Merge tag 'v1.4.8' into develop

Fix an issue with temporary directories.
dputhier · Dec 22, 2023 · 7ac8bc2 · 7ac8bc2
2 parents 42a74f3 + 27424dd
commit 7ac8bc2
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: scigenex
 Type: Package
 Title: The scigenex package (Single-Cell Informative GENe Explorer)
-Version: 1.4.7
+Version: 1.4.8
 Date: 2020-07-22
 Author: J. Bavais, Sebastien Nin, Lionel Spinelli and Denis Puthier
 Maintainer: J. Bavais <julie.bavais@yahoo.fr>

diff --git a/Makefile b/Makefile
@@ -1,5 +1,5 @@
 MAKEFILE=Makefile
-VERSION=1.4.7
+VERSION=1.4.8
 
 .PHONY: help
 
@@ -11,7 +11,7 @@ VERSION=1.4.7
 help:
 	@echo ""
 	@echo "- Available targets:"
-	@echo "- Info: make check VERSION=1.4.2 "
+	@echo "- Info: make check VERSION=1.4.8 "
 	@perl -ne 'if(	/^(\w+):/){print "\t",$$1,"\n"}' $(MAKEFILE)
 	@echo ""
 	@echo ""

diff --git a/R/gene_clustering.R b/R/gene_clustering.R
@@ -64,10 +64,20 @@ gene_clustering <- function(object = NULL,
                             inflation = 2,
                             method=c("closest_neighborhood", "reciprocal_neighborhood"),
                             threads = 1,
-                            output_path = tempdir(),
+                            output_path = NULL,
                             name = NULL,
                             keep_nn = FALSE) {
 
+  if(is.null(output_path)){
+    output_path <- tempdir()
+    dir.create(output_path, recursive = TRUE, showWarnings = FALSE)
+  }else{
+    if (!dir.exists(output_path)) {
+      dir.create(output_path, recursive = TRUE, showWarnings = FALSE)
+    }
+  }
+
+
 
   method <- match.arg(method)
 
@@ -179,19 +189,24 @@ gene_clustering <- function(object = NULL,
 #' @export construct_new_graph
 construct_new_graph <- function(object = NULL,
                                 k = 5,
-                                output_path = tempdir(),
+                                output_path = NULL,
                                 name = NULL) {
+
+  if(is.null(output_path)){
+    output_path <- tempdir()
+    dir.create(output_path, recursive = TRUE, showWarnings = FALSE)
+  }
+
   ## Check format object arg
   check_format_cluster_set(object)
 
-  ## Generate output path
   # Get working directory if output_path is "."
   if (output_path == ".") {
     output_path <- getwd()
   }
-  # Check if output directory exists. If not stop the command.
-  if (!file.exists(output_path)) {
-    stop("Output directory provided does not exist.")
+
+  if (!dir.exists(output_path)) {
+    dir.create(output_path, recursive = TRUE, showWarnings = FALSE)
   }
 
   # Create a random string if name is not provided
@@ -376,17 +391,21 @@ construct_new_graph <- function(object = NULL,
 #' @keywords internal
 #' @export keep_dbf_graph
 keep_dbf_graph <- function(object = NULL,
-                           output_path = tempdir(),
+                           output_path = NULL,
                            name = NULL) {
 
-  ## Generate output path
+  if(is.null(output_path)){
+    output_path <- tempdir()
+    dir.create(output_path, recursive = TRUE, showWarnings = FALSE)
+  }
+
   # Get working directory if output_path is "."
   if (output_path == ".") {
     output_path <- getwd()
   }
-  # Check if output directory exists. If not stop the command.
-  if (!file.exists(output_path)) {
-    stop("Output directory provided does not exist.")
+
+  if (!dir.exists(output_path)) {
+    dir.create(output_path, recursive = TRUE, showWarnings = FALSE)
   }
 
   # Create a random string if name is not provided

diff --git a/README.Rmd b/README.Rmd
@@ -11,6 +11,9 @@ html_preview: false
 library("badger")
 ```
 
+<img src="https://github.com/dputhier/scigenex/raw/master/inst/sticker/scigenex_logo.png" width="150" height="150" align="right"/>
+
+
 ```{r, echo = FALSE, results='asis'}
 cat(
 	badge_lifecycle(stage = "stable", color="green"),

diff --git a/README.md b/README.md
@@ -1,4 +1,8 @@
-<!-- README.md is generated from README.Rmd using devtools::build_readme(). Please edit README.Rmd -->
+<!-- README.md is generated from README.Rmd using devtools::build_readme(). Please edit that file -->
+
+<img src="https://github.com/dputhier/scigenex/raw/master/inst/sticker/scigenex_logo.png" width="150" height="150" align="right"/>
+
+    ## ✔ Setting active project to '/Users/puthier/Documents/git/project_dev/scigenex'
 
