Browse code

Edit links to documentation

unknown authored on 22/10/2020 03:39:09
Showing1 changed files
... ...
@@ -30,7 +30,7 @@ ad <- NULL
30 30
 #' @name sctkPythonInstallConda
31 31
 #' @title Installs Python packages into a Conda environment
32 32
 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package
33
-#' using \code{\link[reticulate]{conda_install}} from package \code{\link{reticulate}}. This
33
+#' using \code{\link{conda_install}} from package \code{\link{reticulate}}. This
34 34
 #' will create a new Conda environment with the name \code{envname} if not already present.
35 35
 #' Note that Anaconda or Miniconda already need to be installed on the local system.
36 36
 #' @param envname Character. Name of the conda environment to create.
... ...
@@ -42,15 +42,15 @@ ad <- NULL
42 42
 #' @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.
43 43
 #'        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
44 44
 #'        to install via pip due to compilation requirements).
45
-#' @param pythonVersion Passed to \code{python_version} variable in \code{\link[reticulate]{conda_install}}. Default NULL.
46
-#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}.
45
+#' @param pythonVersion Passed to \code{python_version} variable in \code{\link{conda_install}}. Default NULL.
46
+#' @param ... Other parameters to pass to \code{\link{conda_install}}.
47 47
 #' @return None. Installation of Conda environment.
48 48
 #' @examples
49 49
 #' \dontrun{
50 50
 #' sctkPythonInstallConda(envname = "sctk-reticulate")
51 51
 #' }
52
-#' @seealso See \code{\link[reticulate]{conda_create}} for more information on creating a Conda environment.
53
-#' See \code{\link[reticulate]{conda_install}} for more description of the installation parameters.
52
+#' @seealso See \code{\link{conda_create}} for more information on creating a Conda environment.
53
+#' See \code{\link{conda_install}} for more description of the installation parameters.
54 54
 #' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.
55 55
 #' See \code{\link[singleCellTK]{selectSCTKConda}} for reloading the Conda environment if R is restarted without
56 56
 #' going through the whole installation process again.
... ...
@@ -88,7 +88,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",
88 88
 #' @name sctkPythonInstallVirtualEnv
89 89
 #' @title Installs Python packages into a virtual environment
90 90
 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package
91
-#' using \code{\link[reticulate]{virtualenv_install}} from package \code{\link{reticulate}}. This
91
+#' using \code{\link{virtualenv_install}} from package \code{\link{reticulate}}. This
92 92
 #' will create a new virtual environment with the name \code{envname} if not already present.
93 93
 #' @param envname Character. Name of the virtual environment to create.
94 94
 #' @param packages Character Vector. List of packages to install.
... ...
@@ -99,8 +99,8 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",
99 99
 #' \dontrun{
100 100
 #' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")
101 101
 #' }
102
-#' @seealso See \code{\link[reticulate]{virtualenv_create}} for more information on creating a Conda environment.
103
-#' See \code{\link[reticulate]{virtualenv_install}} for more description of the installation parameters.
102
+#' @seealso See \code{\link{virtualenv_create}} for more information on creating a Conda environment.
103
+#' See \code{\link{virtualenv_install}} for more description of the installation parameters.
104 104
 #' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.
105 105
 #' See \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} for reloading the virtual environment if R is restarted without
106 106
 #' going through the whole installation process again.
Browse code

bug fix: UMAP

unknown authored on 21/10/2020 18:18:37
Showing1 changed files
... ...
@@ -59,7 +59,7 @@ ad <- NULL
59 59
 sctkPythonInstallConda <- function(envname = "sctk-reticulate",
60 60
                                    conda = "auto",
61 61
                                    packages = c("scipy", "numpy", "astroid", "six"),
62
-                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "anndata", "umap-learn"),
62
+                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "anndata"),
63 63
                                    selectConda = TRUE,
64 64
                                    forge = FALSE,
65 65
                                    pipIgnoreInstalled = TRUE,
... ...
@@ -106,7 +106,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",
106 106
 #' going through the whole installation process again.
107 107
 #' @export
108 108
 sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",
109
-                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "anndata", "umap-learn"),
109
+                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "anndata"),
110 110
                                         selectEnvironment = TRUE,
111 111
                                         python = NULL) {
112 112
 
Browse code

bug fix: install umap-learn

unknown authored on 21/10/2020 18:15:37
Showing1 changed files
... ...
@@ -59,7 +59,7 @@ ad <- NULL
59 59
 sctkPythonInstallConda <- function(envname = "sctk-reticulate",
60 60
                                    conda = "auto",
61 61
                                    packages = c("scipy", "numpy", "astroid", "six"),
62
-                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "anndata"),
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+                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "anndata", "umap-learn"),
63 63
                                    selectConda = TRUE,
64 64
                                    forge = FALSE,
65 65
                                    pipIgnoreInstalled = TRUE,
... ...
@@ -106,7 +106,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",
106 106
 #' going through the whole installation process again.
107 107
 #' @export
108 108
 sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",
109
-                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "anndata"),
109
+                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "anndata", "umap-learn"),
110 110
                                         selectEnvironment = TRUE,
111 111
                                         python = NULL) {
112 112
 
