added citation_cff fn

Author: matthewphamilton

.Rbuildignore

@@ -54,3 +54,4 @@
 ^doc$
 ^Meta$
 ^data-raw/FUNCTIONS\.R$
+^data-raw/WIP\.R$

CITATION.cff

@@ -0,0 +1,12 @@
+cff-version: 1.2.0
+message: "Matthew P Hamilton  (2021). ready4: Implement Open Science Computational Models of Mental Health
+Systems. Version 0.0.0.9089. Zenodo. https://doi.org/10.5281/zenodo.5606250"
+authors:
+  - family-names: "Matthew P"
+    given-names: "Hamilton"
+title: "ready4: Implement Open Science Computational Models of Mental Health
+Systems"
+version: 0.0.0.9089
+doi: 10.5281/zenodo.5606250
+date-released: 2022-02-15
+url: "https://ready4-dev.github.io/ready4/"

DESCRIPTION

@@ -26,7 +26,6 @@ Collate:
     'C4_Ready4Module.R'
     'C4_Ready4Private.R'
     'C4_Ready4Public.R'
-    'add.R'
     'fn_add.R'
     'fn_get.R'
     'fn_make.R'
@@ -36,11 +35,9 @@ Collate:
     'fn_transform.R'
     'fn_update.R'
     'fn_write.R'
-    'get.R'
     'grp_generics.R'
     'imp_fns.R'
     'imp_mthds.R'
-    'make.R'
     'mthd_authorSlot.R'
     'mthd_characterizeSlot.R'
     'mthd_depictSlot.R'
@@ -57,13 +54,7 @@ Collate:
     'mthd_renewSlot.R'
     'mthd_shareSlot.R'
     'pkg_ready4.R'
-    'print.R'
     'ready4-package.R'
-    'remove.R'
-    'rowbind.R'
-    'transform.R'
-    'update.R'
-    'write.R'
 Imports: 
     assertthat,
     bib2df,

NAMESPACE

@@ -85,6 +85,7 @@ export(transform_cls_type_ls)
 export(update_pt_fn_args_ls)
 export(update_tb_r3)
 export(write_all_tbs_in_tbs_r4_to_csvs)
+export(write_citation_cff)
 export(write_dv_fl_to_loc)
 export(write_env_objs_to_dv)
 export(write_fls_from_dv)
@@ -99,6 +100,7 @@ export(write_to_delete_fls)
 export(write_to_dv_from_tbl)
 export(write_to_dv_with_wait)
 export(write_to_publish_dv_ds)
+export(write_words)
 export(write_ws)
 exportClasses(Ready4Module)
 exportClasses(Ready4Private)
@@ -198,6 +200,8 @@ importFrom(stringr,str_locate)
 importFrom(stringr,str_match)
 importFrom(stringr,str_remove)
 importFrom(stringr,str_remove_all)
+importFrom(stringr,str_replace)
+importFrom(stringr,str_replace_all)
 importFrom(stringr,str_sub)
 importFrom(testit,assert)
 importFrom(tibble,as_tibble)

R/fn_write.R

@@ -17,6 +17,41 @@ write_all_tbs_in_tbs_r4_to_csvs <- function (tbs_r4, r4_name_1L_chr, lup_dir_1L_
             r4_name_1L_chr = r4_name_1L_chr, lup_dir_1L_chr = lup_dir_1L_chr, 
             pfx_1L_chr = pfx_1L_chr))
 }
+#' Write citation cff
+#' @description write_citation_cff() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write citation cff. The function is called for its side effects and does not return a value. WARNING: This function writes R scripts to your local environment. Make sure to only use if you want this behaviour
+#' @param pkg_desc_ls Package description (a list)
+#' @param citation_chr Citation (a character vector)
+#' @param publisher_1L_chr Publisher (a character vector of length one), Default: 'Zenodo'
+#' @return NULL
+#' @rdname write_citation_cff
+#' @export 
+#' @importFrom stringr str_sub str_replace_all str_remove str_replace
+#' @importFrom purrr map2_chr
+#' @keywords internal
+write_citation_cff <- function (pkg_desc_ls, citation_chr, publisher_1L_chr = "Zenodo") 
+{
+    meta <- pkg_desc_ls
+    authors_ls <- parse(text = paste0("list(", citation_chr[startsWith(citation_chr, 
+        "  author   = ")] %>% stringr::str_sub(start = 16, end = -3) %>% 
+        stringr::str_replace_all("person", "c"), ")")) %>% eval()
+    citation_cff_chr <- c("cff-version: 1.2.0", paste0("message: \"", 
+        parse(text = citation_chr[which(citation_chr %>% startsWith("  textVersion = ")):(length(citation_chr) - 
+            1)] %>% stringr::str_remove("  textVersion = ") %>% 
+            paste0(collapse = "\n")) %>% eval() %>% stringr::str_replace(paste0(meta$Version, 
+            "."), paste0(meta$Version, ". ", publisher_1L_chr, 
+            ".")), "\""), "authors:", purrr::map2_chr(authors_ls, 
+        1:length(authors_ls), ~paste0("  - family-names: \"", 
+            .x[1], "\"\n", "    given-names: \"", .x[2], ifelse(.y == 
+                length(authors_ls), "\"", "\"\n"))), paste0("title: \"", 
+        paste0(meta$Package, ": ", meta$Title), "\""), paste0("version: ", 
+        meta$Version), paste0("doi: ", citation_chr[startsWith(citation_chr, 
+        "  doi      = ")] %>% stringr::str_sub(start = 15, end = -3)), 
+        paste0("date-released: ", Sys.Date()), paste0("url: \"", 
+            citation_chr[startsWith(citation_chr, "  url      = ")] %>% 
+                stringr::str_sub(start = 15, end = -3), "\""))
+    write_new_files("CITATION.cff", fl_nm_1L_chr = "CITATION", 
+        text_ls = list(citation_cff_chr))
+}
 #' Write dataverse file to local
 #' @description write_dv_fl_to_loc() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write dataverse file to local. The function is called for its side effects and does not return a value. WARNING: This function writes R scripts to your local environment. Make sure to only use if you want this behaviour
 #' @param ds_ui_1L_chr Dataset user interface (a character vector of length one)
@@ -644,6 +679,28 @@ write_to_publish_dv_ds <- function (dv_ds_1L_chr)
         dataverse::publish_dataset(dv_ds_1L_chr, minor = F)
     }
 }
+#' Write words
+#' @description write_words() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write words. The function is called for its side effects and does not return a value. WARNING: This function writes R scripts to your local environment. Make sure to only use if you want this behaviour
+#' @param new_words_chr New words (a character vector)
+#' @param gh_repo_1L_chr Github repository (a character vector of length one), Default: 'ready4-dev/ready4'
+#' @param gh_tag_1L_chr Github tag (a character vector of length one), Default: 'Documentation_0.0'
+#' @return NULL
+#' @rdname write_words
+#' @export 
+#' @importFrom piggyback pb_download_url
+#' @keywords internal
+write_words <- function (new_words_chr, gh_repo_1L_chr = "ready4-dev/ready4", 
+    gh_tag_1L_chr = "Documentation_0.0") 
+{
+    dmt_urls_chr <- piggyback::pb_download_url(repo = gh_repo_1L_chr, 
+        tag = gh_tag_1L_chr, .token = "")
+    b <- readRDS(url(dmt_urls_chr[dmt_urls_chr %>% endsWith("treat_as_words_chr.RDS")]))
+    b <- c(b, new_words_chr) %>% sort()
+    write_env_objs_to_dv(env_objects_ls = list(treat_as_words_chr = b), 
+        descriptions_chr = NULL, ds_url_1L_chr = character(0), 
+        piggyback_desc_1L_chr = "Supplementary Files", piggyback_tag_1L_chr = gh_tag_1L_chr, 
+        piggyback_to_1L_chr = gh_repo_1L_chr, prerelease_1L_lgl = T)
+}
 #' Write workspace
 #' @description write_ws() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write workspace. The function is called for its side effects and does not return a value. WARNING: This function writes R scripts to your local environment. Make sure to only use if you want this behaviour
 #' @param path_1L_chr Path (a character vector of length one)

data-raw/DATASET.R

@@ -8,7 +8,8 @@ x <- ready4fun::make_pkg_desc_ls(pkg_title_1L_chr = "Implement Open Science Comp
                                                     authors_prsn = c(utils::person(
                                                       given = "Matthew",family = "Hamilton", email =
                                                         "matthew.hamilton@orygen.org.au",role = c("aut",
-                                                                                                  "cre"),comment = c(ORCID = "0000-0001-7407-9194")
+                                                                                                  "cre"),
+                                                      comment = c(ORCID = "0000-0001-7407-9194")
                                                     ),
                                                     utils::person("Orygen", role = c("cph", "fnd")),
                                                     utils::person("VicHealth",role = c("fnd")),
@@ -44,9 +45,9 @@ x <- ready4fun::make_pkg_desc_ls(pkg_title_1L_chr = "Implement Open Science Comp
 ## Do you confirm ('Y') that you want to delete these files: [Y|N]
 ## After doing so, all other such prompts should be answered in the affirmative.
 x <- write_self_srvc_pkg(x)
+ # ADD DOI OVERRIDE FOR RELEASES
 #
 # write_extensions() # Required only if extensions have changed since last build
 # write_badges() # Only run if the ready4fun badges table has been updated.
 # Very occasional calls to write_housestyle_fls (four a year tops)
 devtools::build_vignettes()
-#

data-raw/FUNCTIONS.R

@@ -408,6 +408,8 @@ write_self_srvc_pkg <- function(x){
   }
   write_to_delete_dirs("safety")
   write_prototypes()
+  write_citation_cff(packageDescription("ready4"),
+                     citation_chr = readLines("inst/CITATION"))
   return(x)
 }
 write_prototypes <- function(gh_repo_1L_chr = "ready4-dev/ready4",
@@ -458,22 +460,7 @@ write_extensions <- function(gh_repo_1L_chr = "ready4-dev/ready4",
                        piggyback_to_1L_chr = gh_repo_1L_chr,
                        prerelease_1L_lgl = T)
 }
-write_words <- function(new_words_chr,
-                        gh_repo_1L_chr = "ready4-dev/ready4",
-                        gh_tag_1L_chr = "Documentation_0.0"){
-  dmt_urls_chr <- piggyback::pb_download_url(repo = gh_repo_1L_chr,
-                                             tag = gh_tag_1L_chr,
-                                             .token = "")
-  b <- readRDS(url(dmt_urls_chr[dmt_urls_chr %>% endsWith("treat_as_words_chr.RDS")]))
-  b <- c(b,new_words_chr) %>% sort()
-  write_env_objs_to_dv(env_objects_ls = list(treat_as_words_chr = b),
-                       descriptions_chr = NULL,
-                       ds_url_1L_chr = character(0),
-                       piggyback_desc_1L_chr = "Supplementary Files",
-                       piggyback_tag_1L_chr =  gh_tag_1L_chr,
-                       piggyback_to_1L_chr = gh_repo_1L_chr,
-                       prerelease_1L_lgl = T)
-}
+
 
 write_housestyle_fls <- function(){ # Use sparingly [Max 4 times a year]
   X <- ready4use::Ready4useRepos(dv_nm_1L_chr = "ready4fw",

data-raw/WIP.R

@@ -0,0 +1,6 @@
+meta <- packageDescription("ready4")
+citation_chr <- readLines("inst/CITATION")
+publisher_1L_chr <- "Zenodo"
+
+write_citation_cff(packageDescription("ready4"),
+                   citation_chr = readLines("inst/CITATION"))

