[SYN-1520] upgrade python client version and R version (#336)

* upgraded synapseclient version to v4.4.0
* updated R version and package dependencies
* added/extended reference documents for both new and modified functions
* updated Github action to reflect most recent compatible R versions
* resolved infinite recursion issues and package building failures on Ubuntu and Windows

.github/workflows/build.yml

@@ -1,3 +1,4 @@
+
 # build and test synapser. Additionally deploys to  S3 RAN server on GitHub release.
 
 name: build
@@ -28,14 +29,14 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04, macos-13, windows-2022]
-        r: [4.1.3, 4.2.3, 4.3.1]
+        r: [4.1.3, 4.2.3, 4.3.1, 4.4.1]
 
     steps:
       - name: checkout
         uses: actions/checkout@v4
 
       - name: Set up Python Version
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
 
@@ -137,6 +138,10 @@ jobs:
       - name: linux-build-package
         if: ${{runner.os == 'linux'}}
         run: |
+          Rscript -e "install.packages('remotes'); remotes::install_version('reticulate', version = '1.28')"
+          Rscript -e "reticulate::install_miniconda()"
+          echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile
+          Rscript -e "reticulate::conda_create('r-reticulate', packages = c('python==3.10'))"
           R CMD build ./
           R CMD INSTALL ./ --library=$R_LIBS_USER --no-test-load
 
@@ -145,7 +150,7 @@ jobs:
       - name: mac-build-package
         if: ${{runner.os == 'macOS'}}
         run: |
-            Rscript -e "install.packages(c('remotes', 'reticulate'))"
+            Rscript -e "install.packages('remotes'); remotes::install_version('reticulate', version = '1.28')"
             Rscript -e "reticulate::install_miniconda()"
             echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile
             Rscript -e "reticulate::conda_create('r-reticulate', packages = c('python==3.10'))"
@@ -158,6 +163,11 @@ jobs:
         if: ${{runner.os == 'Windows'}}
         shell: bash
         run: |
+          echo "options(repos = c(CRAN = 'https://cloud.r-project.org'))" >> .Rprofile
+          Rscript -e "install.packages('remotes'); remotes::install_version('reticulate', version = '1.28')"
+          Rscript -e "reticulate::install_python(version = '3.10.11')"
+          Rscript -e "reticulate::virtualenv_create(envname='r-reticulate',version = '3.10.11')"
+          Rscript -e "reticulate::use_virtualenv('r-reticulate')"
           R CMD build ./
           R CMD INSTALL --build ${PACKAGE_NAME}_${PACKAGE_VERSION}.tar.gz --library=$R_LIBS_USER --no-test-load --no-multiarch
 
@@ -193,7 +203,7 @@ jobs:
           echo "UPLOAD_NAME=$UPLOAD_NAME" >> $GITHUB_ENV
 
       - name: upload-artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{env.UPLOAD_NAME}}
           path: ${{env.ARTIFACT_NAME}}
@@ -278,7 +288,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04, windows-2022, macos-13]
-        r: [4.1.3, 4.2.3, 4.3.1]
+        r: [4.1.3, 4.2.3, 4.3.1, 4.4.1]
 
     runs-on: ${{ matrix.os }}
 

DESCRIPTION

@@ -15,12 +15,14 @@ Encoding: UTF-8
 License: Apache License 2.0
 Imports:
   reticulate(>= 1.25),
+  reticulate(<= 1.28),
   methods,
   rjson,
   stats,
   utils
 Depends:
-  R(>= 4.0)
+  R(>= 4.1.3),
+  R(< 4.5)
 Remotes:
   [email protected]
 Suggests: pack, R6, testthat, knitr, rmarkdown

R/table.R

@@ -124,7 +124,7 @@
   df <- data.frame(
     Map(.convertToRType, list = df, synapseType = types),
     stringsAsFactors = F)
-
+  
   # The Map function mangles column names (which are in the Schema), so let's fix them
   colnames(df) <- .extractColumnNames(columnSchema)
   df
@@ -137,7 +137,7 @@
   df <- data.frame(
     Map(.convertToSynapseType, list = df, synapseType = types),
     stringsAsFactors = F)
-
+  
   # The Map function mangles column names (which are in the Schema), so let's fix them
   colnames(df) <- .extractColumnNames(columnSchema)
   df
@@ -181,4 +181,4 @@
   } else {
     .saveToCsv(values, file)
   }
-}
+}

R/zzz.R

@@ -12,28 +12,28 @@
       # 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 <- '4.0.0'
+      PYTHON_CLIENT_VERSION <- '4.4.0'
       # 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("pandas>=1.5,<=2.0.3", "jinja2", "markupsafe","numpy<=1.24.4"))
       reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T)
       reticulate::py_run_string("import synapseclient")
     }
   )
-
+  
   reticulate::py_run_string(sprintf("synapserVersion = 'synapser/%s' ", utils::packageVersion("synapser")))
   reticulate::py_run_string("synapseclient.USER_AGENT['User-Agent'] = synapserVersion + ' '+ synapseclient.USER_AGENT['User-Agent']")
   reticulate::py_run_string("synapseclient.core.config.single_threaded = True")
-  reticulate::py_run_string("syn=synapseclient.Synapse(skip_checks=True)")
+  reticulate::py_run_string("syn=synapseclient.Synapse(skip_checks=True, debug=False)")
   # make syn available in the global environment
   syn <<- reticulate::py_eval("syn")
-
+  
   .addPythonAndFoldersToSysPath(system.file(package = "synapser"))
   .defineRPackageFunctions()
   # .defineOverloadFunctions() must come AFTER .defineRPackageFunctions()
   # because it redefines selected generic functions
   .defineOverloadFunctions()
-
+  
   # mute Python warnings
   reticulate::py_run_string("import warnings")
   reticulate::py_run_string("warnings.filterwarnings('ignore')")
@@ -57,7 +57,6 @@
                     assignEnumCallback = .assignEnumCallback,
                     functionFilter = .synapseClassFunctionFilter,
                     functionPrefix = "syn",
-                    transformReturnObject = .objectDefinitionHelper,
                     pySingletonName = "syn")
   # exposing all supporting classes except for Synapse itself and some selected classes.
   generateRWrappers(pyPkg = "synapseclient",
@@ -73,23 +72,25 @@
                     assignEnumCallback = .assignEnumCallback,
                     functionFilter = .cherryPickTableFunctionFilter,
                     classFilter = .removeAllClassesClassFilter,
-                    functionPrefix = "syn",
-                    transformReturnObject = .objectDefinitionHelper)
+                    functionPrefix = "syn")
 }
 
-.objectDefinitionHelper <- function(object) {
-  if (methods::is(object, "CsvFileTable")) {
-    # reading from csv
-    # Removed due to Error in unlockBinding("asDataFrame", object) : no binding for "asDataFrame"
-    # unlockBinding("asDataFrame", object)
-    object$asDataFrame <- function() {
-      .readCsvBasedOnSchema(object)
-    }
-    # Removed due to Error in lockBinding("asDataFrame", object) : no binding for "asDataFrame"
-    # lockBinding("asDataFrame", object)
-  }
-  object
-}
+# TODO: This section is removed since it causes the infinite recursion 
+# issue when reading downloaded entity to a dataframe. Revisit this
+# when deprecating PythonEmbedInR code
+# .objectDefinitionHelper <- function(object) {
+#   if (methods::is(object, "CsvFileTable")) {
+#     # reading from csv
+#     # Removed due to Error in unlockBinding("asDataFrame", object) : no binding for "asDataFrame"
+#     # unlockBinding("asDataFrame", object)
+#     object$asDataFrame <- function() {
+#       .readCsvBasedOnSchema(object)
+#     }
+#     # Removed due to Error in lockBinding("asDataFrame", object) : no binding for "asDataFrame"
+#     # lockBinding("asDataFrame", object)
+#   }
+#   object
+# }
 
 .onAttach <- function(libname, pkgname) {
   tou <- "\nTERMS OF USE NOTICE:
@@ -98,7 +99,7 @@
   2) Not discriminate, identify, or recontact individuals or groups represented by the data.
   3) Use and contribute only data de-identified to HIPAA standards.
   4) Redistribute data only under these same terms of use.\n"
-
+  
   .checkForUpdate()
   packageStartupMessage(tou)
 }
@@ -128,7 +129,7 @@
       Table(schema, file)
     }
   )
-
+  
   methods::setMethod(
     f = "synBuildTable",
     signature = c("ANY", "ANY", "data.frame"),
@@ -144,10 +145,10 @@
     f = "as.data.frame",
     signature = c(x = "CsvFileTable"),
     definition = function(x) {
-      x$asDataFrame()
+      .readCsvBasedOnSchema(x)
     }
   )
-
+  
   methods::setClass("GeneratorWrapper")
   methods::setMethod(
     f = "as.list",
@@ -156,19 +157,19 @@
       x$asList()
     }
   )
-
+  
   methods::setGeneric(
     name = "nextElem",
     def = function(x) {
       standardGeneric("nextElem")
     }
   )
-
+  
   methods::setMethod(
     f = "nextElem",
     signature = c(x = "GeneratorWrapper"),
     definition = function(x) {
       x$nextElem()
     }
   )
-}
+}

auto-man/Project-class.Rd

@@ -18,13 +18,14 @@ Projects in Synapse must be uniquely named. Trying to create a project with a na
 
