bump to 0.99.8

Author: bschilder

.Rhistory

@@ -1,7 +1,7 @@
 Package: rworkflows
 Type: Package
 Title: Test, Document, Containerise, and Deploy R Packages
-Version: 0.99.7
+Version: 0.99.8
 Authors@R:
     c(person(given = "Brian",
            family = "Schilder",
@@ -42,7 +42,11 @@ Imports:
     desc,
     badger,
     renv,
-    biocViews
+    biocViews,
+    tools,
+    methods,
+    BiocPkgTools,
+    data.table
 Suggests:
     markdown,
     rmarkdown,
@@ -51,7 +55,6 @@ Suggests:
     BiocStyle,
     covr,
     testthat (>= 3.0.0),
-    data.table,
     htmltools
 RoxygenNote: 7.2.3
 VignetteBuilder: knitr

DESCRIPTION

@@ -1,7 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
 export(bioc_r_versions)
+export(construct_authors)
 export(construct_runners)
+export(dt_to_desc)
 export(fill_description)
 export(get_description)
 export(get_hex)
@@ -15,16 +17,22 @@ export(use_readme)
 export(use_vignette_docker)
 export(use_vignette_getstarted)
 export(use_workflow)
+import(BiocPkgTools)
 import(badger)
 import(desc)
 importFrom(biocViews,recommendBiocViews)
+importFrom(data.table,":=")
+importFrom(data.table,as.data.table)
 importFrom(desc,desc)
 importFrom(desc,desc_fields)
 importFrom(desc,desc_get_field)
 importFrom(here,here)
+importFrom(methods,is)
 importFrom(renv,dependencies)
 importFrom(stats,setNames)
+importFrom(tools,R_user_dir)
 importFrom(utils,download.file)
+importFrom(utils,person)
 importFrom(yaml,as.yaml)
 importFrom(yaml,read_yaml)
 importFrom(yaml,write_yaml)

NAMESPACE

@@ -1,3 +1,19 @@
+# rworkflows 0.99.8
+
+## New features
+ 
+* `get_description`
+  - Supplying a `description` obj directly to any argument returns that obj.
+  - Reorder strategies so that local ones go first.
+  - Add Liam Neeson reference.
+  - Now caches DESCRIPTION files.
+  - Add validation step at the end.
+  - Upgrade to handle multiple `refs` at once 
+  - Add another subroutine for getting DESCRIPTION files from CRAN/Bioc 
+* `get_hex`
+  - Now iterable
+* Add `output` style arg to vignette functions.
+
 # rworkflows 0.99.7
 
 ## New features
@@ -30,6 +46,7 @@
 * `get_hex`: Remove extra breaks
 * Fix bad quotes in `if` statements when *rworkflows_static* gets saved.
 
+
 # rworkflows 0.99.6
 
 ## New features

NEWS.md

@@ -27,7 +27,7 @@
 #' ver <- bioc_r_versions(bioc_version="devel")
 bioc_r_versions <- function(bioc_version = NULL,
                             depth = NULL){
-  # templateR:::args2vars(bioc_r_versions)
+  # devoptera::args2vars(bioc_r_versions)
 
   yml <- yaml::read_yaml("https://bioconductor.org/config.yaml")
   info <- list(
@@ -69,4 +69,4 @@ bioc_r_versions <- function(bioc_version = NULL,
   # info[["r_latest"]] <- package_version(rversions::r_release()$version)
   # info[["r_devel"]] <- package_version(rversions::r_release()$version)
   return(info)
-}
+}

R/bioc_r_versions.R

@@ -0,0 +1,27 @@
+check_pkg_name_variants <- function(ref,
+                                    pkg_retrieved=NULL,
+                                    verbose=TRUE){
+  # ref <- "neurogenomics/MAGMA_Celltyping"
+  
+  v1 <- basename(ref) |>
+    trimws() |> trimws(whitespace = "^\\.|\\.")
+  v2 <- tolower(v1)
+  v3 <- lapply(c("-","_"," "), function(x){
+    gsub(x,".",v1)
+  })
+  v4 <- lapply(c("-","_"," "), function(x){
+    gsub(x,"",v1)
+  })
+  v <- unlist(c(ref,basename(ref),v1,v2,v3,v4))
+  approximate_match <- pkg_retrieved %in% v
+  if(isFALSE(approximate_match)){
+    messager(
+      paste0(
+        "Requested package (",shQuote(basename(ref)),") ",
+        "!= retrieved package (",shQuote(pkg_retrieved),") in DESCRIPTION. ",
+        "Returning NULL."
+      ),v = verbose
+    )
+  }
+  return(approximate_match)
+}

