diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 3eea8b863..6aebef676 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -26,8 +26,19 @@ on:
 
 jobs:
 
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    - uses: pre-commit/action@v3.0.0
+
+
   # run unit (and integration tests if account secrets available) on our build matrix
   test:
+    needs: [pre-commit]
 
     strategy:
       matrix:
@@ -39,7 +50,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v4
         with:
@@ -65,7 +76,7 @@ jobs:
             ${{ steps.get-dependencies.outputs.site_bin_dir }}
           key: ${{ runner.os }}-${{ matrix.python }}-build-${{ env.cache-name }}-${{ hashFiles('setup.py') }}-v7
 
-      - name: install-py-dependencies
+      - name: Install py-dependencies
         if: steps.cache-dependencies.outputs.cache-hit != 'true'
         shell: bash
         run: |
@@ -80,11 +91,6 @@ jobs:
             pip install numpy
           fi
 
-      # - name: lint
-      #   shell: bash
-      #   run: |
-      #     flake8
-
       - name: run-unit-tests
         shell: bash
         run: |
@@ -133,17 +139,14 @@ jobs:
             export EXTERNAL_S3_BUCKET_AWS_SECRET_ACCESS_KEY="${{secrets.EXTERNAL_S3_BUCKET_AWS_SECRET_ACCESS_KEY}}"
 
              # use loadscope to avoid issues running tests concurrently that share scoped fixtures
-            pytest -sv tests/integration -n auto --dist loadscope
+            pytest -sv tests/integration -n auto --ignore=tests/integration/synapseclient/test_command_line_client.py --dist loadscope
+            # Execute the CLI tests in a non-dist way because they were causing some test instability when being run concurrently
+            pytest -sv tests/integration/synapseclient/test_command_line_client.py
           fi
-  # enforce the code matches the Black code style
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - uses: psf/black@stable
+
   # on a GitHub release, build the pip package and upload it as a GitHub release asset
   package:
-    needs: [test,lint]
+    needs: [test,pre-commit]
 
     runs-on: ubuntu-20.04
 
@@ -154,7 +157,7 @@ jobs:
       bdist-package-name: ${{ steps.build-package.outputs.bdist-package-name }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v4
         with:
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index e154a229a..0f7354dc8 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -38,7 +38,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 10516fc3d..1565af65c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,4 +1,5 @@
-exclude: '^docs/conf.py'
+exclude: '^docs/conf.py|^docs/build/'
+
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 2335ac2e3..8baa4b4ff 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -4,14 +4,20 @@ Welcome, and thanks for your interest in contributing to the Synapse Python clie
 
 By contributing, you are agreeing that we may redistribute your work under this [license](LICENSE.md).
 
+# Table of contents
 - [How to contribute](#how-to-contribute)
-  - [Reporting bugs or feature requests](#reporting-bugs-or-feature-requests)
-  - [The development life cycle](#the-development-life-cycle)
-    - [Fork and clone this repository](#fork-and-clone-this-repository)
-    - [Installing the Python Client in a virtual environment with pipenv](#installing-the-python-client-in-a-virtual-environment-with-pipenv)
-    - [Development](#development)
-    - [Testing](#testing)
-- [Repository Admins](#repository-admins)
+   * [Reporting bugs or feature requests](#reporting-bugs-or-feature-requests)
+- [Getting started](#getting-started)
+    + [Fork and clone this repository](#fork-and-clone-this-repository)
+    + [Installing the Python Client in a virtual environment with pipenv](#installing-the-python-client-in-a-virtual-environment-with-pipenv)
+    + [Set up pre-commit](#set-up-pre-commit)
+    + [Authentication](#authentication)
+- [The development life cycle](#the-development-life-cycle)
+   * [Development](#development)
+   * [Testing](#testing)
+      + [Integration testing agaisnt the `dev` synapse server](#integration-testing-agaisnt-the-dev-synapse-server)
+   * [Code style](#code-style)
+   * [Repository Admins](#repository-admins)
 
 ## I don't want to read this whole thing I just have a question!
 
@@ -36,10 +42,7 @@ Bug reports and feature requests can be made in two ways. The first (preferred)
 
 After a bug report is received, expect a Sage Bionetworks staff member to contact you through the submission method you chose ([Synapse Help Forum](https://www.synapse.org/#!SynapseForum:default)or [Github issue](https://github.com/Sage-Bionetworks/synapsePythonClient/issues)). After ascertaining there is enough detail for the bug report or feature request, a JIRA issue will be opened. If you want to work on fixing the issue or feature yourself, follow the next sections!
 
-### The development life cycle
-
-Developing on the Python client starts with picking a issue to work on in JIRA! The open work items (bugs and new features) are tracked in JIRA in the [SYNPY Project](https://sagebionetworks.jira.com/projects/SYNPY/issues). Issues marked as `Open` are ready for your contributions! Please make sure your assign yourself the ticket and check with the maintainers if the issue you picked is suitable.
-
+## Getting started
 #### Fork and clone this repository
 
 1. See the [Github docs](https://help.github.com/articles/fork-a-repo/) for how to make a copy (a fork) of a repository to your own Github account.
@@ -66,14 +69,35 @@ Perform the following one-time steps to set up your local environment.
     * pipenv
       ```bash
       # Verify you are at the root directory for the cloned repository (ie: `cd synapsePythonClient`)
-      pipenv install
       # To develop locally you want to add --dev
-      # pipenv install --dev
+      pipenv install --dev
+      # Set your active session to the virtual environment you created
       pipenv shell
+      # Note: The 'Python Environment Manager' extension in vscode is reccomended here
       ```
 
 4. Once completed you are ready to start developing. Commands run through the CLI, or through an IDE like visual studio code within the virtual environment will have all required dependencies automatically installed. Try running `synapse -h` in your shell to read over the available CLI commands. Or view the `Usage as a library` section in the README.md to get started using the library to write more python.
-#### Development
+
+#### Set up pre-commit
+Once your virtual environment is created the `pre-commit` command will be available through your terminal. Install `pre-commit` into your git hooks via:
+```
+pre-commit install
+```
+When you commit your files via git it will automatically use the `.pre-commit-config.yaml` to run various checks to enforce style.
+
+If you want to manually run all pre-commit hooks use:
+```
+pre-commit run --all-files
+```
+
+#### Authentication
+Learn about the multiple ways one can login to Synapse [here](https://python-docs.synapse.org/build/html/getting_started/credentials.html).
+
+## The development life cycle
+
+Developing on the Python client starts with picking a issue to work on in JIRA! The open work items (bugs and new features) are tracked in JIRA in the [SYNPY Project](https://sagebionetworks.jira.com/projects/SYNPY/issues). Issues marked as `Open` are ready for your contributions! Please make sure your assign yourself the ticket and check with the maintainers if the issue you picked is suitable.
+
+### Development
 
 Now that you have chosen a JIRA ticket and have your own fork of this repository.  It's time to start development!
 
@@ -83,14 +107,6 @@ Now that you have chosen a JIRA ticket and have your own fork of this repository
 
 
 1. (Assuming you have followed all 4 steps above in the "fork and clone this repository" section). Navigate to your cloned repository on your computer/server.
-1. Make sure your `develop` branch is up to date with the `Sage-Bionetworks/synapsePythonClient` develop branch
-
-    ```
-    cd synapsePythonClient
-    git remote add upstream https://github.com/Sage-Bionetworks/synapsePythonClient.git
-    git checkout develop
-    git pull upstream develop
-    ```
 
 1. Create a feature branch which off the `develop` branch. The branch should be named the same as the JIRA issue you are working on (e.g., `SYNPY-1234-{feature-here}`). I recommend adding details of the actual feature in the branch name so that you don't need to go back and forth between JIRA and GitHub.
 
@@ -112,11 +128,12 @@ Now that you have chosen a JIRA ticket and have your own fork of this repository
     > It is good practice to run `git diff` or `git status` to first view your changes prior to pushing!
 
     ```
+    # Make sure that you have setup `pre-commit` as noted in the getting started section
     git commit changed_file.txt -m "Remove X parameter because it was unused"
     git push
     ```
 
-1. (Make sure you have follow instructions in "Install development dependencies") Once you have made your additions or changes, make sure you write tests and run the test suite. More information on testing below.
+1. Once you have made your additions or changes, make sure you write tests and run the test suite. More information on testing below.
 1. Once you have completed all the steps above, in Github, create a pull request from the feature branch of your fork to the `develop` branch of `Sage-Bionetworks/synapsePythonClient`.
 
     > **Note**
@@ -125,7 +142,7 @@ Now that you have chosen a JIRA ticket and have your own fork of this repository
     >
     > The status of an issue can be tracked in JIRA. Once an issue has passed a code review with a Sage Bionetworks engineer, he/she will update it's status in JIRA appropriately.
 
-#### Testing
+### Testing
 
 All code added to the client must have tests. These might include unit tests (to test specific functionality of code that was added to support fixing the bug or feature), integration tests (to test that the feature is usable - e.g., it should have complete the expected behavior as reported in the feature request or bug report), or both.
 