data-raw/fns/write.R

@@ -9,6 +9,42 @@ write_all_tbs_in_tbs_r4_to_csvs <- function(tbs_r4,
                                 lup_dir_1L_chr = lup_dir_1L_chr,
                                 pfx_1L_chr = pfx_1L_chr))
 }
+write_citation_cff <- function(pkg_desc_ls,
+                               citation_chr,
+                               publisher_1L_chr = "Zenodo"){
+  meta <- pkg_desc_ls
+  authors_ls <- parse(text=paste0("list(",
+                                  citation_chr[startsWith(citation_chr,"  author   = ")] %>%
+                                    stringr::str_sub(start=16, end=-3) %>%
+                                    stringr::str_replace_all("person","c"),
+                                  ")")) %>%
+    eval()
+  citation_cff_chr <- c("cff-version: 1.2.0",
+                        paste0("message: \"",
+                               parse(text = citation_chr[which(citation_chr %>%
+                                                                 startsWith("  textVersion = ")):(length(citation_chr)-1)] %>%
+                                       stringr::str_remove("  textVersion = ") %>%
+                                       paste0(collapse = "\n")) %>%
+                                 eval() %>%
+                                 stringr::str_replace(paste0(meta$Version,"."),
+                                                      paste0(meta$Version,". ",publisher_1L_chr,".")),
+                               "\""),
+                        "authors:",
+                        purrr::map2_chr(authors_ls,
+                                        1:length(authors_ls),
+                                        ~ paste0("  - family-names: \"",.x[1],"\"\n",
+                                                 "    given-names: \"",.x[2],ifelse(.y==length(authors_ls),"\"","\"\n")#"    orcid: ",
+                                        )),
+                        paste0("title: \"",paste0(meta$Package,": ",meta$Title),"\""),
+                        paste0("version: ",meta$Version),
+                        paste0("doi: ",citation_chr[startsWith(citation_chr,"  doi      = ")] %>% stringr::str_sub(start=15,end=-3)),
+                        paste0("date-released: ",Sys.Date()),
+                        paste0("url: \"",citation_chr[startsWith(citation_chr,"  url      = ")] %>% stringr::str_sub(start=15,end=-3),"\""))
+  write_new_files("CITATION.cff",
+                  fl_nm_1L_chr = "CITATION",
+                  text_ls = list(citation_cff_chr))
+
+}
 write_dv_fl_to_loc <- function(ds_ui_1L_chr,
                                fl_nm_1L_chr = NA_character_,
                                fl_id_1L_int = NA_integer_,
@@ -572,6 +608,22 @@ write_to_publish_dv_ds <- function(dv_ds_1L_chr){
                                minor = F)
   }
 }
+write_words <- function(new_words_chr,
+                        gh_repo_1L_chr = "ready4-dev/ready4",
+                        gh_tag_1L_chr = "Documentation_0.0"){
+  dmt_urls_chr <- piggyback::pb_download_url(repo = gh_repo_1L_chr,
+                                             tag = gh_tag_1L_chr,
+                                             .token = "")
+  b <- readRDS(url(dmt_urls_chr[dmt_urls_chr %>% endsWith("treat_as_words_chr.RDS")]))
+  b <- c(b,new_words_chr) %>% sort()
+  write_env_objs_to_dv(env_objects_ls = list(treat_as_words_chr = b),
+                       descriptions_chr = NULL,
+                       ds_url_1L_chr = character(0),
+                       piggyback_desc_1L_chr = "Supplementary Files",
+                       piggyback_tag_1L_chr =  gh_tag_1L_chr,
+                       piggyback_to_1L_chr = gh_repo_1L_chr,
+                       prerelease_1L_lgl = T)
+}
 write_ws <- function(path_1L_chr){
   top_level_chr <- paste0(path_1L_chr,
                           "/ready4/",