Add free_diskspace. increase code coverage

.Rhistory

@@ -1,118 +1,3 @@
-URL <- paste(
-"https://github.com/",
-co_notag,
-"/pkgs/container/",basename(co_notag),
-"/versions?filters%5Bversion_type%5D=tagged"
-)
-x <- rvest::read_html(URL)
-URL
-##### Only works if you have permissions to the repo #####
-# get_ghcr_tags <- function(container) {
-#   url <- paste0("https://ghcr.io/v2/", container, "/tags/list")
-#   response <- jsonlite::fromJSON(url)
-#   tags <- response$tags
-#   return(tags)
-# }
-# get_ghcr_tags("bioconductor/bioconductor_docker")
-#
-URL <- paste0(
-"https://github.com/",
-co_notag,
-"/pkgs/container/",basename(co_notag),
-"/versions?filters%5Bversion_type%5D=tagged"
-)
-x <- rvest::read_html(URL)
-x
-### get all nodes of class "Label"
-tags <- x |> rvest::html_nodes(".Label") |> rvest::html_text()
-tags
-x <- tryCatch({
-rvest::read_html(URL)
-}, error=function(e){
-stopper("Unable to find public container:",co)}
-)
-x
-splt <- strsplit(co,":")[[1]]
-splt
-source("~/Desktop/rworkflows/R/check_tags.R")
-check_tags(tags = tags,
-splt = splt,
-verbose = verbose)
-verbose=T
-check_tags(tags = tags,
-splt = splt,
-verbose = verbose)
-# co <- "ghcr.io/bioconductor/bioconductor_docker:devel"
-co_notag <- gsub("ghcr.io/","",strsplit(co,":")[[1]][1])
-##### Only works if you have permissions to the repo #####
-# get_ghcr_tags <- function(container) {
-#   url <- paste0("https://ghcr.io/v2/", container, "/tags/list")
-#   response <- jsonlite::fromJSON(url)
-#   tags <- response$tags
-#   return(tags)
-# }
-# tags <- get_ghcr_tags("bioconductor/bioconductor_docker")
-#
-URL <- paste0(
-"https://github.com/",
-co_notag,
-"/pkgs/container/",basename(co_notag),
-"/versions?filters%5Bversion_type%5D=tagged"
-)
-x <- tryCatch({
-rvest::read_html(URL)
-}, error=function(e){
-stopper("Unable to find public container:",co)}
-)
-### get all nodes of class "Label"
-tags <- x |> rvest::html_nodes(".Label") |> rvest::html_text()
-if(length(tags)==0){
-stopper("Unable to find public container:",co)
-}
-strsplit(co,":")[[1]]
-strsplit(co,":")[[2]]
-check_tags(tags = tags,
-splt = strsplit(co,":")[[1]],
-verbose = verbose)
-tags
-check_tags(tags = tags,
-splt = strsplit(co,":")[[1]][1],
-verbose = verbose)
-strsplit(co,":")[[1]][1]
-check_tags(tags = tags,
-splt = c("ew","wefwe"),
-verbose = verbose)
-tags
-co
-for(co in cont){
-# co <- "ghcr.io/bioconductor/bioconductor_docker:devel"
-co_notag <- gsub("ghcr.io/","",strsplit(co,":")[[1]][1])
-##### Only works if you have permissions to the repo #####
-# get_ghcr_tags <- function(container) {
-#   url <- paste0("https://ghcr.io/v2/", container, "/tags/list")
-#   response <- jsonlite::fromJSON(url)
-#   tags <- response$tags
-#   return(tags)
-# }
-# tags <- get_ghcr_tags("bioconductor/bioconductor_docker")
-#
-URL <- paste0(
-"https://github.com/",
-co_notag,
-"/pkgs/container/",basename(co_notag),
-"/versions?filters%5Bversion_type%5D=tagged"
-)
-x <- tryCatch({
-rvest::read_html(URL)
-}, error=function(e){
-stopper("Unable to find public container:",co)}
-)
-### get all nodes of class "Label"
-tags <- x |> rvest::html_nodes(".Label") |> rvest::html_text()
-if(length(tags)==0){
-stopper("Unable to find tags for container:",co)
-} else {
-check_tags(tags = tags,
 splt = strsplit(co,":")[[1]][1],
 verbose = verbose)
 }
@@ -510,3 +395,118 @@ path <- use_dockerfile(save_dir=tempdir(), show=TRUE)
 library(rworkflows)
 path <- use_dockerfile(save_dir=tempdir(), show=TRUE)
 library(rworkflows)
+chattr::chattr_app()
+install.packages("chattr")
+chattr::chattr_app()
+remotes::install_github("mlverse/chattr")
+chattr::chattr_app()
+res <- echodeps::dep_graph(pkg = "rworkflows",
+method_seed = "github",
+exclude = c("neurogenomics_rworkflows",
+"neurogenomics_r_workflows"),
+node_size = "total_downloads",
+height="100%",
+reverse = TRUE,
+save_path = here::here("reports","rworkflows_depgraph.html"))
+res <- echodeps::dep_graph(pkg = "rworkflows",
+method_seed = "github",
+exclude = c("neurogenomics_rworkflows",
+"neurogenomics_r_workflows"),
+node_size = "total_downloads",
+height="100%",
+reverse = TRUE,
+save_path = here::here("reports","rworkflows_depgraph.html"))
+res <- echodeps::dep_graph(pkg = "rworkflows",
+method_seed = "github",
+exclude = c("neurogenomics_rworkflows",
+"neurogenomics_r_workflows"),
+node_size = "total_downloads",
+height="100%",
+reverse = TRUE,
+save_path = here::here("reports","rworkflows_depgraph.html"))
+install.packages("githubinstall")
+res <- echodeps::dep_graph(pkg = "rworkflows",
+method_seed = "github",
+exclude = c("neurogenomics_rworkflows",
+"neurogenomics_r_workflows"),
+node_size = "total_downloads",
+height="100%",
+reverse = TRUE,
+save_path = here::here("reports","rworkflows_depgraph.html"))
+res <- echodeps::dep_graph(pkg = "rworkflows",
+method_seed = "github",
+exclude = c("neurogenomics_rworkflows",
+"neurogenomics_r_workflows"),
+node_size = "total_downloads",
+height="100%",
+reverse = TRUE,
+save_path = here::here("reports","rworkflows_depgraph.html"))
+check_gh_url <- function(URL){
+if(sum(grepl("https://github.com",URL))==0) {
+return(NULL)
+} else {
+return(URL)
+}
+}
+devtools::check_man()
+library(rworkflows)
+get_github_url_desc(desc_file = NULL)
+library(rworkflows)
+res <- echodeps::dep_graph(pkg = "rworkflows",
+method_seed = "github",
+exclude = c("neurogenomics_rworkflows",
+"neurogenomics_r_workflows"),
+node_size = "total_downloads",
+height="100%",
+reverse = TRUE,
+save_path = here::here("reports","rworkflows_depgraph.html"))
+res <- echodeps::dep_graph(pkg = "rworkflows",
+method_seed = "github",
+exclude = c("neurogenomics_rworkflows",
+"neurogenomics_r_workflows"),
+node_size = "total_downloads",
+reverse = TRUE,
+save_path = here::here("reports","rworkflows_depgraph.html"))
+echodeps::visnet_save(res$save_path)
+library(rworkflows)
+method_seed = "github",
+res <- echodeps::dep_graph(pkg = "rworkflows",
+method_seed = "github",
+exclude = c("neurogenomics_rworkflows",
+"neurogenomics_r_workflows"),
+#node_size = "total_downloads",
+reverse = TRUE,
+save_path = here::here("reports","rworkflows_depgraph.html"))
+echodeps::visnet_save(res$save_path)
+saveRDS(res, here::here("reports","dep_graph_res.rds"))
+res$report
+res$pkg
+res$graph
+data.frame(res$graph)
+names(data.frame(res$graph))
+unique(names(data.frame(res$graph)))
+sort(names(data.frame(res$graph)))
+echodeps:::report_summary
+res$report
+r_repos_res <- echogithub::r_repos(
+which = echogithub::r_repos_opts(exclude="local"),
+save_path = here::here("reports","r_repos_upset.pdf"),
+width = 9)
+r_repos_res$repo_stats
+formals(rworkflows::use_workflow())
+formals(rworkflows::use_workflow
+)
+length(formals(rworkflows::use_workflow))
+devtools::check_man()
+devtools::check_man()
+library(rworkflows)
+?use_workflow
+devtools::check_man()
+devtools::check_man()
+devtools::check_man()
+library(rworkflows)
+library(rworkflows)
+devtools::check_man()
+?use_workflow
+library(rworkflows)
+library(rworkflows)

.github/workflows/rworkflows_dev.yml

@@ -54,3 +54,4 @@ jobs:
         DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
         runner_os: ${{ runner.os }}
         cache_version: cache-v1
+        free_diskspace: ${{ true }}

.github/workflows/rworkflows_static.yml

@@ -19,17 +19,18 @@ env:
   run_vignettes: ${{ true }}
   has_testthat: ${{ true }}
   run_covr: ${{ true }}
-  run_pkgdown: ${{ false }}
+  run_pkgdown: ${{ true }}
   has_runit: ${{ false }}
   has_latex: ${{ false }}
   tinytex_installer: TinyTeX-1
-  tinytex_version: ''
   pandoc_version: '2.19'
   run_docker: ${{ false }}
+  docker_registry: ghcr.io
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
   cache_version: cache-v1
-  enable_act: ${{ false }}
+  miniforge_variant: ${{ false }}
+  activate_environment: test
 jobs:
   rworkflows_static:
     permissions: write-all
@@ -43,7 +44,7 @@ jobs:
         - os: ubuntu-latest
           bioc: devel
           r: auto
-          cont: bioconductor/bioconductor_docker:devel
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
           rspm: https://packagemanager.rstudio.com/cran/__linux__/latest/release
         - os: macOS-latest
           bioc: release

NEWS.md

@@ -32,6 +32,9 @@
   - Improve logic to catch more GH URLs.
 * *vignettes/depgraph.Rmd*
   - Update plots with new data and resave PNG.
+* New arg `free_diskspace`
+  - *actions.yml*
+  - `use_workflow`
 
 ## Bug fixes
 

action.yml

@@ -154,6 +154,11 @@ inputs:
       https://docs.conda.io/projects/conda/en/latest/user-guide/configuration/
       for more information.
     default: '' 
+  free_diskspace:
+    description: >
+      Free up additional disk space by deleting non-essential sofwares.
+    default: false
+
 runs:
   using: 'composite'
   steps:
@@ -167,12 +172,15 @@ runs:
         echo "NOT_CRAN=${{ !inputs.as_cran }}" >> $GITHUB_ENV
       shell: bash {0}
 
-    - name: Collect Workflow Telemetry 🔭
+    - name: 🔭 Collect Workflow Telemetry 
       uses: runforesight/workflow-telemetry-action@v1
       continue-on-error: true
+
+    - name: 💾 Free Disk Space
+      if: inputs.free_diskspace == 'true'
+      uses: jlumbroso/free-disk-space@v1
 
-    ## 🐍 Setup Miniconda 
-    - name: Setup Miniconda
+    - name: 🐍 Setup Miniconda
       if: inputs.miniforge_variant != 'false'
       uses: conda-incubator/setup-miniconda@v2
       with:

tests/testthat/test-construct_conda_yml.R

@@ -50,6 +50,12 @@ test_that("construct_conda_yml works", {
     testthat::expect_equal(basename(dirname(dirname(out))),envname)
 
 
+    ### Test conda_export
+    exported_yml <- conda_export(envname)
+    testthat::expect_true(file.exists(exported_yml))
+    testthat::expect_gte(length(readLines(exported_yml)),20)
+
+
     #### From requirements.txt ####
     ## Currently fails due to error:
     ## Error: Error creating conda environment [exit code 1]

tests/testthat/test-construct_runners.R

@@ -1,11 +1,13 @@
 test_that("construct_runners works", {
 
+  #### Set up tests ####  
   run_tests <- function(runners){
     testthat::expect_length(runners,3)
     for (r in runners){
       testthat::expect_true(all(c("os","bioc","r") %in% names(r)))
     }
   }
+  #### Defaults ####
   runners <- construct_runners()
   run_tests(runners = runners)
 
@@ -48,4 +50,15 @@ test_that("construct_runners works", {
                                   "typooo"="devel"))
   )
 
+  #### When python versions passed ####
+  python_version <- "3.9"
+  runners <- construct_runners(python_version = python_version)
+  run_tests(runners = runners) 
+  testthat::expect_true(
+    all(sapply(runners, function(x)x$r=="auto"))
+  )
+  testthat::expect_true(
+    all(sapply(runners, function(x)x$`python-version`==python_version))
+  )
+
 })

tests/testthat/test-use_workflow.R

@@ -38,7 +38,38 @@ test_that("use_workflow works", {
                        force_new = TRUE,
                        tinytex_installer = "TinyTeX",
                        save_dir = tempdir())
+  testthat::expect_equal(yml$on,yml3$on)
+  testthat::expect_equal(length(yml$jobs[[1]]$steps),1)
+  testthat::expect_gte(length(yml3$jobs[[1]]$steps),20)
 
+  #### Modify conda args ####
+  environment_file <- construct_conda_yml(dependencies = c("python>=3.9","anndata"),
+                      preview = TRUE, 
+                      save_path = file.path(tempdir(),"conda.yml"))
+  miniforge_variant <- "Mambaforge"
+  yml4 <- use_workflow(return_path = FALSE,
+                       force_new = TRUE,
+                       miniforge_variant = miniforge_variant,
+                       environment_file = environment_file,
+                       save_dir = tempdir())
+  testthat::expect_equal(yml$on,yml4$on)
+  testthat::expect_null(yml$jobs$rworkflows$steps[[1]]$with$miniforge_variant)
+  testthat::expect_equal(yml4$jobs$rworkflows$steps[[1]]$with$miniforge_variant,
+                         miniforge_variant)
+  testthat::expect_equal(yml4$jobs$rworkflows$steps[[1]]$with$environment_file,
+                         environment_file)
+
+  miniforge_variant <- TRUE
+  yml5 <- use_workflow(return_path = FALSE,
+                       force_new = TRUE,
+                       miniforge_variant = miniforge_variant,
+                       environment_file = environment_file,
+                       save_dir = tempdir())
+  testthat::expect_equal(yml$on,yml5$on)
+  testthat::expect_equal(yml5$jobs$rworkflows$steps[[1]]$with$miniforge_variant,
+                         "")
+  testthat::expect_equal(yml5$jobs$rworkflows$steps[[1]]$with$environment_file,
+                         environment_file)
 
   #### Make table out of arguments ####
   # defaults <- eval(formals(rworkflows::use_workflow))