R/check_pkg_name_variants.R

@@ -6,7 +6,7 @@ codecov_graphs <- function(ref,
                            height=50,
                            style="vertical-align: top;",
                            token=NULL){
-  # templateR:::args2vars(codecov_graphs)
+  # devoptera::args2vars(codecov_graphs)
   # ref="neurogenomics/rworkflows";branch="master"
 
 
@@ -40,4 +40,4 @@ codecov_graphs <- function(ref,
       URL
     }
   })
-}
+}

R/codecov_graphs.R

@@ -0,0 +1,28 @@
+#' Construct authors
+#' 
+#' Helper function to construct an author list for a \emph{DESCRIPTION} file.
+#' Returns a template when \code{authors} is not provided (default).
+#' @param template Default value to return when \code{authors=NULL}.
+#' @inheritParams fill_description
+#' @returns Named list in \link[utils]{person} format.
+#' 
+#' @export
+#' @importFrom utils person
+#' @examples 
+#' authors <- construct_authors()
+construct_authors <- function(authors=NULL,
+                              template=c( 
+  utils::person(
+    given = "yourGivenName",
+    family = "yourFamilyName",
+    role = c("cre"),
+    email = "[email protected]",
+    comment = c(ORCID = "yourOrcidId"))
+  )
+){
+  if(is.null(authors)){
+    return(template)
+  } else {
+    return(authors)
+  }
+}

R/construct_authors.R

@@ -56,8 +56,8 @@ construct_runners <- function(os=c("ubuntu-latest",
                               versions_explicit=FALSE
                               ){ 
 
-  # templateR:::source_all()
-  # templateR:::args2vars(construct_runners)
+  # devoptera::args2varssource_all()
+  # devoptera::args2vars(construct_runners)
 
   #### Check args ####
   construct_runners_check_args(os = os, 

R/construct_runners.R

@@ -0,0 +1,53 @@
+#' \link[data.table]{data.table} to \link[desc]{desc}
+#' 
+#' Convert \link[data.table]{data.table} containing the
+#'  parsed \emph{DESCROPTION} file data and convert each of them to 
+#'  to \link[desc]{desc} format.
+#' @param db A \link[data.table]{data.table} where each row is a different R package
+#' and each column is a field from the \emph{DESCROPTION} file.
+#' @param verbose Print messages.
+#' @inheritParams get_description
+#' @returns A named list of \link[desc]{desc} objects.
+#' 
+#' @export
+#' @importFrom stats setNames
+#' @importFrom  data.table as.data.table 
+#' @import desc
+#' @examples 
+#'  db <-   BiocPkgTools::biocPkgList()
+#'  dl <- dt_to_desc(db=db, refs="GenomicRanges")
+dt_to_desc <- function(db,
+                       refs=NULL,
+                       verbose=TRUE){
+  
+  Package <- NULL;
+  
+  
+  db <- data.table::as.data.table(db)
+  if(is.null(refs)){
+    refs <- db$Package
+  }else{
+    refs <- refs[basename(refs) %in% db$Package]
+  }
+  messager("Constructing DESCRIPTION files for",
+           formatC(length(refs),big.mark = ","),"R packages.",v=verbose)
+  valid_fields <-desc::cran_valid_fields
+  lapply(stats::setNames(basename(refs),
+                         refs),
+         function(p){
+           messager("Constructing DESCRIPTION for:",p,v=verbose)
+           db_sub <- db[Package==p,][1,]
+           d <- desc::description$new("!new")
+           for(k in names(db_sub)){ 
+             vals <- db_sub[[k]]
+             if(is.list(vals)) vals <- unlist(vals)
+             vals <- vals[vals!=""]
+             if(k %in% valid_fields &&
+                !all(is.na(vals))){ 
+               d$set_list(key = k, 
+                          list_value = vals)   
+             }
+           }
+           d
+         })
+}