Merge pull request #326 from Sage-Bionetworks/fix-release

[SYNR-1515] Update to synapseclient v3.1.1

.github/workflows/build.yml

@@ -268,8 +268,8 @@ jobs:
 
     strategy:
       matrix:
-        os: [ubuntu-22.04, windows-2022, macos-12]
-        r: [4.1.3, 4.2.2, 4.3.1]
+        os: [ubuntu-22.04, windows-2022, macos-13]
+        r: [4.1.3, 4.2.3, 4.3.1]
 
     runs-on: ${{ matrix.os }}
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: synapser
 Type: Package
 Title: R Language Bindings for Synapse API
-Version: 1.2.0
+Version: 1.3.0
 Date: 2022-01-18
 Authors@R: c(
   person("Bruce", "Hoff", role = c("aut", "cre"), email = "[email protected]"),

NEWS.md

@@ -1,8 +1,15 @@
+## synapser 1.3.0
+
+### Improvements
+
+* Python synapsePythonClient dependency updated to 3.1.1
+
 ## synapser 1.2.0
 
 ### Improvements
 
 * Python synapsePythonClient dependency updated to 3.0.0
+* Use `virtualenv` to install Python dependencies
 
 ## synapser 1.1.0
 

R/zzz.R

@@ -12,10 +12,11 @@
       # Ideally we would source tools/installPythonClient.R to not
       # have to duplicate the synapseclient install code
       # system2(paste("Rscript ", getwd(), "/tools/installPythonClient.R ", getwd(), sep=""))
-      PYTHON_CLIENT_VERSION <- '3.0.0'
-      reticulate::py_install(c("requests", "pandas", "pysftp", "jinja2", "markupsafe"))
+      PYTHON_CLIENT_VERSION <- '3.1.1'
+      reticulate::virtualenv_create('r-reticulate')
+      reticulate::use_virtualenv('r-reticulate')
+      reticulate::py_install(c("requests<3", "pandas~=2.0.0", "pysftp", "jinja2", "markupsafe"))
       reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T)
-      reticulate::py_run_string("import synapseclient")
     }
   )
 

tools/installPythonClient.R

@@ -5,7 +5,7 @@
 # Author: bhoff
 ###############################################################################
 
-PYTHON_CLIENT_VERSION <- '3.0.0'
+PYTHON_CLIENT_VERSION <- '3.1.1'
 
 args <- commandArgs(trailingOnly = TRUE)
 baseDir<-args[1]