Add new conda yml

RajLabMSSM · May 24, 2024 · 2d5e13e · 2d5e13e
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,4 @@
+^auto$
 .*\.Rproj$
 ^\.Rproj\.user$
 ^README.Rmd

diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
@@ -4,14 +4,19 @@ name: rworkflows
     branches:
     - master
     - main
+    - devel
     - RELEASE_**
   pull_request:
     branches:
     - master
     - main
+    - devel
     - RELEASE_**
 jobs:
   rworkflows:
+    permissions:
+      contents: write
+      packages: write
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     container: ${{ matrix.config.cont }}
@@ -20,16 +25,22 @@ jobs:
       matrix:
         config:
         - os: ubuntu-latest
-          r: devel
           bioc: devel
-          cont: bioconductor/bioconductor_docker:devel
-          rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          python: 3.11
         - os: macOS-latest
-          r: latest
           bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+          python: 3.11
         - os: windows-latest
-          r: latest
           bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+          python: 3.11
     steps:
     - uses: neurogenomics/rworkflows@master
       with:
@@ -41,10 +52,9 @@ jobs:
         run_covr: ${{ true }}
         run_pkgdown: ${{ true }}
         has_runit: ${{ false }}
-        GITHUB_TOKEN: ${{ secrets.PAT_GITHUB }}
-        run_docker: ${{ true }}
-        docker_user: bschilder
-        docker_org: neurogenomicslab
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
         DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
         runner_os: ${{ runner.os }}
-        cache_version: cache-master
+        cache_version: cache-v1
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
+auto/
 basilisk/
 # R project files
 *.Rproj
@@ -40,4 +41,4 @@ vignettes/*.R
 *.utf8.md
 *.knit.md
 # R Environment Variables
-.Renviron
+.Renviron
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: echoconda
 Type: Package
 Title: echoverse module: conda environment management
-Version: 0.99.9
+Version: 0.99.10
 Authors@R: 
     c(person(given = "Brian",
            family = "Schilder",
@@ -59,7 +59,7 @@ Suggests:
 Remotes:
     github::MRCIEU/genetics.binaRies,
     github::RajLabMSSM/echodata
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 StagedInstall: no
 VignetteBuilder: knitr
 License: GPL (>= 3)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# echoconda 0.99.10
+
+## New features
+
+* Updated `rworkflows`. 
+
 # echoconda 0.99.9
 
 ## New features

diff --git a/R/basilisk.R b/R/basilisk.R
@@ -22,11 +22,14 @@ create_env_basilisk <- function(yaml_path,
                                 pkgs,
                                 sep="=",
                                 use_subversion=FALSE,
+                                use_nodefaults=TRUE,
                                 start = TRUE){  
     package <- NULL;
     # yaml_path <- tail(ymls$yaml_path,1)
     yaml_txt <- yaml::read_yaml(file = yaml_path) 
     deps <- unlist(yaml_txt$dependencies)
+    #### Omit python ####
+    deps <- deps[!startsWith(deps,"python")]
     #### Check for pip deps ####
     has_pip <- if(!is.null(names(deps))){
         startsWith(names(deps),"pip")
@@ -41,7 +44,7 @@ create_env_basilisk <- function(yaml_path,
     }
     #### Subset to only core packages ####  
     #### Make sure package aren't listed twice ####
-    pkgs <- pkgs[!duplicated(pkgs$package),]
+    pkgs <- pkgs[!duplicated(pkgs$package),]  
     #### Omit subversions for increased flexibility ####
     if(isFALSE(use_subversion)){
         pkgs$version <- stringr::str_split(pkgs$version,"[.]", 
@@ -50,15 +53,18 @@ create_env_basilisk <- function(yaml_path,
     ## Split by pip / non-pip 
     pip_pkgs <- pkgs[package %in% unname(deps[has_pip]),] 
     nonpip_pkgs <- pkgs[package %in% unname(deps[!has_pip]),]
+    channels <-  unique(c(pkgs$channel,
+                          if(use_nodefaults) "nodefaults" else NULL))
+      use_nodefaults
     #### Create basilisk env object ####
     envObj <- basilisk::BasiliskEnvironment(
         envname = yaml_txt$name, 
         pkgname = "echoconda",
         ## Use >= rather than = or == for increased flexibility,
         ## but reduced reproducibility.
-        packages = paste(nonpip_pkgs$package,nonpip_pkgs$version,sep=sep),
-        pip = paste(pip_pkgs$package,pip_pkgs$version,sep=sep),
-        channels = unique(c(pkgs$channel,"nodefaults"))
+        packages = paste(nonpip_pkgs$package, nonpip_pkgs$version, sep=sep),
+        pip = paste(pip_pkgs$package, pip_pkgs$version, sep=sep),
+        channels = channels
     ) 
     if(isTRUE(start)){
         proc <- basilisk::basiliskStart(env = envObj)

diff --git a/R/create_env.R b/R/create_env.R
@@ -1,6 +1,13 @@
 #' Create conda env
 #' 
 #' Create conda env using one of several methods.
+#' @param ... Additional arguments passed to method-specific 
+#' conda env build functions:
+#' \itemize{
+#'  \item \code{basilisk}: \link[echoconda]{create_env_basilisk}
+#'  \item \code{reticulate}: \link[reticulate]{conda_create}
+#'  \item \code{cli}: \link[echoconda]{create_env_cli} 
+#'  }
 #' @keywords internal
 #' @inheritParams yaml_to_env
 #' @inheritParams reticulate::conda_create
@@ -9,7 +16,8 @@ create_env <- function(conda_env,
                        method=c("basilisk","reticulate","cli"),
                        conda="auto",
                        force_new=FALSE,
-                       verbose=TRUE){
+                       verbose=TRUE,
+                       ...){
     messager("echoconda:: Creating conda environment:", conda_env,
              v = verbose
     ) 
@@ -26,7 +34,8 @@ create_env <- function(conda_env,
         if(method=="reticulate"){
             reticulate::conda_create(envname = conda_env,
                                      environment = yaml_path, 
-                                     conda = conda)
+                                     conda = conda,
+                                     ...)
         #### basilisk ####
         } else if(method=="basilisk"){
             pkgs <- data.table::fread(
@@ -35,15 +44,16 @@ create_env <- function(conda_env,
             )  
             envObj <- create_env_basilisk(yaml_path = yaml_path,
                                           pkgs = pkgs,
-                                          start = TRUE)
+                                          ...)
             conda_env <- envObj@envname
 
         #### cli ####
         } else if(method=="cli"){
             conda_env <- create_env_cli(yaml_path = yaml_path,
                                         conda = conda, 
                                         force_new = force_new,
-                                        verbose = verbose)
+                                        verbose = verbose,
+                                        ...)
         } else {
             stp <- paste("method must be one of:",
                          paste("\n -",eval(formals(create_env)$method)))

diff --git a/R/env_to_yaml.R b/R/env_to_yaml.R
@@ -16,11 +16,11 @@
 #' @export
 #' @importFrom reticulate conda_export
 #' @examples
-#' path <- echoconda::env_to_yaml(conda_env="base")
+#' path <- env_to_yaml(conda_env="base")
 env_to_yaml <- function(conda_env,
                         yaml_path = file.path(tempdir(),"conda.yml"),
                         conda  = "auto",
-                        method = c("basilisk","reticulate"),
+                        method = c("reticulate","basilisk"),
                         verbose = TRUE,
                         ...){
 

diff --git a/R/find_env_rlib.R b/R/find_env_rlib.R
@@ -5,10 +5,12 @@
 #'
 #' @family conda
 #' @export
-find_env_rlib <- function(conda_env = "echoR",
+find_env_rlib <- function(conda_env = "echoR_mini",
                           suffix = "lib/R/library/") {
     conda_env <- check_env(conda_env = conda_env)
-    conda_path <- dirname(dirname(find_python_path(conda_env = conda_env)))
+    list.files(conda_env)
+    python <- find_python_path(conda_env = conda_env)
+    conda_path <- dirname(dirname(python))
     if (conda_path == ".") {
         env_Rlib <- .libPaths()
         message("No conda_env='", conda_env, "' not found.")

diff --git a/R/install_conda_basilisk.R b/R/install_conda_basilisk.R
@@ -6,8 +6,8 @@
 #' @keywords internal
 #' @importFrom basilisk.utils installConda
 install_conda_basilisk <- function(verbose=TRUE){
-
-    new_install <- basilisk.utils::installConda()
+    # Sys.setenv("BASILISK_USE_SYSTEM_DIR"=1)
+    new_install <- basilisk.utils::installConda(installed = FALSE)
     if(isTRUE(new_install)){
         messager("echoconda:: Installing conda via basilisk.",v=verbose)
     } else {

diff --git a/R/yaml_to_env.R b/R/yaml_to_env.R
@@ -14,17 +14,19 @@
 #'  overwrite it with a new one (\emph{DEFAULT}: \code{FALSE}).
 #' @param show_contents Show the contents of the yaml file (if used).
 #' @param verbose Print messages.
+#' @inheritParams create_env
 #' @inheritParams reticulate::conda_create
 #' 
 #' @source \href{https://github.com/rstudio/reticulate/issues/779}{GitHub Issue}
 #' @source \href{https://stackoverflow.com/questions/35802939/install-only-available-packages-using-conda-install-yes-file-requirements-t}{
 #' StackOverflow suggestions for cross-platform troubleshooting}
 #' @family conda
+#' 
 #' @export
 #' @importFrom reticulate conda_binary
 #' @importFrom echodata is_local is_url
 #' @examples
-#' conda_env <- echoconda::yaml_to_env()
+#' conda_env <- yaml_to_env()
 yaml_to_env <- function(yaml_path = system.file(
                               package = "echoconda",
                               "conda","echoR_mini.yml"
@@ -33,13 +35,13 @@ yaml_to_env <- function(yaml_path = system.file(
                         conda = "auto",
                         force_new = FALSE,
                         show_contents = FALSE,
-                        verbose = TRUE) {
-    # echoverseTemplate:::source_all()
-    # echoverseTemplate:::args2vars(echoconda::yaml_to_env)
+                        verbose = TRUE,
+                        ...) {
+    # devoptera::args2vars(yaml_to_env)
 
     method <- tolower(method)[1]
-    install_conda(method = method,
-                  verbose = verbose)
+    # install_conda(method = method,
+    #               verbose = verbose)
     start <- Sys.time()  
     #### Check whether env exists #### 
     conda_env <- name_from_yaml(yaml_path = yaml_path,
@@ -87,7 +89,8 @@ yaml_to_env <- function(yaml_path = system.file(
                                     method = method, 
                                     conda = conda, 
                                     force_new = force_new, 
-                                    verbose = verbose)
+                                    verbose = verbose,
+                                    ...)
         }
     }
     conda_env <- check_env(conda_env = conda_env)

diff --git a/README.Rmd b/README.Rmd
@@ -1,25 +1,21 @@
 ---
 title: ""  
-author: "<img src='https://github.com/RajLabMSSM/`r read.dcf('DESCRIPTION', fields = 'Package')[1]`/raw/`r gsub('[*] ','',system('git branch', intern = TRUE)[1])`/inst/hex/hex.png' height='300'><br><br>
-        `r badger::badge_github_version(color = 'black')` 
-        `r badger::badge_github_actions(action = 'rworkflows')`
-        `r badger::badge_last_commit()`
-        `r badger::badge_codecov()` 
-        `r badger::badge_license()` 
-        <h5>Author: <i>Brian M. Schilder</i></h5>" 
+author: "`r rworkflows::use_badges(branch='main')`" 
 date: "<h5>README updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h5>"
 output:
   github_document
 ---
 
 ```{r, echo=FALSE, include=FALSE}
 pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
-description <- read.dcf("DESCRIPTION", fields = "Description")[1]
+description <- read.dcf("DESCRIPTION", fields = "Description")[1] |>
+    gsub(pattern="\n",replacement=" ")
 ```
 
 ## ``r pkg``: `r gsub("echoverse module: ","", description)`
 
-This R package is part of the *echoverse* suite that supports [`echolocatoR`](https://github.com/RajLabMSSM/echolocatoR):
+This R package is part of the *echoverse* suite that supports 
+[`echolocatoR`](https://github.com/RajLabMSSM/echolocatoR):
 an automated genomic fine-mapping pipeline. 
 
 If you use ``r pkg``, please cite: 

diff --git a/README.md b/README.md
@@ -1,17 +1,22 @@
-<img src='https://github.com/RajLabMSSM/echoconda/raw/main/inst/hex/hex.png' height='300'><br><br>
-[![](https://img.shields.io/badge/devel%20version-0.99.9-black.svg)](https://github.com/RajLabMSSM/echoconda)
-[![R build
-status](https://github.com/RajLabMSSM/echoconda/workflows/rworkflows/badge.svg)](https://github.com/RajLabMSSM/echoconda/actions)
-[![](https://img.shields.io/github/last-commit/RajLabMSSM/echoconda.svg)](https://github.com/RajLabMSSM/echoconda/commits/main)
-[![](https://app.codecov.io/gh/RajLabMSSM/echoconda/branch/main/graph/badge.svg)](https://app.codecov.io/gh/RajLabMSSM/echoconda)
+<img src='https://github.com/RajLabMSSM/echoconda/raw/main/inst/hex/hex.png' title='Hex sticker for echoconda' height='300'><br>
 [![License: GPL (\>=
 3)](https://img.shields.io/badge/license-GPL%20(%3E=%203)-blue.svg)](https://cran.r-project.org/web/licenses/GPL%20(%3E=%203))
-¶ <h5> ¶ Author: <i>Brian M. Schilder</i> ¶ </h5>
-<h5> ¶ README updated: <i>Dec-22-2022</i> ¶ </h5>
-
-## `echoconda`: Various utility functions to find, build,
-
-and use conda environments from within R.
+[![](https://img.shields.io/badge/devel%20version-0.99.10-black.svg)](https://github.com/RajLabMSSM/echoconda)
+[![](https://img.shields.io/github/languages/code-size/RajLabMSSM/echoconda.svg)](https://github.com/RajLabMSSM/echoconda)
+[![](https://img.shields.io/github/last-commit/RajLabMSSM/echoconda.svg)](https://github.com/RajLabMSSM/echoconda/commits/main)
+<br> [![R build
+status](https://github.com/RajLabMSSM/echoconda/workflows/rworkflows/badge.svg)](https://github.com/RajLabMSSM/echoconda/actions)
+[![](https://codecov.io/gh/RajLabMSSM/echoconda/branch/main/graph/badge.svg)](https://app.codecov.io/gh/RajLabMSSM/echoconda)
+<br>
+<a href='https://app.codecov.io/gh/RajLabMSSM/echoconda/tree/main' target='_blank'><img src='https://codecov.io/gh/RajLabMSSM/echoconda/branch/main/graphs/icicle.svg' title='Codecov icicle graph' width='200' height='50' style='vertical-align: top;'></a>  
+<h4>  
+Authors: <i>Brian Schilder, Jack Humphrey, Towfique Raj</i>  
+</h4>
+<h5>  
+README updated: <i>Feb-11-2024</i>  
+</h5>
+
+## `echoconda`: Various utility functions to find, build, and use conda environments from within R.
 
 This R package is part of the *echoverse* suite that supports
 [`echolocatoR`](https://github.com/RajLabMSSM/echolocatoR): an automated

diff --git a/inst/conda/ontogpt.yml b/inst/conda/ontogpt.yml
@@ -0,0 +1,10 @@
+name: ontogpt
+channels:
+  - conda-forge
+  - bioconda 
+  - nodefaults
+dependencies:  
+  - python>=3.9  
+  - poetry
+  - pip:
+    - ontogpt
diff --git a/inst/conda/plotly.yml b/inst/conda/plotly.yml
@@ -0,0 +1,13 @@
+name: plotly
+channels:
+  - conda-forge
+  - bioconda 
+  - plotly 
+  - nodefaults  
+dependencies:
+  - python>=3.7 
+  - plotly  
+  - plotly-orca
+  - python-kaleido
+  - r-plotly
+  - pip