Browse code

Merge branch 'master' of github.com:compbiomed/singleCellTK

Yusuke Koga authored on 16/10/2020 00:27:01
Showing0 changed files
Browse code

remove scgen

Yichen Wang authored on 08/10/2020 19:33:36
Showing1 changed files
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@@ -9,7 +9,6 @@ scipy <- NULL
9 9
 sparse <- NULL
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 numpy <- NULL
11 11
 scnrm <- NULL
12
-scgen <- NULL
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 sc <- NULL
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 bbknn <- NULL
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 pkg_resources <- NULL
... ...
@@ -22,7 +21,6 @@ ad <- NULL
22 21
   sparse <<- reticulate::import("scipy.sparse", delay_load = TRUE)
23 22
   numpy <<- reticulate::import("numpy", delay_load = TRUE)
24 23
   scnrm <<- reticulate::import("scanorama", delay_load = TRUE)
25
-  scgen <<- reticulate::import("scgen", delay_load = TRUE)
26 24
   sc <<- reticulate::import("scanpy", delay_load = TRUE)
27 25
   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)
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   pkg_resources <<- reticulate::import('pkg_resources',delay_load = TRUE)
... ...
@@ -60,7 +58,7 @@ ad <- NULL
60 58
 sctkPythonInstallConda <- function(envname = "sctk-reticulate",
61 59
                                    conda = "auto",
62 60
                                    packages = c("scipy", "numpy", "astroid", "six"),
63
-                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "scgen","anndata"),
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+                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "anndata"),
64 62
                                    selectConda = TRUE,
65 63
                                    forge = FALSE,
66 64
                                    pipIgnoreInstalled = TRUE,
... ...
@@ -106,7 +104,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",
106 104
 #' going through the whole installation process again.
107 105
 #' @export
108 106
 sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",
109
-                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "scgen","anndata"),
107
+                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "anndata"),
110 108
                                         selectEnvironment = TRUE,
111 109
                                         python = NULL) {
112 110
 
Browse code

resolving merge conflict : anndata import in reticulate_setup

Shruthi Bandyadka authored on 08/07/2020 19:02:03
Showing1 changed files
... ...
@@ -25,15 +25,10 @@ ad <- NULL
25 25
   scgen <<- reticulate::import("scgen", delay_load = TRUE)
26 26
   sc <<- reticulate::import("scanpy", delay_load = TRUE)
27 27
   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)
28
-<<<<<<< HEAD
29 28
   pkg_resources <<- reticulate::import('pkg_resources',delay_load = TRUE)
30 29
   ad <<- reticulate::import('anndata',delay_load = TRUE,convert = FALSE)
31
-=======
32
-  pkg_resources <<- reticulate::import('pkg_resources', delay_load = TRUE)
33
->>>>>>> 4127090a0c04ab251d1357d8787f6c0ea2c648d5
34 30
 }
35 31
 
36
-
37 32
 #' @name sctkPythonInstallConda
38 33
 #' @title Installs Python packages into a Conda environment
39 34
 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package
Browse code

merging conflicts

Shruthi Bandyadka authored on 08/07/2020 18:56:07
Showing0 changed files
Browse code

fixing metadata slot for anndata import

Shruthi Bandyadka authored on 08/07/2020 16:46:54
Showing1 changed files
... ...
@@ -28,7 +28,6 @@ ad <- NULL
28 28
   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)
29 29
   pkg_resources <<- reticulate::import('pkg_resources',delay_load = TRUE)
30 30
   ad <<- reticulate::import('anndata',delay_load = TRUE,convert = FALSE)
31
-  blt <<- reticulate::import_builtins()
32 31
 }
33 32
 
34 33
 
Browse code

Fixed conflict

Joshua D. Campbell authored on 28/06/2020 19:20:05
Showing0 changed files
Browse code

Updated doubletFinder calls and example. Fixed problem with reticulate

Joshua D. Campbell authored on 27/06/2020 01:51:00
Showing1 changed files
... ...
@@ -9,7 +9,6 @@ scipy <- NULL
9 9
 sparse <- NULL
10 10
 numpy <- NULL
11 11
 scnrm <- NULL
12
-blt <- NULL
13 12
 scgen <- NULL
14 13
 sc <- NULL
15 14
 bbknn <- NULL
... ...
@@ -25,8 +24,7 @@ pkg_resources <- NULL
25 24
   scgen <<- reticulate::import("scgen", delay_load = TRUE)
26 25
   sc <<- reticulate::import("scanpy", delay_load = TRUE)
27 26
   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)
28
-  pkg_resources <<- reticulate::import('pkg_resources',delay_load = TRUE)
29
-  blt <<- reticulate::import_builtins()
27
+  pkg_resources <<- reticulate::import('pkg_resources', delay_load = TRUE)
30 28
 }
31 29
 
