@@ -30,7 +30,7 @@ ad <- NULL

 #' @name sctkPythonInstallConda

 #' @title Installs Python packages into a Conda environment

 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package

-#' using \code{\link[reticulate]{conda_install}} from package \code{\link{reticulate}}. This

+#' using \code{\link{conda_install}} from package \code{\link{reticulate}}. This

 #' will create a new Conda environment with the name \code{envname} if not already present.

 #' Note that Anaconda or Miniconda already need to be installed on the local system.

 #' @param envname Character. Name of the conda environment to create.

@@ -42,15 +42,15 @@ ad <- NULL

 #' @param pipIgnoreInstalled Boolean. Ignore installed versions when using pip. This is TRUE by default so that specific package versions can be installed even if they are downgrades.

 #'        The FALSE option is useful for situations where you don't want a pip install to attempt an overwrite of a conda binary package (e.g. SciPy on Windows which is very difficult

 #'        to install via pip due to compilation requirements).

-#' @param pythonVersion Passed to \code{python_version} variable in \code{\link[reticulate]{conda_install}}. Default NULL.

-#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}.

+#' @param pythonVersion Passed to \code{python_version} variable in \code{\link{conda_install}}. Default NULL.

+#' @param ... Other parameters to pass to \code{\link{conda_install}}.

 #' @return None. Installation of Conda environment.

 #' @examples

 #' \dontrun{

 #' sctkPythonInstallConda(envname = "sctk-reticulate")

 #' }

-#' @seealso See \code{\link[reticulate]{conda_create}} for more information on creating a Conda environment.

-#' See \code{\link[reticulate]{conda_install}} for more description of the installation parameters.

+#' @seealso See \code{\link{conda_create}} for more information on creating a Conda environment.

+#' See \code{\link{conda_install}} for more description of the installation parameters.

 #' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.

 #' See \code{\link[singleCellTK]{selectSCTKConda}} for reloading the Conda environment if R is restarted without

 #' going through the whole installation process again.

@@ -88,7 +88,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",

 #' @name sctkPythonInstallVirtualEnv

 #' @title Installs Python packages into a virtual environment

 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package

-#' using \code{\link[reticulate]{virtualenv_install}} from package \code{\link{reticulate}}. This

+#' using \code{\link{virtualenv_install}} from package \code{\link{reticulate}}. This

 #' will create a new virtual environment with the name \code{envname} if not already present.

 #' @param envname Character. Name of the virtual environment to create.

 #' @param packages Character Vector. List of packages to install.

@@ -99,8 +99,8 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",

 #' \dontrun{

 #' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")

 #' }

-#' @seealso See \code{\link[reticulate]{virtualenv_create}} for more information on creating a Conda environment.

-#' See \code{\link[reticulate]{virtualenv_install}} for more description of the installation parameters.

+#' @seealso See \code{\link{virtualenv_create}} for more information on creating a Conda environment.

+#' See \code{\link{virtualenv_install}} for more description of the installation parameters.

 #' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.

 #' See \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} for reloading the virtual environment if R is restarted without

 #' going through the whole installation process again.

@@ -59,7 +59,7 @@ ad <- NULL

 sctkPythonInstallConda <- function(envname = "sctk-reticulate",

                                    conda = "auto",

                                    packages = c("scipy", "numpy", "astroid", "six"),

-                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "anndata", "umap-learn"),

+                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "anndata"),

                                    selectConda = TRUE,

                                    forge = FALSE,

                                    pipIgnoreInstalled = TRUE,

@@ -106,7 +106,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",

 #' going through the whole installation process again.

 #' @export

 sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",

-                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "anndata", "umap-learn"),

+                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "anndata"),

                                         selectEnvironment = TRUE,

                                         python = NULL) {

@@ -59,7 +59,7 @@ ad <- NULL

 sctkPythonInstallConda <- function(envname = "sctk-reticulate",

                                    conda = "auto",

                                    packages = c("scipy", "numpy", "astroid", "six"),

-                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "anndata"),

+                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "anndata", "umap-learn"),

                                    selectConda = TRUE,

                                    forge = FALSE,

                                    pipIgnoreInstalled = TRUE,

@@ -106,7 +106,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",

 #' going through the whole installation process again.

 #' @export

 sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",

-                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "anndata"),

+                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "anndata", "umap-learn"),

                                         selectEnvironment = TRUE,

                                         python = NULL) {

@@ -9,7 +9,6 @@ scipy <- NULL

 sparse <- NULL

 numpy <- NULL

 scnrm <- NULL

-scgen <- NULL

 sc <- NULL

 bbknn <- NULL

 pkg_resources <- NULL

@@ -22,7 +21,6 @@ ad <- NULL

   sparse <<- reticulate::import("scipy.sparse", delay_load = TRUE)

   numpy <<- reticulate::import("numpy", delay_load = TRUE)

   scnrm <<- reticulate::import("scanorama", delay_load = TRUE)

-  scgen <<- reticulate::import("scgen", delay_load = TRUE)

   sc <<- reticulate::import("scanpy", delay_load = TRUE)

   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)

   pkg_resources <<- reticulate::import('pkg_resources',delay_load = TRUE)

@@ -60,7 +58,7 @@ ad <- NULL

 sctkPythonInstallConda <- function(envname = "sctk-reticulate",

                                    conda = "auto",

                                    packages = c("scipy", "numpy", "astroid", "six"),

-                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "scgen","anndata"),

+                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "anndata"),

                                    selectConda = TRUE,

                                    forge = FALSE,

                                    pipIgnoreInstalled = TRUE,

@@ -106,7 +104,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",

 #' going through the whole installation process again.

 #' @export

 sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",

-                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "scgen","anndata"),

+                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "anndata"),

                                         selectEnvironment = TRUE,

                                         python = NULL) {

@@ -25,15 +25,10 @@ ad <- NULL

   scgen <<- reticulate::import("scgen", delay_load = TRUE)

   sc <<- reticulate::import("scanpy", delay_load = TRUE)

   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)

-<<<<<<< HEAD

   pkg_resources <<- reticulate::import('pkg_resources',delay_load = TRUE)

   ad <<- reticulate::import('anndata',delay_load = TRUE,convert = FALSE)

-=======

-  pkg_resources <<- reticulate::import('pkg_resources', delay_load = TRUE)

->>>>>>> 4127090a0c04ab251d1357d8787f6c0ea2c648d5

 }

-

 #' @name sctkPythonInstallConda

 #' @title Installs Python packages into a Conda environment

 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package

@@ -28,7 +28,6 @@ ad <- NULL

   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)

   pkg_resources <<- reticulate::import('pkg_resources',delay_load = TRUE)

   ad <<- reticulate::import('anndata',delay_load = TRUE,convert = FALSE)

-  blt <<- reticulate::import_builtins()

 }

@@ -9,7 +9,6 @@ scipy <- NULL

 sparse <- NULL

 numpy <- NULL

 scnrm <- NULL

-blt <- NULL

 scgen <- NULL

 sc <- NULL

 bbknn <- NULL

@@ -25,8 +24,7 @@ pkg_resources <- NULL

   scgen <<- reticulate::import("scgen", delay_load = TRUE)

   sc <<- reticulate::import("scanpy", delay_load = TRUE)

   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)

-  pkg_resources <<- reticulate::import('pkg_resources',delay_load = TRUE)

-  blt <<- reticulate::import_builtins()

+  pkg_resources <<- reticulate::import('pkg_resources', delay_load = TRUE)

 }

@@ -3,13 +3,12 @@

 ## https://rstudio.github.io/reticulate/articles/package.html

 ## Meant to delay loading of python environmnet so user can set the python environment

-# python modules to use 

+# python modules to use

 scrublet <- NULL

 scipy <- NULL

 sparse <- NULL

 numpy <- NULL

 scnrm <- NULL

-blt <- NULL

 scgen <- NULL

 sc <- NULL

 bbknn <- NULL

@@ -26,7 +25,6 @@ pkg_resources <- NULL

   sc <<- reticulate::import("scanpy", delay_load = TRUE)

   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)

   pkg_resources <<- reticulate::import('pkg_resources',delay_load = TRUE)

-  blt <<- reticulate::import_builtins()

 }

@@ -35,30 +33,30 @@ pkg_resources <- NULL

 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package

 #' using \code{\link[reticulate]{conda_install}} from package \code{\link{reticulate}}. This

 #' will create a new Conda environment with the name \code{envname} if not already present.

-#' Note that Anaconda or Miniconda already need to be installed on the local system. 

+#' Note that Anaconda or Miniconda already need to be installed on the local system.

 #' @param envname Character. Name of the conda environment to create.

 #' @param conda Character. Path to conda executable. Usue "auto" to find conda using the PATH and other conventional install locations. Default 'auto'.

-#' @param packages Character Vector. List of packages to install from Conda. 

+#' @param packages Character Vector. List of packages to install from Conda.

 #' @param pipPackages Character Vector. List of packages to install into the Conda environment using 'pip'.

 #' @param selectConda Boolean. Run \code{\link[singleCellTK]{selectSCTKConda}} after installing all packages to select the Conda environment. Default TRUE.

 #' @param forge Boolean. Include the Conda Forge repository.

 #' @param pipIgnoreInstalled Boolean. Ignore installed versions when using pip. This is TRUE by default so that specific package versions can be installed even if they are downgrades.

 #'        The FALSE option is useful for situations where you don't want a pip install to attempt an overwrite of a conda binary package (e.g. SciPy on Windows which is very difficult

 #'        to install via pip due to compilation requirements).

-#' @param pythonVersion Passed to \code{python_version} variable in \code{\link[reticulate]{conda_install}}. Default NULL.        

-#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}. 

+#' @param pythonVersion Passed to \code{python_version} variable in \code{\link[reticulate]{conda_install}}. Default NULL.

+#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}.

 #' @examples

 #' \dontrun{

 #' sctkPythonInstallConda(envname = "sctk-reticulate")

 #' }

-#' @seealso See \code{\link[reticulate]{conda_create}} for more information on creating a Conda environment. 

+#' @seealso See \code{\link[reticulate]{conda_create}} for more information on creating a Conda environment.

 #' See \code{\link[reticulate]{conda_install}} for more description of the installation parameters.

 #' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.

-#' See \code{\link[singleCellTK]{selectSCTKConda}} for reloading the Conda environment if R is restarted without 

-#' going through the whole installation process again. 

+#' See \code{\link[singleCellTK]{selectSCTKConda}} for reloading the Conda environment if R is restarted without

+#' going through the whole installation process again.

 #' See \url{https://docs.conda.io/en/latest/} for more information on Conda environments.

 #' @export

-sctkPythonInstallConda <- function(envname = "sctk-reticulate", 

+sctkPythonInstallConda <- function(envname = "sctk-reticulate",

                                    conda = "auto",

                                    packages = c("scipy", "numpy", "astroid", "six"),

                                    pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "scgen"),

@@ -67,21 +65,21 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",

                                    pipIgnoreInstalled = TRUE,

                                    pythonVersion = NULL,

                                    ...) {

-  

+

   path <- reticulate::conda_create(envname = envname, packages = "python", conda = conda)

-  

+

   for(i in packages) {

-    reticulate::conda_install(envname = envname, packages = i, conda = conda, 

+    reticulate::conda_install(envname = envname, packages = i, conda = conda,

                   pip = FALSE, pip_ignore_installed = pipIgnoreInstalled,

                   python_version = pythonVersion, ...)

   }

-  

+

   reticulate::conda_install(envname = envname, packages = pipPackages,

                 pip = TRUE, pip_ignore_installed = pipIgnoreInstalled,

                 python_version = pythonVersion, ...)

-  

+

   if(isTRUE(selectConda)) selectSCTKConda(envname = envname)

-  

+

   invisible(path)

 }

@@ -93,32 +91,32 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",

 #' using \code{\link[reticulate]{virtualenv_install}} from package \code{\link{reticulate}}. This

 #' will create a new virtual environment with the name \code{envname} if not already present.

 #' @param envname Character. Name of the virtual environment to create.

-#' @param packages Character Vector. List of packages to install. 

+#' @param packages Character Vector. List of packages to install.

 #' @param selectEnvironment Boolean. Run \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} after installing all packages to select the virtual environment. Default TRUE.

 #' @param python The path to a Python interpreter, to be used with the created virtual environment. When NULL, the Python interpreter associated with the current session will be used. Default NULL.

 #' @examples

 #' \dontrun{

 #' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")

 #' }

-#' @seealso See \code{\link[reticulate]{virtualenv_create}} for more information on creating a Conda environment. 

+#' @seealso See \code{\link[reticulate]{virtualenv_create}} for more information on creating a Conda environment.

 #' See \code{\link[reticulate]{virtualenv_install}} for more description of the installation parameters.

 #' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.

-#' See \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} for reloading the virtual environment if R is restarted without 

-#' going through the whole installation process again. 

+#' See \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} for reloading the virtual environment if R is restarted without

+#' going through the whole installation process again.

 #' @export

 sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",

                                         packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "scgen"),

                                         selectEnvironment = TRUE,

                                         python = NULL) {

-  

+

   path <- reticulate::virtualenv_create(envname = envname, python = python)

-  

+

   for(i in packages) {

     reticulate::virtualenv_install(envname = envname, packages = i, ignore_installed = TRUE)

   }

-  

+

   if(isTRUE(selectEnvironment)) selectSCTKVirtualEnvironment(envname = envname)

-  

+

   invisible(path)

 }

@@ -142,7 +140,7 @@ sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",

 selectSCTKConda <- function(envname = "sctk-reticulate") {

   condaList <- reticulate::conda_list()

   ix <- condaList$name == envname

-  

+

   if(!any(ix)) {

     stop(paste0("Environment '", envname, "', not found. Run sctkPythonInstallConda(envname = '", envname, "') to install Python packages into a conda environmanet with this name."))

   }

@@ -150,7 +148,7 @@ selectSCTKConda <- function(envname = "sctk-reticulate") {

     envs <- paste(condaList[ix,"python"], collapse="\n")

     warning(paste0("More than one Conda environment detected with the name '", envname, "'. Selecting the first one in the list:\n", envs))

   }

-  

+

   reticulate::use_condaenv(condaenv = envname, required = TRUE)

 }

@@ -172,13 +170,13 @@ selectSCTKConda <- function(envname = "sctk-reticulate") {

 selectSCTKVirtualEnvironment <- function(envname = "sctk-reticulate") {

   res <- reticulate::virtualenv_list()

   ix <- res == envname

-  

+

   if(!any(ix)) {

     stop(paste0("Environmnet '", envname, "', not found. Run selectSCTKVirtualEnvironment(envname = '", envname, "') to install Python packages into a virtual environmanet with this name."))

   }

   if(sum(ix) > 1) {

     warning(paste0("More than one virtual environment detected with the name '", envname, "'. Selecting the first one in the list."))

   }

-  

+

   reticulate::use_virtualenv(res[which(ix)[1]], required = TRUE)

 }

@@ -14,6 +14,7 @@ scgen <- NULL

 sc <- NULL

 bbknn <- NULL

 pkg_resources <- NULL

+ad <- NULL

 .onLoad <- function(libname, pkgname) {

   # use superassignment to update global reference to scipy

@@ -26,6 +27,7 @@ pkg_resources <- NULL

   sc <<- reticulate::import("scanpy", delay_load = TRUE)

   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)

   pkg_resources <<- reticulate::import('pkg_resources',delay_load = TRUE)

+  ad <<- reticulate::import('anndata',delay_load = TRUE,convert = FALSE)

   blt <<- reticulate::import_builtins()

 }

@@ -61,7 +63,7 @@ pkg_resources <- NULL

 sctkPythonInstallConda <- function(envname = "sctk-reticulate", 

                                    conda = "auto",

                                    packages = c("scipy", "numpy", "astroid", "six"),

-                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "scgen"),

+                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "scgen","anndata"),

                                    selectConda = TRUE,

                                    forge = FALSE,

                                    pipIgnoreInstalled = TRUE,

@@ -107,7 +109,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",

 #' going through the whole installation process again. 

 #' @export

 sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",

-                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "scgen"),

+                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "scgen","anndata"),

                                         selectEnvironment = TRUE,

                                         python = NULL) {

@@ -96,7 +96,6 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",

 #' @param packages Character Vector. List of packages to install. 

 #' @param selectEnvironment Boolean. Run \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} after installing all packages to select the virtual environment. Default TRUE.

 #' @param python The path to a Python interpreter, to be used with the created virtual environment. When NULL, the Python interpreter associated with the current session will be used. Default NULL.

-#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}. 

 #' @examples

 #' \dontrun{

 #' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")

@@ -13,6 +13,7 @@ blt <- NULL

 scgen <- NULL

 sc <- NULL

 bbknn <- NULL

+pkg_resources <- NULL

 .onLoad <- function(libname, pkgname) {

   # use superassignment to update global reference to scipy

@@ -24,7 +25,7 @@ bbknn <- NULL

   scgen <<- reticulate::import("scgen", delay_load = TRUE)

   sc <<- reticulate::import("scanpy", delay_load = TRUE)

   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)

-  pkg_resources <- reticulate::import('pkg_resources',delay_load = TRUE)

+  pkg_resources <<- reticulate::import('pkg_resources',delay_load = TRUE)

   blt <<- reticulate::import_builtins()

 }

@@ -24,6 +24,7 @@ bbknn <- NULL

   scgen <<- reticulate::import("scgen", delay_load = TRUE)

   sc <<- reticulate::import("scanpy", delay_load = TRUE)

   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)

+  pkg_resources <- reticulate::import('pkg_resources',delay_load = TRUE)

   blt <<- reticulate::import_builtins()

 }

@@ -8,6 +8,11 @@ scrublet <- NULL

 scipy <- NULL

 sparse <- NULL

 numpy <- NULL

+scnrm <- NULL

+blt <- NULL

+scgen <- NULL

+sc <- NULL

+bbknn <- NULL

 .onLoad <- function(libname, pkgname) {

   # use superassignment to update global reference to scipy

@@ -15,6 +20,11 @@ numpy <- NULL

   scipy <<- reticulate::import("scipy", delay_load = TRUE)

   sparse <<- reticulate::import("scipy.sparse", delay_load = TRUE)

   numpy <<- reticulate::import("numpy", delay_load = TRUE)

+  scnrm <<- reticulate::import("scanorama", delay_load = TRUE)

+  scgen <<- reticulate::import("scgen", delay_load = TRUE)

+  sc <<- reticulate::import("scanpy", delay_load = TRUE)

+  bbknn <<- reticulate::import("bbknn", delay_load = TRUE)

+  blt <<- reticulate::import_builtins()

 }

@@ -49,7 +59,7 @@ numpy <- NULL

 sctkPythonInstallConda <- function(envname = "sctk-reticulate", 

                                    conda = "auto",

                                    packages = c("scipy", "numpy", "astroid", "six"),

-                                   pipPackages = c("scrublet"),

+                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "scgen"),

                                    selectConda = TRUE,

                                    forge = FALSE,

                                    pipIgnoreInstalled = TRUE,

@@ -96,7 +106,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",

 #' going through the whole installation process again. 

 #' @export

 sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",

-                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet"),

+                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "scgen"),

                                         selectEnvironment = TRUE,

                                         python = NULL) {

@@ -23,7 +23,7 @@ numpy <- NULL

 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package

 #' using \code{\link[reticulate]{conda_install}} from package \code{\link{reticulate}}. This

 #' will create a new Conda environment with the name \code{envname} if not already present.

-#' Note that Conda or Miniconda already need to be installed on the local system.

+#' Note that Anaconda or Miniconda already need to be installed on the local system. 

 #' @param envname Character. Name of the conda environment to create.

 #' @param conda Character. Path to conda executable. Usue "auto" to find conda using the PATH and other conventional install locations. Default 'auto'.

 #' @param packages Character Vector. List of packages to install from Conda. 

@@ -18,15 +18,156 @@ numpy <- NULL

 }

-#' @name sctk_py_install

-#' @title Installs Python packages

+#' @name sctkPythonInstallConda

+#' @title Installs Python packages into a Conda environment

 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package

-#' using \code{\link[reticulate]{py_install}} from package \code{\link{reticulate}}.

-#' @param packages List of packages to install

-#' @param ... Other parameters to pass to \code{\link[reticulate]{py_install}}. Can be useful for

-#' selecting which environment to install these packages into. If no parameters are supplied,

-#' then packages will be installed into default Python environment chosen by \code{\link{reticulate}}.

+#' using \code{\link[reticulate]{conda_install}} from package \code{\link{reticulate}}. This

+#' will create a new Conda environment with the name \code{envname} if not already present.

+#' Note that Conda or Miniconda already need to be installed on the local system.

+#' @param envname Character. Name of the conda environment to create.

+#' @param conda Character. Path to conda executable. Usue "auto" to find conda using the PATH and other conventional install locations. Default 'auto'.

+#' @param packages Character Vector. List of packages to install from Conda. 

+#' @param pipPackages Character Vector. List of packages to install into the Conda environment using 'pip'.

+#' @param selectConda Boolean. Run \code{\link[singleCellTK]{selectSCTKConda}} after installing all packages to select the Conda environment. Default TRUE.

+#' @param forge Boolean. Include the Conda Forge repository.

+#' @param pipIgnoreInstalled Boolean. Ignore installed versions when using pip. This is TRUE by default so that specific package versions can be installed even if they are downgrades.

+#'        The FALSE option is useful for situations where you don't want a pip install to attempt an overwrite of a conda binary package (e.g. SciPy on Windows which is very difficult

+#'        to install via pip due to compilation requirements).

+#' @param pythonVersion Passed to \code{python_version} variable in \code{\link[reticulate]{conda_install}}. Default NULL.        

+#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}. 

+#' @examples

+#' \dontrun{

+#' sctkPythonInstallConda(envname = "sctk-reticulate")

+#' }

+#' @seealso See \code{\link[reticulate]{conda_create}} for more information on creating a Conda environment. 

+#' See \code{\link[reticulate]{conda_install}} for more description of the installation parameters.

+#' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.

+#' See \code{\link[singleCellTK]{selectSCTKConda}} for reloading the Conda environment if R is restarted without 

+#' going through the whole installation process again. 

+#' See \url{https://docs.conda.io/en/latest/} for more information on Conda environments.

 #' @export

-sctk_py_install = function(packages = c("scipy", "scrublet"), ...) {

-  reticulate::py_install(packages, ...)

-}

\ No newline at end of file

+sctkPythonInstallConda <- function(envname = "sctk-reticulate", 

+                                   conda = "auto",

+                                   packages = c("scipy", "numpy", "astroid", "six"),

+                                   pipPackages = c("scrublet"),

+                                   selectConda = TRUE,

+                                   forge = FALSE,

+                                   pipIgnoreInstalled = TRUE,

+                                   pythonVersion = NULL,

+                                   ...) {

+  

+  path <- reticulate::conda_create(envname = envname, packages = "python", conda = conda)

+  

+  for(i in packages) {

+    reticulate::conda_install(envname = envname, packages = i, conda = conda, 

+                  pip = FALSE, pip_ignore_installed = pipIgnoreInstalled,

+                  python_version = pythonVersion, ...)

+  }

+  

+  reticulate::conda_install(envname = envname, packages = pipPackages,

+                pip = TRUE, pip_ignore_installed = pipIgnoreInstalled,

+                python_version = pythonVersion, ...)

+  

+  if(isTRUE(selectConda)) selectSCTKConda(envname = envname)

+  

+  invisible(path)

+}

+

+

+

+#' @name sctkPythonInstallVirtualEnv

+#' @title Installs Python packages into a virtual environment

+#' @description Install all Python packages used in the \code{\link{singleCellTK}} package

+#' using \code{\link[reticulate]{virtualenv_install}} from package \code{\link{reticulate}}. This

+#' will create a new virtual environment with the name \code{envname} if not already present.

+#' @param envname Character. Name of the virtual environment to create.

+#' @param packages Character Vector. List of packages to install. 

+#' @param selectEnvironment Boolean. Run \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} after installing all packages to select the virtual environment. Default TRUE.

+#' @param python The path to a Python interpreter, to be used with the created virtual environment. When NULL, the Python interpreter associated with the current session will be used. Default NULL.

+#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}. 

+#' @examples

+#' \dontrun{

+#' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")

+#' }

+#' @seealso See \code{\link[reticulate]{virtualenv_create}} for more information on creating a Conda environment. 

+#' See \code{\link[reticulate]{virtualenv_install}} for more description of the installation parameters.

+#' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.

+#' See \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} for reloading the virtual environment if R is restarted without 

+#' going through the whole installation process again. 

+#' @export

+sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",

+                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet"),

+                                        selectEnvironment = TRUE,

+                                        python = NULL) {

+  

+  path <- reticulate::virtualenv_create(envname = envname, python = python)

+  

+  for(i in packages) {

+    reticulate::virtualenv_install(envname = envname, packages = i, ignore_installed = TRUE)

+  }

+  

+  if(isTRUE(selectEnvironment)) selectSCTKVirtualEnvironment(envname = envname)

+  

+  invisible(path)

+}

+

+

+#' @name selectSCTKConda

+#' @title Selects a Conda environment

+#' @description Selects a Conda environment with Python packages used in \code{\link{singleCellTK}}.

+#' @param envname Character. Name of the conda environment to activate.

+#' @examples

+#' \dontrun{

+#' sctkPythonInstallConda(envname = "sctk-reticulate", selectConda = FALSE)

+#' selectSCTKConda(envname = "sctk-reticulate")

+#' }

+#' @seealso \code{\link[reticulate]{conda-tools}} for more information on using Conda environments with package \code{\link{reticulate}}.

+#' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.

+#' @export

+#' @seealso See \code{\link[singleCellTK]{sctkPythonInstallConda}} for installation of Python modules into a Conda environment.

+#' See\code{\link[reticulate]{conda-tools}} for more information on using Conda environments with package \code{\link{reticulate}}.

+#' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.

+#' See \url{https://docs.conda.io/en/latest/} for more information on Conda environments.

+selectSCTKConda <- function(envname = "sctk-reticulate") {

+  condaList <- reticulate::conda_list()

+  ix <- condaList$name == envname

+  

+  if(!any(ix)) {

+    stop(paste0("Environment '", envname, "', not found. Run sctkPythonInstallConda(envname = '", envname, "') to install Python packages into a conda environmanet with this name."))

+  }

+  if(sum(ix) > 1) {

+    envs <- paste(condaList[ix,"python"], collapse="\n")

+    warning(paste0("More than one Conda environment detected with the name '", envname, "'. Selecting the first one in the list:\n", envs))

+  }

+  

+  reticulate::use_condaenv(condaenv = envname, required = TRUE)

+}

+

+

+

+#' @name selectSCTKVirtualEnvironment

+#' @title Selects a virtual environment

+#' @description Selects a virtual environment with Python packages used in \code{\link{singleCellTK}}

+#' @param envname Character. Name of the virtual environment to activate.

+#' @examples

+#' \dontrun{

+#' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate", selectEnvironment = FALSE)

+#' selectSCTKVirtualEnvironment(envname = "sctk-reticulate")

+#' }

+#' @seealso See \code{\link[singleCellTK]{sctkPythonInstallVirtualEnv}} for installation of Python modules into a virtual environment.

+#' See\code{\link[reticulate]{virtualenv-tools}} for more information on using virtual environments with package \code{\link{reticulate}}.

+#' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.

+#' @export

+selectSCTKVirtualEnvironment <- function(envname = "sctk-reticulate") {

+  res <- reticulate::virtualenv_list()

+  ix <- res == envname

+  

+  if(!any(ix)) {

+    stop(paste0("Environmnet '", envname, "', not found. Run selectSCTKVirtualEnvironment(envname = '", envname, "') to install Python packages into a virtual environmanet with this name."))

+  }

+  if(sum(ix) > 1) {

+    warning(paste0("More than one virtual environment detected with the name '", envname, "'. Selecting the first one in the list."))

+  }

+  

+  reticulate::use_virtualenv(res[which(ix)[1]], required = TRUE)

+}

@@ -6,11 +6,15 @@

 # python modules to use 

 scrublet <- NULL

 scipy <- NULL

+sparse <- NULL

+numpy <- NULL

 .onLoad <- function(libname, pkgname) {

   # use superassignment to update global reference to scipy

-#  scrublet <<- reticulate::import("scrublet", delay_load = TRUE)

-#  scipy <<- reticulate::import("scipy", delay_load = TRUE)

+  scrublet <<- reticulate::import("scrublet", delay_load = TRUE)

+  scipy <<- reticulate::import("scipy", delay_load = TRUE)

+  sparse <<- reticulate::import("scipy.sparse", delay_load = TRUE)

+  numpy <<- reticulate::import("numpy", delay_load = TRUE)

 }

@@ -9,8 +9,8 @@ scipy <- NULL

 .onLoad <- function(libname, pkgname) {

   # use superassignment to update global reference to scipy

-  scrublet <<- reticulate::import("scrublet", delay_load = TRUE)

-  scipy <<- reticulate::import("scipy", delay_load = TRUE)

+#  scrublet <<- reticulate::import("scrublet", delay_load = TRUE)

+#  scipy <<- reticulate::import("scipy", delay_load = TRUE)

 }

@@ -8,7 +8,21 @@ scrublet <- NULL

 scipy <- NULL

 .onLoad <- function(libname, pkgname) {

-  # delay load foo module (will only be loaded when accessed via $)

-  scrublet <<- import("scrublet", delay_load = TRUE)

-  scipy <<- import("scipy", delay_load = TRUE)

+  # use superassignment to update global reference to scipy

+  scrublet <<- reticulate::import("scrublet", delay_load = TRUE)

+  scipy <<- reticulate::import("scipy", delay_load = TRUE)

+}

+

+

+#' @name sctk_py_install

+#' @title Installs Python packages

+#' @description Install all Python packages used in the \code{\link{singleCellTK}} package

+#' using \code{\link[reticulate]{py_install}} from package \code{\link{reticulate}}.

+#' @param packages List of packages to install

+#' @param ... Other parameters to pass to \code{\link[reticulate]{py_install}}. Can be useful for

+#' selecting which environment to install these packages into. If no parameters are supplied,

+#' then packages will be installed into default Python environment chosen by \code{\link{reticulate}}.

+#' @export

+sctk_py_install = function(packages = c("scipy", "scrublet"), ...) {

+  reticulate::py_install(packages, ...)

 }

\ No newline at end of file

new file mode 100644

@@ -0,0 +1,14 @@

+

+## Code taken from:

+## https://rstudio.github.io/reticulate/articles/package.html

+## Meant to delay loading of python environmnet so user can set the python environment

+

+# python modules to use 

+scrublet <- NULL

+scipy <- NULL

+

+.onLoad <- function(libname, pkgname) {

+  # delay load foo module (will only be loaded when accessed via $)

+  scrublet <<- import("scrublet", delay_load = TRUE)

+  scipy <<- import("scipy", delay_load = TRUE)

+}

\ No newline at end of file