install packages in inst/python-packages

R/shared.R

@@ -3,28 +3,6 @@
 # Author: bhoff
 ###############################################################################
 
-.getPythonFolderPath<-function(rootDir) {
-	file.path(rootDir, "python")
-}
-
-.addEggsToPath<-function(dir){
-	# modules with .egg extensions (such as future and synapseClient) need to be explicitly added to the sys.path
-	pyImport("sys")
-	pyImport("glob")
-	pyExec(sprintf("sys.path+=glob.glob('%s/*.egg')", dir))
-}
-
-.addPythonAndLibFoldersToSysPath<-function(srcDir) {
-	pyImport("sys")
-	pyExec(sprintf("sys.path.append('%s')", .getPythonFolderPath(srcDir)))
-	pyExec(sprintf("sys.path.append('%s')", file.path(srcDir, "lib")))
-	pyExec(sprintf("sys.path.append('%s')", file.path(srcDir, "lib/python3.5")))
-	sitePackageDir <- file.path(srcDir, "lib/python3.5/site-packages")
-	pyExec(sprintf("sys.path.append('%s')", sitePackageDir))
-	#add all .eggs to paths
-	.addEggsToPath(sitePackageDir)
-}
-
 .addSynPrefix<-function(name) {
 	paste("syn", toupper(substring(name,1,1)), substring(name,2,nchar(name)), sep="")
 }
@@ -38,7 +16,6 @@
 # rootDir is the folder containing the 'python' folder
 #
 .getSynapseFunctionInfo<-function(rootDir) {
-	#pyImport("sys")
 	pyExec(sprintf("sys.path.append(\"%s\")", file.path(rootDir, "python")))
 	pyImport("functionInfo")	
 

R/zzz.R

@@ -1,31 +1,41 @@
 # package initialization
 #
-# 
 # Author: bhoff
 ###############################################################################
 
-# TODO the package should be able to return the version of the underlying Python package
-# i.e. the value of synapseclient.__version__
 .onLoad <- function(libname, pkgname) { 
-	.addPythonAndLibFoldersToSysPath(system.file(package="synapser"))
+	.addPythonAndFoldersToSysPath(system.file(package="synapser"))
 
 	# TODO This line is in '.onLoad' in PythonEmbedInR but fails to persist on Windows
 	# long term, need to determine why and fix it
 	Sys.setenv(PYTHONPATH=system.file("lib", package="PythonEmbedInR"))
 	# TODO to be on the safe side, we repeat this too.  Long term we need to look at the root cause.
 	Sys.setenv(PYTHONHOME=system.file(package="PythonEmbedInR"))
 
-
 	.defineRPackageFunctions()
 
-	# TODO fix module import failure
-	#pyImport("urllib3")
-	#pyExec("urllib3.disable_warnings()")
-
 	pyImport("synapseclient")
 	pyExec("syn=synapseclient.Synapse()")
+	message("synapseclient version:", pyGet("synapseclient.__version__"))
+}
+
+.addEggsToPath<-function(dir) {
+	# modules with .egg extensions (such as future and synapseClient) need to be explicitly added to the sys.path
+	pyImport("sys")
+	pyImport("glob")
+	pyExec(sprintf("sys.path+=glob.glob('%s/*.egg')", dir))
 }
 
+.addPythonAndFoldersToSysPath<-function(srcDir) {
+	pyImport("sys")
+	pyExec(sprintf("sys.path.append('%s')", file.path(srcDir, "python")))
+	packageDir<-file.path(srcDir, "python-packages")
+	pyExec(sprintf("sys.path.append('%s')", packageDir))
+	#add all .eggs to paths
+	.addEggsToPath(packageDir)
+}
+
+
 .defineFunction<-function(synName, pyName) {
 	force(synName)
 	force(pyName)
@@ -47,9 +57,7 @@
 	}
 }
 
-.onAttach <-
-		function(libname, pkgname)
-{
+.onAttach <- function(libname, pkgname) {
 	tou <- "\nTERMS OF USE NOTICE:
 	When using Synapse, remember that the terms and conditions of use require that you:
 	1) Attribute data contributors when discussing these data or results from these data.

cleanup

@@ -0,0 +1,3 @@
+#!/bin/sh
+rm -rf inst/python/__pycache__
+rm -rf inst/python-packages

cleanup.win

@@ -0,0 +1,2 @@
+#!/bin/sh
+./cleanup

configure

@@ -4,15 +4,10 @@ set -e
 
 export PWD_FROM_R=${ALT_PWD-`pwd`}
 
-# This code is for linking the package to the R Python client
-rm -rf inst/lib
-rm -rf inst/bin
 rm -rf inst/python/__pycache__
+rm -rf inst/python-packages
 
