0.1.6 work (ropensci#89)

* add pre-commit hook for DESCRIPTION vs codemeta.json * oops had forgotten the dependencies 😱 * had also forgotten to import the function * puts the code in the right place and documents what the first call to write_codemeta will do * add rOpenSci and myself as authors * remove MIT licence * change licence * add that the code is GPL-3 * replaces devtools with usethis where possible * mostly French snobism 😉 * add uses_git origin * cf ropensci#62 * ropensci#62 * only adds hook once! * start using desc cf ropensci#41 * various fixes * better example? * document * removes reference to deleted function * cf ropensci#63 * cf ropensci#64, parses more possible roles * updates codemeta.json in particular more people/orgs appear * start work on opinions cf ropensci#76 * document * oops * oops again * gives opinion when verbose=TRUE and otherwise just uses robust code * cleans up tests * more tests of plain authors&maintainer * work on tests * corrects documentation * better if the pkg exists 😁 * update codemeta * adds a message to get a devtools release question * fix? * new try * removes httr dependency in favor of crul cf ropensci#83 * checks URLs in DESCRIPTION cf ropensci#68 * oops fixes test * uses dev version of jsonld * adds coercion to character to repair bug introduced by jsonld new version cf ropensci#88 * clean up cache * yay encoding * close ropensci#84 by deleting now useless licences.R file * appveyor * oh, Appveyor * start filling NEWS.md * better checks when several URLs * more space * generate review metadata cf ropensci#23 * oops * cf ropensci#63 * @jeroen said that this might help 🙏 * thanks again @jeroen * test on patched R version * CRAN and Bioconductor links for dependencies cf ropensci#81 * add tests of dependencies URL creation * add canonic URL for the package itself cf ropensci#81 * borrows jsonlite code cf ropensci#84 * makes it a bit more specific * badge parsing cf ropensci#130 * uses badge parsing function in guess_metadata * opinions about README cf 98 * add check of provider cf ropensci#81 * oops * oops again * R CMD Check NOTEs * oops * update contributor list cf ropensci#95 * several relatedLinks cf ropensci#99 * add the URL only once * oops repairs test * update NEWS * add ability to provide relatedLink for packages installed from CRAN or Bioconductor * add link to commit if available * only one maintainer currently cf ropensci#109 * oops this was wrong! * mmmh there was a mistake here * Travis fix? * remotes cf ropensci#96 * Travis fix? * export the badge extraction function cf ropensci#107 and update docs and correct a test * status as URL cf ropensci#102 * now one can extract lifecycle status * not only Travis CI as contIntegration cf ropensci#111 * update NEWs * update NEWS * repairs handling of additional terms cf ropensci#112 and adds corresponding test * correct test
noamross · Apr 23, 2018 · 4ab555a · 4ab555a
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diff --git a/.travis.yml b/.travis.yml
@@ -8,3 +8,5 @@ apt_packages:
 
 after_success:
   - Rscript -e 'covr::codecov()'
+
+r_github_packages: ropensci/jsonld
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,50 +1,77 @@
 Package: codemetar
 Type: Package
 Title: Generate 'CodeMeta' Metadata for R Packages
-Version: 0.1.5
-Authors@R: c(person("Carl", "Boettiger", 
-                  role=c("aut", "cre", "cph"), 
-                  email="cboettig@gmail.com", 
-                  comment=c(ORCID = "0000-0002-1642-628X")),
-          person("Anna", "Krystalli", 
-                  role = "rev",
-                  comment=c(ORCID = "0000-0002-2378-4915")),       
-          person("Toph", "Allen", 
-                  role = "rev",
-                  comment=c(ORCID = "0000-0003-4580-091X")))
+Version: 0.1.6
+Authors@R: 
+    c(person(given = "Carl",
+             family = "Boettiger",
+             role = c("aut", "cre", "cph"),
+             email = "cboettig@gmail.com",
+             comment = structure("0000-0002-1642-628X", .Names = "ORCID")),
+      person(given = "Anna",
+             family = "Krystalli",
+             role = c("rev", "ctb"),
+             comment = structure("0000-0002-2378-4915", .Names = "ORCID")),
+      person(given = "Toph",
+             family = "Allen",
+             role = "rev",
+             comment = structure("0000-0003-4580-091X", .Names = "ORCID")),
+      person(given = "Maëlle",
+             family = "Salmon",
+             role = c("ctb", "aut"),
+             comment = structure("0000-0002-2815-0399", .Names = "ORCID")),
+      person(given = "rOpenSci",
+             role = "fnd",
+             comment = "https://ropensci.org/"),
+      person(given = "Katrin",
+             family = "Leinweber",
+             role = "ctb"),
+      person(given = "Noam",
+             family = "Ross",
+             role = "ctb"),
+      person(given = "Arfon",
+             family = "Smith",
+             role = "ctb"))
 Description: The 'Codemeta' Project defines a 'JSON-LD' format for describing
   software metadata, as detailed at <https://codemeta.github.io>. This package
   provides utilities to generate, parse, and modify 'codemeta.json' files 
   automatically for R packages, as well as tools and examples for working with
   'codemeta.json' 'JSON-LD' more generally.
-License: MIT + file LICENSE
-URL: https://github.com/ropensci/codemetar
+License: GPL-3
+URL: https://github.com/ropensci/codemetar,https://codemeta.github.io/codemetar
 BugReports: https://github.com/ropensci/codemetar/issues
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 6.0.1.9000
 Depends: R (>= 3.0.0)
-Imports: jsonlite (>= 1.3),
+Imports: 
+    jsonlite (>= 1.3),
     jsonld,
     git2r,
     devtools,
     methods,
     stats,
     stringi,
-    readr
-Suggests: testthat,
+    readr,
+    desc,
+    usethis,
+    whisker,
+    tibble,
+    crul,
+    gh,
+    stringr,
+    sessioninfo
+Suggests: 
+    testthat,
     jsonvalidate,
     covr,
     knitr,
     rmarkdown,
-    httr,
     magrittr,
     xml2,
     dplyr (>= 0.7.0),
-    tibble,
     purrr,
     printr
 VignetteBuilder: knitr
 X-schema.org-keywords: metadata, codemeta, ropensci, citation, credit, linked-data
 X-schema.org-isPartOf: https://ropensci.org
-X-schema.org-relatedLink: https://codemeta.github.io/codemetar
diff --git a/LICENSE b/LICENSE
diff --git a/NAMESPACE b/NAMESPACE
@@ -6,17 +6,16 @@ export(create_codemeta)
 export(crosswalk)
 export(crosswalk_table)
 export(drop_context)
+export(extract_badges)
+export(give_opinions)
 export(write_codemeta)
-importFrom(devtools,build)
-importFrom(devtools,use_build_ignore)
 importFrom(git2r,branches)
 importFrom(git2r,repository)
 importFrom(jsonld,jsonld_compact)
 importFrom(jsonld,jsonld_expand)
 importFrom(jsonlite,fromJSON)
 importFrom(jsonlite,read_json)
 importFrom(jsonlite,toJSON)
-importFrom(jsonlite,write_json)
 importFrom(methods,is)
 importFrom(readr,cols)
 importFrom(readr,read_csv)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,27 @@
+# codemetar 0.1.6 2018-04
+
+* Use desc to parse DESCRIPTION files.
+
+* Writing codemeta.json for the first time adds a git pre-commit hook and suggests adding a release question for devtools::release.
+
+* License changed to GPL because of code borrowed from usethis
+
+* Add give_opinion function giving opiniated advice about package metadata
+
+* Replace httr with crul and use crul to check URLs.
+
+* relatedLink field now include provider URL and URL(s) from DESCRIPTION that are not the code repository
+
+* add an extract_badges function for extracting information from all badges in a Markdown file.
+
+* now if more than one CI service among Travis, Appveyor and Circle CI are used and shown via a README badge they're all added to the contIntegration field.
+
+* now ability to parse all CRAN-allowed MARC roles.
+
+* if there is a badge for an rOpenSci onboarding review and the review issue is closed, basic review metadata is added to codemeta.json
+
+* For dependencies, if the provider guessed is CRAN or BioConductor, their canonic CRAN/BioConductor URL is added to codemeta.json as sameAs, unless there's a GitHub repo mentioned for them in Remotes in DESCRIPTION, in which case sameAs is that GitHub repo.
+
 # codemetar 0.1.5 2018-03-21
 
 * Default to DOI-based schema. (previous CN issues now resolved)

diff --git a/R/codemeta_description.R b/R/codemeta_description.R
@@ -17,40 +17,63 @@ new_codemeta <- function() {
 codemeta_description <-
   function(f, id = NULL, codemeta = new_codemeta()) {
     if (file.exists(f)) {
-      descr <- cm_read_dcf(f)
+      descr <- desc::desc(f)
     } else {
       return(codemeta)
     }
 
-    if (is.null(descr) || length(descr) == 0) {
-      return(codemeta)
-    }
 
     ## FIXME define an S3 class based on the codemeta list of lists?
     if (is.null(id)) {
-      id <- descr$Package
+      id <- descr$get("Package")
     }
 
     if (is_IRI(id)) {
       codemeta$`@id` <- id
     }
 
-    codemeta$identifier <- descr$Package
-    codemeta$description <- descr$Description
-    codemeta$name <- paste0(descr$Package, ": ", descr$Title)
+    codemeta$identifier <- descr$get("Package")
+    codemeta$description <- descr$get("Description")
+    codemeta$name <- paste0(descr$get("Package"), ": ",
+                            descr$get("Title"))
+
+
+    ## Get URLs
+    code_repo <- descr$get_urls()
+    if (!is.na(code_repo[1])){
+
+      if(length(code_repo) == 1){
+        # only one, easy
+        codemeta$codeRepository <- code_repo
+      }else{
+        # try to identify a GitHub or Gitlab repo
+        actual_code_repo <- code_repo[grepl("github\\.com", code_repo)|
+                                        grepl("gitlab\\.com", code_repo)][1]
+        # otherwise take the first URL arbitrarily
+        if(is.null(codemeta$Repository)){
+          codemeta$codeRepository <- actual_code_repo
+        }
+
+        # add other URLs as related links
+        codemeta$relatedLink <- unique(c(codemeta$relatedLink,
+                                         code_repo[code_repo != actual_code_repo]))
+      }
+    }
+
+    issue_tracker <- descr$get("BugReports")
+    if (!is.na(issue_tracker)){
+      codemeta$issueTracker <- issue_tracker
+    }
+
 
-    ## Will later guess these these a la devtools::use_github_links
-    codemeta$codeRepository <- descr$URL
-    codemeta$issueTracker <- descr$BugReports
 
     ## According to crosswalk, codemeta$dateModified and
     ## codemeta$dateCreated are not crosswalked in DESCRIPTION
-    codemeta$datePublished <-
-      descr$Date # probably not avaialable as descr$Date.
+    codemeta$datePublished <- NULL
 
-    codemeta$license <- spdx_license(descr$License)
+    codemeta$license <- spdx_license(descr$get("License"))
 
-    codemeta$version <- descr$Version
+    codemeta$version <- as.character(descr$get_version())
     codemeta$programmingLanguage <-
       list(
         "@type" = "ComputerLanguage",
@@ -64,33 +87,60 @@ codemeta_description <-
     codemeta$runtimePlatform <- R.version.string
 
     if (is.null(codemeta$provider))
-      codemeta$provider <- guess_provider(descr$Package)
-    if ("Authors@R" %in% names(descr)) {
+      codemeta$provider <- guess_provider(descr$get("Package"))
+    authors <- try(descr$get_authors(), silent = TRUE)
+    if (!inherits(authors,'try-error')) {
       codemeta <-
-        parse_people(eval(parse(text = descr$`Authors@R`)), codemeta)
+        parse_people(authors, codemeta)
     } else {
-      codemeta <- parse_people(as.person(descr$Author), codemeta)
-      ## maintainer must come second in case Author list also specifies
-      ## maintainer by role [cre] without email
-      codemeta$maintainer <-
-        person_to_schema(as.person(descr$Maintainer))
+      # get authors and maintainer from their fields
+      # and don't get maintainer twice!
+      authors <- as.person(descr$get("Author"))
+      maintainer <- descr$get_maintainer()
+      maintainer <- as.person(paste(maintainer))
+      maintainer$role <- "cre"
+      authors_strings <- paste(authors$given, authors$family)
+      maintainer_strings <- paste(maintainer$given, maintainer$family)
+      # for now only one maintainer
+      if(length(maintainer) > 1){
+
+        authors <- c(authors[!authors_strings %in% maintainer_strings[1]],
+                     maintainer[2:length(maintainer)])
+        maintainer <- maintainer[1]
+      }else{
+        authors <- authors[!authors_strings %in% maintainer_strings]
+      }
 
+      authors <- c(authors, maintainer)
+      codemeta <-
+        parse_people(authors, codemeta)
     }
 
-    codemeta$softwareSuggestions <- parse_depends(descr$Suggests)
-    codemeta$softwareRequirements <-
-      c(parse_depends(descr$Imports),
-        parse_depends(descr$Depends))
+    dependencies <- descr$get_deps()
+    suggests <- dependencies[dependencies$type == "Suggests",]
+    requirements <- dependencies[dependencies$type %in%
+                                   c("Imports", "Depends"),]
+
+    remotes <- descr$get_remotes()
+
+    suggests$remote_provider <- unlist(lapply(suggests$package,
+                                              add_remote_to_dep, remotes = remotes))
+    requirements$remote_provider <- unlist(lapply(requirements$package,
+                                                  add_remote_to_dep, remotes = remotes))
+
+    codemeta$softwareSuggestions <- parse_depends(suggests)
+    codemeta$softwareRequirements <- parse_depends(requirements)
 
 
 
     ## add any additional codemeta terms found in the DESCRIPTION metadata
+
     for(term in additional_codemeta_terms){
       ## in DESCRIPTION, these terms must be *prefixed*:
       X_term <- paste0("X-schema.org-", term)
-      if(!is.null(descr[[X_term]])){
+      if(!is.na(descr$get(X_term))){
         codemeta[[term]] <- gsub("\\s+", "",
-                                 strsplit(descr[[X_term]], ",")[[1]])
+                                 strsplit(descr$get(X_term), ",")[[1]])
       }
     }
Original file line number	Diff line number	Diff line change
Expand Up		@@ -8,3 +8,5 @@ apt_packages:

		after_success:
		- Rscript -e 'covr::codecov()'

		r_github_packages: ropensci/jsonld