 Attributes:
     name: The name of the project
+    alias: The project alias for use in friendly project urls.
     properties: A map of Synapse properties
     annotations: A map of user defined annotations
     local_state: Internal use only
 }
 \section{Methods}{
 \itemize{
-\item \code{Project(name=NULL, properties=NULL, annotations=NULL, local_state=NULL)}: Constructor for \code{\link{Project}}
+\item \code{Project(name=NULL, properties=NULL, annotations=NULL, local_state=NULL, alias=NULL)}: Constructor for \code{\link{Project}}
 \item \code{local_state(state=NULL)}: Set or get the object's internal state, excluding properties, or annotations.\cr
 \cr
 Arguments:\cr

auto-man/Project.Rd

@@ -17,18 +17,20 @@ Projects in Synapse must be uniquely named. Trying to create a project with a na
 
 Attributes:
     name: The name of the project
+    alias: The project alias for use in friendly project urls.
     properties: A map of Synapse properties
     annotations: A map of user defined annotations
     local_state: Internal use only
 }
 \usage{
-Project(name=NULL, properties=NULL, annotations=NULL, local_state=NULL)
+Project(name=NULL, properties=NULL, annotations=NULL, local_state=NULL, alias=NULL)
 }
 \arguments{
 \item{name}{}
 \item{properties}{}
 \item{annotations}{}
 \item{local_state}{}
+\item{alias}{}
 }
 \value{
 An object of type Project

auto-man/synCreateExternalS3FileHandle.Rd

@@ -23,12 +23,13 @@ Arguments:
     storage_location_id: Explicit storage location id to create the file handle in, mutually exclusive
             with parent
     mimetype: Mimetype of the file, if known
+    md5: MD5 of the file, if known
 
 Raises:
     ValueError: If neither parent nor storage_location_id is specified, or if both are specified.
 }
 \usage{
-synCreateExternalS3FileHandle(bucket_name, s3_file_key, file_path, parent=NULL, storage_location_id=NULL, mimetype=NULL)
+synCreateExternalS3FileHandle(bucket_name, s3_file_key, file_path, parent=NULL, storage_location_id=NULL, mimetype=NULL, md5=NULL)
 }
 \arguments{
 \item{bucket_name}{}
@@ -37,6 +38,7 @@ synCreateExternalS3FileHandle(bucket_name, s3_file_key, file_path, parent=NULL,
 \item{parent}{}
 \item{storage_location_id}{}
 \item{mimetype}{}
+\item{md5}{}
 }
 \value{
 

auto-man/synCreateTeam.Rd

@@ -0,0 +1,39 @@
+%
+%  Auto-generated file, do not modify.
+%  Instead, copy this file to the man/ folder, remove this warning, and edit freely.
+%  Use Git to identify changes in this file which suggest where to change your edited copy.
+%
+\name{synCreateTeam}
+\alias{synCreateTeam}
+\docType{methods}
+\title{
+synCreateTeam
+}
+\description{
+Creates a new team.
+
+Arguments:
+    name: The name of the team to create.
+    description: A description of the team.
+    icon: The FileHandleID of the icon to be used for the team.
+    canPublicJoin: Whether the team can be joined by anyone. Defaults to False.
+    canRequestMembership: Whether the team can request membership. Defaults to True.
+
+Returns:
+    An object of type [synapseclient.team.Team][]
+}
+\usage{
+synCreateTeam(name, description=NULL, icon=NULL, can_public_join=FALSE, can_request_membership=TRUE)
+}
+\arguments{
+\item{name}{}
+\item{description}{}
+\item{icon}{}
+\item{can_public_join}{}
+\item{can_request_membership}{}
+}
+\value{
+
+}
+
+

auto-man/synDeleteTeam.Rd

@@ -0,0 +1,28 @@
+%
+%  Auto-generated file, do not modify.
+%  Instead, copy this file to the man/ folder, remove this warning, and edit freely.
+%  Use Git to identify changes in this file which suggest where to change your edited copy.
+%
+\name{synDeleteTeam}
+\alias{synDeleteTeam}
+\docType{methods}
+\title{
+synDeleteTeam
+}
+\description{
+Deletes a team.
+
+Arguments:
+    id: The ID of the team to delete.
+}
+\usage{
+synDeleteTeam(id)
+}
+\arguments{
+\item{id}{}
+}
+\value{
+
+}
+
+