32 30
 
Browse code

SeuratInt update: use altExp; Python related update: cleaner style in Scanorama & remove blt; Remove typo in runMAST

Yichen Wang authored on 23/06/2020 00:09:38
Showing1 changed files
... ...
@@ -3,13 +3,12 @@
3 3
 ## https://rstudio.github.io/reticulate/articles/package.html
4 4
 ## Meant to delay loading of python environmnet so user can set the python environment
5 5
 
6
-# python modules to use 
6
+# python modules to use
7 7
 scrublet <- NULL
8 8
 scipy <- NULL
9 9
 sparse <- NULL
10 10
 numpy <- NULL
11 11
 scnrm <- NULL
12
-blt <- NULL
13 12
 scgen <- NULL
14 13
 sc <- NULL
15 14
 bbknn <- NULL
... ...
@@ -26,7 +25,6 @@ pkg_resources <- NULL
26 25
   sc <<- reticulate::import("scanpy", delay_load = TRUE)
27 26
   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)
28 27
   pkg_resources <<- reticulate::import('pkg_resources',delay_load = TRUE)
29
-  blt <<- reticulate::import_builtins()
30 28
 }
31 29
 
32 30
 
... ...
@@ -35,30 +33,30 @@ pkg_resources <- NULL
35 33
 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package
36 34
 #' using \code{\link[reticulate]{conda_install}} from package \code{\link{reticulate}}. This
37 35
 #' will create a new Conda environment with the name \code{envname} if not already present.
38
-#' Note that Anaconda or Miniconda already need to be installed on the local system. 
36
+#' Note that Anaconda or Miniconda already need to be installed on the local system.
39 37
 #' @param envname Character. Name of the conda environment to create.
40 38
 #' @param conda Character. Path to conda executable. Usue "auto" to find conda using the PATH and other conventional install locations. Default 'auto'.
41
-#' @param packages Character Vector. List of packages to install from Conda. 
39
+#' @param packages Character Vector. List of packages to install from Conda.
42 40
 #' @param pipPackages Character Vector. List of packages to install into the Conda environment using 'pip'.
43 41
 #' @param selectConda Boolean. Run \code{\link[singleCellTK]{selectSCTKConda}} after installing all packages to select the Conda environment. Default TRUE.
44 42
 #' @param forge Boolean. Include the Conda Forge repository.
45 43
 #' @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.
46 44
 #'        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
47 45
 #'        to install via pip due to compilation requirements).
48
-#' @param pythonVersion Passed to \code{python_version} variable in \code{\link[reticulate]{conda_install}}. Default NULL.        
49
-#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}. 
46
+#' @param pythonVersion Passed to \code{python_version} variable in \code{\link[reticulate]{conda_install}}. Default NULL.
47
+#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}.
50 48
 #' @examples
51 49
 #' \dontrun{
52 50
 #' sctkPythonInstallConda(envname = "sctk-reticulate")
53 51
 #' }
54
-#' @seealso See \code{\link[reticulate]{conda_create}} for more information on creating a Conda environment. 
52
+#' @seealso See \code{\link[reticulate]{conda_create}} for more information on creating a Conda environment.
55 53
 #' See \code{\link[reticulate]{conda_install}} for more description of the installation parameters.
56 54
 #' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.
57
-#' See \code{\link[singleCellTK]{selectSCTKConda}} for reloading the Conda environment if R is restarted without 
58
-#' going through the whole installation process again. 
55
+#' See \code{\link[singleCellTK]{selectSCTKConda}} for reloading the Conda environment if R is restarted without
56
+#' going through the whole installation process again.
59 57
 #' See \url{https://docs.conda.io/en/latest/} for more information on Conda environments.
60 58
 #' @export
61
-sctkPythonInstallConda <- function(envname = "sctk-reticulate", 
59
+sctkPythonInstallConda <- function(envname = "sctk-reticulate",
62 60
                                    conda = "auto",
63 61
                                    packages = c("scipy", "numpy", "astroid", "six"),
64 62
                                    pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "scgen"),
... ...
@@ -67,21 +65,21 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",
67 65
                                    pipIgnoreInstalled = TRUE,
68 66
                                    pythonVersion = NULL,
69 67
                                    ...) {
70
-  
68
+
71 69
   path <- reticulate::conda_create(envname = envname, packages = "python", conda = conda)
72
-  
70
+
73 71
   for(i in packages) {
74
-    reticulate::conda_install(envname = envname, packages = i, conda = conda, 
72
+    reticulate::conda_install(envname = envname, packages = i, conda = conda,
75 73
                   pip = FALSE, pip_ignore_installed = pipIgnoreInstalled,
76 74
                   python_version = pythonVersion, ...)
77 75
   }
78
-  
76
+
79 77
   reticulate::conda_install(envname = envname, packages = pipPackages,
80 78
                 pip = TRUE, pip_ignore_installed = pipIgnoreInstalled,
81 79
                 python_version = pythonVersion, ...)
82
-  
80
+
83 81
   if(isTRUE(selectConda)) selectSCTKConda(envname = envname)
84
-  
82
+
85 83
   invisible(path)
86 84
 }
87 85
 
... ...
@@ -93,32 +91,32 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",
93 91
 #' using \code{\link[reticulate]{virtualenv_install}} from package \code{\link{reticulate}}. This
94 92
 #' will create a new virtual environment with the name \code{envname} if not already present.
95 93
 #' @param envname Character. Name of the virtual environment to create.
96
-#' @param packages Character Vector. List of packages to install. 
94
+#' @param packages Character Vector. List of packages to install.
97 95
 #' @param selectEnvironment Boolean. Run \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} after installing all packages to select the virtual environment. Default TRUE.
98 96
 #' @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.
99 97
 #' @examples
100 98
 #' \dontrun{
101 99
 #' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")
102 100
 #' }
103
-#' @seealso See \code{\link[reticulate]{virtualenv_create}} for more information on creating a Conda environment. 
101
+#' @seealso See \code{\link[reticulate]{virtualenv_create}} for more information on creating a Conda environment.
104 102
 #' See \code{\link[reticulate]{virtualenv_install}} for more description of the installation parameters.
105 103
 #' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.
106
-#' See \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} for reloading the virtual environment if R is restarted without 
107
-#' going through the whole installation process again. 
104
+#' See \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} for reloading the virtual environment if R is restarted without
105
+#' going through the whole installation process again.
108 106
 #' @export
109 107
 sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",
110 108
                                         packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "scgen"),
111 109
                                         selectEnvironment = TRUE,
112 110
                                         python = NULL) {
113
-  
111
+
114 112
   path <- reticulate::virtualenv_create(envname = envname, python = python)
115
-  
113
+
116 114
   for(i in packages) {
117 115
     reticulate::virtualenv_install(envname = envname, packages = i, ignore_installed = TRUE)
118 116
   }
119
-  
117
+
120 118
   if(isTRUE(selectEnvironment)) selectSCTKVirtualEnvironment(envname = envname)
121
-  
119
+
122 120
   invisible(path)
123 121
 }
124 122
 
... ...
@@ -142,7 +140,7 @@ sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",
142 140
 selectSCTKConda <- function(envname = "sctk-reticulate") {
143 141
   condaList <- reticulate::conda_list()
144 142
   ix <- condaList$name == envname
145
-  
143
+
146 144
   if(!any(ix)) {
147 145
     stop(paste0("Environment '", envname, "', not found. Run sctkPythonInstallConda(envname = '", envname, "') to install Python packages into a conda environmanet with this name."))
148 146
   }
... ...
@@ -150,7 +148,7 @@ selectSCTKConda <- function(envname = "sctk-reticulate") {
150 148
     envs <- paste(condaList[ix,"python"], collapse="\n")
151 149
     warning(paste0("More than one Conda environment detected with the name '", envname, "'. Selecting the first one in the list:\n", envs))
152 150
   }
153
-  
151
+
154 152
   reticulate::use_condaenv(condaenv = envname, required = TRUE)
155 153
 }
156 154
 
... ...
@@ -172,13 +170,13 @@ selectSCTKConda <- function(envname = "sctk-reticulate") {
172 170
 selectSCTKVirtualEnvironment <- function(envname = "sctk-reticulate") {
173 171
   res <- reticulate::virtualenv_list()
174 172
   ix <- res == envname
175
-  
173
+
176 174
   if(!any(ix)) {
177 175
     stop(paste0("Environmnet '", envname, "', not found. Run selectSCTKVirtualEnvironment(envname = '", envname, "') to install Python packages into a virtual environmanet with this name."))
178 176
   }
179 177
   if(sum(ix) > 1) {
180 178
     warning(paste0("More than one virtual environment detected with the name '", envname, "'. Selecting the first one in the list."))
181 179
   }
182
-  
180
+
183 181
   reticulate::use_virtualenv(res[which(ix)[1]], required = TRUE)
184 182
 }
Browse code

import anndata as SCE.