-#export MODULE_INSTALLATION_FOLDER=$PWD/inst
-#mkdir -p $MODULE_INSTALLATION_FOLDER
-#export PYTHONUSERBASE=$MODULE_INSTALLATION_FOLDER
-
+# This code is for linking the package to the R Python client
 Rscript --vanilla tools/installPythonClient.R $PWD_FROM_R
 
 # build the .Rd files

inst/python/installPythonClient.py

@@ -26,32 +26,29 @@ def main(path):
     else:
         print('No PYTHONPATH env variable')
 
-    moduleInstallationFolder=path+os.sep+"inst"
+    moduleInstallationFolder=path+os.sep+"inst"+os.sep+"python-packages"
     sys.path.insert(0, moduleInstallationFolder)
     # The preferred approach is to use pip...
 
-    call_pip(['install', 'pip',  '--upgrade', '--quiet'])
-    call_pip(['install', '--user', 'urllib3',  '--upgrade', '--quiet'])
-    call_pip(['install', '--user', 'requests',  '--upgrade', '--quiet'])
-    call_pip(['install', '--user', 'six',  '--upgrade', '--quiet'])
-    call_pip(['install', '--user', 'backports.csv',  '--upgrade', '--quiet'])
+    call_pip('pip', moduleInstallationFolder)
+    call_pip('urllib3', moduleInstallationFolder)
+    call_pip('requests', moduleInstallationFolder)
+    call_pip('six', moduleInstallationFolder)
+    call_pip('backports.csv', moduleInstallationFolder)
 
     # ...but - for some reason - pip breaks when we install future and the python synapse client
     # my guess is that pip 'shells out' to call setup.py and hops to another version of
     # python on the machine
 
-
-    #pip.main(['install', '--user', 'future',  '--upgrade'])
     packageName = "future-0.15.2"
     linkPrefix = "https://pypi.python.org/packages/5a/f4/99abde815842bc6e97d5a7806ad51236630da14ca2f3b1fce94c0bb94d3d/"
-    installPackage(packageName, linkPrefix, path)
+    installPackage(packageName, linkPrefix, path, moduleInstallationFolder)
 
-    #pip.main(['install', '--user', 'synapseclient',  '--upgrade'])
-    packageName = "synapseclient-1.6.1"
-    linkPrefix = "https://pypi.python.org/packages/37/fd/5672e85abc68f4323e19e470cb7eeb0f8dc610566f124c930c3026404fb9/"
-    installPackage(packageName, linkPrefix, path)
+    packageName = "synapseclient-1.7.1"
+    linkPrefix = "https://pypi.python.org/packages/56/da/e489aad73886e6572737ccfe679b3a2bc9e68b05636d4ac30302d0dcf261/"
+    installPackage(packageName, linkPrefix, path, moduleInstallationFolder)
 
-def installPackage(packageName, linkPrefix, path):
+def installPackage(packageName, linkPrefix, path, moduleInstallationFolder):
     # download 
     zipFileName = packageName + ".tar.gz"
     x = urllib.request.urlopen(linkPrefix+zipFileName)
@@ -82,13 +79,13 @@ def installPackage(packageName, linkPrefix, path):
 
             sys.argv=['setup.py', 'install', '--user'] 
             # TODO how do we get 'setup.py' to install into inst/lib?
-            distutils.core.run_setup(script_name='setup.py', script_args=['install', '--user', '--upgrade', '--quiet'])
+            distutils.core.run_setup(script_name='setup.py', script_args=['install', '--upgrade', '--quiet', '--target', moduleInstallationFolder])
             # step back one level before remove the directory
             os.chdir(path)
             shutil.rmtree(packageDir)
         else:
             os.chdir(path)
-            call_pip(['install', '--user', localZipFile,  '--upgrade', '--quiet'])
+            call_pip(['install', localZipFile,  '--upgrade', '--quiet', '--target', moduleInstallationFolder])
             os.remove(localZipFile)
     finally:
         time.sleep(10)
@@ -107,7 +104,7 @@ def installPackage(packageName, linkPrefix, path):
         # os we'll let the system remove the temp file
         # os.remove(outfilepath)
 
-def call_pip(args):
+def call_pip(packageName, moduleInstallationFolder):
     origStdout=sys.stdout
     origStderr=sys.stderr 
     outfile=tempfile.mkstemp()
@@ -118,7 +115,7 @@ def call_pip(args):
     sys.stderr = outfilehandle
 
     try:
-        rc = pip.main(args)
+        rc = pip.main(['install', packageName,  '--upgrade', '--quiet', '--target', moduleInstallationFolder])
         if rc!=0:
             raise Exception('pip.main returned '+str(rc))
     finally: