation_format <- cff_to_bibentry(cff_format) class(citation_format) citation_format toBibtex(citation_format) ``` -## BibTeX definitions +## BibTeX Definitions -@patashnik1988 provides a comprehensive explanation of the BibTeX formats. We can distinguish between **Entries** and -**Fields**. +@patashnik1988 provides a comprehensive explanation of the **BibTeX** formats. +Let's distinguish between **Entries** and **Fields**. ### Entries {#entries} -Each entry type defines a different type of work. The 14 entry types defined on BibTeX[^2] are: - -[^2]: Other implementations similar to BibTeX, as [BibLaTeX](https://www.ctan.org/pkg/biblatex), expand the definitions - of entries including other types as **online**, **software** or **dataset**. On BibTeX these entries should be - reclassified to **misc**. - -- **\@article**: An article from a journal or magazine. -- **\@book**: A book with an explicit publisher. -- **\@booklet**: A work that is printed and bound, but without a named publisher or sponsoring institution. -- **\@conference**: The same as **\@inproceedings**, included for Scribe compatibility. -- **\@inbook**: A part of a book, which may be a chapter (or section or whatever) and/or a range of pages. -- **\@incollection**: A part of a book having its own title. -- **\@inproceedings**: An article in a conference proceedings. -- **\@manual**: Technical documentation. -- **\@mastersthesis**: A Master's thesis. -- **\@misc**: Use this type when nothing else fits. -- **\@phdthesis**: A PhD thesis. -- **\@proceedings**: The proceedings of a conference. -- **\@techreport**: A report published by a school or other institution, usually numbered within a series. -- **\@unpublished**: A document having an author and title, but not formally published. - -Regarding the entries, `bibentry()` **R** function does not implement **\@conference** . However, we can replace that -key by **\@inproceedings** given that the definition is identical. - -### Fields - -As in the case of Entries, @patashnik1988 provides also a definition for each of the possible standard BibTeX -fields[^3]. An entry can include other fields that would be ignored on the raw implementation of BibTeX: - -[^3]: As in the case of the entries, other implementations based on BibTeX may recognize additional fields. - -- **address**: Usually the address of the **publisher** or other of **institution**. -- **annote**: An annotation. It is not used by the standard bibliography styles, but may be used by others that - produce an annotated bibliography. -- **author**: The name(s) of the author(s), in the format described in the LaTeX book [@lamport86latex]. -- **booktitle**: Title of a book, part of which is being cited. For **\@book** entries, use the **title** field - instead. -- **chapter**: A chapter (or section or whatever) number. -- **crossref**: The database key of the entry being cross referenced. -- **edition**: The edition of a **\@book**, for example, "Second". This should be an ordinal, and should have the - first letter capitalized, the standard styles convert to lower case when necessary. -- **editor**: Name(s) of editor(s), typed as indicated in the LaTeX book [@lamport86latex]. If there is also an - **author** field, then the editor field gives the editor of the book or collection in which the reference appears. -- **howpublished**: How something strange has been published. The first word should be capitalized. -- **institution**: The sponsoring institution of a technical report. -- **journal**: A journal name. -- **key**: Used for alphabetizing, cross referencing, and creating a label when the **author** information is missing. -- **month**: The month in which the work was published or, for an unpublished work, in which it was written. You - should use the standard three-letter abbreviation, as described in Appendix B.1.3 of the LaTeX book - [@lamport86latex] (i.e. `jan, feb, mar`). -- **note**: Any additional information that can help the reader. The first word should be capitalized. -- **number**: The number of a journal, magazine, technical report, or of a work in a series. An issue of a journal or - magazine is usually identified by its **volume**: and number; the organization that issues a technical report - usually gives it a number; and sometimes books are given numbers in a named series. -- **organization**: The organization that sponsors a **\@conference** or that publishes a manual. -- **pages**: One or more page numbers or range of numbers, such as `42--111` or `7,41,73--97` or `43+`. -- **publisher**: The publisher's name. -- **school**: The name of the school where a thesis was written. -- **series**: The name of a series or set of books. When citing an entire book, the **title** field gives its title - and an optional **series** field gives the name of a series or multi-volume set in which the book is published. -- **title**: The work's title. -- **type**: The type of a technical report, for example, "Research Note". -- **volume**: The volume of a journal or multivolume book. -- **year**: The year of publication or, for an unpublished work, the year it was written. Generally it should consist - of four numerals, such as `1984`. - -There is a strict relation between Entries and Fields on BibTeX. Depending on the type of entries, some fields are -required while others are optional or even ignored. On the following table, required field are flagged as **x** and -optional fields are flagged as **o**. Fields on parenthesis (**(x), (o)**) denotes that there are some degree of -flexibility on the requirement of the field, see @patashnik1988 for more information. +Each entry type defines a different type of work. The 14 entry types defined in +**BibTeX** are: + +1. **\@article**: An article from a journal or magazine. +2. **\@book**: A book with an explicit publisher. +3. **\@booklet**: A work that is printed and bound, but without a named + publisher or sponsoring institution. +4. **\@conference**: Equivalent to **\@inproceedings**, included for + [Scribe](https://en.wikipedia.org/wiki/Scribe_(markup_language)) + compatibility. +5. **\@inbook**: A part of a book, which may be a chapter (or section) and/or a + range of pages. +6. **\@incollection**: A part of a book having its own title. +7. **\@inproceedings**: An article in conference proceedings. +8. **\@manual**: Technical documentation. +9. **\@mastersthesis**: A Master's thesis. +10. **\@misc**: Use this type when nothing else fits. +11. **\@phdthesis**: A PhD thesis. +12. **\@proceedings**: The proceedings of a conference. +13. **\@techreport**: A report published by a school or other institution, + usually numbered within a series. +14. **\@unpublished**: A document having an author and title, but not formally + published. + +Other implementations similar to **BibTeX**, such as **BibLaTeX** +[@biblatexpack], expand the definitions of entries to include other types such +as online resources, software, or datasets. In **BibTeX**, these entries should +be reclassified as **\@misc**. + +In **R**, the `bibentry()` base function does not implement **\@conference**. +However, we can use **\@inproceedings**, instead given that the definition is +identical. + +### Fields {#fields} + +Similar to the **Entries**, @patashnik1988 also provides definitions for each of +the possible standard **BibTeX fields**. While an entry must include certain +required fields, it can also include additional fields that might be ignored in +the raw implementation of **BibTeX**. Let's explore some of these fields: + +1. **address**: Typically represents the address of the **publisher** or + another **institution**. In the case of **\@conference**, + **\@inproceedings** and **\@proceedings** this field indicates where the + conference was held. +2. **annote**: An annotation. Although not used by standard bibliography + styles, it may be relevant for producing annotated bibliographies. +3. **author**: Contains the name(s) of the author(s), following the format + described in the LaTeX book [@lamport86latex]. +4. **booktitle**: Refers to the title of a book, part of which is being cited. + For **\@book** entries, use the **title** field instead. +5. **chapter**: Indicates a chapter (or section) number. +6. **crossref**: Refers to the database key of the entry being + cross-referenced. +7. **edition**: Specifies the edition of a **\@book**, e.g., `"Second"`. The + ordinal should have the first letter capitalized; standard styles convert to + lowercase when necessary. +8. **editor**: Contains the name(s) of editor(s), following the conventions in + the LaTeX book [@lamport86latex]. If there is also an **author** field, the + **editor** field specifies the editor of the book or collection where the + reference appears. +9. **howpublished**: Describes how something unusual has been published. The + first word should be capitalized. +10. **institution**: Represents the sponsoring institution of a technical + report. +11. **journal**: Refers to the name of a journal. +12. **key**: Used for alphabetizing, cross-referencing, and creating a label + when **author** information is missing. +13. **month**: Indicates the month in which the work was published or, for an + unpublished work, when it was written. Use the standard three-letter + abbreviation (e.g., `jan`, `feb`, `mar`) as described in **Appendix B.1.3** + of the LaTeX book [@lamport86latex]. +14. **note**: Provides any additional information that can assist the reader. + The first word should be capitalized. +15. **number**: Represents the number of a journal, magazine, technical report, + or a work in a series. An issue of a journal or magazine is usually + identified by its **volume** and number. Organizations issuing technical + reports often assign them numbers, and sometimes books are given numbers + within a named series. +16. **organization**: Refers to the organization that sponsors a + **\@conference** or publishes a manual. +17. **pages**: Specifies one or more page numbers or a range of numbers (e.g., + `42--111` or `7,41,73--97` or `43+`). +18. **publisher**: Indicates the publisher's name. +19. **school**: Provides the name of the school where a thesis was written. +20. **series**: Specifies the name of a series or set of books. When citing an + entire book, the **title** field gives its title, and an optional **series** + field provides the name of a series or multi-volume set in which the book is + published. +21. **title**: Represents the work's title. +22. **type**: Describes the type of a technical report (e.g., "Research Note"). +23. **volume**: Refers to the volume of a journal or multi-volume book. +24. **year**: Indicates the year of publication or, for an unpublished work, the + year it was written. Generally, it should consist of four numerals (e.g., + `1984`). + +As in the case of the **Entries**, other implementations such as **BibLaTeX** +recognize additional fields. + +In **BibTeX**, there exists a strict relationship between **Entries** and +**Fields**. Depending on the type of entry, certain fields are required, while +others are optional or even ignored. + +The following table summarizes the relationship between **Entries** and +**Fields** in **BibTeX**. Required fields are flagged as **x**, and optional +fields are flagged as **o**. For more detailed information, refer to +@patashnik1988. ```{r entry_fields1, echo=FALSE} -bibtex_field_entry <- read.csv( - system.file("extdata/bibtex_field_entry.csv", - package = "cffr" - ), - sep = "," +df_table <- table_master[table_master$table == "entry_fields", -1] + +nms <- c( + "**field**", "**\\@article**", "**\\@book**", "**\\@booklet**", + "**\\@inbook**", "**\\@incollection**", "**\\@conference, \\@inproceedings**", + "**\\@manual**", "**\\@mastersthesis, phdthesis**", "**\\@misc**", + "**\\@proceedings**", "**\\@techreport**", "**\\@unpublished**" ) -t1 <- bibtex_field_entry[, c(1:7)] + +df_table[is.na(df_table)] <- "" +row.names(df_table) <- NULL +t1 <- df_table[, c(1:7)] +nm1 <- nms[1:7] knitr::kable(t1, - col.names = gsub("\\.", ",", names(t1)), - align = c("l", rep("c", 6)), - caption = "BibTeX, required fields by entry" + col.names = nm1, row.names = NA, align = c("l", rep("c", 6)), + caption = "**BibTeX**, required fields by entry" ) ``` ```{r entry_fields2, echo=FALSE} -t2 <- bibtex_field_entry[, c(1, 8:13)] - +t2 <- df_table[, c(1, 8:13)] +nm2 <- nms[c(1, 8:13)] knitr::kable(t2, - col.names = gsub("\\.", ",", names(t2)), - align = c("l", rep("c", 6)), - caption = "(cont) BibTeX, required fields by entry" + col.names = nm2, row.names = NA, align = c("l", rep("c", 6)), + caption = "(cont) **BibTeX**, required fields by entry" ) ``` -It can be observed that just a subset of fields is required in any of the Entries. For example, **title**, **year** and -**author** are either required or optional on almost every entry, while **crossref**, **annote** or **key** are never -required. +It can be seen that only a subset of fields is necessary for any entry. For +instance, **title**, **year**, and **author** are either required or optional in +almost every entry, whereas **crossref**, **annote**, or **key** are never +mandatory. ## Citation File Format -[Citation File Format (CFF](https://citation-file-format.github.io/)) [@druskat_citation_2021] are plain text files with -human- and machine-readable citation information for software (and datasets). Among the [valid keys of -CFF](https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#valid-keys) there are two -keys, `preferred-citation` and `references` of special interest for citing and referring to related works[^4]: - -[^4]: See [Guide to Citation File Format schema version - 1.2.0](https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#preferred-citation). - -- **`preferred-citation`**: A reference to another work that should be cited instead of the software or dataset - itself. - -- **`references`**: Reference(s) to other creative works. Similar to a list of references in a paper, references of - the software or dataset may include other software (dependencies), or other research products that the software or - dataset builds on, but not work describing the software or dataset. - -These two keys are expected to be -[`definition.reference`](https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#definitionsreference) -objects, therefore they may contain the following keys: +[Citation File Format (CFF](https://citation-file-format.github.io/)) +[@druskat_citation_2021] consists of plain text files containing both human- and +machine-readable citation information for software and datasets. Within +[CFF]{.underline}, there are two important keys: `preferred-citation` and +`references`, which play a crucial role in citing and referring to related +works: + +- `preferred-citation`: Refers to another work that should be cited instead of + the software or dataset itself. +- `references`: Includes reference(s) to other creative works related to the + software or dataset. Similar to a list of references in a scholarly paper, + these references may encompass papers describing the abstract concepts of + the software or algorithms implemented in the software version. + +These two keys are expected to be `definition.reference objects`, as defined in +the [Guide to Citation File Format schema version +1.2.0](https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#preferred-citation), +and they may contain the following keys: ```{r refkeys, echo=FALSE, message=FALSE, warning=FALSE, results='asis'} library(cffr) # Fill with whites -l <- c(cff_schema_definitions_refs(), rep("", 4)) +init <- paste0("[", cff_schema_definitions_refs(), "]{.underline}") + +l <- c(init, rep("", 4)) refkeys <- matrix(l, ncol = 5, byrow = TRUE) knitr::kable(refkeys, - caption = "Valid keys on CFF `definition-reference` objects" + row.names = NA, + caption = "Valid keys on [CFF]{underline} `definition-reference` objects" +) +``` + +These keys are equivalent to the **BibTeX** [fields](#fields), with the +exception of the key [type]{.underline}. In [CFF]{.underline}, this key defines +the type of work[^2], making it analogous to the **BibTeX** [entries](#0). + +[^2]: See a complete list of possible values of [CFF]{.underline} + [type]{.underline} in [Appendix B](#appendix_cff_type). + +## Proposed Crosswalk + +The **cffr** package [@hernangomez2021] provides utilities for converting +**BibTeX** entries (via the **R** base function `bibentry()`) to +[CFF]{.underline} files and vice versa. This section describes how the +conversion between both formats has been implemented. The crosswalk is partially +based on @Haines_Ruby_CFF_Library_2021[^3]. + +[^3]: Note that this software performs only the conversion from + [CFF]{.underline} to **BibTeX**, however **cffr** can perform the conversion + in both directions. + +In the following two sections, I present an overview of the proposed mapping +between the **Entries** and **Fields** of **BibTeX** and the [CFF]{.underline} +keys. After this initial mapping, I propose further transformations to enhance +compatibility between both systems using different [Entry Models](#entrymodels). + +For better clarity, when a field is in **bold** (e.g., **\@book, edition**), it +corresponds to **BibTeX**, and when the field is [underlined]{.underline} (e.g., +[book, edition]{.underline}), it corresponds to [CFF]{.underline}. + +### Entry/Type Crosswalk + +For converting general **BibTeX** entries to [CFF]{.underline} +[types]{.underline}, the following crosswalk is proposed: + +```{r entry_bib2cff, echo=FALSE, results='asis'} +df_table <- table_master[table_master$table == "entry_bib2cff", c(2:4)] +df_table[is.na(df_table)] <- "" +# fix links +df_table$f3 <- gsub("link_to_entry_models", "#entrymodels", df_table$f3) +row.names(df_table) <- NULL + +knitr::kable(df_table, + col.names = c("**BibTeX** Entry", "[**CFF key: type**]{.underline}", "Notes"), + row.names = NA, + caption = "Entry/Type crosswalk: From **BibTeX** to [CFF]{.underline}" +) +``` + +The previous crosswalk has the following specifications: + +- **\@book**, **\@inbook**, and **\@incollection** are closely related in + **BibTeX**[^4]. While **\@inbook** and **\@incollection** both reference + parts of a **\@book**, the former is used for citing sections, chapters, + pages, or other specific parts, whereas the latter is used for citing parts + with a specific title. Since [CFF]{.underline} allows keys `type:book` and + `collection-type: book`, we may utilize a combination of these fields to tag + each entry type in [CFF]{.underline} accordingly. +- **\@mastersthesis** and **\@phdthesis** would be tagged using a combination + of `type:thesis` and `thesis-type`. + +[^4]: Note that **BibLaTeX** [@biblatexpack] handles **\@inbook** differently, + see [Appendix A](#appendix_inbook). + +Additionally, considering that [CFF]{.underline} allows for a wide range of +values[^5] for the [type]{.underline} field, the following conversion would be +applied from [CFF]{.underline} to **BibTeX**: + +[^5]: See [Appendix B](#appendix_cff_type) for all possible values. Information + extracted from @druskat2019. + +```{r entry_cff2bib, echo=FALSE,results='asis'} +df_table <- table_master[table_master$table == "entry_cff2bib", c(2:4)] +df_table[is.na(df_table)] <- "" +# fix links +df_table$f3 <- gsub("link_to_entry_models", "#entrymodels", df_table$f3) +row.names(df_table) <- NULL + +knitr::kable(df_table, + col.names = c("[**CFF key: type**]{.underline}", "**BibTeX** Entry", "Notes"), + caption = "Entry/Type crosswalk: From [CFF]{.underline} to **BibTeX**" +) +``` + +### Fields/Key Crosswalk + +There is a significant similarity between the definitions and names of certain +**BibTeX** fields and [CFF]{.underline} keys. While the equivalence is +straightforward in some cases, there are instances where certain keys need to be +processed depending on the **entry** type. + +```{r fields_bib2cff, echo=FALSE,results='asis'} +df_table <- table_master[table_master$table == "fields_bib2cff", c(2:4)] +df_table[is.na(df_table)] <- "" +# fix links +df_table$f3 <- gsub("link_to_entry_models", "#entrymodels", df_table$f3) +row.names(df_table) <- NULL + +knitr::kable(df_table, + col.names = c("**BibTeX Field**", "[CFF key]{.underline}", "Notes"), + caption = "**BibTeX** - [CFF]{.underline} Field/Key crosswalk" +) +``` + +We provide more detail on some of the mappings presented in the table above: + +- Some fields are not mapped because there is no clear equivalence with + [CFF]{.underline} keys (such as **annote**, **crossref**, and **key**). + Regarding the **type** field, the [CFF]{.underline} key [type]{.underline} + corresponds to the identifier of the work (similar to an entry in + **BibTeX**), therefore, **BibTeX type** won't be mapped. These fields are + always optional in **BibTeX**. + +- For the **address** field, its intended use in **BibTeX** varies depending + on the entry type (e.g., for **\@inproceedings**, it denotes the **address** + of the **conference**, while for **\@mastersthesis/\@phdthesis**, is the + **address** of the **school**, etc.). Mapping between **BibTeX** and + [CFF]{.underline} becomes more complex when related to institutions, + resulting in varying final mappings in [CFF]{.underline}. When converting + from [CFF]{.underline} to **BibTeX**, we propose to follow the same + entry-based logic, using the key [location]{.underline} as a fallback value + when converting to **address**. + +- In relation with this complexity mentioned above, **institution, + organization** and **school** would be mapped to [institution]{.underline}. + +- **series** would be mapped to [collection-title]{.underline} only on those + entries that does not requires **booktitle**. In practice, this means that + collection-title would correspond to **booktitle** for **incollection** and + **inproceedings**, and in the rest of cases it would correspond to series. A + consequence of this is that series information would be lost for + incollection and inproceedings, but on those cases is an optional field. + +- Regarding **series**, it would be mapped to [collection-title]{.underline} + only for those entries that do not require **booktitle**. In practice, this + means that [collection-title]{.underline} would correspond to **booktitle** + for **\@incollection** and **\@inproceedings**, while in other cases it + would correspond to **series**. As a consequence, **series** information + would be lost for **\@incollection** and **\@inproceedings**, but in those + cases, it is an optional field. + +- When converting from [CFF]{.underline} to **BibTeX**, we propose to use + [date-published]{.underline} as a fallback for extracting **month** and + **year** fields. + +- When **pages** is provided as a range separated by `--`, i.e, **pages = + {3--5}** would be parsed as [start: 3]{.underline}, [end: 5]{.underline} in + [CFF]{.underline}. + +Additionally, there are other [CFF]{.underline} keys that correspond to +**BibLaTeX** fields. We propose to include these fields in the crosswalk[^6], +even though they are not part of the core **BibTeX** fields definition. + +[^6]: See @biblatexcheatsheet for a preview of the accepted **BibLaTeX** fields. + +```{r fields_biblatex2cff, echo=FALSE,results='asis'} +df_table <- table_master[table_master$table == "fields_biblatex2cff", c(2:3)] +df_table[is.na(df_table)] <- "" +# fix links +df_table$f2 <- gsub("link_to_entry_models", "#entrymodels", df_table$f2) +row.names(df_table) <- NULL + +knitr::kable(df_table, + col.names = c("**BibLaTeX Field**", "[CFF key]{.underline}"), + caption = "**BibLaTeX** - [CFF]{.underline} Field/Key crosswalk" ) ``` -These keys are the equivalent to the fields of BibTeX (see [Fields]), with the exception of the key **type**. On CFF, -this key defines the type of work[^5], therefore this is the equivalent to the BibTeX entries (see [Entries](#entries)). - -[^5]: See a complete list of possible values of CFF type on the [Guide to Citation File Format schema version - 1.2.0](https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#definitionsreferencetype). - -## Proposed crosswalk - -The **cffr** package [@hernangomez2021] provides utilities from converting BibTeX entries (via the **R** base function -`bibentry()`) to CFF files and vice-versa. This section describes how the conversion between both formats have been -implemented. This crosswalk is based partially on @Haines_Ruby_CFF_Library_2021[^6]. - -[^6]: Note that this software performs only the conversion from CFF to BibTeX, however **cffr** can perform the - conversion in both directions. - -On the following two section I present an overview of the proposed mapping between the Entries and Fields of BibTeX and -the CFF keys. After this initial mapping, I propose further transformations to improve the compatibility between both -systems using different [Entry Models]. - -For a better understanding of this paper, when a field is in **bold** (i.e. **\@book**, **edition**) the field -correspond to **BibTex** and when the field is [underlined]{.underline} (i.e. [book]{.underline}, [edition]{.underline}) -the field correspond to [CFF]{.underline}. - -### Entry/Type crosswalk - -For converting general **BibTeX** entries to [CFF]{.underline} types, the following crosswalk is proposed: - -+----------------------------+-----------------------------------------------------------+----------------------------+ -| BibTeX Entry | [**Value of CFF key: type**]{.underline} | Notes | -+============================+===========================================================+============================+ -| **\@article** | [article]{.underline} | | -+----------------------------+-----------------------------------------------------------+----------------------------+ -| **\@book** | [book]{.underline} | | -+----------------------------+-----------------------------------------------------------+----------------------------+ -| **\@booklet** | [pamphlet]{.underline} | | -+----------------------------+-----------------------------------------------------------+----------------------------+ -| **\@conference** | [conference-paper]{.underline} | | -+----------------------------+-----------------------------------------------------------+----------------------------+ -| **\@inbook** | [book]{.underline} | See [Entry Models] | -+----------------------------+-----------------------------------------------------------+----------------------------+ -| **\@incollection** | [generic]{.underline} | See [Entry Models] | -+----------------------------+-----------------------------------------------------------+----------------------------+ -| **\@inproceedings** | [conference-paper]{.underline} | | -+----------------------------+-----------------------------------------------------------+----------------------------+ -| **\@manual** | [manual]{.underline} | | -+----------------------------+-----------------------------------------------------------+----------------------------+ -| **\@mastersthesis** | [thesis]{.underline} | See [Entry Models] | -+----------------------------+-----------------------------------------------------------+----------------------------+ -| **\@misc** | [generic]{.underline} | | -+----------------------------+-----------------------------------------------------------+----------------------------+ -| **\@phdthesis** | [thesis]{.underline} | See [Entry Models] | -+----------------------------+-----------------------------------------------------------+----------------------------+ -| **\@proceedings** | [proceedings]{.underline} | | -+----------------------------+-----------------------------------------------------------+----------------------------+ -| **\@techreport** | [report]{.underline} | | -+----------------------------+-----------------------------------------------------------+----------------------------+ -| **\@unpublished** | [unpublished]{.underline} | | -+----------------------------+-----------------------------------------------------------+----------------------------+ - -: Entry/Type crosswalk: From **BibTeX** to [CFF]{.underline} - -Also, given that CFF provides with a [wide range of allowed -values](https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#definitionsreferencetype) -on type, the following conversion would be performed from [CFF]{.underline} to **BibTeX**: - -+------------------------------------+---------------------------------+---------------------------------------------+ -| [Value of CFF key: | BibTeX Entry | Notes | -| type]{.underline} | | | -+====================================+=================================+=============================================+ -| [book]{.underline} | **\@book** **/ \@inbook** | See [Entry Models] | -+------------------------------------+---------------------------------+---------------------------------------------+ -| [conference]{.underline} | **\@inproceedings** | | -+------------------------------------+---------------------------------+---------------------------------------------+ -| [conference-paper]{.underline} | **\@inproceedings** | | -+------------------------------------+---------------------------------+---------------------------------------------+ -| [magazine-article]{.underline} | **\@article** | | -+------------------------------------+---------------------------------+---------------------------------------------+ -| [manual]{.underline} | **\@manual** | | -+------------------------------------+---------------------------------+---------------------------------------------+ -| [newspaper-article]{.underline} | **\@article** | | -+------------------------------------+---------------------------------+---------------------------------------------+ -| [pamphlet]{.underline} | **\@booklet** | | -+------------------------------------+---------------------------------+---------------------------------------------+ -| [proceedings]{.underline} | **\@proceedings** | | -+------------------------------------+---------------------------------+---------------------------------------------+ -| [report]{.underline} | **\@techreport** | | -+------------------------------------+---------------------------------+---------------------------------------------+ -| [thesis]{.underline} | **\@mastersthesis / | See [Entry Models] | -| | \@phdthesis** | | -+------------------------------------+---------------------------------+---------------------------------------------+ -| [unpublished]{.underline} | **\@unpublished** | | -+------------------------------------+---------------------------------+---------------------------------------------+ -| [generic]{.underline} | **\@misc / \@incollection** | Under specific conditions, see [Entry | -| | | Models] | -+------------------------------------+---------------------------------+---------------------------------------------+ -| \ | **\@misc** | | -+------------------------------------+---------------------------------+---------------------------------------------+ - -: Entry/Type crosswalk: From [CFF]{.underline} to **BibTeX** - -### Fields/Key crosswalk - -There is a large degree of similarity between the definition and names of some **BibTeX** fields and [CFF]{.underline} -keys. On the following cases, the equivalence is almost straightforward: - -| BibTeX Field | [CFF key]{.underline} | -|------------------|-----------------------------------------| -| **address** | See [Entry Models] | -| ***annote*** | \- | -| **author** | [authors]{.underline} | -| **booktitle** | [collection-title]{.underline} | -| **chapter** | [section]{.underline} | -| ***crossref*** | \- | -| **edition** | [edition]{.underline} | -| **editor** | [editors]{.underline} | -| **howpublished** | [medium]{.underline} | -| **institution** | See [Entry Models] | -| **journal** | [journal]{.underline} | -| ***key*** | \- | -| **month** | [month]{.underline} | -| **note** | [notes]{.underline} | -| **number** | [issue]{.underline} | -| **organization** | See [Entry Models] | -| **pages** | [start]{.underline} & [end]{.underline} | -| **publisher** | [publisher]{.underline} | -| **school** | See [Entry Models] | -| **series** | See [Entry Models] | -| **title** | [title]{.underline} | -| ***type*** | \- | -| **volume** | [volume]{.underline} | -| **year** | [year]{.underline} | - -: BibTeX - CFF Field/Key crosswalk - -Additionally, there are other additional CFF keys that have a correspondence with BibLaTeX fields. We propose also to -include these fields on the crosswalk[^7], although they are not part of the core BibTeX fields definition. - -[^7]: See @biblatexcheatsheet for a preview of the accepted BibLaTeX fields. - -| BibLaTeX Field | [CFF key]{.underline} | -|----------------|------------------------------| -| **abstract** | [abstract]{.underline} | -| **date** | [date-published]{.underline} | -| **doi** | [doi]{.underline} | -| **file** | [filename]{.underline} | -| **isbn** | [isbn]{.underline} | -| **issn** | [issn]{.underline} | -| **issuetitle** | [issue-title]{.underline} | -| **pagetotal** | [pages]{.underline} | -| **translator** | [translators]{.underline} | -| **url** | [url]{.underline} | -| **urldate** | [date-accessed]{.underline} | -| **version** | [version]{.underline} | - -: BibLaTeX - CFF Field/Key crosswalk - -## Entry Models - -This section presents the specific mapping proposed for each of the BibTeX entries, providing further information on how -each field is treated. Examples are adapted from the [xampl.bib](https://tug.org/texmf-docs/bibtex/xampl.bib) file -provided with the bibtex package [@patashnik]. - -### article +## Entry Models {#entrymodels} + +This section presents the specific mapping proposed for each of the **BibTeX** +entries, providing further information on how each field is treated. Examples +are adapted from the [xampl.bib](https://tug.org/texmf-docs/bibtex/xampl.bib) +file provided with the **bibtex** package [@patashnik]. + +### \@article {#article} The crosswalk of **\@article** does not require any special treatment. -+------------------------+------------------------------------------+------------------------------------------------+ -| BibTeX | [CFF]{.underline} | Note | -+========================+==========================================+================================================+ -| **\@article** | [type: article]{.underline} | When converting CFF to BibTeX, [type | -| | | magazine-article]{.underline} and | -| | | [newspaper-article]{.underline} are converted | -| | | to **\@article**. | -+------------------------+------------------------------------------+------------------------------------------------+ -| **author\*** | [authors]{.underline} | | -+------------------------+------------------------------------------+------------------------------------------------+ -| **title\*** | [title]{.underline} | | -+------------------------+------------------------------------------+------------------------------------------------+ -| **journal\*** | [journal]{.underline} | | -+------------------------+------------------------------------------+------------------------------------------------+ -| **year\*** | [year]{.underline} | | -+------------------------+------------------------------------------+------------------------------------------------+ -| **volume** | [volume]{.underline} | | -+------------------------+------------------------------------------+------------------------------------------------+ -| **number** | [issue]{.underline} | | -+------------------------+------------------------------------------+------------------------------------------------+ -| **pages** | [start]{.underline} and | Separated by `--`, i.e, **pages = {3\--5}** | -| | [end]{.underline} | would be parsed as: | -| | | | -| | | - [start: 3]{.underline} | -| | | | -| | | - [end: 5]{.underline} | -+------------------------+------------------------------------------+------------------------------------------------+ -| **month** | [month]{.underline} | As a fallback, **month** could be extracted | -| | | also from **date** (BibLaTeX field) or | -| | | [date-published]{.underline} | -+------------------------+------------------------------------------+------------------------------------------------+ -| **note** | [notes]{.underline} | | -+------------------------+------------------------------------------+------------------------------------------------+ - -: **\@article** Model +```{r model_article, echo=FALSE, results='asis'} +df_table <- table_master[table_master$table == "model_article", c(2:4)] +df_table[is.na(df_table)] <- "" + +# fix links +df_table$f3 <- gsub("link_to_entry_models", "#entrymodels", df_table$f3) +df_table$f3 <- gsub("link_to_article", "#article", df_table$f3) +df_table$f3 <- gsub("link_to_booklet", "#booklet", df_table$f3) +df_table$f3 <- gsub("link_to_book", "#book-inbook", df_table$f3) + +row.names(df_table) <- NULL +knitr::kable(df_table, + col.names = c("**BibTeX**", "[CFF]{.underline}", "Notes"), + caption = "**\\@article** Model" +) +``` **Examples** -[*BibTeX entry*]{.underline} +**BibTeX entry** ``` bibtex @article{article-full, @@ -502,7 +557,7 @@ The crosswalk of **\@article** does not require any special treatment. } ``` -[*CFF entry*]{.underline} +[CFF entry]{.underline} ```{r echo=FALSE} bib <- "@article{article-full, @@ -519,69 +574,53 @@ bib <- "@article{article-full, cff_from_bibtex(bib) ``` -[*From CFF to BibTeX*]{.underline} +From [CFF]{.underline} to **BibTeX** ```{r echo=FALSE} -toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) -``` - -### book/inbook - -In terms of field required on BibTeX, the only difference between **\@book** and **\@inbook** is that the latter -requires also a **chapter** or **pages**, while for **\@book** these fields are not even optional. So we propose here to -identify an **\@inbook** on CFF as a [book]{.underline} with [section]{.underline} and -[start]{.underline}-[end]{.underline} fields (CFF). - -Another specificity is that **series** field is mapped to [collection-title]{.underline} and **address** is mapped as -the [address]{.underline} of the [publisher]{.underline} (CFF). - -+----------------------+---------------------------+------------------------------------------------------------------+ -| BibTeX | [CFF]{.underline} | Note | -+======================+===========================+==================================================================+ -| **\@book** | [type: book]{.underline} | | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **\@inbook** | [type: book]{.underline} | For identifying an **\@inbook** in CFF, assess if | -| | | [section]{.underline} or [start/end]{.underline} information is | -| | | available | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **author\*** | [authors]{.underline} | | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **editor\*** | [editors]{.underline} | | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **title\*** | [title]{.underline} | | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **publisher\*** | [publisher]{.underline} | | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **year\*** | [year]{.underline} | | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **chapter\*** | [section]{.underline} | Only required on **\@inbook** | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **pages\*** | [start]{.underline} and | Only required on **\@inbook** | -| | [end]{.underline} | | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **volume** | [volume]{.underline} | | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **number** | [issue]{.underline} | | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **series** | [coll | | -| | ection-title]{.underline} | | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **address** | [address]{.underline} | As a fallback, the field [location]{.underline} can be used | -| | property of | | -| | [publisher]{.underline} | | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **edition** | [edition]{.underline} | | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **month** | [month]{.underline} | See **Note** on [article] | -+----------------------+---------------------------+------------------------------------------------------------------+ -| **note** | [notes]{.underline} | | -+----------------------+---------------------------+------------------------------------------------------------------+ - -: **\@book/\@inbook** Model - -**Examples: book** - -[*BibTeX entry*]{.underline} +toBibtex(cff_to_bibentry(cff_from_bibtex(bib))) +``` + +### \@book / \@inbook {#book-inbook} + +In terms of the fields required in BibTeX, the primary difference between +**\@book** and **\@inbook** is that **\@inbook** requires a **chapter** or +**page** field, while **\@book** does not even allow these fields as optional. +Therefore, we propose that an **\@inbook** entry in [CFF]{.underline} be treated +as a **\@book** with the following supplementary fields: + +1. [section]{.underline}: To denote the specific **chapter** within the book. +2. [start-end]{.underline}: To indicate the range of **pages** covered by the + section. + +Additionally, note that in [CFF]{.underline}, the **series** field corresponds +to [collection-title]{.underline}, and the **address** field represents the +[publisher]{.underline}'s [address]{.underline}. By last, the key +[collection-type]{.underline} would be populated with [book-series]{.underline}. + +```{r model_book, echo=FALSE, results='asis'} +df_table <- table_master[table_master$table == "model_book", c(2:4)] +df_table[is.na(df_table)] <- "" + +# fix links +df_table$f3 <- gsub("link_to_entry_models", "#entrymodels", df_table$f3) +df_table$f3 <- gsub("link_to_article", "#article", df_table$f3) +df_table$f3 <- gsub("link_to_booklet", "#booklet", df_table$f3) +df_table$f3 <- gsub("link_to_book", "#book-inbook", df_table$f3) + +row.names(df_table) <- NULL +knitr::kable(df_table, + col.names = c("**BibTeX**", "[CFF]{.underline}", "Notes"), + caption = "**\\@book / \\@inbook** Model" +) +``` + +There are notable differences in how **BibTeX** and **BibLaTeX** handle the +**\@inbook** entry (further discussed in the [Appendix A](#appendix_inbook)). We +propose to treat a **BibLaTeX \@inbook** as a **BibTeX \@incollection.** + +**Examples: \@book** + +**BibTeX entry** ``` bibtex @book{book-full, @@ -598,7 +637,7 @@ the [address]{.underline} of the [publisher]{.underline} (CFF). } ``` -[*CFF entry*]{.underline} +[CFF entry]{.underline} ```{r echo=FALSE} bib <- "@book{book-full, @@ -617,15 +656,15 @@ bib <- "@book{book-full, cff_from_bibtex(bib) ``` -[*From CFF to BibTeX*]{.underline} +From [CFF]{.underline} to **BibTeX** ```{r, echo=FALSE} -toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) +toBibtex(cff_to_bibentry(cff_from_bibtex(bib))) ``` -**Examples: inbook** +**Examples: \@inbook** -[*BibTeX entry*]{.underline} +**BibTeX entry** ``` bibtex @inbook{inbook-full, @@ -645,7 +684,7 @@ toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) } ``` -[*CFF entry*]{.underline} +[CFF entry]{.underline} ```{r echo=FALSE,} bib <- "@inbook{inbook-full, @@ -667,47 +706,36 @@ bib <- "@inbook{inbook-full, cff_from_bibtex(bib) ``` -[*From CFF to BibTeX*]{.underline} +From [CFF]{.underline} to **BibTeX** ```{r echo=FALSE,} -toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) +toBibtex(cff_to_bibentry(cff_from_bibtex(bib))) ``` -### booklet +### \@booklet {#booklet} In **\@booklet** **address** is mapped to [location]{.underline}. -+---------------------+---------------------+--------------------------------------------------------------------------+ -| BibTeX | [CFF]{.underline} | Note | -+=====================+=====================+==========================================================================+ -| **\@booklet** | [type: | | -| | pa | | -| | mphlet]{.underline} | | -+---------------------+---------------------+--------------------------------------------------------------------------+ -| **title\*** | [title]{.underline} | | -+---------------------+---------------------+--------------------------------------------------------------------------+ -| **author\*** | [a | | -| | uthors]{.underline} | | -+---------------------+---------------------+--------------------------------------------------------------------------+ -| **howpublished** | [ | | -| | medium]{.underline} | | -+---------------------+---------------------+--------------------------------------------------------------------------+ -| **address** | [lo | | -| | cation]{.underline} | | -+---------------------+---------------------+--------------------------------------------------------------------------+ -| **month** | [month]{.underline} | See **Note** on [article] | -+---------------------+---------------------+--------------------------------------------------------------------------+ -| **year** | [year]{.underline} | As a fallback, **year** could be extracted also from **date** (BibLaTeX | -| | | field)/ [date-published]{.underline} | -+---------------------+---------------------+--------------------------------------------------------------------------+ -| **note** | [notes]{.underline} | | -+---------------------+---------------------+--------------------------------------------------------------------------+ - -: **\@booklet** Model +```{r model_booklet, echo=FALSE, results='asis'} +df_table <- table_master[table_master$table == "model_booklet", c(2:4)] +df_table[is.na(df_table)] <- "" + +# fix links +df_table$f3 <- gsub("link_to_entry_models", "#entrymodels", df_table$f3) +df_table$f3 <- gsub("link_to_article", "#article", df_table$f3) +df_table$f3 <- gsub("link_to_booklet", "#booklet", df_table$f3) +df_table$f3 <- gsub("link_to_book", "#book-inbook", df_table$f3) + +row.names(df_table) <- NULL +knitr::kable(df_table, + col.names = c("**BibTeX**", "[CFF]{.underline}", "Notes"), + caption = "**\\@booklet** Model" +) +``` **Examples** -[*BibTeX entry*]{.underline} +**BibTeX entry** ``` bibtex @booklet{booklet-full, @@ -721,7 +749,7 @@ In **\@booklet** **address** is mapped to [location]{.underline}. } ``` -[*CFF entry*]{.underline} +[CFF entry]{.underline} ```{r echo=FALSE, } bib <- "@booklet{booklet-full, @@ -737,61 +765,38 @@ bib <- "@booklet{booklet-full, cff_from_bibtex(bib) ``` -[*From CFF to BibTeX*]{.underline} +From [CFF]{.underline} to **BibTeX** ```{r echo=FALSE, } -toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) -``` - -### conference/inproceedings - -Note that in this case, **organization** is mapped to [institution]{.underline}, as BibTeX does not prescribe the use of -**institution** on these entries. - -+---------------------------+----------------------------+-------------------------------------------------------------+ -| BibTeX | CFF | Note | -+===========================+============================+=============================================================+ -| **\@conference / | [type: | CFF entries with [type; conference]{.underline} are mapped | -| \@inproceedings** | con | back to **\@inproceedings**. | -| | ference-paper]{.underline} | | -+---------------------------+----------------------------+-------------------------------------------------------------+ -| **author\*** | [authors]{.underline} | | -+---------------------------+----------------------------+-------------------------------------------------------------+ -| **title\*** | [title]{.underline} | | -+---------------------------+----------------------------+-------------------------------------------------------------+ -| **booktitle\*** | [col | | -| | lection-title]{.underline} | | -+---------------------------+----------------------------+-------------------------------------------------------------+ -| **year\*** | [year]{.underline} | | -+---------------------------+----------------------------+-------------------------------------------------------------+ -| **editor** | [editors]{.underline} | | -+---------------------------+----------------------------+-------------------------------------------------------------+ -| **volume** | [volume]{.underline} | | -+---------------------------+----------------------------+-------------------------------------------------------------+ -| **number** | [issue]{.underline} | | -+---------------------------+----------------------------+-------------------------------------------------------------+ -| **series** | [conference]{.underline} | | -+---------------------------+----------------------------+-------------------------------------------------------------+ -| **pages** | [start]{.underline} and | See **Note** on [article] | -| | [end]{.underline} | | -+---------------------------+----------------------------+-------------------------------------------------------------+ -| **address** | [location]{.underline} | As a fallback, [address]{.underline} property of | -| | | [conference]{.underline} can be used | -+---------------------------+----------------------------+-------------------------------------------------------------+ -| **month** | [month]{.underline} | See **Note** on [article] | -+---------------------------+----------------------------+-------------------------------------------------------------+ -| **organization** | [institution]{.underline} | | -+---------------------------+----------------------------+-------------------------------------------------------------+ -| **publisher** | [publisher]{.underline} | | -+---------------------------+----------------------------+-------------------------------------------------------------+ -| **note** | [notes]{.underline} | | -+---------------------------+----------------------------+-------------------------------------------------------------+ - -: **\@conference/\@inproceedings** Model +toBibtex(cff_to_bibentry(cff_from_bibtex(bib))) +``` + +### \@conference / \@inproceedings {#conf_inproc} + +Note that in this case, **organization** is mapped to [institution]{.underline}. +Additionally, **series** would be ignored as there is not clear mapping on +[CFF]{.underline} for this field. + +```{r model_inproceedings, echo=FALSE, results='asis'} +df_table <- table_master[table_master$table == "model_inproceedings", c(2:4)] +df_table[is.na(df_table)] <- "" + +# fix links +df_table$f3 <- gsub("link_to_entry_models", "#entrymodels", df_table$f3) +df_table$f3 <- gsub("link_to_article", "#article", df_table$f3) +df_table$f3 <- gsub("link_to_booklet", "#booklet", df_table$f3) +df_table$f3 <- gsub("link_to_book", "#book-inbook", df_table$f3) + +row.names(df_table) <- NULL +knitr::kable(df_table, + col.names = c("**BibTeX**", "[CFF]{.underline}", "Notes"), + caption = "**\\@conference / \\@inproceedings** Model" +) +``` **Examples** -[*BibTeX entry*]{.underline} +**BibTeX entry** ``` bibtex @inproceedings{inproceedings-full, @@ -810,7 +815,7 @@ Note that in this case, **organization** is mapped to [institution]{.underline}, } ``` -[*CFF entry*]{.underline} +[CFF entry]{.underline} ```{r echo=FALSE,} bib <- "@inproceedings{inproceedings-full, @@ -831,63 +836,42 @@ bib <- "@inproceedings{inproceedings-full, cff_from_bibtex(bib) ``` -[*From CFF to BibTeX*]{.underline} +From [CFF]{.underline} to **BibTeX** ```{r echo=FALSE,} -toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) -``` - -### incollection - -As **booktitle** is a required field, we propose to map that field to [collection-title]{.underline} and the -[type]{.underline} to [generic]{.underline}. Therefore, an **\@incollection** is a [type: generic]{.underline} with a -[collection-title]{.underline} key. - -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **BibTeX** | [CFF]{.underline} | Note | -+=========================+=================================================+=========================================+ -| **\@incollection** | [type: generic]{.underline} | Including a | -| | | [collection-title]{.underline} value | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **author\*** | [authors]{.underline} | | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **title\*** | [title]{.underline} | | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **booktitle\*** | [collection-title]{.underline} | | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **publisher\*** | [publisher]{.underline} | | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **year\*** | [year]{.underline} | | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **editor** | [editors]{.underline} | | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **volume** | [volume]{.underline} | | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **number** | [issue]{.underline} | | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **series** | [series]{.underline} | | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **type** | \- | Ignored | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **chapter** | [section]{.underline} | | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **pages** | [start]{.underline} and [end]{.underline} | See **Note** on [article] | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **address** | [address]{.underline} property of | See **Note** on [book/inbook] | -| | [publisher]{.underline} | | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **edition** | [edition]{.underline} | | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **month** | [month]{.underline} | See **Note** on [article] | -+-------------------------+-------------------------------------------------+-----------------------------------------+ -| **note** | [notes]{.underline} | | -+-------------------------+-------------------------------------------------+-----------------------------------------+ - -: **\@incollection** Model +toBibtex(cff_to_bibentry(cff_from_bibtex(bib))) +``` + +### \@incollection {#incol} + +As **booktitle** is a required field, we propose to map that field to +[collection-title]{.underline} and the [type]{.underline} to +[generic]{.underline}. Therefore, an **\@incollection** is a [type: +generic]{.underline} with a [collection-title]{.underline} key. + +Additionally, **series** and **type** would be ignored as there is not clear +mapping on [CFF]{.underline} for this field. + +```{r model_incollection, echo=FALSE, results='asis'} +df_table <- table_master[table_master$table == "model_incollection", c(2:4)] +df_table[is.na(df_table)] <- "" + +# fix links +df_table$f3 <- gsub("link_to_entry_models", "#entrymodels", df_table$f3) +df_table$f3 <- gsub("link_to_article", "#article", df_table$f3) +df_table$f3 <- gsub("link_to_booklet", "#booklet", df_table$f3) +df_table$f3 <- gsub("link_to_book", "#book-inbook", df_table$f3) + +row.names(df_table) <- NULL +knitr::kable(df_table, + col.names = c("**BibTeX**", "[CFF]{.underline}", "Notes"), + caption = "**\\@incollection** Model" +) +``` **Examples** -[*BibTeX entry*]{.underline} +**BibTeX entry** ``` bibtex @incollection{incollection-full, @@ -909,7 +893,7 @@ As **booktitle** is a required field, we propose to map that field to [collectio } ``` -[*CFF entry*]{.underline} +[CFF entry]{.underline} ```{r echo=FALSE,} bib <- "@incollection{incollection-full, @@ -933,46 +917,40 @@ bib <- "@incollection{incollection-full, cff_from_bibtex(bib) ``` -[*From CFF to BibTeX*]{.underline} +From [CFF]{.underline} to **BibTeX** ```{r echo=FALSE,} -toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) -``` - -### manual - -As in the case of [conference/inproceedings], **organization** is mapped to [institution]{.underline}. - -+----------------------------+--------------------------------------------+-------------------------------------------+ -| **BibTeX** | [CFF]{.underline} | Note | -+============================+============================================+===========================================+ -| **\@manual** | [type: manual]{.underline} | | -+----------------------------+--------------------------------------------+-------------------------------------------+ -| **title\*** | [title]{.underline} | | -+----------------------------+--------------------------------------------+-------------------------------------------+ -| **author** | [authors]{.underline} | | -+----------------------------+--------------------------------------------+-------------------------------------------+ -| **organization** | [institution]{.underline} | | -+----------------------------+--------------------------------------------+-------------------------------------------+ -| **address** | [location]{.underline} | | -+----------------------------+--------------------------------------------+-------------------------------------------+ -| **edition** | [edition]{.underline} | | -+----------------------------+--------------------------------------------+-------------------------------------------+ -| **month** | [month]{.underline} | See **Note** on [article] | -+----------------------------+--------------------------------------------+-------------------------------------------+ -| **year** | [year]{.underline} | See **Note** on [booklet] | -+----------------------------+--------------------------------------------+-------------------------------------------+ -| **note** | [notes]{.underline} | | -+----------------------------+--------------------------------------------+-------------------------------------------+ - -: **\@manual** Model +toBibtex(cff_to_bibentry(cff_from_bibtex(bib))) +``` + +### \@manual + +As in the case of [**\@conference** / **\@inproceedings**](#conf_inproc), +**organization** is mapped to [institution]{.underline}. + +```{r model_manual, echo=FALSE, results='asis'} +df_table <- table_master[table_master$table == "model_manual", c(2:4)] +df_table[is.na(df_table)] <- "" + +# fix links +df_table$f3 <- gsub("link_to_entry_models", "#entrymodels", df_table$f3) +df_table$f3 <- gsub("link_to_article", "#article", df_table$f3) +df_table$f3 <- gsub("link_to_booklet", "#booklet", df_table$f3) +df_table$f3 <- gsub("link_to_book", "#book-inbook", df_table$f3) + +row.names(df_table) <- NULL +knitr::kable(df_table, + col.names = c("**BibTeX**", "[CFF]{.underline}", "Notes"), + caption = "**\\@manual** Model" +) +``` **Examples** -[*BibTeX entry*]{.underline} +**BibTeX entry** -Note that **month** can't be parsed to a single integer in the range `1--12` as required on CFF, so it is not parsed to -avoid validation errors. +Note that **month** can't be parsed to a single integer in the range `1--12` as +required on CFF, so it is not parsed to avoid validation errors. ``` bibtex @manual{manual-full, @@ -987,7 +965,7 @@ avoid validation errors. } ``` -[*CFF entry*]{.underline} +[CFF entry]{.underline} ```{r echo=FALSE,} bib <- "@manual{manual-full, @@ -1004,52 +982,44 @@ bib <- "@manual{manual-full, cff_from_bibtex(bib) ``` -[*From CFF to BibTeX*]{.underline} +From [CFF]{.underline} to **BibTeX** ```{r echo=FALSE,} -toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) -``` - -### mastersthesis/phdthesis - -In terms of field required on BibTeX, it is identical for both **\@mastersthesis** and **\@phdthesis.** - -We propose here to identify each type of thesis using the field [thesis-type]{.underline} (CFF). So if -[thesis-type]{.underline} contains a [regex pattern](https://regex101.com/r/mBWfbs/1) `(?i)(phd)` it would be recognized -as **\@phdthesis**. - -+------------------------+------------------------------------------+-------------------------------------------------+ -| BibTeX | [CFF]{.underline} | Note | -+========================+==========================================+=================================================+ -| **\@mastersthesis** | [type: thesis]{.underline} | Use also [thesis-type]{.underline} for | -| | | identifying the thesis type. | -+------------------------+------------------------------------------+-------------------------------------------------+ -| **\@phdthesis** | [type: thesis]{.underline} | Use also [thesis-type]{.underline} for | -| | | identifying the thesis type. | -+------------------------+------------------------------------------+-------------------------------------------------+ -| **author\*** | [authors]{.underline} | | -+------------------------+------------------------------------------+-------------------------------------------------+ -| **title\*** | [title]{.underline} | | -+------------------------+------------------------------------------+-------------------------------------------------+ -| **school\*** | [institution]{.underline} | | -+------------------------+------------------------------------------+-------------------------------------------------+ -| **year\*** | [year]{.underline} | | -+------------------------+------------------------------------------+-------------------------------------------------+ -| **type** | | | -+------------------------+------------------------------------------+-------------------------------------------------+ -| **address** | [address]{.underline} property of | See **Note** on [book/inbook] | -| | [institution]{.underline} | | -+------------------------+------------------------------------------+-------------------------------------------------+ -| **month** | [month]{.underline} | See **Note** on [article] | -+------------------------+------------------------------------------+-------------------------------------------------+ -| **note** | [notes]{.underline} | | -+------------------------+------------------------------------------+-------------------------------------------------+ - -: **\@mastersthesis/phdthesis** Model - -**Examples: mastersthesis** - -[*BibTeX entry*]{.underline} +toBibtex(cff_to_bibentry(cff_from_bibtex(bib))) +``` + +### \@mastersthesis / \@phdthesis + +In terms of field required on BibTeX, it is identical for both +**\@mastersthesis** and **\@phdthesis.