Add -autolink_bare_uris to use_vignette_docker

Author: bschilder

NEWS.md

@@ -4,29 +4,16 @@
 
 * Synchronise `rworkflows` package versioning with `rworkflows` action 
 Release versioning.
+* `use_vignette_docker`/`use_vignette_getstarted`
+  - Autofill `package` arg if not provided.
+  
+## Bug fixes
 
-# rworkflows 0.99.15
-
-## New features
-
-* Add *.devcontainer/devcontainer.json*
-* `use_vignette_docker`
-  - New helper func: `infer_docker_org`
-
-## Bug fixes 
+* *inst/template/docker.Rmd*
+  - Remove the need to include `construct_cont`, 
+    as not everyone will have `rworkfows` installed on the machine where
+    the vignette is being rendered.
 
-* `infer_deps` 
-  - Pass `infer_deps` the *DESCRIPTION* path directly 
-    within the `fill_description` func. 
-  - Fix unit tests.
-* `conda_*`
-  - Try to get reticularte to find the path to conda 
-  installed by `setup-miniconda`.
-* New func: `use_codespace`
-  - Create dev container config file.
-* *.Rprofile*
-  - Added to avoid CRAN issues with bioc packages.
-  
 # rworkflows 0.99.14
 
 ## New features
@@ -68,6 +55,9 @@ Release versioning.
 * `use_workflow`
   - `template` arg can now be "rworkflows_static:dev" to use the "dev" branch's 
   version of *action.yml* as a workflow template.
+* Add *.devcontainer/devcontainer.json*
+* `use_vignette_docker`
+  - New helper func: `infer_docker_org`
 
 ## Bug fixes
 
@@ -81,6 +71,19 @@ Release versioning.
 * *action.yml*
   - Remove unnecessary  export:`echo "GITHUB_TOKEN=${{ inputs.GITHUB_TOKEN }}" >> $GITHUB_ENV`
   - Fix `runforesight/workflow-telemetry-action` step and move to top.
+* `infer_deps` 
+  - Pass `infer_deps` the *DESCRIPTION* path directly 
+    within the `fill_description` func. 
+  - Fix unit tests.
+* `conda_*`
+  - Try to get reticularte to find the path to conda 
+  installed by `setup-miniconda`.
+* New func: `use_codespace`
+  - Create dev container config file.
+* *.Rprofile*
+  - Added to avoid CRAN issues with bioc packages.
+
+
 
 # rworkflows 0.99.13
 

R/use_vignette_docker.R

@@ -3,6 +3,7 @@
 #' Creates a vignette rmarkdown file demonstrates how to create a
 #'  Docker/Singularity image from a container stored in 
 #' \href{https://hub.docker.com/}{Dockerhub}.
+#' @param package R package name.
 #' @param docker_org Docker registry organization name. 
 #' Can simply be your registry username instead.
 #' If \code{NULL}, \code{docker_org} will be inferred as the R package's GitHub 
@@ -27,42 +28,54 @@
 #' @param output Vignette output style. 
 #' Defaults to \link[BiocStyle]{html_document}.
 #' @inheritParams use_workflow
+#' @inheritParams construct_runners
 #' @returns Path to vignette file.
 #' 
 #' @export
 #' @importFrom yaml read_yaml as.yaml
 #' @importFrom here here
 #' @examples
-#' path <- use_vignette_docker(docker_org = "neurogenomics",
+#' path <- use_vignette_docker(package = "mypackage",
+#'                             docker_org = "neurogenomics",
 #'                             ## use default save_dir in practice
 #'                             save_dir = tempdir())
-use_vignette_docker <- function(docker_org = NULL,
+use_vignette_docker <- function(package = names(get_description()),
+                                docker_org = NULL,
                                 docker_registry="ghcr.io",
+                                cont = construct_cont(
+                                  cont = paste(docker_org,
+                                               package,
+                                               sep="/"),
+                                  default_registry =docker_registry)[[1]],
                                 title="Docker/Singularity Containers",
                                 vignette_index_entry="docker",
                                 save_dir=here::here(),
                                 path=file.path(save_dir,
                                                "vignettes",
                                                "docker.Rmd"),
-                                output="BiocStyle::html_document",
+                                output=list(
+                                  "BiocStyle::html_document"= list(
+                                    "md_extensions"="-autolink_bare_uris"
+                                    )
+                                  ),
                                 port_in=8787,
                                 port_out=8900,
                                 force_new=FALSE,
                                 show=FALSE,
                                 verbose=TRUE){
   # devoptera::args2vars(use_vignette_docker, reassign = TRUE)
-  
-  force(docker_org)
-  #### Infer docker_org
-  docker_org <- infer_docker_org(docker_org=docker_org,
-                                 docker_registry=docker_registry,
-                                 verbose=verbose)
+
   #### Check if file exists already ####
   if(file.exists(path) &
      isFALSE(force_new)){
     messager("Using existing vignette file:",path,v=verbose)
   } else {
     messager("Creating new vignette file ==>",path,v=verbose)
+    force(docker_org)
+    #### Infer docker_org
+    docker_org <- infer_docker_org(docker_org=docker_org,
+                                   docker_registry=docker_registry,
+                                   verbose=verbose) 
     dir.create(dirname(path), showWarnings = FALSE, recursive = TRUE)
     #### get the template ####
     template_path <- system.file("templates","docker.Rmd",
@@ -73,6 +86,8 @@ use_vignette_docker <- function(docker_org = NULL,
                      rev(grep("---",l))[1] ) 
     yml <- yaml::read_yaml(text = l[yml_lines])
     #### Set params ####
+    ## cont
+    yml$params$cont$value <- cont
     ## docker_registry
     yml$params$docker_registry$value <- docker_registry
     ## docker_org

R/use_vignette_getstarted.R

@@ -12,7 +12,7 @@
 #' path <- use_vignette_getstarted(package = "mypackage",
 #'                                 ## use default save_dir in practice
 #'                                 save_dir = tempdir())
-use_vignette_getstarted <- function(package,
+use_vignette_getstarted <- function(package = names(get_description()),
                                     title="Get started",
                                     vignette_index_entry=package,
                                     save_dir=here::here(),

README.Rmd

@@ -1,6 +1,6 @@
 ---
 title: ""  
-author: "`r rworkflows::use_badges(add_actions=c('rworkflows','rworkflows_static','rworkflows_dev'), add_cran_release = TRUE, add_cran_checks = TRUE, add_cran_download_month=TRUE, add_cran_download_total=TRUE, add_codecov_graphs='icicle', hex_height=350, add_doi='https://doi.org/10.21203/rs.3.rs-2399015/v1')`" 
+author: "`r rworkflows::use_badges(add_actions=c('rworkflows','rworkflows_static','rworkflows_dev'), add_cran_release = TRUE, add_cran_checks = TRUE, add_cran_download_month=TRUE, add_cran_download_total=TRUE, add_codecov_graphs='icicle', hex_height=350, add_doi='https://doi.org/10.5281/zenodo.10048573')`" 
 date: "<h4>README updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
 output:
   github_document

README.md

@@ -6,9 +6,9 @@ checks](https://badges.cranchecks.info/summary/rworkflows.svg)](https://cran.r-p
 [![](http://cranlogs.r-pkg.org/badges/grand-total/rworkflows?color=black)](https://cran.r-project.org/package=rworkflows)
 [![License:
 GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3)
-[![](https://img.shields.io/badge/doi-https://doi.org/10.21203/rs.3.rs--2399015/v1-blue.svg)](https://doi.org/https://doi.org/10.21203/rs.3.rs-2399015/v1)
+[![](https://img.shields.io/badge/doi-https://doi.org/10.5281/zenodo.10048573-blue.svg)](https://doi.org/https://doi.org/10.5281/zenodo.10048573)
 <br>
-[![](https://img.shields.io/badge/devel%20version-0.99.14-black.svg)](https://github.com/neurogenomics/rworkflows)
+[![](https://img.shields.io/badge/devel%20version-1.0.0-black.svg)](https://github.com/neurogenomics/rworkflows)
 [![](https://img.shields.io/github/languages/code-size/neurogenomics/rworkflows.svg)](https://github.com/neurogenomics/rworkflows)
 [![](https://img.shields.io/github/last-commit/neurogenomics/rworkflows.svg)](https://github.com/neurogenomics/rworkflows/commits/master)
 <br> [![R build
@@ -24,7 +24,7 @@ status](https://github.com/neurogenomics/rworkflows/workflows/rworkflows_dev/bad
 Authors: <i>Brian Schilder, Alan Murphy, Nathan Skene</i>  
 </h4>
 <h4>  
-README updated: <i>Oct-28-2023</i>  
+README updated: <i>Nov-01-2023</i>  
 </h4>
 
 ## Intro
@@ -84,7 +84,7 @@ options to enable/disable/modify each step):
     [**DockerHub**](https://hub.docker.com/)).
 11. 🔭 Generates [workflow
     telemetry](https://github.com/runforesight/workflow-telemetry-action)
-    report.
+    report.  
 12. 🎖 Updates relevant badges added to your README with
     `rworkflows::use_badges()`.
 
@@ -317,7 +317,7 @@ utils::sessionInfo()
     ## [25] rlang_1.1.1         utf8_1.2.4          cachem_1.0.8       
     ## [28] badger_0.2.3        xfun_0.40           fs_1.6.3           
     ## [31] memoise_2.0.1.9000  cli_3.6.1           magrittr_2.0.3     
-    ## [34] rworkflows_0.99.14  digest_0.6.33       grid_4.3.1         
+    ## [34] rworkflows_1.0.0    digest_0.6.33       grid_4.3.1         
     ## [37] rstudioapi_0.15.0   lifecycle_1.0.3     vctrs_0.6.4        
     ## [40] data.table_1.14.8   evaluate_0.22       glue_1.6.2         
     ## [43] fansi_1.0.5         colorspace_2.1-0    rmarkdown_2.25     

inst/templates/docker.Rmd

@@ -8,6 +8,8 @@ output:
       "-autolink_bare_uris" 
     ]
 params:
+  cont:
+    value: NULL
   docker_registry:
     value: "ghcr.io"
   docker_org: 
@@ -28,10 +30,8 @@ library(PKG, character.only = TRUE)
 pkg <- tolower(PKG)
 #### Username of DockerHub account ####
 docker_org <- params$docker_org
-docker_registry <- params$docker_registry
-
-cont <- construct_cont(cont = paste(docker_org,pkg,sep="/"),
-                       default_registry =docker_registry)[[1]]
+docker_registry <- params$docker_registry 
+cont <- params$cont 
 docker_url <- if(grepl("ghcr.io",docker_registry)){
   paste("https://ghcr.io",cont,sep="/")
 } else {

man/use_vignette_docker.Rd

@@ -1,11 +1,13 @@
 test_that("use_vignette_docker works", {
 
-  path <- use_vignette_docker(docker_org = "neurogenomicslab",
+  path <- use_vignette_docker(package = "mypackage",
+                              docker_org = "neurogenomicslab",
                               save_dir = tempdir())
   testthat::expect_true(file.exists(path))
 
   out <- testthat::capture_output_lines({
-    path2 <- use_vignette_docker(docker_org = "neurogenomicslab",
+    path2 <- use_vignette_docker(package = "mypackage",
+                                 docker_org = "neurogenomicslab",
                                  save_dir = tempdir(), 
                                  show = TRUE)
   })

man/use_vignette_getstarted.Rd

@@ -4,8 +4,12 @@ author: '<h4>Authors: <i>`r auths <- eval(parse(text = gsub("person","c",read.dc
   fields = "Authors@R"))));paste(auths[names(auths)=="given"],auths[names(auths)=="family"],
   collapse = ", ")`</i></h4>'
 date: '<h4>Vignette updated: <i>`r format( Sys.Date(), "%b-%d-%Y")`</i></h4>'
-output: BiocStyle::html_document
+output:
+  BiocStyle::html_document:
+    md_extensions: -autolink_bare_uris
 params:
+  cont:
+    value: ghcr.io/neurogenomics/rworkflows
   docker_registry:
     value: ghcr.io
   docker_org:
@@ -25,10 +29,8 @@ library(PKG, character.only = TRUE)
 pkg <- tolower(PKG)
 #### Username of DockerHub account ####
 docker_org <- params$docker_org
-docker_registry <- params$docker_registry
-
-cont <- construct_cont(cont = paste(docker_org,pkg,sep="/"),
-                       default_registry =docker_registry)[[1]]
+docker_registry <- params$docker_registry 
+cont <- params$cont 
 docker_url <- if(grepl("ghcr.io",docker_registry)){
   paste("https://ghcr.io",cont,sep="/")
 } else {