Add force=TRUE when installing local repo [skip ci]

neurogenomics · Oct 11, 2023 · 059489c · 059489c
1 parent c0dabce
commit 059489c
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Showing 16 changed files with 614 additions and 549 deletions.
diff --git a/.Rhistory b/.Rhistory
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -57,7 +57,8 @@ Suggests:
     jsonlite,
     BiocStyle,
     BiocPkgTools,
-    biocViews
+    biocViews,
+    reticulate
 VignetteBuilder: knitr
 License: GPL-3
 Config/testthat/edition: 3

diff --git a/NEWS.md b/NEWS.md
@@ -12,9 +12,21 @@
     - `channels`
   - New function to construct conda env yaml files:
     - `construct_conda_yml`
+  - New unit tests to test `construct_conda_yml` and building conda envs 
+  from the generated yamls.
 * `fill_yaml` 
   - Add subfunction `is_default`
 
+## Bug fixes
+
+* `no visible global function definition for internal function check_miniconda_args`
+  - This weird error only came up during Rstudio R CMD checks. 
+  The function `check_miniconda_args` was clearly defined in its own file. 
+  The only way to fix it was copying the function into the same one where it
+  was called `fill_yaml`.
+  - Thought it might be a permissions issues with *check_miniconda_args.R* but 
+  the permissions are identical with all the others.
+
 # rworkflows 0.99.13
 
 ## New features

diff --git a/R/check_miniconda_args.R b/R/check_miniconda_args.R
diff --git a/R/conda_installed.R b/R/conda_installed.R
@@ -0,0 +1,4 @@
+conda_installed <- function(){
+  requireNamespace("reticulate")
+  utils::getFromNamespace("conda_installed","reticulate")()
+}
diff --git a/R/condaenv_exists.R b/R/condaenv_exists.R
@@ -0,0 +1,4 @@
+condaenv_exists <- function(...){
+  requireNamespace("reticulate")
+ utils::getFromNamespace("condaenv_exists","reticulate")(...) 
+}
diff --git a/R/construct_conda_yml.R b/R/construct_conda_yml.R
@@ -17,9 +17,11 @@
 #' @export
 #' @importFrom yaml read_yaml
 #' @examples
-#' yml <- construct_conda_yml(name="sc_env",
+#' yml <- construct_conda_yml(name="myenv",
 #'                            dependencies=c("anndata","scanpy"),
-#'                            return_path = FALSE)
+#'                            return_path = FALSE,  
+#'                            ## Writing to temp only for example
+#'                            save_path=tempfile(fileext="myenv_conda.yml"))
 construct_conda_yml <- function(name = "test",
                                 channels = list("conda-forge", 
                                                 "nodefaults"),
@@ -34,13 +36,16 @@ construct_conda_yml <- function(name = "test",
                                 ){
   # devoptera::args2vars(construct_conda_yml) 
 
+  if(is.vector(dependencies)) dependencies <- as.list(dependencies)
+  if(is.vector(pip)) pip <- as.list(pip)
   yml <- list(
     name=name,
     channels=channels,
     dependencies=dependencies
   )
   if(!is.null(pip)){
-    yml[["pip"]] <- pip
+    yml[["dependencies"]] <- c(unique(c(yml[["dependencies"]],"pip")),
+                               list(list(pip=pip))) 
   }
   #### Preview ####
   if(isTRUE(preview)){
@@ -50,6 +55,7 @@ construct_conda_yml <- function(name = "test",
   path_or_yaml <- return_yaml(yml=yml,
                               path=save_path,
                               return_path=return_path,
-                              verbose=verbose)
+                              verbose=verbose, 
+                              indent.mapping.sequence = TRUE)
   return(path_or_yaml)
 }
diff --git a/R/fill_yaml.R b/R/fill_yaml.R
@@ -106,3 +106,50 @@ fill_yaml <- function(## function-level args
   }
   return(yml) 
 }
+
+
+#' Check Miniconda arguments
+#' 
+#' Check Miniconda arguments for compatibility with one another.
+#' @inheritParams use_workflow
+#' @returns Named list of updated args.
+#' 
+#' @keywords internal
+check_miniconda_args <- function(runners, 
+                                 miniforge_variant,
+                                 miniforge_version,
+                                 activate_environment,
+                                 environment_file,
+                                 channels,
+                                 verbose=TRUE){
+
+  for(a in c("miniforge_version",
+             "environment_file",
+             "activate_environment")){
+    if(!is_default(arg=a, val=get(a), func="use_workflow") && 
+       isFALSE(miniforge_variant)){
+      messager(a,"supplied. Enabling miniforge.", v=verbose)
+      miniforge_variant <- TRUE
+    }
+  }
+  #### Check if python-version set ####
+  if(isTRUE(miniforge_variant)) { 
+    #### Check runners ####
+    for(r in runners){
+      if(is.null(r$`python-version`)){
+        messager("python-version not set for runner",
+                 paste0("os=",shQuote(r$os),"."),
+                 "Using default.",v=verbose)
+      }
+    }
+  }
+  if(isTRUE(miniforge_variant)) miniforge_variant <- ""
+  return(list( 
+    miniforge_variant=miniforge_variant,
+    miniforge_version=miniforge_version,
+    activate_environment=activate_environment,
+    environment_file=environment_file,
+    channels=channels
+  ))
+}
+
diff --git a/R/return_yaml.R b/R/return_yaml.R
@@ -1,11 +1,15 @@
 return_yaml <- function(yml,
                         path,
                         return_path,
-                        verbose=TRUE){
+                        handlers=NULL,
+                        verbose=TRUE, 
+                        ...){
   if(!is.null(path)){  
     save_yaml(yml=yml,
               path=path,
-              verbose=verbose)
+              handlers=handlers,
+              verbose=verbose,
+              ...)
     #### Return ####
     if(isTRUE(return_path)){
       return(path)

diff --git a/R/save_yaml.R b/R/save_yaml.R
@@ -1,14 +1,16 @@
 save_yaml <- function(yml,
                       path,
-                      verbose=TRUE){
+                      handlers=NULL,
+                      verbose=TRUE,
+                      ...){
 
   dir.create(dirname(path),showWarnings = FALSE, recursive = TRUE)
   messager("Saving yaml ==>",path,v=verbose)
   #### Write bools as true/false rather than yes/no (default) ####
-  handlers2 <- list('bool#yes' = function(x){"${{ true }}"},
-                    'bool#no' = function(x){"${{ false }}"})
-  yml2 <- yaml::yaml.load(yaml::as.yaml(yml), 
-                          handlers = handlers2)
-  yaml::write_yaml(x = yml2,
+  if(!is.null(handlers)){
+    yml <- yaml::yaml.load(yaml::as.yaml(yml), 
+                           handlers = handlers)
+  } 
+  yaml::write_yaml(x = yml,
                    file = path)
 }
diff --git a/R/use_workflow.R b/R/use_workflow.R
@@ -242,9 +242,12 @@ use_workflow <- function(## action-level args
     preview_yaml(yml=yml) 
   }
   #### Save yaml #### 
+  handlers <- list('bool#yes' = function(x){"${{ true }}"},
+                   'bool#no' = function(x){"${{ false }}"})
   path_or_yaml <- return_yaml(yml=yml,
                               path=path,
                               return_path=return_path,
+                              handlers=handlers,
                               verbose=verbose)
   return(path_or_yaml)
 }
diff --git a/action.yml b/action.yml
@@ -303,7 +303,7 @@ runs:
          install.packages(c("rmarkdown","BiocManager"), dependencies = TRUE)
          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies****'))
          repos <- BiocManager::repositories()
-         remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE)
+         remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=TRUE)
       continue-on-error: true
       shell: Rscript {0}
 
@@ -314,7 +314,7 @@ runs:
         options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout"))
         message(paste('****', Sys.time(), 'pass number 2 at installing dependencies****'))
         repos <- BiocManager::repositories()
-        remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE)
+        remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=TRUE)
       shell: Rscript {0}
 
     - name: Install RUnit (via BiocGenerics) 🛠

diff --git a/man/check_miniconda_args.Rd b/man/check_miniconda_args.Rd
diff --git a/man/construct_conda_yml.Rd b/man/construct_conda_yml.Rd
diff --git a/tests/testthat/test-construct_conda_yml.R b/tests/testthat/test-construct_conda_yml.R
@@ -1,24 +1,47 @@
 test_that("construct_conda_yml works", {
 
-  path1 <- construct_conda_yml(name="sc_env",
+  save_path <- tempfile(fileext = "myenv_conda.yml")
+  path1 <- construct_conda_yml(name="myenv",
                               dependencies=c("anndata","scanpy"),
-                              return_path = TRUE)
+                              return_path = TRUE,
+                              save_path = save_path)
   testthat::expect_true(file.exists(path1)) 
 
-  yml1 <- construct_conda_yml(name="sc_env",
+  yml1 <- construct_conda_yml(name="myenv",
                               dependencies=c("anndata","scanpy"),
-                              return_path = FALSE)
+                              return_path = FALSE,
+                              save_path = save_path)
   testthat::expect_true(all(c("name","channels","dependencies") %in% names(yml1)))
 
-  yml2 <- construct_conda_yml(name="sc_env",
+  yml2 <- construct_conda_yml(name="myenv",
                               dependencies=c("anndata>=1.0","scanpy<20.1.1"),
                               pip = c("pip","mytool1","mtool2"), 
-                              return_path = FALSE)
+                              return_path = FALSE,
+                              save_path = save_path)
   testthat::expect_true(all(c("name","channels","dependencies","pip") %in% names(yml2)))
 
-  yml3 <- construct_conda_yml(name="sc_env",
+  yml3 <- construct_conda_yml(name="myenv",
                               dependencies=c("anndata","scanpy"),
                               save_path = NULL,
-                              return_path = TRUE)
+                              preview = TRUE,
+                              return_path = TRUE,
+                              save_path = save_path)
   testthat::expect_true(all(c("name","channels","dependencies") %in% names(yml3)))
+
+
+  #### Construct an actual conda env ####
+  if(conda_installed() && is_gha()){ 
+    envname <- "testenv"
+    if(condaenv_exists(envname)){
+      reticulate::conda_remove(envname = envname)
+    }
+    path2 <- construct_conda_yml(name=envname,
+                                 dependencies=list("python"),
+                                 pip=list("requests"),
+                                 preview = TRUE,
+                                 return_path = TRUE,
+                                 save_path = save_path)
+    out <- reticulate::conda_create(environment = path2)
+  }
+
 })
diff --git a/tests/testthat/test-infer_biocviews.R b/tests/testthat/test-infer_biocviews.R
@@ -12,7 +12,7 @@ test_that("infer_biocviews works", {
     )
   } else {
     testthat::expect_equal(infer_biocviews(include_branch = FALSE),
-                           "WorkflowManagement")  
+                           c("`Software","WorkflowManagement"))  
   }
   biocviews_manual = c("Software","Genetics","Transcriptomics") 
   if(testthat::is_testing() && !is_gha()){