Update to use python client 3.1.1

Sage-Bionetworks · Nov 1, 2023 · d0d32ac · d0d32ac
1 parent 27492e5
commit d0d32ac
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Showing 4 changed files with 17 additions and 7 deletions.
diff --git a/DESCRIPTION b/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]"),

diff --git a/NEWS.md b/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
 

diff --git a/R/zzz.R b/R/zzz.R
@@ -12,10 +12,12 @@
       # 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"))
-      reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T)
-      reticulate::py_run_string("import synapseclient")
+      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)
+      system('pip3 install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "synapseclient[pandas]"')
     }
   )
 

diff --git a/tools/installPythonClient.R b/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]
@@ -19,4 +19,5 @@ reticulate::use_virtualenv('r-reticulate')
 # reticulate::py_run_string("import sys")
 # reticulate::py_run_string(sprintf("sys.path.append(\"%s\")", file.path(baseDir, "inst", "python")))
 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_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T)
+system('pip3 install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "synapseclient[pandas]"')