Shruthi Bandyadka authored on 12/06/2020 20:12:54
Showing1 changed files
... ...
@@ -14,6 +14,7 @@ scgen <- NULL
14 14
 sc <- NULL
15 15
 bbknn <- NULL
16 16
 pkg_resources <- NULL
17
+ad <- NULL
17 18
 
18 19
 .onLoad <- function(libname, pkgname) {
19 20
   # use superassignment to update global reference to scipy
... ...
@@ -26,6 +27,7 @@ pkg_resources <- NULL
26 27
   sc <<- reticulate::import("scanpy", delay_load = TRUE)
27 28
   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)
28 29
   pkg_resources <<- reticulate::import('pkg_resources',delay_load = TRUE)
30
+  ad <<- reticulate::import('anndata',delay_load = TRUE,convert = FALSE)
29 31
   blt <<- reticulate::import_builtins()
30 32
 }
31 33
 
... ...
@@ -61,7 +63,7 @@ pkg_resources <- NULL
61 63
 sctkPythonInstallConda <- function(envname = "sctk-reticulate", 
62 64
                                    conda = "auto",
63 65
                                    packages = c("scipy", "numpy", "astroid", "six"),
64
-                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "scgen"),
66
+                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "scgen","anndata"),
65 67
                                    selectConda = TRUE,
66 68
                                    forge = FALSE,
67 69
                                    pipIgnoreInstalled = TRUE,
... ...
@@ -107,7 +109,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",
107 109
 #' going through the whole installation process again. 
108 110
 #' @export
109 111
 sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",
110
-                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "scgen"),
112
+                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "scgen","anndata"),
111 113
                                         selectEnvironment = TRUE,
112 114
                                         python = NULL) {
113 115
   
Browse code

Updated documentation. Set warnings as errors in travis

Joshua D. Campbell authored on 30/04/2020 20:18:27
Showing1 changed files
... ...
@@ -96,7 +96,6 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",
96 96
 #' @param packages Character Vector. List of packages to install. 
97 97
 #' @param selectEnvironment Boolean. Run \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} after installing all packages to select the virtual environment. Default TRUE.
98 98
 #' @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.
99
-#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}. 
100 99
 #' @examples
101 100
 #' \dontrun{
102 101
 #' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")
Browse code

update scrublet: fix parameter names, assignment operators

Shruthi Bandyadka authored on 22/04/2020 15:47:00
Showing1 changed files
... ...
@@ -13,6 +13,7 @@ blt <- NULL
13 13
 scgen <- NULL
14 14
 sc <- NULL
15 15
 bbknn <- NULL
16
+pkg_resources <- NULL
16 17
 
17 18
 .onLoad <- function(libname, pkgname) {
18 19
   # use superassignment to update global reference to scipy
... ...
@@ -24,7 +25,7 @@ bbknn <- NULL
24 25
   scgen <<- reticulate::import("scgen", delay_load = TRUE)
25 26
   sc <<- reticulate::import("scanpy", delay_load = TRUE)
26 27
   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)
27
-  pkg_resources <- reticulate::import('pkg_resources',delay_load = TRUE)
28
+  pkg_resources <<- reticulate::import('pkg_resources',delay_load = TRUE)
28 29
   blt <<- reticulate::import_builtins()
29 30
 }
30 31
 
Browse code

updated scrublet: add UMAP, TSNE coordinates to sce reducedDims, and scrublet version to metadata

Shruthi Bandyadka authored on 22/04/2020 14:33:28
Showing1 changed files
... ...
@@ -24,6 +24,7 @@ bbknn <- NULL
24 24
   scgen <<- reticulate::import("scgen", delay_load = TRUE)
25 25
   sc <<- reticulate::import("scanpy", delay_load = TRUE)
26 26
   bbknn <<- reticulate::import("bbknn", delay_load = TRUE)
27
+  pkg_resources <- reticulate::import('pkg_resources',delay_load = TRUE)
27 28
   blt <<- reticulate::import_builtins()
28 29
 }
29 30
 
Browse code

move to branch

Yichen Wang authored on 04/03/2020 20:32:17
Showing1 changed files
... ...
@@ -8,6 +8,11 @@ scrublet <- NULL
8 8
 scipy <- NULL
9 9
 sparse <- NULL
10 10
 numpy <- NULL
11
+scnrm <- NULL
12
+blt <- NULL
13
+scgen <- NULL
14
+sc <- NULL
15
+bbknn <- NULL
11 16
 
12 17
 .onLoad <- function(libname, pkgname) {
13 18
   # use superassignment to update global reference to scipy
... ...
@@ -15,6 +20,11 @@ numpy <- NULL
15 20
   scipy <<- reticulate::import("scipy", delay_load = TRUE)
16 21
   sparse <<- reticulate::import("scipy.sparse", delay_load = TRUE)
17 22
   numpy <<- reticulate::import("numpy", delay_load = TRUE)
23
+  scnrm <<- reticulate::import("scanorama", delay_load = TRUE)
24
+  scgen <<- reticulate::import("scgen", delay_load = TRUE)
25
+  sc <<- reticulate::import("scanpy", delay_load = TRUE)
26
+  bbknn <<- reticulate::import("bbknn", delay_load = TRUE)
27
+  blt <<- reticulate::import_builtins()
18 28
 }
19 29
 
20 30
 
... ...
@@ -49,7 +59,7 @@ numpy <- NULL
49 59
 sctkPythonInstallConda <- function(envname = "sctk-reticulate", 
50 60
                                    conda = "auto",
51 61
                                    packages = c("scipy", "numpy", "astroid", "six"),
52
-                                   pipPackages = c("scrublet"),
62
+                                   pipPackages = c("scrublet", "scanpy", "bbknn", "scanorama", "scgen"),
53 63
                                    selectConda = TRUE,
54 64
                                    forge = FALSE,
55 65
                                    pipIgnoreInstalled = TRUE,
... ...
@@ -96,7 +106,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",
96 106
 #' going through the whole installation process again. 
97 107
 #' @export
98 108
 sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",
99
-                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet"),
109
+                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet", "scanpy", "scanorama", "bbknn", "scgen"),
100 110
                                         selectEnvironment = TRUE,
101 111
                                         python = NULL) {
102 112
   
Browse code

updated documentation

Joshua D. Campbell authored on 17/02/2020 15:08:51
Showing1 changed files
... ...
@@ -23,7 +23,7 @@ numpy <- NULL
23 23
 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package
24 24
 #' using \code{\link[reticulate]{conda_install}} from package \code{\link{reticulate}}. This
25 25
 #' will create a new Conda environment with the name \code{envname} if not already present.
26
-#' Note that Conda or Miniconda already need to be installed on the local system.
26
+#' Note that Anaconda or Miniconda already need to be installed on the local system. 
27 27
 #' @param envname Character. Name of the conda environment to create.
28 28
 #' @param conda Character. Path to conda executable. Usue "auto" to find conda using the PATH and other conventional install locations. Default 'auto'.
29 29
 #' @param packages Character Vector. List of packages to install from Conda. 
Browse code

Added new functions for automatically installing all python dependencies in a virtual or conda environment

Joshua D. Campbell authored on 17/02/2020 04:45:25
Showing1 changed files
... ...
@@ -18,15 +18,156 @@ numpy <- NULL
18 18
 }
19 19
 
20 20
 
21
-#' @name sctk_py_install
22
-#' @title Installs Python packages
21
+#' @name sctkPythonInstallConda
22
+#' @title Installs Python packages into a Conda environment
23 23
 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package
24
-#' using \code{\link[reticulate]{py_install}} from package \code{\link{reticulate}}.
25
-#' @param packages List of packages to install
26
-#' @param ... Other parameters to pass to \code{\link[reticulate]{py_install}}. Can be useful for
27
-#' selecting which environment to install these packages into. If no parameters are supplied,
28
-#' then packages will be installed into default Python environment chosen by \code{\link{reticulate}}.
24
+#' using \code{\link[reticulate]{conda_install}} from package \code{\link{reticulate}}. This
25
+#' will create a new Conda environment with the name \code{envname} if not already present.
26
+#' Note that Conda or Miniconda already need to be installed on the local system.
27
+#' @param envname Character. Name of the conda environment to create.
28
+#' @param conda Character. Path to conda executable. Usue "auto" to find conda using the PATH and other conventional install locations. Default 'auto'.
29
+#' @param packages Character Vector. List of packages to install from Conda. 
30
+#' @param pipPackages Character Vector. List of packages to install into the Conda environment using 'pip'.
31
+#' @param selectConda Boolean. Run \code{\link[singleCellTK]{selectSCTKConda}} after installing all packages to select the Conda environment. Default TRUE.
32
+#' @param forge Boolean. Include the Conda Forge repository.
33
+#' @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.
34
+#'        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
35
+#'        to install via pip due to compilation requirements).
36
+#' @param pythonVersion Passed to \code{python_version} variable in \code{\link[reticulate]{conda_install}}. Default NULL.        
37
+#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}. 
38
+#' @examples
39
+#' \dontrun{
40
+#' sctkPythonInstallConda(envname = "sctk-reticulate")
41
+#' }
42
+#' @seealso See \code{\link[reticulate]{conda_create}} for more information on creating a Conda environment. 
43
+#' See \code{\link[reticulate]{conda_install}} for more description of the installation parameters.
44
+#' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.
45
+#' See \code{\link[singleCellTK]{selectSCTKConda}} for reloading the Conda environment if R is restarted without 
46
+#' going through the whole installation process again. 
47
+#' See \url{https://docs.conda.io/en/latest/} for more information on Conda environments.
29 48
 #' @export
30
-sctk_py_install = function(packages = c("scipy", "scrublet"), ...) {
31
-  reticulate::py_install(packages, ...)
32
-}
33 49
\ No newline at end of file
50
+sctkPythonInstallConda <- function(envname = "sctk-reticulate", 
51
+                                   conda = "auto",
52
+                                   packages = c("scipy", "numpy", "astroid", "six"),
53
+                                   pipPackages = c("scrublet"),
54
+                                   selectConda = TRUE,
55
+                                   forge = FALSE,
56
+                                   pipIgnoreInstalled = TRUE,
57
+                                   pythonVersion = NULL,
58
+                                   ...) {
59
+  
60
+  path <- reticulate::conda_create(envname = envname, packages = "python", conda = conda)
61
+  
62
+  for(i in packages) {
63
+    reticulate::conda_install(envname = envname, packages = i, conda = conda, 
64
+                  pip = FALSE, pip_ignore_installed = pipIgnoreInstalled,
65
+                  python_version = pythonVersion, ...)
66
+  }
67
+  
68
+  reticulate::conda_install(envname = envname, packages = pipPackages,
69
+                pip = TRUE, pip_ignore_installed = pipIgnoreInstalled,
70
+                python_version = pythonVersion, ...)
71
+  
72
+  if(isTRUE(selectConda)) selectSCTKConda(envname = envname)
73
+  
74
+  invisible(path)
75
+}
76
+
77
+
78
+
79
+#' @name sctkPythonInstallVirtualEnv
80
+#' @title Installs Python packages into a virtual environment
81
+#' @description Install all Python packages used in the \code{\link{singleCellTK}} package
82
+#' using \code{\link[reticulate]{virtualenv_install}} from package \code{\link{reticulate}}. This
83
+#' will create a new virtual environment with the name \code{envname} if not already present.
84
+#' @param envname Character. Name of the virtual environment to create.
85
+#' @param packages Character Vector. List of packages to install. 
86
+#' @param selectEnvironment Boolean. Run \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} after installing all packages to select the virtual environment. Default TRUE.
87
+#' @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.
88
+#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}. 
89
+#' @examples
90
+#' \dontrun{
91
+#' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")
92
+#' }
93
+#' @seealso See \code{\link[reticulate]{virtualenv_create}} for more information on creating a Conda environment. 
94
+#' See \code{\link[reticulate]{virtualenv_install}} for more description of the installation parameters.
95
+#' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.
96
+#' See \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} for reloading the virtual environment if R is restarted without 
97
+#' going through the whole installation process again. 
98
+#' @export
99
+sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",
100
+                                        packages = c("scipy", "numpy", "astroid", "six", "scrublet"),
101
+                                        selectEnvironment = TRUE,
102
+                                        python = NULL) {
103
+  
104
+  path <- reticulate::virtualenv_create(envname = envname, python = python)
105
+  
106
+  for(i in packages) {
107
+    reticulate::virtualenv_install(envname = envname, packages = i, ignore_installed = TRUE)
108
+  }
109
+  
110
+  if(isTRUE(selectEnvironment)) selectSCTKVirtualEnvironment(envname = envname)
111
+  
112
+  invisible(path)
113
+}
114
+
115
+
116
+#' @name selectSCTKConda
117
+#' @title Selects a Conda environment
118
+#' @description Selects a Conda environment with Python packages used in \code{\link{singleCellTK}}.
119
+#' @param envname Character. Name of the conda environment to activate.
120
+#' @examples
121
+#' \dontrun{
122
+#' sctkPythonInstallConda(envname = "sctk-reticulate", selectConda = FALSE)
123
+#' selectSCTKConda(envname = "sctk-reticulate")
124
+#' }
125
+#' @seealso \code{\link[reticulate]{conda-tools}} for more information on using Conda environments with package \code{\link{reticulate}}.
126
+#' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.
127
+#' @export
128
+#' @seealso See \code{\link[singleCellTK]{sctkPythonInstallConda}} for installation of Python modules into a Conda environment.
129
+#' See\code{\link[reticulate]{conda-tools}} for more information on using Conda environments with package \code{\link{reticulate}}.
130
+#' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.
131
+#' See \url{https://docs.conda.io/en/latest/} for more information on Conda environments.
132
+selectSCTKConda <- function(envname = "sctk-reticulate") {
133
+  condaList <- reticulate::conda_list()
134
+  ix <- condaList$name == envname
135
+  
136
+  if(!any(ix)) {
137
+    stop(paste0("Environment '", envname, "', not found. Run sctkPythonInstallConda(envname = '", envname, "') to install Python packages into a conda environmanet with this name."))
138
+  }
139
+  if(sum(ix) > 1) {
140
+    envs <- paste(condaList[ix,"python"], collapse="\n")
141
+    warning(paste0("More than one Conda environment detected with the name '", envname, "'. Selecting the first one in the list:\n", envs))
142
+  }
143
+  
144
+  reticulate::use_condaenv(condaenv = envname, required = TRUE)
145
+}
146
+
147
+
148
+
149
+#' @name selectSCTKVirtualEnvironment
150
+#' @title Selects a virtual environment
151
+#' @description Selects a virtual environment with Python packages used in \code{\link{singleCellTK}}
152
+#' @param envname Character. Name of the virtual environment to activate.
153
+#' @examples
154
+#' \dontrun{
155
+#' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate", selectEnvironment = FALSE)
156
+#' selectSCTKVirtualEnvironment(envname = "sctk-reticulate")
157
+#' }
158
+#' @seealso See \code{\link[singleCellTK]{sctkPythonInstallVirtualEnv}} for installation of Python modules into a virtual environment.
159
+#' See\code{\link[reticulate]{virtualenv-tools}} for more information on using virtual environments with package \code{\link{reticulate}}.
160
+#' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.
161
+#' @export
162
+selectSCTKVirtualEnvironment <- function(envname = "sctk-reticulate") {
163
+  res <- reticulate::virtualenv_list()
164
+  ix <- res == envname
165
+  
166
+  if(!any(ix)) {
167
+    stop(paste0("Environmnet '", envname, "', not found. Run selectSCTKVirtualEnvironment(envname = '", envname, "') to install Python packages into a virtual environmanet with this name."))
168
+  }
169
+  if(sum(ix) > 1) {
170
+    warning(paste0("More than one virtual environment detected with the name '", envname, "'. Selecting the first one in the list."))
171
+  }
172
+  
173
+  reticulate::use_virtualenv(res[which(ix)[1]], required = TRUE)
174
+}
Browse code

Updated reticulate import calls for importOptimus

Joshua D. Campbell authored on 15/02/2020 01:58:48
Showing1 changed files
... ...
@@ -6,11 +6,15 @@
6 6
 # python modules to use 
7 7
 scrublet <- NULL
8 8
 scipy <- NULL
9
+sparse <- NULL
10
+numpy <- NULL
9 11
 
10 12
 .onLoad <- function(libname, pkgname) {
11 13
   # use superassignment to update global reference to scipy
12
-#  scrublet <<- reticulate::import("scrublet", delay_load = TRUE)
13
-#  scipy <<- reticulate::import("scipy", delay_load = TRUE)
14
+  scrublet <<- reticulate::import("scrublet", delay_load = TRUE)
15
+  scipy <<- reticulate::import("scipy", delay_load = TRUE)
16
+  sparse <<- reticulate::import("scipy.sparse", delay_load = TRUE)
17
+  numpy <<- reticulate::import("numpy", delay_load = TRUE)
14 18
 }
15 19
 
16 20
 
Browse code

Move python import calls to reticulate_setup.R

Joshua D. Campbell authored on 14/02/2020 04:33:31
Showing1 changed files
... ...
@@ -9,8 +9,8 @@ scipy <- NULL
9 9
 
10 10
 .onLoad <- function(libname, pkgname) {
11 11
   # use superassignment to update global reference to scipy
12
-  scrublet <<- reticulate::import("scrublet", delay_load = TRUE)
13
-  scipy <<- reticulate::import("scipy", delay_load = TRUE)
12
+#  scrublet <<- reticulate::import("scrublet", delay_load = TRUE)
13
+#  scipy <<- reticulate::import("scipy", delay_load = TRUE)
14 14
 }
15 15
 
16 16
 
Browse code

Added functionality/support for reticulate

Joshua D. Campbell authored on 05/02/2020 16:26:46
Showing1 changed files
... ...
@@ -8,7 +8,21 @@ scrublet <- NULL
8 8
 scipy <- NULL
9 9
 
10 10
 .onLoad <- function(libname, pkgname) {
11
-  # delay load foo module (will only be loaded when accessed via $)
12
-  scrublet <<- import("scrublet", delay_load = TRUE)
13
-  scipy <<- import("scipy", delay_load = TRUE)
11
+  # use superassignment to update global reference to scipy
12
+  scrublet <<- reticulate::import("scrublet", delay_load = TRUE)
13
+  scipy <<- reticulate::import("scipy", delay_load = TRUE)
14
+}
15
+
16
+
17
+#' @name sctk_py_install
18
+#' @title Installs Python packages
19
+#' @description Install all Python packages used in the \code{\link{singleCellTK}} package
20
+#' using \code{\link[reticulate]{py_install}} from package \code{\link{reticulate}}.
21
+#' @param packages List of packages to install
22
+#' @param ... Other parameters to pass to \code{\link[reticulate]{py_install}}. Can be useful for
23
+#' selecting which environment to install these packages into. If no parameters are supplied,
24
+#' then packages will be installed into default Python environment chosen by \code{\link{reticulate}}.
25
+#' @export
26
+sctk_py_install = function(packages = c("scipy", "scrublet"), ...) {
27
+  reticulate::py_install(packages, ...)
14 28
 }
15 29
\ No newline at end of file
Browse code

Added control for initializing reticulate

Joshua D. Campbell authored on 04/02/2020 02:52:59
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,14 @@
1
+
2
+## Code taken from:
3
+## https://rstudio.github.io/reticulate/articles/package.html
4
+## Meant to delay loading of python environmnet so user can set the python environment
5
+
6
+# python modules to use 
7
+scrublet <- NULL
8
+scipy <- NULL
9
+
10
+.onLoad <- function(libname, pkgname) {
11
+  # delay load foo module (will only be loaded when accessed via $)
12
+  scrublet <<- import("scrublet", delay_load = TRUE)
13
+  scipy <<- import("scipy", delay_load = TRUE)
14
+}
0 15
\ No newline at end of file