test miniforge_variant

Author: bschilder

.Rhistory

@@ -53,3 +53,4 @@ jobs:
         DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
         runner_os: ${{ runner.os }}
         cache_version: cache-v1
+        miniforge_variant: ""

.github/workflows/rworkflows.yml

@@ -1,7 +1,7 @@
 Package: rworkflows
 Type: Package
 Title: Test, Document, Containerise, and Deploy R Packages
-Version: 0.99.13
+Version: 0.99.14
 Authors@R:
     c(person(given = "Brian",
            family = "Schilder",
@@ -58,8 +58,6 @@ Suggests:
     BiocStyle,
     BiocPkgTools,
     biocViews
-Remotes:
-  github::Bioconductor/BiocStyle
 VignetteBuilder: knitr
 License: GPL-3
 Config/testthat/edition: 3

DESCRIPTION

@@ -1,3 +1,16 @@
+# rworkflows 0.99.14
+
+## New features
+
+* Add step to enable conda envs: #78
+  - Add subfunction: `gha_python_versions()` within `construct_runners`
+  - Add new *action.yml*:
+    - `miniforge_variant`
+    - `miniforge_version`
+    - `activate_environment`
+    - `environment_file`
+    - `channels`
+
 # rworkflows 0.99.13
 
 ## New features

NEWS.md

@@ -53,9 +53,9 @@ bioc_r_versions <- function(bioc_version = NULL,
     return(opts)
   } else if(is.null(bioc_version)){
     return(info)
-  } else if (bioc_version=="devel") {
+  } else if (bioc_version %in% c("devel","dev")) {
     return(info$devel)
-  } else if (bioc_version=="release") {
+  } else if (bioc_version %in% c("release","latest")) {
     return(info$release)
   } else if (bioc_version %in% names(info$r_ver_for_bioc_ver)){ 
     if(grepl("RELEASE_",bioc_version,ignore.case = TRUE)){

R/bioc_r_versions.R

@@ -13,6 +13,11 @@
 #'   for a list of all official Bioconductor Docker container versions.
 #' @param rspm Which R repository manager to use on each OS
 #'  (\code{NULL} means the default will be used for that OS).
+#' @param python_version Which python version to use on each OS.
+#'  (\code{NULL} means python will not be installed on that OS).
+#'  See 
+#'  \href{https://github.com/marketplace/actions/setup-miniconda}{here} for
+#'  details.
 #' @param versions_explicit Specify R/Bioc versions explicitly
 #'  (e.g. \code{r: 4.2.0, bioc: 3.16}) 
 #'  as opposed to flexibly (e.g. \code{r: "latest", bioc: "release"}).
@@ -33,6 +38,9 @@ construct_runners <- function(os=c("ubuntu-latest",
                               r = list("auto",
                                        "auto",
                                        "auto"),
+                              python_version = list(NULL,
+                                                    NULL,
+                                                    NULL),
                               versions_explicit = FALSE, 
                               run_check_cont = FALSE,
                               cont = construct_cont(
@@ -53,7 +61,8 @@ construct_runners <- function(os=c("ubuntu-latest",
                                        bioc = bioc, 
                                        r = r, 
                                        cont = cont,
-                                       rspm = rspm)   
+                                       rspm = rspm,
+                                       python_version = python_version)   
   #### Set runners ####
   runners <- lapply(os, function(o){
     if(isTRUE(versions_explicit)){
@@ -65,16 +74,22 @@ construct_runners <- function(os=c("ubuntu-latest",
     } 
     #### Check container settings ####
     if(isTRUE(run_check_cont)){
-      cont <- check_cont(cont=cont, 
-                         verbose=verbose)
-    }
+      args$cont[[o]] <- check_cont(cont=args$cont[[o]], 
+                                   verbose=verbose)
+    } 
     #### Construct new list ####
-    list(os = o,
-         bioc = info$bioc,
-         r = info$r,
-         cont = args$cont[[o]],
-         rspm = args$rspm[[o]]
+    l <- list(os = o,
+              bioc = info$bioc,
+              r = info$r,
+              cont = args$cont[[o]],
+              rspm = args$rspm[[o]]
          )
+    #### Check python settings ####
+    python_version <- if(!is.null(args$python_version)){
+      l[["python-version"]] <- gha_python_versions(
+        python_version=args$python_version[[o]])
+    } 
+    return(l)
   })
   return(runners) 
 }

R/construct_runners.R

@@ -3,12 +3,14 @@ construct_runners_check_args <- function(os,
                                          r,
                                          cont,
                                          rspm,
+                                         python_version,
                                          versions_explicit=FALSE,
                                          verbose=TRUE){
 
 
   #### Fill names ####
-  args <- list(os=os, bioc=bioc, r=r, cont=cont, rspm=rspm)
+  args <- list(os=os, bioc=bioc, r=r, cont=cont, rspm=rspm, 
+               python_version=python_version)
   args2 <- lapply(stats::setNames(names(args),
                                   names(args)), 
          function(nm){

R/construct_runners_check_args.R

@@ -0,0 +1,39 @@
+gha_python_versions <- function(python_version=NULL){
+  yml <- yaml::read_yaml(paste0(
+    "https://raw.githubusercontent.com/actions/python-versions/",
+    "main/versions-manifest.json")
+    )
+  
+  if(!is.null(python_version)){
+    python_version <- as.character(python_version[1]) 
+    #### Get all versions (minor and major) ####
+    versions <- sapply(yml, function(x){x$version}) 
+    versions_major <- unique(sapply(strsplit(versions,'\\.'),
+                                    function(x)paste(x[1],x[2],sep="."))
+                             )
+    versions_x <- unique(sapply(strsplit(versions,'\\.'),
+                                function(x)paste(x[1],"x",sep="."))
+    )
+    versions_opts <- c(versions,versions_major,versions_x)
+    #### Get devel version ####
+    if(python_version %in% c("devel","dev")){
+      python_version <- versions[sapply(yml, function(x){x$stable==FALSE})][1]
+    #### Get release version ####
+    } else if (python_version %in% c("latest","release")){
+      python_version <- versions[sapply(yml, function(x){x$stable==TRUE})][1]
+    #### Get specific version ####
+    } else if(python_version=="3"){
+      python_version <- "3.x"
+    }else {
+      if(!python_version %in% versions_opts){
+        stopper(paste0("python_version=",shQuote(python_version),
+                       "is not available.",
+                       "Must be one of:",
+                       paste("\n - ",shQuote(versions_opts),collapse = "")))
+      }  
+    } 
+    return(python_version)
+  } else {
+    return(yml)
+  } 
+}

R/gha_python_versions.R

@@ -100,10 +100,56 @@ inputs:
       The maximum time to wait for long R processes like 
       dependency installations, downloads, and code checks.
     default: 2000
+  miniforge_variant:
+    description: >
+      If provided, this variant of Miniforge will be downloaded and installed.
+      If `miniforge_variant=false`, Miniforge will not be instaled at all.
+      If `miniforge_variant=""`, the "Miniforge3" variant will be installed.
+      If `miniforge_version` is not provided, the `latest` version will be used.
+      Currently-known values: - Miniforge3 (default) - Miniforge-pypy3 -
+      Mambaforge - Mambaforge-pypy3 Visit
+      https://github.com/conda-forge/miniforge/releases/ for more information on
+      available variants.
+    default: false
+   miniforge_version:
+    description: >
+      If provided, this version of the given Miniforge variant will be
+      downloaded and installed. If `miniforge_variant` is not provided,
+      `Miniforge3` will be used. Visit
+      https://github.com/conda-forge/miniforge/releases/ for more information on
+      available versions.
+    default: ""
+  activate_environment:
+    description: >
+      Environment name (or path) to activate on all shells. Default is `test`
+      which will be created in `$CONDA/envs/test`. If an empty string is used,
+      no environment is activated by default (For `base` activation see the
+      `auto-activate-base` option). If the environment does not exist, it will
+      be created and activated. If `environment-file` is used and you want that
+      to be the environment used, you need to explicitely provide the name of
+      that environment on `activate-environment`. If using sh/bash/cmd.exe
+      shells please read the IMPORTANT! section on the README.md! to properly
+      activate conda environments on these shells.
+    default: "test"
+  environment_file: 
+    description: >
+      Path or URL to a .yml file to build the conda environment with. 
+      For more information see: 
+      https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file
+    default:
+      ""
+  channels: 
+    description: >
+      Conda configuration. Comma separated list of channels to use in order of
+      priority. See
+      https://docs.conda.io/projects/conda/en/latest/user-guide/configuration/
+      for more information.
+    default:
+      "" 
 runs:
   using: 'composite'
   steps:
-    - name: Set GitHub environment variables 🏞️
+    - name: Set GitHub environment variables ️🌎
       run: | 
         echo "GITHUB_TOKEN=${{ inputs.GITHUB_TOKEN }}" >> $GITHUB_ENV
         echo "RGL_USE_NULL=TRUE" >> $GITHUB_ENV
@@ -113,6 +159,19 @@ runs:
         echo "NOT_CRAN=${{ !inputs.as_cran }}" >> $GITHUB_ENV
       shell: bash {0}
 
+    ## Setup Miniconda 🐍
+    - name: Setup Miniconda
+      if: inputs.miniforge_variant != 'false'
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: false
+        python-version: ${{ matrix.python-version }}
+        miniforge-variant: ${{ inputs.miniforge_variant }}
+        miniforge-version: ${{ inputs.miniforge_version }}
+        activate-environment: ${{ inputs.activate_environment }}
+        environment-file: ${{ inputs.environment_file }}
+        channels: ${{ inputs.channels }}
+    
     ## Set the R library to the directory matching the
     ## R packages cache step further below when running on Docker (Linux).
     - name: Set R library home on Linux 📚