Fix merge conflicts

.github/workflows/build.yml

@@ -246,7 +246,7 @@ jobs:
           echo "deploy_target=$DEPLOY_TARGET" >> $GITHUB_OUTPUT
 
       - name: download-artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         if: ${{steps.check-deployment-target.outputs.deploy_target != ''}}
         with:
           path: deploy_artifacts
@@ -300,7 +300,14 @@ jobs:
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.r }}
-
+
+      - name: setup-r-dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache: true
+          cache-version: 2
+          architecture: 'x64'
+
       - name: check-install
         shell: bash
         run: |
@@ -309,8 +316,9 @@ jobs:
           PACKAGE="synapser"
           echo "if (available.packages(repos='$RAN')['$PACKAGE','Version'] != '$VERSION_TO_CHECK') { quit(save = 'no', status = 1) }" > test.R
           echo "try(remove.packages('$PACKAGE'), silent=T)" >> test.R
-          echo "install.packages('reticulate', repos=c('https://cloud.r-project.org/'))" >> test.R
-          echo "reticulate::virtualenv_create('r-reticulate')" >> test.R
+          echo "install.packages('remotes', repos = 'https://cloud.r-project.org'); remotes::install_version('reticulate', version = '1.28', repos = 'https://cloud.r-project.org')" >> test.R
+          echo "reticulate::install_python(version = '3.10.11')" >> test.R
+          echo "reticulate::virtualenv_create(envname='r-reticulate',version = '3.10.11')" >> test.R
           echo "reticulate::use_virtualenv('r-reticulate')" >> test.R
           echo "install.packages('$PACKAGE', repos=c('$RAN', 'https://cloud.r-project.org/'))" >> test.R
           echo "library('$PACKAGE')" >> test.R

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: synapser
 Type: Package
 Title: R Language Bindings for Synapse API
-Version: 2.0.0
-Date: 2022-01-18
+Version: 2.1.0
+Date: 2024-07-31
 Authors@R: c(
-  person("Tom", "Yu", role = c("cre"), email = "[email protected]"),
+  person("Dan", "Lu", role = c("aut", "cre"), email = "[email protected]"),
+  person("Tom", "Yu", role = c("aut"), email = "[email protected]"),
   person("Bruce", "Hoff", role = c("aut"), email = "[email protected]"),
   person("Sage Bionetworks", role = c("cph"))
   )
-Maintainer: Bruce Hoff <[email protected]>
 BugReports: https://github.com/Sage-Bionetworks/synapser/issues
 Description: Provides R language bindings for Synapse RESTful web services.
 Encoding: UTF-8

NEWS.md

@@ -1,9 +1,35 @@
+## synapser 2.1.0
+
+### Improvements
+
+* Upgraded to the synapsePythonClient v4.4.0.
+* Now support R 4.4.1.
+* The data upload and download algorithm in synapsePythonClient have been revamped for enhanced stability, reliability, and performance.
+* Updated reference documents and code examples for both new and modified functions. 
+
+#### New Functions
+* `synCreateTeam` and `synDeleteTeam` have been added to manage team. 
+* `synRestGetAsync`, `synRestDeleteAsync`, `synRestPostAsync` and `synRestPutAsync` have been added to allow interaction with Synapse server utilizing [asynchronous](https://python-docs.synapse.org/reference/oop/models_async/) models.
+
+#### Minor behavior changes: 
+* Credentials passed by command line argument will now be evaluated before credentials stored in the `~/.synapseConfig` file.
+* Using syn123.version notation is now supported with `synGet` and `synSetProvenance`.
+* File entities will no longer have their version incremented during no-op changes. Only when file content, or fields on the file has been updated will a version number be incremented.
+* New parameters have been added to allow more features: 
+  + Defining the project alias used in project url is now supported in `Project`.
+  + Setting the annotations on the entity is now supported in `synStore`.
+  + The MD5 of the file can now be used when creating S3 file handle in `synCreateExternalS3FileHandle`. 
+
+
+For more changes, please view the [Release Notes](https://python-docs.synapse.org/news/) on the Python client documentation.
+
 ## synapser 2.0.0
 
 ### Improvements
 
 * Python synapsePythonClient dependency updated to 4.0.0
 * You can only login via a Synapse Personal Access token now.  All other forms of authentication have been disabled for security purposes.
+* `rememberMe` has been deprecated in `synLogin`. 
 * `synSetAnnotations` removed as it is not working as expected due to implementation in the Python API.
 * For more changes, please view the 3.2.0 and 4.0.0 changes on the [Python client documentation](https://python-docs.synapse.org/news/).