** + +We propose here to identify each type of thesis using the key +[thesis-type]{.underline} So if [thesis-type]{.underline} contains a [regex +pattern](https://regex101.com/r/mBWfbs/1) `(?i)(phd)` it would be recognized as +**\@phdthesis**. + +Additionally, **school** would be mapped to [institution]{.underline}. + +```{r model_thesis, echo=FALSE, results='asis'} +df_table <- table_master[table_master$table == "model_thesis", c(2:4)] +df_table[is.na(df_table)] <- "" + +# fix links +df_table$f3 <- gsub("link_to_entry_models", "#entrymodels", df_table$f3) +df_table$f3 <- gsub("link_to_article", "#article", df_table$f3) +df_table$f3 <- gsub("link_to_booklet", "#booklet", df_table$f3) +df_table$f3 <- gsub("link_to_book", "#book-inbook", df_table$f3) + +row.names(df_table) <- NULL +knitr::kable(df_table, + col.names = c("**BibTeX**", "[CFF]{.underline}", "Notes"), + caption = "**\\@mastersthesis / \\@phdthesis** Model" +) +``` + +**Examples: \@mastersthesis** + +**BibTeX entry** ``` bibtex @mastersthesis{mastersthesis-full, @@ -1064,7 +1034,7 @@ as **\@phdthesis**. } ``` -[*CFF entry*]{.underline} +[CFF entry]{.underline} ```{r echo=FALSE} bib <- "@mastersthesis{mastersthesis-full, @@ -1081,15 +1051,15 @@ bib <- "@mastersthesis{mastersthesis-full, cff_from_bibtex(bib) ``` -[*From CFF to BibTeX*]{.underline} +From [CFF]{.underline} to **BibTeX** ```{r, echo=FALSE} -toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) +toBibtex(cff_to_bibentry(cff_from_bibtex(bib))) ``` -**Examples: phdthesis** +**Examples: \@phdthesis** -[*BibTeX entry*]{.underline} +**BibTeX entry** ``` bibtex @phdthesis{phdthesis-full, @@ -1104,7 +1074,7 @@ toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) } ``` -[*CFF entry*]{.underline} +[CFF entry]{.underline} ```{r echo=FALSE,} bib <- "@phdthesis{phdthesis-full, @@ -1121,42 +1091,42 @@ bib <- "@phdthesis{phdthesis-full, cff_from_bibtex(bib) ``` -[*From CFF to BibTeX*]{.underline} +From [CFF]{.underline} to **BibTeX** ```{r echo=FALSE,} -toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) +toBibtex(cff_to_bibentry(cff_from_bibtex(bib))) ``` -### misc +### \@misc -The crosswalk of **\@misc** does not require any special treatment. This entry does not require any field. +The crosswalk of **\@misc** does not require any special treatment. This +**entry** does not require any **field**. -Note also that it is mapped to [type: generic]{.underline} as [incollection], but in this case **booktitle** is not even -an option, so the proposed definition should cover both **\@misc** and **\@incollection** without problems. +Note also that it is mapped to [type: generic]{.underline} as +[**\@incollection**](#incol), but in this case **booktitle** is not even an +option, so the proposed definition should cover both **\@misc** and +**\@incollection** without problems. -+----------------------------+---------------------------------------------+------------------------------------------+ -| **BibTeX** | [CFF]{.underline} | Note | -+============================+=============================================+==========================================+ -| **\@misc** | [type: generic]{.underline} | | -+----------------------------+---------------------------------------------+------------------------------------------+ -| **author** | [authors]{.underline} | | -+----------------------------+---------------------------------------------+------------------------------------------+ -| **title** | [title]{.underline} | | -+----------------------------+---------------------------------------------+------------------------------------------+ -| **howpublished** | [medium]{.underline} | | -+----------------------------+---------------------------------------------+------------------------------------------+ -| **month** | [month]{.underline} | See **Note** on [article] | -+----------------------------+---------------------------------------------+------------------------------------------+ -| **year** | [year]{.underline} | See **Note** on [booklet] | -+----------------------------+---------------------------------------------+------------------------------------------+ -| **note** | [notes]{.underline} | | -+----------------------------+---------------------------------------------+------------------------------------------+ +```{r model_misc, echo=FALSE, results='asis'} +df_table <- table_master[table_master$table == "model_misc", c(2:4)] +df_table[is.na(df_table)] <- "" -: **\@misc** Model +# fix links +df_table$f3 <- gsub("link_to_entry_models", "#entrymodels", df_table$f3) +df_table$f3 <- gsub("link_to_article", "#article", df_table$f3) +df_table$f3 <- gsub("link_to_booklet", "#booklet", df_table$f3) +df_table$f3 <- gsub("link_to_book", "#book-inbook", df_table$f3) + +row.names(df_table) <- NULL +knitr::kable(df_table, + col.names = c("**BibTeX**", "[CFF]{.underline}", "Notes"), + caption = "**\\@misc** Model" +) +``` **Examples** -[*BibTeX entry*]{.underline} +**BibTeX entry** ``` bibtex @misc{misc-full, @@ -1169,7 +1139,7 @@ an option, so the proposed definition should cover both **\@misc** and **\@incol } ``` -[*CFF entry*]{.underline} +[CFF entry]{.underline} ```{r echo=FALSE,} bib <- "@misc{misc-full, @@ -1184,61 +1154,45 @@ bib <- "@misc{misc-full, cff_from_bibtex(bib) ``` -[*From CFF to BibTeX*]{.underline} +From [CFF]{.underline} to **BibTeX** ```{r echo=FALSE,} -toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) +toBibtex(cff_to_bibentry(cff_from_bibtex(bib))) ``` -### proceedings +### \@proceedings -The proposed model is similar to [conference/inproceedings]. Note that **\@proceedings** does not prescribe a **author** -field. On this cases, as [authors]{.underline} is required on CFF, we would use *anonymous*[^8] when converting to CFF -and omit it on the conversion back to CFF. +The proposed model is consistent with [**\@conference** / +**\@inproceedings**](#conf_inproc). Note that **\@proceedings** does not +prescribe a **author** field. On this cases, as [authors]{.underline} is +required on [CFF]{.underline}, we would use *anonymous*[^7] when converting to +[CFF]{.underline} and omit it on the conversion from [CFF]{.underline} to +**BibTeX**. -[^8]: As proposed on [*How to deal with unknown individual +[^7]: As proposed on [*How to deal with unknown individual authors?*](https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#how-to-deal-with-unknown-individual-authors), **(Guide to Citation File Format schema version 1.2.0)** -+-----------------------+-----------------------+--------------------------------------------------------------------+ -| BibTeX | [CFF]{.underline} | Note | -+=======================+=======================+====================================================================+ -| **\@proceedings** | [type: | | -| | pro | | -| | ceedings]{.underline} | | -+-----------------------+-----------------------+--------------------------------------------------------------------+ -| **title\*** | [title]{.underline} | | -+-----------------------+-----------------------+--------------------------------------------------------------------+ -| **year\*** | [year]{.underline} | | -+-----------------------+-----------------------+--------------------------------------------------------------------+ -| **editor** | [editors]{.underline} | | -+-----------------------+-----------------------+--------------------------------------------------------------------+ -| **volume** | [volume]{.underline} | | -+-----------------------+-----------------------+--------------------------------------------------------------------+ -| **number** | [issue]{.underline} | | -+-----------------------+-----------------------+--------------------------------------------------------------------+ -| **series** | [co | | -| | nference]{.underline} | | -+-----------------------+-----------------------+--------------------------------------------------------------------+ -| **address** | [ | As a fallback, [address]{.underline} property of | -| | location]{.underline} | [conference]{.underline} can be used | -+-----------------------+-----------------------+--------------------------------------------------------------------+ -| **month** | [month]{.underline} | See **Note** on [article] | -+-----------------------+-----------------------+--------------------------------------------------------------------+ -| **organization** | [ins | | -| | titution]{.underline} | | -+-----------------------+-----------------------+--------------------------------------------------------------------+ -| **publisher** | [p | | -| | ublisher]{.underline} | | -+-----------------------+-----------------------+--------------------------------------------------------------------+ -| **note** | [notes]{.underline} | | -+-----------------------+-----------------------+--------------------------------------------------------------------+ - -: **\@conference/\@inproceedings** Model +```{r model_proceedings, echo=FALSE, results='asis'} +df_table <- table_master[table_master$table == "model_proceedings", c(2:4)] +df_table[is.na(df_table)] <- "" + +# fix links +df_table$f3 <- gsub("link_to_entry_models", "#entrymodels", df_table$f3) +df_table$f3 <- gsub("link_to_article", "#article", df_table$f3) +df_table$f3 <- gsub("link_to_booklet", "#booklet", df_table$f3) +df_table$f3 <- gsub("link_to_book", "#book-inbook", df_table$f3) + +row.names(df_table) <- NULL +knitr::kable(df_table, + col.names = c("**BibTeX**", "[CFF]{.underline}", "Notes"), + caption = "**\\@proceedings** Model" +) +``` **Examples** -[*BibTeX entry*]{.underline} +**BibTeX entry** ``` bibtex @proceedings{proceedings-full, @@ -1274,44 +1228,36 @@ bib <- "@proceedings{proceedings-full, cff_from_bibtex(bib) ``` -[*From CFF to BibTeX*]{.underline} +From [CFF]{.underline} to **BibTeX** ```{r echo=FALSE,} -toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) -``` - -### techreport - -+-------------------------+-------------------------------------------------------------+-----------------------------+ -| **BibTeX** | [CFF]{.underline} | Note | -+=========================+=============================================================+=============================+ -| **\@techreport** | [type: report]{.underline} | | -+-------------------------+-------------------------------------------------------------+-----------------------------+ -| **author\*** | [authors]{.underline} | | -+-------------------------+-------------------------------------------------------------+-----------------------------+ -| **title\*** | [title]{.underline} | | -+-------------------------+-------------------------------------------------------------+-----------------------------+ -| **institution\*** | [institution]{.underline} | | -+-------------------------+-------------------------------------------------------------+-----------------------------+ -| **year\*** | [year]{.underline} | | -+-------------------------+-------------------------------------------------------------+-----------------------------+ -| **type** | \- | Ignored | -+-------------------------+-------------------------------------------------------------+-----------------------------+ -| **number** | [issue]{.underline} | | -+-------------------------+-------------------------------------------------------------+-----------------------------+ -| **address** | [address]{.underline} property of [institution]{.underline} | See **Note** on | -| | | [book/inbook] | -+-------------------------+-------------------------------------------------------------+-----------------------------+ -| **month** | [month]{.underline} | See **Note** on [article] | -+-------------------------+-------------------------------------------------------------+-----------------------------+ -| **note** | [notes]{.underline} | | -+-------------------------+-------------------------------------------------------------+-----------------------------+ - -: **\@techreport** Model +toBibtex(cff_to_bibentry(cff_from_bibtex(bib))) +``` + +### \@techreport + +The crosswalk of **\@techreport** does not require any special treatment. + +```{r model_techreport, echo=FALSE, results='asis'} +df_table <- table_master[table_master$table == "model_techreport", c(2:4)] +df_table[is.na(df_table)] <- "" + +# fix links +df_table$f3 <- gsub("link_to_entry_models", "#entrymodels", df_table$f3) +df_table$f3 <- gsub("link_to_article", "#article", df_table$f3) +df_table$f3 <- gsub("link_to_booklet", "#booklet", df_table$f3) +df_table$f3 <- gsub("link_to_book", "#book-inbook", df_table$f3) + +row.names(df_table) <- NULL +knitr::kable(df_table, + col.names = c("**BibTeX**", "[CFF]{.underline}", "Notes"), + caption = "**\\@techreport** Model" +) +``` **Examples** -[*BibTeX entry*]{.underline} +**BibTeX entry** ``` bibtex @techreport{techreport-full, @@ -1327,7 +1273,7 @@ toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) } ``` -[*CFF entry*]{.underline} +[CFF entry]{.underline} ```{r echo=FALSE,} bib <- "@techreport{techreport-full, @@ -1345,35 +1291,36 @@ bib <- "@techreport{techreport-full, cff_from_bibtex(bib) ``` -[*From CFF to BibTeX*]{.underline} +From [CFF]{.underline} to **BibTeX** ```{r echo=FALSE,} -toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) +toBibtex(cff_to_bibentry(cff_from_bibtex(bib))) ``` -### unpublished +### \@unpublished + +The crosswalk of **\@unpublished** does not require any special treatment. + +```{r model_unpublished, echo=FALSE, results='asis'} +df_table <- table_master[table_master$table == "model_unpublished", c(2:4)] +df_table[is.na(df_table)] <- "" -+----------------------------+------------------------------------------------+---------------------------------------+ -| **BibTeX** | [CFF]{.underline} | Note | -+============================+================================================+=======================================+ -| **\@unpublished** | [type: unpublished]{.underline} | | -+----------------------------+------------------------------------------------+---------------------------------------+ -| **author\*** | [authors]{.underline} | | -+----------------------------+------------------------------------------------+---------------------------------------+ -| **title\*** | [title]{.underline} | | -+----------------------------+------------------------------------------------+---------------------------------------+ -| **note\*** | [notes]{.underline} | | -+----------------------------+------------------------------------------------+---------------------------------------+ -| **month** | [month]{.underline} | See **Note** on [article] | -+----------------------------+------------------------------------------------+---------------------------------------+ -| **year** | [year]{.underline} | See **Note** on [booklet] | -+----------------------------+------------------------------------------------+---------------------------------------+ +# fix links +df_table$f3 <- gsub("link_to_entry_models", "#entrymodels", df_table$f3) +df_table$f3 <- gsub("link_to_article", "#article", df_table$f3) +df_table$f3 <- gsub("link_to_booklet", "#booklet", df_table$f3) +df_table$f3 <- gsub("link_to_book", "#book-inbook", df_table$f3) -: **\@unpublished** Model +row.names(df_table) <- NULL +knitr::kable(df_table, + col.names = c("**BibTeX**", "[CFF]{.underline}", "Notes"), + caption = "**\\@unpublished** Model" +) +``` **Examples** -[*BibTeX entry*]{.underline} +**BibTeX entry** ``` bibtex @unpublished{unpublished-minimal, @@ -1383,7 +1330,7 @@ toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) } ``` -[*CFF entry*]{.underline} +[CFF entry]{.underline} ```{r echo=FALSE,} bib <- "@unpublished{unpublished-minimal, @@ -1395,10 +1342,98 @@ bib <- "@unpublished{unpublished-minimal, cff_from_bibtex(bib) ``` -[*From CFF to BibTeX*]{.underline} +From [CFF]{.underline} to **BibTeX** + +```{r echo=FALSE,} +toBibtex(cff_to_bibentry(cff_from_bibtex(bib))) +``` + +## Appendix A: **\@inbook** in BibTeX and BibLaTeX {#appendix_inbook} + +The definition of **\@inbook** and **\@incollection** in **BibTeX** +[@patashnik1988] is as follows: + +> - **\@inbook**: A part of a book, which may be a chapter (or section) and/or +> a range of pages. Required fields: author or editor, title, chapter and/or +> pages, publisher, year (...) +> +> - **\@incollection**: A part of a book having its own title. Required +> fields: author, title, booktitle, publisher, year (...) + +Whereas **BibLaTeX** [@biblatexpack] specifies: + +> - **\@inbook:** A part of a book which forms a self-contained unit with its +> own title. Note that the [profile]{.underline} of this entry type is +> [different from standard BibTeX]{.underline}, see § 2.3.1. Required +> fields: author, title, booktitle, year/date (...). + +When considering required fields, an important difference is **booktitle** +requirement in **BibLaTeX**. Notably, **BibTeX \@incollection** requires also +this field. Moreover, both **BibTeX \@incollection** and **BibLaTeX \@inbook** +emphasize its reference to *"a part of a book (...) with its own title"*. + +In this document, the proposed crosswalk ensures full compatibility with +**BibTeX**. Hence, we propose to consider a **BibLaTeX \@inbook** entry as +equivalent to a **BibTeX \@incollection**, given the congruence in their +definitions and field requirements. + +**Examples** + +**BibTeX entry** + +``` bibtex +@inbook{inbook-biblatex, + author = {Yihui Xie and Christophe Dervieux and Emily Riederer}, + title = {Bibliographies and citations}, + booktitle = {{R} Markdown Cookbook}, + date = {2023-12-30}, + publisher = {Chapman and Hall/CRC}, + address = {Boca Raton, Florida}, + series = {The {R} Series}, + isbn = 9780367563837, + url = {https://bookdown.org/yihui/rmarkdown-cookbook}, + chapter = {4.5} +} +``` + +[CFF entry]{.underline} + +```{r echo=FALSE,} +bib <- "@inbook{inbook-biblatex, + author = {Yihui Xie and Christophe Dervieux and Emily Riederer}, + title = {Bibliographies and citations}, + booktitle = {{R} Markdown Cookbook}, + date = {2023-12-30}, + publisher = {Chapman and Hall/CRC}, + address = {Boca Raton, Florida}, + series = {The {R} Series}, + isbn = 9780367563837, + url = {https://bookdown.org/yihui/rmarkdown-cookbook}, + chapter = {4.5} +}" + +cff_from_bibtex(bib) +``` + +From [CFF]{.underline} to **BibTeX** ```{r echo=FALSE,} -toBibtex(cff_to_bibtex(cff_from_bibtex(bib))) +toBibtex(cff_to_bibentry(cff_from_bibtex(bib))) +``` + +## Appendix B: [CFF key:type]{.underline} values {#appendix_cff_type} + +From @druskat2019 Table 4: Complete list of [CFF]{.underline} reference types. + +```{r cff_types, echo=FALSE, results='asis'} +df_table <- table_master[table_master$table == "cff_types", c(2:3)] +df_table[is.na(df_table)] <- "" +row.names(df_table) <- NULL +knitr::kable(df_table, + col.names = c("Reference type string", "Description"), + row.names = NA, + caption = "Complete list of [CFF]{.underline} reference types." +) ``` ## References diff --git a/vignettes/cffr.Rmd b/vignettes/cffr.Rmd index c6b97152..030c065a 100644 --- a/vignettes/cffr.Rmd +++ b/vignettes/cffr.Rmd @@ -254,7 +254,7 @@ simplified as: allkeys <- list( "url" = "https://ropensci.org/", "version" = "0.0.1", - "repository" = "https://github.com/user/repo", + "repository" = "https://github.com/ropensci/cffr", # If the field is already present, it would be overridden title = "Modifying a 'cff' object", authors = newauthors, diff --git a/vignettes/crosswalk.Rmd b/vignettes/crosswalk.Rmd index 0acf2d20..e1cb1741 100644 --- a/vignettes/crosswalk.Rmd +++ b/vignettes/crosswalk.Rmd @@ -3,7 +3,7 @@ title: "From R to CFF" subtitle: "Crosswalk" description: > A comprehenshive description of the internal mappings performed by `cffr`. -author: Diego Hernangómez ORCID logo +author: Diego Hernangómez bibliography: REFERENCES.bib link-citations: yes output: