Add docker_registry argument

neurogenomics · Oct 27, 2023 · 1eceb31 · 1eceb31
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diff --git a/.Rhistory b/.Rhistory
diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
@@ -14,8 +14,7 @@ name: rworkflows
     - RELEASE_**
 jobs:
   rworkflows:
-    permissions:
-      contents: write
+    permissions: write-all
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     container: ${{ matrix.config.cont }}

diff --git a/.github/workflows/rworkflows_static.yml b/.github/workflows/rworkflows_static.yml
@@ -32,8 +32,7 @@ env:
   enable_act: ${{ false }}
 jobs:
   rworkflows_static:
-    permissions:
-      contents: write
+    permissions: write-all
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     container: ${{ matrix.config.cont }}

diff --git a/NEWS.md b/NEWS.md
@@ -23,6 +23,15 @@
   - Make registry explicit.
   - New arg: `default_registry`
   - New subfunction: `check_registry`
+* Add `docker_registry` arg to let users choose which registry to push to. 
+  Defaults to "ghcr.io" instead of "docker.io" so that no additional credentials 
+  are needed.
+  - *actions.yml*
+  - `use_workflow`
+* `get_github_url_desc`
+  - Improve logic to catch more GH URLs.
+* *vignettes/depgraph.Rmd*
+  - Update plots with new data and resave PNG.
 
 ## Bug fixes
 

diff --git a/R/fill_yaml.R b/R/fill_yaml.R
@@ -31,6 +31,7 @@ fill_yaml <- function(## function-level args
                       tinytex_version,
                       pandoc_version,
                       run_docker,  
+                      docker_registry,
                       github_token,
                       docker_user,
                       docker_org,
@@ -43,6 +44,7 @@ fill_yaml <- function(## function-level args
                       channels){
   # devoptera::args2vars(use_workflow)
 
+  docker_registry <- docker_registry[1]
   #### name ####
   yml$name <- name
   #### on ####

diff --git a/R/get_github_url_desc.R b/R/get_github_url_desc.R
@@ -2,27 +2,41 @@ get_github_url_desc <- function(desc_file){
   ## These fields sometimes contain >1 link.
   ## Find the one that's actually for the GitHub repo.
   if(is.null(desc_file)) return (desc_file)
+  check_gh_url <- function(URL){
+    if(sum(grepl("https://github.com",URL))==0) {
+      return(NULL)
+    } else {
+      return(URL)
+    }
+  }
   get_gh <- function(URL){
     urls <- trimws(strsplit(URL,",")[[1]])
     (
       grep("https://github.com", urls, value = TRUE)[1] |>
-        strsplit("#")
-    )[[1]][1]
+        strsplit("#") |>
+        gsub(pattern="issues$",replacement="") |>
+        trimws(whitespace = "/")
+    )[[1]][1] |>
+      check_gh_url()
   }
   #### Parse ####
+  ## From URL field
   if(desc_file$has_fields("URL")){ 
-    return(get_gh(desc_file$get_field("URL")))
-  } else if (desc_file$has_fields("BugReports")){
-    return(
-      trimws(gsub("issues$","",get_gh(desc_file$get_field("BugReports"))),
-             whitespace = "/") 
-    )
-  } else if (desc_file$has_fields("git_url")){
-    return(
-      paste("https://github.com",
-            strsplit(desc_file$get_field("git_url"),"[.]")[[1]][[2]],
-            basename(desc_file$get_field("git_url")),sep="/")
-    ) 
+    gh_url <- get_gh(desc_file$get_field("URL"))
+    if(!is.null(gh_url)) return(gh_url)
+  } 
+  ## From BugReports field
+  if (desc_file$has_fields("BugReports")){
+    gh_url <- get_gh(desc_file$get_field("BugReports"))
+    if(!is.null(gh_url)) return(gh_url)
+  } 
+  ## From git_url field
+  if (desc_file$has_fields("git_url")){
+    gh_url <- paste("https://github.com",
+                    strsplit(desc_file$get_field("git_url"),"[.]")[[1]][[2]],
+                    basename(desc_file$get_field("git_url")),sep="/")
+    gh_url <- check_gh_url(gh_url)
+    if(!is.null(gh_url)) return(gh_url)
   } else {
     return(NULL)
   }

diff --git a/R/use_workflow.R b/R/use_workflow.R
@@ -41,7 +41,6 @@
 #' @param run_pkgdown Knit the \emph{README.Rmd} (if available), 
 #' build documentation website, and deploy to \emph{gh-pages} branch.
 #' @param has_runit Run R Unit tests.
-#' @param run_docker Whether to build and push a Docker container to DockerHub.
 #' @param has_latex Install a suite of LaTeX dependencies used for 
 #' rendering Sweave (.rnw) and other documentation files.
 #' @param tinytex_installer  Which release of tinytex (bundles of LaTeX
@@ -66,13 +65,24 @@
 #' Read 
 #' \href{https://docs.github.com/en/actions/security-guides/automatic-token-authentication}{
 #' here for more details}.
-#' @param docker_user DockerHub username.
-#' @param docker_org DockerHub organization name. 
+#' @param run_docker Whether to build and push a Docker container to DockerHub.
+#' @param docker_registry Docker container registry to push to. 
+#' Options include:
+#' \itemize{
+#'  \item{"ghcr.io"} : \href{https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry}{
+#'  GitHub Container Registry}
+#'  \item{"docker.io"} : \href{https://hub.docker.com/}{DockerHub} 
+#' }
+#' @param docker_user Docker registry username.
+#' Not used when \code{docker_registry="ghcr.io"}.
+#' @param docker_org Docker registry organization name. 
 #' Is the same as \code{docker_user} by default.
-#' @param docker_token DockerHub token.
+#' Not used when \code{docker_registry="ghcr.io"}.
+#' @param docker_token Docker registry token.
+#' Not used when \code{docker_registry="ghcr.io"}.
+#' 
 #' @param force_new If the GHA workflow yaml already exists, 
 #' overwrite with new one (default: \code{FALSE}).
-#' 
 #' @param save_dir Directory to save workflow to.
 #' @param return_path Return the path to the saved \emph{yaml} workflow file
 #' (default: \code{TRUE}), or return the \emph{yaml} object directly.
@@ -160,6 +170,7 @@ use_workflow <- function(## action-level args
                          run_pkgdown=TRUE,   
                          ### Container
                          run_docker=FALSE,  
+                         docker_registry="ghcr.io",
                          docker_user=NULL,
                          docker_org=docker_user,
                          docker_token="${{ secrets.DOCKER_TOKEN }}",
@@ -213,6 +224,7 @@ use_workflow <- function(## action-level args
                    branches=branches,
                    runners=runners,
                    ## workflow-level args
+                   github_token=github_token,
                    run_bioccheck=run_bioccheck,
                    run_rcmdcheck=run_rcmdcheck, 
                    as_cran=as_cran,
@@ -226,7 +238,7 @@ use_workflow <- function(## action-level args
                    tinytex_version=tinytex_version,
                    pandoc_version=pandoc_version,
                    run_docker=run_docker,  
-                   github_token=github_token,
+                   docker_registry=docker_registry,
                    docker_user=docker_user,
                    docker_org=docker_org,
                    docker_token=docker_token,

diff --git a/action.yml b/action.yml
@@ -68,20 +68,23 @@ inputs:
     default: false
   docker_registry: 
     description: >
-      Docker container registry. 
+      Docker container registry to push to. 
       Options include:
-      - ghcr.io : [GitHub Container Registry](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry}{GitHub Container Registry)
-      - docker.io : [DockerHub](https://hub.docker.com/) 
+      - ghcr.io : GitHub Container Registry (https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry)
+      - docker.io : DockerHub (https://hub.docker.com/) 
     default: 'ghcr.io'
   docker_user: 
     description: >
-      DockerHub username. 
+      Docker registry username. 
+      Not used when `docker_registry="ghcr.io"`.
   docker_org: 
     description: >
-      DockerHub organization name. Can be the same as Docker username.
+      Docker registry organization name. Can be the same as `docker_user`.
+      Not used when `docker_registry="ghcr.io"`.
   DOCKER_TOKEN:
     description: >
-      DockerHub authentication token.
+      Docker registry authentication token.
+      Not used when `docker_registry="ghcr.io"`.
   GITHUB_TOKEN:
     description: >
       GitHub authentication token with permissions to push 

diff --git a/inst/templates/Dockerfile b/inst/templates/Dockerfile
@@ -44,22 +44,10 @@ RUN echo $PKG
 RUN mkdir -p /$PKG
 ADD . /$PKG
 WORKDIR /$PKG
-# Install dependencies with AnVil (faster)
+#### Install package dependencies ####
 RUN Rscript -e 'options(download.file.method="libcurl", crayon.enabled=TRUE, timeout=2000); \
                 if(!require("BiocManager")) install.packages("BiocManager"); \
-                if(!require("AnVIL"))  {BiocManager::install("AnVIL", ask = FALSE)}; \
-                AnVIL::install(c("remotes","devtools")); \
-                try({remotes::install_github("bergant/rapiclient")}); \
-                bioc_ver <- BiocManager::version(); \
-                options(repos = c(AnVIL::repositories(),\
-                                  AnVIL = file.path("https://bioconductordocker.blob.core.windows.net/packages",bioc_ver,"bioc"),\
-                                  CRAN = "https://cran.rstudio.com/"),\
-                                  download.file.method = "libcurl", Ncpus = 2); \
-                deps <- remotes::dev_package_deps(dependencies = TRUE)$package; \
-                AnVIL::install(pkgs = deps,  ask = FALSE); \
-                deps_left <- deps[!deps %in% rownames(installed.packages())]; \
-                if(length(deps_left)>0) devtools::install_dev_deps(dependencies = TRUE, upgrade = "never");' 
-# Install R package from source
-RUN R -e 'options(crayon.enabled = TRUE); \
-          remotes::install_local(upgrade="never")'
+                if(!require("remotes")) install.packages("remotes");
+                repos <- BiocManager::repositories()
+                remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=TRUE)'
 RUN rm -rf /$PKG
diff --git a/man/use_workflow.Rd b/man/use_workflow.Rd
diff --git a/reports/dep_graph_res.rds b/reports/dep_graph_res.rds
diff --git a/reports/r_repos_upset.pdf b/reports/r_repos_upset.pdf
diff --git a/reports/rworkflows_depgraph.html b/reports/rworkflows_depgraph.html
diff --git a/reports/rworkflows_depgraph.png b/reports/rworkflows_depgraph.png
diff --git a/vignettes/depgraph.Rmd b/vignettes/depgraph.Rmd
@@ -34,15 +34,18 @@ res <- echodeps::dep_graph(pkg = "rworkflows",
                            method_seed = "github",
                            exclude = c("neurogenomics_rworkflows",
                                        "neurogenomics_r_workflows"),
-                           node_size = "total_downloads",
-                           height="100%",
+                           #node_size = "total_downloads", 
                            reverse = TRUE,
-                           save_path = here::here("reports","rworkflows_depgraph.html"))
+                           save_path = here::here("reports","rworkflows_depgraph.html")) 
 ```
 
 ## Save data
 
 ``` r
+## Save network plot as PNG
+echodeps::visnet_save(res$save_path)
+
+## Save all data and plots
 saveRDS(res, here::here("reports","dep_graph_res.rds"))
 ```