 [![](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![Project Status: Active - The project has reached a stable, usable
@@ -7,11 +11,10 @@ developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.re
 [![License:
 MIT](https://img.shields.io/badge/license-MIT-blue.svg)](https://cran.r-project.org/web/licenses/MIT)
 [![](https://img.shields.io/github/last-commit/dputhier/scigenex.svg)](https://github.com/dputhier/scigenex/commits/main)
-[![Codecov test coverage](https://codecov.io/gh/dputhier/scigenex/branch/main/graph/badge.svg)](https://app.codecov.io/gh/dputhier/scigenex?branch=main)
 
 # SciGeneX repository
 
-## :arrow_double_down: Installation
+## :arrow\_double\_down: Installation
 
 ### System requirements
 
@@ -48,7 +51,7 @@ You may skip this step as the latest versions of SciGeneX will call
 `scigenex::install_mcl()`to install MCL in `~/.scigenex` directory if
 this program is not found in the PATH.
 
-#### Installation of MCL using install_mcl()
+#### Installation of MCL using install\_mcl()
 
 The `install_mcl()` has been developed to ease MCL installation. This
 function should be call automatically from within R when calling the
@@ -80,15 +83,15 @@ should be available in your PATH from within R.
 ## Example
 
 The scigenex library contains several datasets including the
-pbmc3k_medium which is a subset from pbmc3k 10X dataset.
+pbmc3k\_medium which is a subset from pbmc3k 10X dataset.
 
     library(Seurat)
     library(scigenex)
     set_verbosity(1)
-
+    
     # Load a dataset
     load_example_dataset("7871581/files/pbmc3k_medium")
-
+    
     # Select informative genes
     res <- select_genes(pbmc3k_medium,
                          distance = "pearson",

diff --git a/changelog.md b/changelog.md
@@ -1,6 +1,10 @@
 
 # Changelog
 
+## v1.4.8
+
+* Fix an issue with temp dir.
+
 ## v1.4.7
 
 * Change k_g argument to 's' in `gene_clustering()` function for clarity purpose.

diff --git a/codecov.yml b/codecov.yml
@@ -1,14 +1,11 @@
 comment: false
 
-coverage:
-  status:
-    project:
-      default:
-        target: auto
-        threshold: 1%
-        informational: true
-    patch:
-      default:
-        target: auto
-        threshold: 1%
-        informational: true
+language: R
+
+sudo: false
+
+cache: packages
+
+after_success:
+
+- Rscript -e 'covr::codecov()'
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/usage.html b/docs/articles/usage.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">scigenex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.4.7</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.4.8</span>
       </span>
     </div>
 
@@ -193,7 +193,7 @@ <h3 id="extracting-gene-modules-using-scigenex">Extracting gene modules using Sc
 <span><span class="co">##               *  seed  =  123 </span></span>
 <span><span class="co">##               *  keep_nn  =  FALSE </span></span>
 <span><span class="co">##               *  k_mcl_graph  =  5 </span></span>
-<span><span class="co">##               *  output_path  =  /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//Rtmp6UgYV7 </span></span>
+<span><span class="co">##               *  output_path  =  /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpDSTiJs </span></span>
 <span><span class="co">##               *  name  =  s8gZ5uYQ33 </span></span>
 <span><span class="co">##               *  inflation  =  2</span></span></code></pre>
 <p>There are various methods associated with the <code>ClusterSet</code> objects.</p>
@@ -567,7 +567,7 @@ <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#s
 <span><span class="co">## </span></span>
 <span><span class="co">## other attached packages:</span></span>
 <span><span class="co">##  [1] tidyr_1.3.0                dplyr_1.1.3               </span></span>
-<span><span class="co">##  [3] scigenex_1.4.7             stxKidney.SeuratData_0.1.0</span></span>
+<span><span class="co">##  [3] scigenex_1.4.8             stxKidney.SeuratData_0.1.0</span></span>
 <span><span class="co">##  [5] stxBrain.SeuratData_0.1.1  pbmc3k.SeuratData_3.1.4   </span></span>
 <span><span class="co">##  [7] SeuratData_0.2.2           SeuratObject_4.1.3        </span></span>
 <span><span class="co">##  [9] Seurat_4.3.0               patchwork_1.1.2           </span></span>

diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/changelog.html b/docs/changelog.html