@@ -139,7 +156,7 @@ Here's how to run the test suite:
 # Unit tests
 pytest -vs tests/unit
 
-# Integration tests
+# Integration tests - The integration tests should be run against the `dev` synapse server
 pytest -vs tests/integration
 ```
 
@@ -150,6 +167,22 @@ To test a specific feature, specify the full path to the function to run:
 pytest -vs tests/integration/synapseclient/test_command_line_client.py::test_table_query
 ````
 
+#### Integration testing against the `dev` synapse server
+The easiest way to specify the HTTP endpoints to use for all synapse requests is to modify the `~/.synapseConfig` file and modify a few key-value pairs such as below. Not this is also where you will specify the dev authentication:
+```
+[authentication]
+username=<dev username>
+authtoken=<dev authtoken>
+
+[endpoints]
+repoEndpoint=https://repo-dev.dev.sagebase.org/repo/v1
+authEndpoint=https://repo-dev.dev.sagebase.org/auth/v1
+fileHandleEndpoint=https://repo-dev.dev.sagebase.org/file/v1
+```
+
+#### Integration testing for external collaborators
+As an external collaborator you will not have access to a development account and environment to run the integration tests agaisnt. Either request that a Sage Bionetworks staff member run your integration tests via a pull request, or, contact us via the [Service Desk](https://sagebionetworks.jira.com/servicedesk/customer/portal/9) to requisition a development account for integration testing only.
+
 ### Code style
 
 The Synapse Python Client uses [`flake8`](https://pypi.org/project/flake8/) to enforce
diff --git a/Pipfile.lock b/Pipfile.lock
index b3390f03a..6d63c6968 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -84,119 +84,128 @@
         },
         "charset-normalizer": {
             "hashes": [
-                "sha256:02673e456dc5ab13659f85196c534dc596d4ef260e4d86e856c3b2773ce09843",
-                "sha256:02af06682e3590ab952599fbadac535ede5d60d78848e555aa58d0c0abbde786",
-                "sha256:03680bb39035fbcffe828eae9c3f8afc0428c91d38e7d61aa992ef7a59fb120e",
-                "sha256:0570d21da019941634a531444364f2482e8db0b3425fcd5ac0c36565a64142c8",
-                "sha256:09c77f964f351a7369cc343911e0df63e762e42bac24cd7d18525961c81754f4",
-                "sha256:0d3d5b7db9ed8a2b11a774db2bbea7ba1884430a205dbd54a32d61d7c2a190fa",
-                "sha256:1063da2c85b95f2d1a430f1c33b55c9c17ffaf5e612e10aeaad641c55a9e2b9d",
-                "sha256:12ebea541c44fdc88ccb794a13fe861cc5e35d64ed689513a5c03d05b53b7c82",
-                "sha256:153e7b6e724761741e0974fc4dcd406d35ba70b92bfe3fedcb497226c93b9da7",
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@@ -546,99 +555,99 @@
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+                "sha256:baec8148d6b8bd5cee1ae138ba658c71f5b03e0d69d5907703e3e1df96db5e41",
+                "sha256:bb06098d019766ca16fc915ecaa455c1f1cd594204e7f840cd6258237b5079a8",
+                "sha256:bc791ec3fd0c4309a753f95bb6c749ef0d8ea3aea91f07ee1cf06b7b02118f2f",
+                "sha256:bd28b31730f0e982ace8663d108e01199098432a30a4c410d06fe08fdb9e93f4",
+                "sha256:be4d9c2770044a59715eb57c1144dedea7c5d5ae80c68fb9959515037cde2008",
+                "sha256:c0c72d34e7de5604df0fde3644cc079feee5e55464967d10b24b1de268deceb9",
+                "sha256:c0e842112fe3f1a4ffcf64b06dc4c61a88441c2f02f373367f7b4c1aa9be2ad5",
+                "sha256:c15070ebf11b8b7fd1bfff7217e9324963c82dbdf6182ff7050519e350e7ad9f",
+                "sha256:c2000c54c395d9e5e44c99dc7c20a64dc371f777faf8bae4919ad3e99ce5253e",
+                "sha256:c30187840d36d0ba2893bc3271a36a517a717f9fd383a98e2697ee890a37c273",
+                "sha256:cb7cd68814308aade9d0c93c5bd2ade9f9441666f8ba5aa9c2d4b389cb5e2a45",
+                "sha256:cd805513198304026bd379d1d516afbf6c3c13f4382134a2c526b8b854da1c2e",
+                "sha256:d0bf89afcbcf4d1bb2652f6580e5e55a840fdf87384f6063c4a4f0c95e378656",
+                "sha256:d9137a876020661972ca6eec0766d81aef8a5627df628b664b234b73396e727e",
+                "sha256:dbd95e300367aa0827496fe75a1766d198d34385a58f97683fe6e07f89ca3e3c",
+                "sha256:dced27917823df984fe0c80a5c4ad75cf58df0fbfae890bc08004cd3888922a2",
+                "sha256:de0b4caa1c8a21394e8ce971997614a17648f94e1cd0640fbd6b4d14cab13a72",
+                "sha256:debb633f3f7856f95ad957d9b9c781f8e2c6303ef21724ec94bea2ce2fcbd056",
+                "sha256:e372d7dfd154009142631de2d316adad3cc1c36c32a38b16a4751ba78da2a397",
+                "sha256:ecd26be9f112c4f96718290c10f4caea6cc798459a3a76636b817a0ed7874e42",
+                "sha256:edc0202099ea1d82844316604e17d2b175044f9bcb6b398aab781eba957224bd",
+                "sha256:f194cce575e59ffe442c10a360182a986535fd90b57f7debfaa5c845c409ecc3",
+                "sha256:f5fb672c396d826ca16a022ac04c9dce74e00a1c344f6ad1a0fdc1ba1f332213",
+                "sha256:f6a02a3c7950cafaadcd46a226ad9e12fc9744652cc69f9e5534f98b47f3bbcf",
+                "sha256:fe81b35c33772e56f4b6cf62cf4aedc1762ef7162a31e6ac7fe5e40d0149eb67"
             ],
             "markers": "python_full_version >= '3.7.0'",
-            "version": "==3.3.0"
+            "version": "==3.3.1"
         },
         "click": {
             "hashes": [
@@ -650,23 +659,32 @@
         },
         "cryptography": {
             "hashes": [
-                "sha256:0d7b69674b738068fa6ffade5c962ecd14969690585aaca0a1b1fc9058938a72",
-                "sha256:1bd0ccb0a1ed775cd7e2144fe46df9dc03eefd722bbcf587b3e0616ea4a81eff",
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-                "sha256:5a60d3780149e13b7a6ff7ad6526b38846354d11a15e21068e57073e29e19bed",
-                "sha256:7951a966613c4211b6612b0352f5bf29989955ee592c4a885d8c7d0f830d0433",
-                "sha256:922f9602d67c15ade470c11d616f2b2364950602e370c76f0c94c94ae672742e",
-                "sha256:a0f0b96c572fc9f25c3f4ddbf4688b9b38c69836713fb255f4a2715d93cbaf44",
-                "sha256:a777c096a49d80f9d2979695b835b0f9c9edab73b59e4ceb51f19724dda887ed",
-                "sha256:a9a4ac9648d39ce71c2f63fe7dc6db144b9fa567ddfc48b9fde1b54483d26042",
-                "sha256:aa4969f24d536ae2268c902b2c3d62ab464b5a66bcb247630d208a79a8098e9b",
-                "sha256:c7390f9b2119b2b43160abb34f63277a638504ef8df99f11cb52c1fda66a2e6f",
-                "sha256:e18e6ab84dfb0ab997faf8cca25a86ff15dfea4027b986322026cc99e0a892da"
+                "sha256:0c327cac00f082013c7c9fb6c46b7cc9fa3c288ca702c74773968173bda421bf",
+                "sha256:0d2a6a598847c46e3e321a7aef8af1436f11c27f1254933746304ff014664d84",
+                "sha256:227ec057cd32a41c6651701abc0328135e472ed450f47c2766f23267b792a88e",
+                "sha256:22892cc830d8b2c89ea60148227631bb96a7da0c1b722f2aac8824b1b7c0b6b8",
+                "sha256:392cb88b597247177172e02da6b7a63deeff1937fa6fec3bbf902ebd75d97ec7",
+                "sha256:3be3ca726e1572517d2bef99a818378bbcf7d7799d5372a46c79c29eb8d166c1",
+                "sha256:573eb7128cbca75f9157dcde974781209463ce56b5804983e11a1c462f0f4e88",
+                "sha256:580afc7b7216deeb87a098ef0674d6ee34ab55993140838b14c9b83312b37b86",
+                "sha256:5a70187954ba7292c7876734183e810b728b4f3965fbe571421cb2434d279179",
+                "sha256:73801ac9736741f220e20435f84ecec75ed70eda90f781a148f1bad546963d81",
+                "sha256:7d208c21e47940369accfc9e85f0de7693d9a5d843c2509b3846b2db170dfd20",
+                "sha256:8254962e6ba1f4d2090c44daf50a547cd5f0bf446dc658a8e5f8156cae0d8548",
+                "sha256:88417bff20162f635f24f849ab182b092697922088b477a7abd6664ddd82291d",
+                "sha256:a48e74dad1fb349f3dc1d449ed88e0017d792997a7ad2ec9587ed17405667e6d",
+                "sha256:b948e09fe5fb18517d99994184854ebd50b57248736fd4c720ad540560174ec5",
+                "sha256:c707f7afd813478e2019ae32a7c49cd932dd60ab2d2a93e796f68236b7e1fbf1",
+                "sha256:d38e6031e113b7421db1de0c1b1f7739564a88f1684c6b89234fbf6c11b75147",
+                "sha256:d3977f0e276f6f5bf245c403156673db103283266601405376f075c849a0b936",
+                "sha256:da6a0ff8f1016ccc7477e6339e1d50ce5f59b88905585f77193ebd5068f1e797",
+                "sha256:e270c04f4d9b5671ebcc792b3ba5d4488bf7c42c3c241a3748e2599776f29696",
+                "sha256:e886098619d3815e0ad5790c973afeee2c0e6e04b4da90b88e6bd06e2a0b1b72",
+                "sha256:ec3b055ff8f1dce8e6ef28f626e0972981475173d7973d63f271b29c8a2897da",
+                "sha256:fba1e91467c65fe64a82c689dc6cf58151158993b13eb7a7f3f4b7f395636723"
             ],
-            "markers": "sys_platform == 'linux'",
-            "version": "==3.3.2"
+            "markers": "python_version >= '3.7'",
+            "version": "==41.0.5"
         },
         "deprecated": {
             "hashes": [
@@ -701,11 +719,11 @@
         },
         "filelock": {
             "hashes": [
-                "sha256:08c21d87ded6e2b9da6728c3dff51baf1dcecf973b768ef35bcbc3447edb9ad4",
-                "sha256:2e6f249f1f3654291606e046b09f1fd5eac39b360664c27f5aad072012f8bcbd"
+                "sha256:521f5f56c50f8426f5e03ad3b281b490a87ef15bc6c526f168290f0c7148d44e",
+                "sha256:57dbda9b35157b05fb3e58ee91448612eb674172fab98ee235ccb0b5bee19a1c"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==3.12.4"
+            "version": "==3.13.1"
         },
         "flake8": {
             "hashes": [
@@ -714,13 +732,19 @@
             ],
             "version": "==3.9.2"
         },
+        "func-timeout": {
+            "hashes": [
+                "sha256:74cd3c428ec94f4edfba81f9b2f14904846d5ffccc27c92433b8b5939b5575dd"
+            ],
+            "version": "==4.3.5"
+        },
         "identify": {
             "hashes": [
-                "sha256:afe67f26ae29bab007ec21b03d4114f41316ab9dd15aa8736a167481e108da54",
-                "sha256:f302a4256a15c849b91cfcdcec052a8ce914634b2f77ae87dad29cd749f2d88d"
+                "sha256:7736b3c7a28233637e3c36550646fc6389bedd74ae84cb788200cc8e2dd60b75",
+                "sha256:90199cb9e7bd3c5407a9b7e81b4abec4bb9d249991c79439ec8af740afc6293d"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==2.5.30"
+            "version": "==2.5.31"
         },
         "idna": {
             "hashes": [
@@ -1102,6 +1126,13 @@
             ],
             "version": "==3.12.0"
         },
+        "pytest-rerunfailures": {
+            "hashes": [
+                "sha256:784f462fa87fe9bdf781d0027d856b47a4bfe6c12af108f6bd887057a917b48e",
+                "sha256:9a1afd04e21b8177faf08a9bbbf44de7a0fe3fc29f8ddbe83b9684bd5f8f92a9"
+            ],
+            "version": "==12.0"
+        },
         "pytest-xdist": {
             "extras": [
                 "psutil"
@@ -1337,11 +1368,11 @@
         },
         "virtualenv": {
             "hashes": [
-                "sha256:b80039f280f4919c77b30f1c23294ae357c4c8701042086e3fc005963e4e537b",
-                "sha256:e8361967f6da6fbdf1426483bfe9fca8287c242ac0bc30429905721cefbff752"
+                "sha256:02ece4f56fbf939dbbc33c0715159951d6bf14aaf5457b092e4548e1382455af",
+                "sha256:520d056652454c5098a00c0f073611ccbea4c79089331f60bf9d7ba247bb7381"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==20.24.5"
+            "version": "==20.24.6"
         },
         "wrapt": {
             "hashes": [
diff --git a/README.md b/README.md
index 79e5c6578..406418b1b 100644
--- a/README.md
+++ b/README.md
@@ -93,7 +93,7 @@ The Synapse client can be used to write software that interacts with the Sage Bi
 
     syn = synapseclient.Synapse()
 
-    ## log in using username and password
+    ## log in using auth token
     syn.login(authToken='auth_token')
 
     ## retrieve a 100 by 4 matrix
@@ -124,6 +124,8 @@ Authentication toward [Synapse](https://www.synapse.org/#RegisterAccount:0) can
 
 Authentication via passwords and API keys will be deprecated early 2024.
 
+Learn about the multiple ways one can login to Synapse [here](https://python-docs.synapse.org/build/html/getting_started/credentials.html).
+
 
 Synapse Utilities (synapseutils)
 --------------------------------
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
index fa3d336b1..e2c49c82a 100644
--- a/docs/build/html/.buildinfo
+++ b/docs/build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: e61f33e16f39e8cbda346a2c639c4799
+config: 90d422e4b09fda20663a5d255dc16438
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_static/documentation_options.js b/docs/build/html/_static/documentation_options.js
index 5a7903e99..056ece08f 100644
--- a/docs/build/html/_static/documentation_options.js
+++ b/docs/build/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '3.1.0',
+    VERSION: '3.1.1',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/docs/build/html/api/Activity.html b/docs/build/html/api/Activity.html
index 32e51be25..3155a0ed4 100644
--- a/docs/build/html/api/Activity.html
+++ b/docs/build/html/api/Activity.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Provenance &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Provenance &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -247,7 +247,7 @@ <h2>Activity<a class="headerlink" href="#activity" title="Permalink to this head
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -268,7 +268,7 @@ <h2>Activity<a class="headerlink" href="#activity" title="Permalink to this head
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/api/Annotations.html b/docs/build/html/api/Annotations.html
index 8c50f1235..47775884c 100644
--- a/docs/build/html/api/Annotations.html
+++ b/docs/build/html/api/Annotations.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Annotations &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Annotations &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -199,7 +199,7 @@ <h2>Classes<a class="headerlink" href="#classes" title="Permalink to this headli
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -220,7 +220,7 @@ <h2>Classes<a class="headerlink" href="#classes" title="Permalink to this headli
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/api/Client.html b/docs/build/html/api/Client.html
index 6dad80b2a..e5863f33c 100644
--- a/docs/build/html/api/Client.html
+++ b/docs/build/html/api/Client.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Client &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Client &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -1643,7 +1643,7 @@ <h2>More information<a class="headerlink" href="#more-information" title="Permal
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -1664,7 +1664,7 @@ <h2>More information<a class="headerlink" href="#more-information" title="Permal
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/api/Entity.html b/docs/build/html/api/Entity.html
index 376848267..3000c3e8b 100644
--- a/docs/build/html/api/Entity.html
+++ b/docs/build/html/api/Entity.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Entity &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Entity &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -461,7 +461,7 @@ <h2>Properties and annotations, implementation details<a class="headerlink" href
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -482,7 +482,7 @@ <h2>Properties and annotations, implementation details<a class="headerlink" href
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/api/Evaluation.html b/docs/build/html/api/Evaluation.html
index c7bb3d0eb..f627b27fe 100644
--- a/docs/build/html/api/Evaluation.html
+++ b/docs/build/html/api/Evaluation.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Evaluations &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Evaluations &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -277,7 +277,7 @@ <h2>Submission Status<a class="headerlink" href="#submission-status" title="Perm
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -298,7 +298,7 @@ <h2>Submission Status<a class="headerlink" href="#submission-status" title="Perm
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/api/JsonSchema.html b/docs/build/html/api/JsonSchema.html
index 3f5660095..a24a3b93a 100644
--- a/docs/build/html/api/JsonSchema.html
+++ b/docs/build/html/api/JsonSchema.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>JSON Schema &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>JSON Schema &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -709,7 +709,7 @@ <h1>JSON Schema<a class="headerlink" href="#json-schema" title="Permalink to thi
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -730,7 +730,7 @@ <h1>JSON Schema<a class="headerlink" href="#json-schema" title="Permalink to thi
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/api/Table.html b/docs/build/html/api/Table.html
index c4bdd722e..01d5b5534 100644
--- a/docs/build/html/api/Table.html
+++ b/docs/build/html/api/Table.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Tables &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Tables &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -975,7 +975,7 @@ <h2>Module level methods<a class="headerlink" href="#module-level-methods" title
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -996,7 +996,7 @@ <h2>Module level methods<a class="headerlink" href="#module-level-methods" title
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/api/Team.html b/docs/build/html/api/Team.html
index c5d6e16be..f86a49c7b 100644
--- a/docs/build/html/api/Team.html
+++ b/docs/build/html/api/Team.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Teams &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Teams &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -204,7 +204,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -225,7 +225,7 @@
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/api/Views.html b/docs/build/html/api/Views.html
index 0493a0703..9daaf7a99 100644
--- a/docs/build/html/api/Views.html
+++ b/docs/build/html/api/Views.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Views &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Views &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -200,7 +200,7 @@ <h2>Updating Annotations using View<a class="headerlink" href="#updating-annotat
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -221,7 +221,7 @@ <h2>Updating Annotations using View<a class="headerlink" href="#updating-annotat
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/api/Wiki.html b/docs/build/html/api/Wiki.html
index 1ccf7e93c..f63c3c613 100644
--- a/docs/build/html/api/Wiki.html
+++ b/docs/build/html/api/Wiki.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Wiki &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Wiki &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -218,7 +218,7 @@ <h2>Wiki methods<a class="headerlink" href="#wiki-methods" title="Permalink to t
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -239,7 +239,7 @@ <h2>Wiki methods<a class="headerlink" href="#wiki-methods" title="Permalink to t
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/api/core.html b/docs/build/html/api/core.html
index 8aad412e8..7aa7f771d 100644
--- a/docs/build/html/api/core.html
+++ b/docs/build/html/api/core.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Core &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Core &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -487,6 +487,18 @@ <h1>Core<a class="headerlink" href="#core" title="Permalink to this headline">
 </dl>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="synapseclient.core.utils.md5_fn">
+<span class="sig-prename descclassname"><span class="pre">synapseclient.core.utils.</span></span><span class="sig-name descname"><span class="pre">md5_fn</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">part</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">_</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#synapseclient.core.utils.md5_fn" title="Permalink to this definition"></a></dt>
+<dd><p>Calculate the MD5 of a file-like object.</p>
+<p>:part – A file-like object to read from.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The MD5</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="synapseclient.core.utils.md5_for_file">
 <span class="sig-prename descclassname"><span class="pre">synapseclient.core.utils.</span></span><span class="sig-name descname"><span class="pre">md5_for_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">block_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2097152</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">callback</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#synapseclient.core.utils.md5_for_file" title="Permalink to this definition"></a></dt>
@@ -676,7 +688,7 @@ <h3>Version Functions<a class="headerlink" href="#version-functions" title="Perm
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -697,7 +709,7 @@ <h3>Version Functions<a class="headerlink" href="#version-functions" title="Perm
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/articles/Upload.html b/docs/build/html/articles/Upload.html
index 6a5b7ad87..00fa2b8c2 100644
--- a/docs/build/html/articles/Upload.html
+++ b/docs/build/html/articles/Upload.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>File Upload &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>File Upload &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -35,7 +35,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -181,7 +181,7 @@ <h2>Downloading a Specific Version<a class="headerlink" href="#downloading-a-spe
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -202,7 +202,7 @@ <h2>Downloading a Specific Version<a class="headerlink" href="#downloading-a-spe
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/articles/api.html b/docs/build/html/articles/api.html
index 973f68300..834531976 100644
--- a/docs/build/html/articles/api.html
+++ b/docs/build/html/articles/api.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Accessing the API &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Accessing the API &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -129,7 +129,7 @@ <h1>Accessing the API<a class="headerlink" href="#accessing-the-api" title="Perm
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -150,7 +150,7 @@ <h1>Accessing the API<a class="headerlink" href="#accessing-the-api" title="Perm
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/articles/cli.html b/docs/build/html/articles/cli.html
index 0ffcea8aa..d367edd3c 100644
--- a/docs/build/html/articles/cli.html
+++ b/docs/build/html/articles/cli.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Command Line Client &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Command Line Client &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -158,8 +158,7 @@ <h2>Usage<a class="headerlink" href="#usage" title="Permalink to this headline">
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="p">[</span><span class="n">command</span><span class="p">]</span> <span class="o">-</span><span class="n">h</span>
 </pre></div>
 </div>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">synapse</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">version</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">u</span> <span class="n">SYNAPSEUSER</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">p</span> <span class="n">SYNAPSEPASSWORD</span><span class="p">]</span>
-               <span class="p">[</span><span class="o">-</span><span class="n">c</span> <span class="n">CONFIGPATH</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">debug</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">silent</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">s</span><span class="p">]</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">synapse</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">version</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">u</span> <span class="n">SYNAPSEUSER</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">p</span> <span class="n">SYNAPSEPASSWORD</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">c</span> <span class="n">CONFIGPATH</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">debug</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">silent</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">s</span><span class="p">]</span>
                <span class="p">{</span><span class="n">get</span><span class="p">,</span><span class="n">manifest</span><span class="p">,</span><span class="n">sync</span><span class="p">,</span><span class="n">store</span><span class="p">,</span><span class="n">add</span><span class="p">,</span><span class="n">mv</span><span class="p">,</span><span class="n">cp</span><span class="p">,</span><span class="n">get</span><span class="o">-</span><span class="n">download</span><span class="o">-</span><span class="nb">list</span><span class="p">,</span><span class="n">associate</span><span class="p">,</span><span class="n">delete</span><span class="p">,</span><span class="n">query</span><span class="p">,</span><span class="n">submit</span><span class="p">,</span><span class="n">show</span><span class="p">,</span><span class="n">cat</span><span class="p">,</span><span class="nb">list</span><span class="p">,</span><span class="n">config</span><span class="p">,</span><span class="nb">set</span><span class="o">-</span><span class="n">provenance</span><span class="p">,</span><span class="n">get</span><span class="o">-</span><span class="n">provenance</span><span class="p">,</span><span class="nb">set</span><span class="o">-</span><span class="n">annotations</span><span class="p">,</span><span class="n">get</span><span class="o">-</span><span class="n">annotations</span><span class="p">,</span><span class="n">create</span><span class="p">,</span><span class="n">store</span><span class="o">-</span><span class="n">table</span><span class="p">,</span><span class="n">onweb</span><span class="p">,</span><span class="n">login</span><span class="p">,</span><span class="n">test</span><span class="o">-</span><span class="n">encoding</span><span class="p">,</span><span class="n">get</span><span class="o">-</span><span class="n">sts</span><span class="o">-</span><span class="n">token</span><span class="p">,</span><span class="n">migrate</span><span class="p">}</span>
                <span class="o">...</span>
 </pre></div>
@@ -209,8 +208,7 @@ <h3>Sub-commands:<a class="headerlink" href="#Sub-commands:" title="Permalink to
 <section id="get">
 <h4>get<a class="headerlink" href="#get" title="Permalink to this headline"></a></h4>
 <p>downloads a file from Synapse</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">get</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">q</span> <span class="n">queryString</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">v</span> <span class="n">VERSION</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">r</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">followLink</span><span class="p">]</span>
-            <span class="p">[</span><span class="o">--</span><span class="n">limitSearch</span> <span class="n">projId</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">downloadLocation</span> <span class="n">path</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">multiThreaded</span><span class="p">]</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">get</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">q</span> <span class="n">queryString</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">v</span> <span class="n">VERSION</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">r</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">followLink</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">limitSearch</span> <span class="n">projId</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">downloadLocation</span> <span class="n">path</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">multiThreaded</span><span class="p">]</span>
             <span class="p">[</span><span class="o">--</span><span class="n">manifest</span> <span class="p">{</span><span class="nb">all</span><span class="p">,</span><span class="n">root</span><span class="p">,</span><span class="n">suppress</span><span class="p">}]</span>
             <span class="p">[</span><span class="n">local</span> <span class="n">path</span><span class="p">]</span>
 </pre></div>
@@ -320,10 +318,8 @@ <h5>options<a class="headerlink" href="#options_repeat3" title="Permalink to thi
 <h4>store<a class="headerlink" href="#store" title="Permalink to this headline"></a></h4>
 <p>uploads and adds a file to Synapse</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">store</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">(</span><span class="o">--</span><span class="n">parentid</span> <span class="n">syn123</span> <span class="o">|</span> <span class="o">--</span><span class="nb">id</span> <span class="n">syn123</span> <span class="o">|</span> <span class="o">--</span><span class="nb">type</span> <span class="n">TYPE</span><span class="p">)</span> <span class="p">[</span><span class="o">--</span><span class="n">name</span> <span class="n">NAME</span><span class="p">]</span>
-              <span class="p">[</span><span class="o">--</span><span class="n">description</span> <span class="n">DESCRIPTION</span> <span class="o">|</span> <span class="o">--</span><span class="n">descriptionFile</span> <span class="n">DESCRIPTION_FILE_PATH</span><span class="p">]</span>
-              <span class="p">[</span><span class="o">--</span><span class="n">used</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span> <span class="p">[</span><span class="o">--</span><span class="n">executed</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span>
-              <span class="p">[</span><span class="o">--</span><span class="n">limitSearch</span> <span class="n">projId</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">noForceVersion</span><span class="p">]</span>
-              <span class="p">[</span><span class="o">--</span><span class="n">annotations</span> <span class="n">ANNOTATIONS</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">replace</span><span class="p">]</span>
+              <span class="p">[</span><span class="o">--</span><span class="n">description</span> <span class="n">DESCRIPTION</span> <span class="o">|</span> <span class="o">--</span><span class="n">descriptionFile</span> <span class="n">DESCRIPTION_FILE_PATH</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">used</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span> <span class="p">[</span><span class="o">--</span><span class="n">executed</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span>
+              <span class="p">[</span><span class="o">--</span><span class="n">limitSearch</span> <span class="n">projId</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">noForceVersion</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">annotations</span> <span class="n">ANNOTATIONS</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">replace</span><span class="p">]</span>
               <span class="p">[</span><span class="n">FILE</span><span class="p">]</span>
 </pre></div>
 </div>
@@ -384,10 +380,8 @@ <h5>options<a class="headerlink" href="#options_repeat4" title="Permalink to thi
 <h4>add<a class="headerlink" href="#add" title="Permalink to this headline"></a></h4>
 <p>uploads and adds a file to Synapse</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">add</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">(</span><span class="o">--</span><span class="n">parentid</span> <span class="n">syn123</span> <span class="o">|</span> <span class="o">--</span><span class="nb">id</span> <span class="n">syn123</span> <span class="o">|</span> <span class="o">--</span><span class="nb">type</span> <span class="n">TYPE</span><span class="p">)</span> <span class="p">[</span><span class="o">--</span><span class="n">name</span> <span class="n">NAME</span><span class="p">]</span>
-            <span class="p">[</span><span class="o">--</span><span class="n">description</span> <span class="n">DESCRIPTION</span> <span class="o">|</span> <span class="o">--</span><span class="n">descriptionFile</span> <span class="n">DESCRIPTION_FILE_PATH</span><span class="p">]</span>
-            <span class="p">[</span><span class="o">--</span><span class="n">used</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span> <span class="p">[</span><span class="o">--</span><span class="n">executed</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span>
-            <span class="p">[</span><span class="o">--</span><span class="n">limitSearch</span> <span class="n">projId</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">noForceVersion</span><span class="p">]</span>
-            <span class="p">[</span><span class="o">--</span><span class="n">annotations</span> <span class="n">ANNOTATIONS</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">replace</span><span class="p">]</span>
+            <span class="p">[</span><span class="o">--</span><span class="n">description</span> <span class="n">DESCRIPTION</span> <span class="o">|</span> <span class="o">--</span><span class="n">descriptionFile</span> <span class="n">DESCRIPTION_FILE_PATH</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">used</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span> <span class="p">[</span><span class="o">--</span><span class="n">executed</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span>
+            <span class="p">[</span><span class="o">--</span><span class="n">limitSearch</span> <span class="n">projId</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">noForceVersion</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">annotations</span> <span class="n">ANNOTATIONS</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">replace</span><span class="p">]</span>
             <span class="p">[</span><span class="n">FILE</span><span class="p">]</span>
 </pre></div>
 </div>
@@ -465,8 +459,7 @@ <h5>options<a class="headerlink" href="#options_repeat6" title="Permalink to thi
 <section id="cp">
 <h4>cp<a class="headerlink" href="#cp" title="Permalink to this headline"></a></h4>
 <p>Copies specific versions of synapse content such as files, folders and projects by recursively copying all sub-content</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">cp</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="o">--</span><span class="n">destinationId</span> <span class="n">syn123</span> <span class="p">[</span><span class="o">--</span><span class="n">version</span> <span class="mi">1</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">setProvenance</span> <span class="n">traceback</span><span class="p">]</span>
-           <span class="p">[</span><span class="o">--</span><span class="n">updateExisting</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">skipCopyAnnotations</span><span class="p">]</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">cp</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="o">--</span><span class="n">destinationId</span> <span class="n">syn123</span> <span class="p">[</span><span class="o">--</span><span class="n">version</span> <span class="mi">1</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">setProvenance</span> <span class="n">traceback</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">updateExisting</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">skipCopyAnnotations</span><span class="p">]</span>
            <span class="p">[</span><span class="o">--</span><span class="n">excludeTypes</span> <span class="p">[</span><span class="n">file</span> <span class="n">table</span> <span class="o">...</span><span class="p">]]</span> <span class="p">[</span><span class="o">--</span><span class="n">skipCopyWiki</span><span class="p">]</span>
            <span class="n">syn123</span>
 </pre></div>
@@ -602,11 +595,9 @@ <h5>Positional Arguments<a class="headerlink" href="#Positional Arguments_repeat
 <section id="submit">
 <h4>submit<a class="headerlink" href="#submit" title="Permalink to this headline"></a></h4>
 <p>submit an entity or a file for evaluation</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">submit</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">evaluationID</span> <span class="n">EVALUATIONID</span><span class="p">]</span>
-               <span class="p">[</span><span class="o">--</span><span class="n">evaluationName</span> <span class="n">EVALUATIONNAME</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">entity</span> <span class="n">ENTITY</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">file</span> <span class="n">FILE</span><span class="p">]</span>
-               <span class="p">[</span><span class="o">--</span><span class="n">parentId</span> <span class="n">PARENTID</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">name</span> <span class="n">NAME</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">teamName</span> <span class="n">TEAMNAME</span><span class="p">]</span>
-               <span class="p">[</span><span class="o">--</span><span class="n">submitterAlias</span> <span class="n">ALIAS</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">used</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span>
-               <span class="p">[</span><span class="o">--</span><span class="n">executed</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span> <span class="p">[</span><span class="o">--</span><span class="n">limitSearch</span> <span class="n">projId</span><span class="p">]</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">submit</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">evaluationID</span> <span class="n">EVALUATIONID</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">evaluationName</span> <span class="n">EVALUATIONNAME</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">entity</span> <span class="n">ENTITY</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">file</span> <span class="n">FILE</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">parentId</span> <span class="n">PARENTID</span><span class="p">]</span>
+               <span class="p">[</span><span class="o">--</span><span class="n">name</span> <span class="n">NAME</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">teamName</span> <span class="n">TEAMNAME</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">submitterAlias</span> <span class="n">ALIAS</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">used</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span> <span class="p">[</span><span class="o">--</span><span class="n">executed</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span>
+               <span class="p">[</span><span class="o">--</span><span class="n">limitSearch</span> <span class="n">projId</span><span class="p">]</span>
 </pre></div>
 </div>
 <section id="options_repeat11">
@@ -736,10 +727,8 @@ <h4>config<a class="headerlink" href="#config" title="Permalink to this headline
 <section id="set-provenance">
 <h4>set-provenance<a class="headerlink" href="#set-provenance" title="Permalink to this headline"></a></h4>
 <p>create provenance records</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="nb">set</span><span class="o">-</span><span class="n">provenance</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="o">--</span><span class="nb">id</span> <span class="n">syn123</span> <span class="p">[</span><span class="o">--</span><span class="n">name</span> <span class="n">NAME</span><span class="p">]</span>
-                       <span class="p">[</span><span class="o">--</span><span class="n">description</span> <span class="n">DESCRIPTION</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">o</span> <span class="p">[</span><span class="n">OUTPUT_FILE</span><span class="p">]]</span>
-                       <span class="p">[</span><span class="o">--</span><span class="n">used</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span> <span class="p">[</span><span class="o">--</span><span class="n">executed</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span>
-                       <span class="p">[</span><span class="o">--</span><span class="n">limitSearch</span> <span class="n">projId</span><span class="p">]</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="nb">set</span><span class="o">-</span><span class="n">provenance</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="o">--</span><span class="nb">id</span> <span class="n">syn123</span> <span class="p">[</span><span class="o">--</span><span class="n">name</span> <span class="n">NAME</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">description</span> <span class="n">DESCRIPTION</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">o</span> <span class="p">[</span><span class="n">OUTPUT_FILE</span><span class="p">]]</span> <span class="p">[</span><span class="o">--</span><span class="n">used</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span>
+                       <span class="p">[</span><span class="o">--</span><span class="n">executed</span> <span class="p">[</span><span class="n">target</span> <span class="o">...</span><span class="p">]]</span> <span class="p">[</span><span class="o">--</span><span class="n">limitSearch</span> <span class="n">projId</span><span class="p">]</span>
 </pre></div>
 </div>
 <section id="options_repeat15">
@@ -833,9 +822,7 @@ <h5>options<a class="headerlink" href="#options_repeat18" title="Permalink to th
 <section id="create">
 <h4>create<a class="headerlink" href="#create" title="Permalink to this headline"></a></h4>
 <p>Creates folders or projects on Synapse</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">create</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">parentid</span> <span class="n">syn123</span><span class="p">]</span> <span class="o">--</span><span class="n">name</span> <span class="n">NAME</span>
-               <span class="p">[</span><span class="o">--</span><span class="n">description</span> <span class="n">DESCRIPTION</span> <span class="o">|</span> <span class="o">--</span><span class="n">descriptionFile</span> <span class="n">DESCRIPTION_FILE_PATH</span><span class="p">]</span>
-               <span class="nb">type</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">create</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">parentid</span> <span class="n">syn123</span><span class="p">]</span> <span class="o">--</span><span class="n">name</span> <span class="n">NAME</span> <span class="p">[</span><span class="o">--</span><span class="n">description</span> <span class="n">DESCRIPTION</span> <span class="o">|</span> <span class="o">--</span><span class="n">descriptionFile</span> <span class="n">DESCRIPTION_FILE_PATH</span><span class="p">]</span> <span class="nb">type</span>
 </pre></div>
 </div>
 <section id="Positional Arguments_repeat12">
@@ -932,8 +919,7 @@ <h4>test-encoding<a class="headerlink" href="#test-encoding" title="Permalink to
 <section id="get-sts-token">
 <h4>get-sts-token<a class="headerlink" href="#get-sts-token" title="Permalink to this headline"></a></h4>
 <p>Get an STS token for access to AWS S3 storage underlying Synapse</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">get</span><span class="o">-</span><span class="n">sts</span><span class="o">-</span><span class="n">token</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">o</span> <span class="p">{</span><span class="n">json</span><span class="p">,</span><span class="n">boto</span><span class="p">,</span><span class="n">shell</span><span class="p">,</span><span class="n">bash</span><span class="p">,</span><span class="n">cmd</span><span class="p">,</span><span class="n">powershell</span><span class="p">}]</span>
-                      <span class="nb">id</span> <span class="p">{</span><span class="n">read_write</span><span class="p">,</span><span class="n">read_only</span><span class="p">}</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">get</span><span class="o">-</span><span class="n">sts</span><span class="o">-</span><span class="n">token</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">o</span> <span class="p">{</span><span class="n">json</span><span class="p">,</span><span class="n">boto</span><span class="p">,</span><span class="n">shell</span><span class="p">,</span><span class="n">bash</span><span class="p">,</span><span class="n">cmd</span><span class="p">,</span><span class="n">powershell</span><span class="p">}]</span> <span class="nb">id</span> <span class="p">{</span><span class="n">read_write</span><span class="p">,</span><span class="n">read_only</span><span class="p">}</span>
 </pre></div>
 </div>
 <section id="Positional Arguments_repeat14">
@@ -960,11 +946,8 @@ <h5>options<a class="headerlink" href="#options_repeat22" title="Permalink to th
 <section id="migrate">
 <h4>migrate<a class="headerlink" href="#migrate" title="Permalink to this headline"></a></h4>
 <p>Migrate Synapse entities to a different storage location</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">migrate</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span>
-                <span class="p">[</span><span class="o">--</span><span class="n">source_storage_location_ids</span> <span class="p">[</span><span class="n">SOURCE_STORAGE_LOCATION_IDS</span> <span class="o">...</span><span class="p">]]</span>
-                <span class="p">[</span><span class="o">--</span><span class="n">file_version_strategy</span> <span class="n">FILE_VERSION_STRATEGY</span><span class="p">]</span>
-                <span class="p">[</span><span class="o">--</span><span class="n">include_table_files</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">continue_on_error</span><span class="p">]</span>
-                <span class="p">[</span><span class="o">--</span><span class="n">csv_log_path</span> <span class="n">CSV_LOG_PATH</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">dryRun</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">force</span><span class="p">]</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">migrate</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">source_storage_location_ids</span> <span class="p">[</span><span class="n">SOURCE_STORAGE_LOCATION_IDS</span> <span class="o">...</span><span class="p">]]</span> <span class="p">[</span><span class="o">--</span><span class="n">file_version_strategy</span> <span class="n">FILE_VERSION_STRATEGY</span><span class="p">]</span>
+                <span class="p">[</span><span class="o">--</span><span class="n">include_table_files</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">continue_on_error</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">csv_log_path</span> <span class="n">CSV_LOG_PATH</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">dryRun</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">force</span><span class="p">]</span>
                 <span class="nb">id</span> <span class="n">dest_storage_location_id</span> <span class="n">db_path</span>
 </pre></div>
 </div>
@@ -1037,7 +1020,7 @@ <h5>options<a class="headerlink" href="#options_repeat23" title="Permalink to th
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -1058,7 +1041,7 @@ <h5>options<a class="headerlink" href="#options_repeat23" title="Permalink to th
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/articles/data_storage.html b/docs/build/html/articles/data_storage.html
index 229f40770..9d3724944 100644
--- a/docs/build/html/articles/data_storage.html
+++ b/docs/build/html/articles/data_storage.html
@@ -4,7 +4,7 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Data Storage &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Data Storage &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
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@@ -37,7 +37,7 @@
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           </a>
               <div class="version">
-                3.1.0
+                3.1.1
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 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -455,7 +455,7 @@ <h3>Configure your client<a class="headerlink" href="#configure-your-client" tit
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -476,7 +476,7 @@ <h3>Configure your client<a class="headerlink" href="#configure-your-client" tit
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/articles/permissions.html b/docs/build/html/articles/permissions.html
index 9043667fd..405d671b2 100644
--- a/docs/build/html/articles/permissions.html
+++ b/docs/build/html/articles/permissions.html
@@ -4,7 +4,7 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Access Control &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Access Control &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -35,7 +35,7 @@
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           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -122,7 +122,7 @@ <h1>Access Control<a class="headerlink" href="#access-control" title="Permalink
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -143,7 +143,7 @@ <h1>Access Control<a class="headerlink" href="#access-control" title="Permalink
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/articles/reticulate.html b/docs/build/html/articles/reticulate.html
index a6a108238..6d0fd9b61 100644
--- a/docs/build/html/articles/reticulate.html
+++ b/docs/build/html/articles/reticulate.html
@@ -4,7 +4,7 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Using synapseclient with R through reticulate &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Using synapseclient with R through reticulate &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -35,7 +35,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -614,7 +614,7 @@ <h2>Using with a Shiny App<a class="headerlink" href="#using-with-a-shiny-app" t
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -635,7 +635,7 @@ <h2>Using with a Shiny App<a class="headerlink" href="#using-with-a-shiny-app" t
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/articles/synapseutils.html b/docs/build/html/articles/synapseutils.html
index 4fda87e7b..fa6583f5e 100644
--- a/docs/build/html/articles/synapseutils.html
+++ b/docs/build/html/articles/synapseutils.html
@@ -4,7 +4,7 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Synapse Utils &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Synapse Utils &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -870,7 +870,7 @@ <h2>Overview<a class="headerlink" href="#overview" title="Permalink to this head
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -891,7 +891,7 @@ <h2>Overview<a class="headerlink" href="#overview" title="Permalink to this head
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/articles/tables.html b/docs/build/html/articles/tables.html
index b0b3cb87e..4ccacf002 100644
--- a/docs/build/html/articles/tables.html
+++ b/docs/build/html/articles/tables.html
@@ -4,7 +4,7 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Tables &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Tables &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
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@@ -35,7 +35,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -124,7 +124,7 @@ <h1>Tables<a class="headerlink" href="#tables" title="Permalink to this headline
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -145,7 +145,7 @@ <h1>Tables<a class="headerlink" href="#tables" title="Permalink to this headline
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/articles/validate_annotations.html b/docs/build/html/articles/validate_annotations.html
index 97e2eaa72..622bf7edb 100644
--- a/docs/build/html/articles/validate_annotations.html
+++ b/docs/build/html/articles/validate_annotations.html
@@ -4,7 +4,7 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Validate Annotations &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Validate Annotations &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
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@@ -37,7 +37,7 @@
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           </a>
               <div class="version">
-                3.1.0
+                3.1.1
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 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -219,7 +219,7 @@ <h2>Create a JSON Schema organization<a class="headerlink" href="#create-a-json-
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -240,7 +240,7 @@ <h2>Create a JSON Schema organization<a class="headerlink" href="#create-a-json-
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
index 65448db48..cda45754d 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Index &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Index &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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@@ -34,7 +34,7 @@
               <img src="_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
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 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -562,6 +562,8 @@ <h2 id="M">M</h2>
       <li><a href="api/core.html#synapseclient.core.utils.make_bogus_binary_file">make_bogus_binary_file() (in module synapseclient.core.utils)</a>
 </li>
       <li><a href="api/core.html#synapseclient.core.utils.make_bogus_data_file">make_bogus_data_file() (in module synapseclient.core.utils)</a>
+</li>
+      <li><a href="api/core.html#synapseclient.core.utils.md5_fn">md5_fn() (in module synapseclient.core.utils)</a>
 </li>
       <li><a href="api/core.html#synapseclient.core.utils.md5_for_file">md5_for_file() (in module synapseclient.core.utils)</a>
 </li>
@@ -990,7 +992,7 @@ <h2 id="W">W</h2>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -1011,7 +1013,7 @@ <h2 id="W">W</h2>
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/getting_started/basics.html b/docs/build/html/getting_started/basics.html
index 21ea92869..cf11298bc 100644
--- a/docs/build/html/getting_started/basics.html
+++ b/docs/build/html/getting_started/basics.html
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Tutorial &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Tutorial &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
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@@ -37,7 +37,7 @@
               <img src="../_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
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     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
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     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
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+      <span class="lastupdated">Last updated on Oct 30, 2023.
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     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
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     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
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-<li class="toctree-l2"><a class="reference internal" href="#id1">3.1.0 (2023-10-20)</a><ul>
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+<li class="toctree-l3"><a class="reference internal" href="#stories">Stories</a></li>
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+<li class="toctree-l3"><a class="reference internal" href="#id7">Bug Fixes</a></li>
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+<li class="toctree-l3"><a class="reference internal" href="#id10">Highlights</a></li>
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-<li class="toctree-l3"><a class="reference internal" href="#id9">Highlights</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id11">2.7.1 (2023-04-11)</a><ul>
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-<li class="toctree-l3"><a class="reference internal" href="#id13">Stories</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id13">2.7.0 (2022-09-16)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id14">Highlights</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id15">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id16">Stories</a></li>
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-<li class="toctree-l3"><a class="reference internal" href="#id17">Stories</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id18">Tasks</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id17">2.6.0 (2022-04-19)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id18">Highlights</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id19">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id20">Stories</a></li>
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-<li class="toctree-l3"><a class="reference internal" href="#id22">Stories</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id22">2.5.1 (2021-12-02)</a><ul>
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+<li class="toctree-l3"><a class="reference internal" href="#id24">Bug Fixes</a></li>
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-<li class="toctree-l3"><a class="reference internal" href="#id26">Stories</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id27">Tasks</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id26">2.5.0 (2021-10-05)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id27">Highlights</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id28">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id29">Stories</a></li>
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-<li class="toctree-l3"><a class="reference internal" href="#id30">Bug Fixes</a></li>
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+<li class="toctree-l3"><a class="reference internal" href="#id33">Bug Fixes</a></li>
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-<li class="toctree-l3"><a class="reference internal" href="#id31">Tasks</a></li>
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-<li class="toctree-l3"><a class="reference internal" href="#id35">Improvements</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id35">2.3.1 (2021-04-13)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id36">Highlights</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id37">Bug Fixes</a></li>
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-<li class="toctree-l3"><a class="reference internal" href="#id38">Bug Fixes</a></li>
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+<li class="toctree-l3"><a class="reference internal" href="#id41">Bug Fixes</a></li>
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-<li class="toctree-l3"><a class="reference internal" href="#id39">Improvements</a></li>
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-<li class="toctree-l3"><a class="reference internal" href="#id44">Improvements</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id43">2.2.2 (2020-10-18)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id44">Highlights</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id45">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id46">New Features</a></li>
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-<li class="toctree-l3"><a class="reference internal" href="#id49">Tasks</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id48">2.2.0 (2020-08-31)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id49">Highlights</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id50">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id51">Improvements</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id52">Tasks</a></li>
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-<li class="toctree-l3"><a class="reference internal" href="#id53">Improvements</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id53">2.1.1 (2020-07-10)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id54">Highlights</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id55">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id56">Improvements</a></li>
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-<li class="toctree-l2"><a class="reference internal" href="#id54">2.1.0 (2020-06-16)</a><ul>
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-<li class="toctree-l3"><a class="reference internal" href="#id56">Bug Fixes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id57">Improvements</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id58">Tasks</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id57">2.1.0 (2020-06-16)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id58">Highlights</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id59">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id60">Improvements</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id61">Tasks</a></li>
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-<li class="toctree-l2"><a class="reference internal" href="#id59">2.0.0 (2020-03-23)</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id60">Highlights:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id62">2.0.0 (2020-03-23)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id63">Highlights:</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#bugs-fixes">Bugs Fixes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id61">Tasks</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id62">Improvements</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id64">Tasks</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id65">Improvements</a></li>
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-<li class="toctree-l2"><a class="reference internal" href="#id63">1.9.4 (2019-06-28)</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id64">Bug Fixes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id65">New Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id66">Improvements</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id66">1.9.4 (2019-06-28)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id67">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id68">New Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id69">Improvements</a></li>
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-<li class="toctree-l2"><a class="reference internal" href="#id67">1.9.3 (2019-06-28)</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id68">Bug Fixes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id70">1.9.3 (2019-06-28)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id71">Bug Fixes</a></li>
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-<li class="toctree-l2"><a class="reference internal" href="#id69">1.9.2 (2019-02-15)</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#id72">1.9.2 (2019-02-15)</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#features">Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id70">Bug Fixes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id71">Tasks</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id72">Improvements</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id73">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id74">Tasks</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id75">Improvements</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="#id73">1.9.1 (2019-01-20)</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id74">Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id75">Bug Fixes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id76">Tasks</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id77">Improvements</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id76">1.9.1 (2019-01-20)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id77">Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id78">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id79">Tasks</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id80">Improvements</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="#id78">1.9.0 (2018-09-28)</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id79">Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id80">Bug Fixes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id81">Tasks</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id82">Improvements</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id81">1.9.0 (2018-09-28)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id82">Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id83">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id84">Tasks</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id85">Improvements</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="#id83">1.8.2 (2018-08-17)</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id84">Bug Fixes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id85">Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id86">Tasks</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id87">Improvements</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id86">1.8.2 (2018-08-17)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id87">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id88">Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id89">Tasks</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id90">Improvements</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="#id88">1.8.1 (2018-05-17)</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id89">Bug Fixes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id91">1.8.1 (2018-05-17)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id92">Bug Fixes</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="#id90">1.8.0 (2018-05-07)</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id91">Bug Fixes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id92">Tasks</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id93">Improvements</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id93">1.8.0 (2018-05-07)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id94">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id95">Tasks</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id96">Improvements</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="#id94">1.7.5 (2018-01-31)</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#id95">1.7.4 (2018-01-29)</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id96">Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id97">Improvements</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id98">Bug Fixes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id99">Tasks</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id97">1.7.5 (2018-01-31)</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id98">1.7.4 (2018-01-29)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id99">Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id100">Improvements</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id101">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id102">Tasks</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="#id100">1.7.3 (2017-12-08)</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id101">Bug Fixes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id102">Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id104">Tasks</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id105">Improvements</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id103">1.7.3 (2017-12-08)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id104">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id105">Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id107">Tasks</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id108">Improvements</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="#id108">1.7.1 (2017-11-17)</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id109">Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id110">Improvements</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id111">Bug Fixes</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id112">Tasks</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#id111">1.7.1 (2017-11-17)</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id112">Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id113">Improvements</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id114">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id115">Tasks</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="#id113">1.6.1 (2016-11-02)</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#id116">1.6.1 (2016-11-02)</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#what-is-new">What is New</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id114">Improvements</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id115">Bug Fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id117">Improvements</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id118">Bug Fixes</a></li>
 </ul>
 </li>
 </ul>
@@ -285,18 +290,36 @@
   <section id="release-notes">
 <h1>Release Notes<a class="headerlink" href="#release-notes" title="Permalink to this headline"></a></h1>
 <section id="id1">
-<h2>3.1.0 (2023-10-20)<a class="headerlink" href="#id1" title="Permalink to this headline"></a></h2>
+<h2>3.1.1 (2023-10-30)<a class="headerlink" href="#id1" title="Permalink to this headline"></a></h2>
 <section id="highlights">
 <h3>Highlights<a class="headerlink" href="#highlights" title="Permalink to this headline"></a></h3>
 <ul class="simple">
+<li><p>A fix to dowloads when file names match but content does not when <cite>ifcollision=overwrite.local</cite></p></li>
+</ul>
+</section>
+<section id="bug-fixes">
+<h3>Bug Fixes<a class="headerlink" href="#bug-fixes" title="Permalink to this headline"></a></h3>
+<ul class="simple">
+<li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1316">SYNPY-1316</a>] -
+Calling <cite>syn.get</cite> with <cite>ifcollision=’overwrite.local</cite> does not always overwrite previous file</p></li>
+<li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1298">SYNPY-1298</a>] -
+Resolve unstable integration tests</p></li>
+</ul>
+</section>
+</section>
+<section id="id2">
+<h2>3.1.0 (2023-10-20)<a class="headerlink" href="#id2" title="Permalink to this headline"></a></h2>
+<section id="id3">
+<h3>Highlights<a class="headerlink" href="#id3" title="Permalink to this headline"></a></h3>
+<ul class="simple">
 <li><p>A fix to authentication when using a Personal Access token or API Key.
 <cite>synapse login</cite> and <cite>synapse config</cite> correctly work as a result.</p></li>
 <li><p>Replacement of custom <cite>&#64;memoize</cite> decorator with <cite>&#64;functools.lru_cache</cite> decorator.</p></li>
 <li><p>Introduction of pipfile for easy creation of a virtual environment for development.</p></li>
 </ul>
 </section>
-<section id="bug-fixes">
-<h3>Bug Fixes<a class="headerlink" href="#bug-fixes" title="Permalink to this headline"></a></h3>
+<section id="id4">
+<h3>Bug Fixes<a class="headerlink" href="#id4" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1283">SYNPY-1283</a>] -
 Fix dead link in docs</p></li>
@@ -322,10 +345,10 @@ <h3>Stories<a class="headerlink" href="#stories" title="Permalink to this headli
 </ul>
 </section>
 </section>
-<section id="id2">
-<h2>3.0.0 (2023-09-09)<a class="headerlink" href="#id2" title="Permalink to this headline"></a></h2>
-<section id="id3">
-<h3>Highlights<a class="headerlink" href="#id3" title="Permalink to this headline"></a></h3>
+<section id="id5">
+<h2>3.0.0 (2023-09-09)<a class="headerlink" href="#id5" title="Permalink to this headline"></a></h2>
+<section id="id6">
+<h3>Highlights<a class="headerlink" href="#id6" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>Removed all camel case or non-standard single dash long command line interface (cli)
 parameters.
@@ -336,8 +359,8 @@ <h3>Highlights<a class="headerlink" href="#id3" title="Permalink to this headlin
 <li><p>Support Synapse JSON schema services</p></li>
 </ul>
 </section>
-<section id="id4">
-<h3>Bug Fixes<a class="headerlink" href="#id4" title="Permalink to this headline"></a></h3>
+<section id="id7">
+<h3>Bug Fixes<a class="headerlink" href="#id7" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-570">SYNPY-570</a>] -
 warning messages when downloading if files in the cache already</p></li>
@@ -351,8 +374,8 @@ <h3>Bug Fixes<a class="headerlink" href="#id4" title="Permalink to this headline
 Integration test failure against release-458</p></li>
 </ul>
 </section>
-<section id="id5">
-<h3>Stories<a class="headerlink" href="#id5" title="Permalink to this headline"></a></h3>
+<section id="id8">
+<h3>Stories<a class="headerlink" href="#id8" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-737">SYNPY-737</a>] -
 deprecate single dash, multi-letter named params in command line client</p></li>
@@ -377,10 +400,10 @@ <h3>Stories<a class="headerlink" href="#id5" title="Permalink to this headline">
 </ul>
 </section>
 </section>
-<section id="id6">
-<h2>2.7.2 (2023-06-02)<a class="headerlink" href="#id6" title="Permalink to this headline"></a></h2>
-<section id="id7">
-<h3>Highlights<a class="headerlink" href="#id7" title="Permalink to this headline"></a></h3>
+<section id="id9">
+<h2>2.7.2 (2023-06-02)<a class="headerlink" href="#id9" title="Permalink to this headline"></a></h2>
+<section id="id10">
+<h3>Highlights<a class="headerlink" href="#id10" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1267">SYNPY-1267</a>] -
 Lock down urllib3</p></li>
@@ -401,10 +424,10 @@ <h3>Highlights<a class="headerlink" href="#id7" title="Permalink to this headlin
 </ul>
 </section>
 </section>
-<section id="id8">
-<h2>2.7.1 (2023-04-11)<a class="headerlink" href="#id8" title="Permalink to this headline"></a></h2>
-<section id="id9">
-<h3>Highlights<a class="headerlink" href="#id9" title="Permalink to this headline"></a></h3>
+<section id="id11">
+<h2>2.7.1 (2023-04-11)<a class="headerlink" href="#id11" title="Permalink to this headline"></a></h2>
+<section id="id12">
+<h3>Highlights<a class="headerlink" href="#id12" title="Permalink to this headline"></a></h3>
 <ul>
 <li><p>Locked down pandas version to only support pandas <cite>&lt;</cite> 1.5</p></li>
 <li><p>Next major release (3.0.0)…</p>
@@ -424,10 +447,10 @@ <h3>Highlights<a class="headerlink" href="#id9" title="Permalink to this headlin
 </ul>
 </section>
 </section>
-<section id="id10">
-<h2>2.7.0 (2022-09-16)<a class="headerlink" href="#id10" title="Permalink to this headline"></a></h2>
-<section id="id11">
-<h3>Highlights<a class="headerlink" href="#id11" title="Permalink to this headline"></a></h3>
+<section id="id13">
+<h2>2.7.0 (2022-09-16)<a class="headerlink" href="#id13" title="Permalink to this headline"></a></h2>
+<section id="id14">
+<h3>Highlights<a class="headerlink" href="#id14" title="Permalink to this headline"></a></h3>
 <ul>
 <li><p>Added support for Datasets</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># from python</span>
@@ -485,8 +508,8 @@ <h3>Highlights<a class="headerlink" href="#id11" title="Permalink to this headli
 will be changed to <cite>–parent-id</cite>.</p></li>
 </ul>
 </section>
-<section id="id12">
-<h3>Bug Fixes<a class="headerlink" href="#id12" title="Permalink to this headline"></a></h3>
+<section id="id15">
+<h3>Bug Fixes<a class="headerlink" href="#id15" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-226">SYNPY-226</a>] -
 isConsistent fails as parameter for table query</p></li>
@@ -502,8 +525,8 @@ <h3>Bug Fixes<a class="headerlink" href="#id12" title="Permalink to this headlin
 as_table_columns function is mishandling mixed data types</p></li>
 </ul>
 </section>
-<section id="id13">
-<h3>Stories<a class="headerlink" href="#id13" title="Permalink to this headline"></a></h3>
+<section id="id16">
+<h3>Stories<a class="headerlink" href="#id16" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-63">SYNPY-63</a>] -
 py: use metaclass to replace the _entity_type_to_class hack</p></li>
@@ -535,10 +558,10 @@ <h3>Tasks<a class="headerlink" href="#tasks" title="Permalink to this headline">
 </ul>
 </section>
 </section>
-<section id="id14">
-<h2>2.6.0 (2022-04-19)<a class="headerlink" href="#id14" title="Permalink to this headline"></a></h2>
-<section id="id15">
-<h3>Highlights<a class="headerlink" href="#id15" title="Permalink to this headline"></a></h3>
+<section id="id17">
+<h2>2.6.0 (2022-04-19)<a class="headerlink" href="#id17" title="Permalink to this headline"></a></h2>
+<section id="id18">
+<h3>Highlights<a class="headerlink" href="#id18" title="Permalink to this headline"></a></h3>
 <ul>
 <li><p>Next major release (3.0.0) there will be major cosmetic changes to the cli such as
 removing all camel case or non-standard single dash long command line interface (cli)
@@ -569,15 +592,15 @@ <h3>Highlights<a class="headerlink" href="#id15" title="Permalink to this headli
 </li>
 </ul>
 </section>
-<section id="id16">
-<h3>Bug Fixes<a class="headerlink" href="#id16" title="Permalink to this headline"></a></h3>
+<section id="id19">
+<h3>Bug Fixes<a class="headerlink" href="#id19" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1204">SYNPY-1204</a>] -
 Python 3.10 compatibility</p></li>
 </ul>
 </section>
-<section id="id17">
-<h3>Stories<a class="headerlink" href="#id17" title="Permalink to this headline"></a></h3>
+<section id="id20">
+<h3>Stories<a class="headerlink" href="#id20" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-728">SYNPY-728</a>] -
 Improve error message when pandas is not available</p></li>
@@ -587,8 +610,8 @@ <h3>Stories<a class="headerlink" href="#id17" title="Permalink to this headline"
 Support for MaterializedViews in Py Client</p></li>
 </ul>
 </section>
-<section id="id18">
-<h3>Tasks<a class="headerlink" href="#id18" title="Permalink to this headline"></a></h3>
+<section id="id21">
+<h3>Tasks<a class="headerlink" href="#id21" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1174">SYNPY-1174</a>] -
 Add function to create Synapse config file</p></li>
@@ -607,10 +630,10 @@ <h3>Tasks<a class="headerlink" href="#id18" title="Permalink to this headline">
 </ul>
 </section>
 </section>
-<section id="id19">
-<h2>2.5.1 (2021-12-02)<a class="headerlink" href="#id19" title="Permalink to this headline"></a></h2>
-<section id="id20">
-<h3>Highlights<a class="headerlink" href="#id20" title="Permalink to this headline"></a></h3>
+<section id="id22">
+<h2>2.5.1 (2021-12-02)<a class="headerlink" href="#id22" title="Permalink to this headline"></a></h2>
+<section id="id23">
+<h3>Highlights<a class="headerlink" href="#id23" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>Next major release (3.0.0) there will be major cosmetic changes to the cli such as
 removing all camel case or non-standard single dash long command line interface (cli)
@@ -620,15 +643,15 @@ <h3>Highlights<a class="headerlink" href="#id20" title="Permalink to this headli
 will be changed to <cite>–parent-id</cite>.</p></li>
 </ul>
 </section>
-<section id="id21">
-<h3>Bug Fixes<a class="headerlink" href="#id21" title="Permalink to this headline"></a></h3>
+<section id="id24">
+<h3>Bug Fixes<a class="headerlink" href="#id24" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1197">SYNPY-1197</a>] -
 Schema is a string and strings don’t have columns_to_store attributes</p></li>
 </ul>
 </section>
-<section id="id22">
-<h3>Stories<a class="headerlink" href="#id22" title="Permalink to this headline"></a></h3>
+<section id="id25">
+<h3>Stories<a class="headerlink" href="#id25" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-772">SYNPY-772</a>] -
 update statement that appears on PyPi about Synapse to be consistent</p></li>
@@ -637,10 +660,10 @@ <h3>Stories<a class="headerlink" href="#id22" title="Permalink to this headline"
 </ul>
 </section>
 </section>
-<section id="id23">
-<h2>2.5.0 (2021-10-05)<a class="headerlink" href="#id23" title="Permalink to this headline"></a></h2>
-<section id="id24">
-<h3>Highlights<a class="headerlink" href="#id24" title="Permalink to this headline"></a></h3>
+<section id="id26">
+<h2>2.5.0 (2021-10-05)<a class="headerlink" href="#id26" title="Permalink to this headline"></a></h2>
+<section id="id27">
+<h3>Highlights<a class="headerlink" href="#id27" title="Permalink to this headline"></a></h3>
 <ul>
 <li><p>Added ability to generate a manifest file from your local directory structure.</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># from the command line</span>
@@ -695,8 +718,8 @@ <h3>Highlights<a class="headerlink" href="#id24" title="Permalink to this headli
 will be changed to <cite>–parent-id</cite>.</p></li>
 </ul>
 </section>
-<section id="id25">
-<h3>Bug Fixes<a class="headerlink" href="#id25" title="Permalink to this headline"></a></h3>
+<section id="id28">
+<h3>Bug Fixes<a class="headerlink" href="#id28" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-669">SYNPY-669</a>] -
 Signing of Synapse authentication header does not correctly URL encode the URL path</p></li>
@@ -710,8 +733,8 @@ <h3>Bug Fixes<a class="headerlink" href="#id25" title="Permalink to this headlin
 datetimes in a Pandas dataframe are not properly stored to Synapse</p></li>
 </ul>
 </section>
-<section id="id26">
-<h3>Stories<a class="headerlink" href="#id26" title="Permalink to this headline"></a></h3>
+<section id="id29">
+<h3>Stories<a class="headerlink" href="#id29" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-726">SYNPY-726</a>] -
 mirror local folder structure for bulk upload</p></li>
@@ -723,8 +746,8 @@ <h3>Stories<a class="headerlink" href="#id26" title="Permalink to this headline"
 Support for Quick Summary Statistics on CSV and TSV files</p></li>
 </ul>
 </section>
-<section id="id27">
-<h3>Tasks<a class="headerlink" href="#id27" title="Permalink to this headline"></a></h3>
+<section id="id30">
+<h3>Tasks<a class="headerlink" href="#id30" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1169">SYNPY-1169</a>] -
 Integration tests failures in develop branch against stack-371</p></li>
@@ -737,10 +760,10 @@ <h3>Tasks<a class="headerlink" href="#id27" title="Permalink to this headline">
 </ul>
 </section>
 </section>
-<section id="id28">
-<h2>2.4.0 (2021-07-08)<a class="headerlink" href="#id28" title="Permalink to this headline"></a></h2>
-<section id="id29">
-<h3>Highlights<a class="headerlink" href="#id29" title="Permalink to this headline"></a></h3>
+<section id="id31">
+<h2>2.4.0 (2021-07-08)<a class="headerlink" href="#id31" title="Permalink to this headline"></a></h2>
+<section id="id32">
+<h3>Highlights<a class="headerlink" href="#id32" title="Permalink to this headline"></a></h3>
 <ul>
 <li><p>Added ability to authenticate from a <code class="code docutils literal notranslate"><span class="pre">SYNAPSE_AUTH_TOKEN</span></code> environment variable set with a valid <a class="reference external" href="https://help.synapse.org/docs/Managing-Your-Account.2055405596.html#ManagingYourAccount-PersonalAccessTokens">personal access token</a>.</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># e.g. set environment variable prior to invoking a Synapse command or running a program that uses synapseclient</span>
@@ -770,8 +793,8 @@ <h3>Highlights<a class="headerlink" href="#id29" title="Permalink to this headli
 reset progress bar.</p></li>
 </ul>
 </section>
-<section id="id30">
-<h3>Bug Fixes<a class="headerlink" href="#id30" title="Permalink to this headline"></a></h3>
+<section id="id33">
+<h3>Bug Fixes<a class="headerlink" href="#id33" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-198">SYNPY-198</a>] -
 get: Unmet access requirement should not raise error if entity not downloadable</p></li>
@@ -816,8 +839,8 @@ <h3>Improvements<a class="headerlink" href="#improvements" title="Permalink to t
 When using boto3 client to upload a file, also include ACL to give bucket owner full access</p></li>
 </ul>
 </section>
-<section id="id31">
-<h3>Tasks<a class="headerlink" href="#id31" title="Permalink to this headline"></a></h3>
+<section id="id34">
+<h3>Tasks<a class="headerlink" href="#id34" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-948">SYNPY-948</a>] -
 command line client set-annotations does not return proper error code when there’s a problem</p></li>
@@ -828,10 +851,10 @@ <h3>Tasks<a class="headerlink" href="#id31" title="Permalink to this headline">
 </ul>
 </section>
 </section>
-<section id="id32">
-<h2>2.3.1 (2021-04-13)<a class="headerlink" href="#id32" title="Permalink to this headline"></a></h2>
-<section id="id33">
-<h3>Highlights<a class="headerlink" href="#id33" title="Permalink to this headline"></a></h3>
+<section id="id35">
+<h2>2.3.1 (2021-04-13)<a class="headerlink" href="#id35" title="Permalink to this headline"></a></h2>
+<section id="id36">
+<h3>Highlights<a class="headerlink" href="#id36" title="Permalink to this headline"></a></h3>
 <ul>
 <li><p>Entities can be annotated with boolean datatypes, for example:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">file</span> <span class="o">=</span> <span class="n">synapseclient</span><span class="o">.</span><span class="n">File</span><span class="p">(</span><span class="s1">&#39;/path/to/file&#39;</span><span class="p">,</span> <span class="n">parentId</span><span class="o">=</span><span class="s1">&#39;syn123&#39;</span><span class="p">,</span> <span class="n">synapse_is_great</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
@@ -842,8 +865,8 @@ <h3>Highlights<a class="headerlink" href="#id33" title="Permalink to this headli
 <li><p>synapseclient is additionally packaged as a Python wheel.</p></li>
 </ul>
 </section>
-<section id="id34">
-<h3>Bug Fixes<a class="headerlink" href="#id34" title="Permalink to this headline"></a></h3>
+<section id="id37">
+<h3>Bug Fixes<a class="headerlink" href="#id37" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-829">SYNPY-829</a>] -
 syn.store always updates annotations</p></li>
@@ -851,8 +874,8 @@ <h3>Bug Fixes<a class="headerlink" href="#id34" title="Permalink to this headlin
 If versionComment is left blank, previous version comment populates</p></li>
 </ul>
 </section>
-<section id="id35">
-<h3>Improvements<a class="headerlink" href="#id35" title="Permalink to this headline"></a></h3>
+<section id="id38">
+<h3>Improvements<a class="headerlink" href="#id38" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1120">SYNPY-1120</a>] -
 Build wheel distributions</p></li>
@@ -861,10 +884,10 @@ <h3>Improvements<a class="headerlink" href="#id35" title="Permalink to this head
 </ul>
 </section>
 </section>
-<section id="id36">
-<h2>2.3.0 (2021-03-03)<a class="headerlink" href="#id36" title="Permalink to this headline"></a></h2>
-<section id="id37">
-<h3>Highlights<a class="headerlink" href="#id37" title="Permalink to this headline"></a></h3>
+<section id="id39">
+<h2>2.3.0 (2021-03-03)<a class="headerlink" href="#id39" title="Permalink to this headline"></a></h2>
+<section id="id40">
+<h3>Highlights<a class="headerlink" href="#id40" title="Permalink to this headline"></a></h3>
 <ul>
 <li><p>The <a class="reference external" href="synapseutils.html#synapseutils.migrate_functions.index_files_for_migration">index_files_for_migration</a> and
 <a class="reference external" href="synapseutils.html#synapseutils.migrate_functions.migrate_indexed_files">migrate_indexed_files</a> functions are added
@@ -895,8 +918,8 @@ <h3>Highlights<a class="headerlink" href="#id37" title="Permalink to this headli
 <li><p>This version has been tested with Python 3.9.</p></li>
 </ul>
 </section>
-<section id="id38">
-<h3>Bug Fixes<a class="headerlink" href="#id38" title="Permalink to this headline"></a></h3>
+<section id="id41">
+<h3>Bug Fixes<a class="headerlink" href="#id41" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1039">SYNPY-1039</a>] -
 tableQuery asDataFrame() results with TYPE_LIST columns should be lists and not literal strings</p></li>
@@ -923,8 +946,8 @@ <h3>New Features<a class="headerlink" href="#new-features" title="Permalink to t
 Add function to get user certification status</p></li>
 </ul>
 </section>
-<section id="id39">
-<h3>Improvements<a class="headerlink" href="#id39" title="Permalink to this headline"></a></h3>
+<section id="id42">
+<h3>Improvements<a class="headerlink" href="#id42" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-885">SYNPY-885</a>] -
 Public interface to customize CACHE_ROOT_DIR</p></li>
@@ -937,17 +960,17 @@ <h3>Improvements<a class="headerlink" href="#id39" title="Permalink to this head
 </ul>
 </section>
 </section>
-<section id="id40">
-<h2>2.2.2 (2020-10-18)<a class="headerlink" href="#id40" title="Permalink to this headline"></a></h2>
-<section id="id41">
-<h3>Highlights<a class="headerlink" href="#id41" title="Permalink to this headline"></a></h3>
+<section id="id43">
+<h2>2.2.2 (2020-10-18)<a class="headerlink" href="#id43" title="Permalink to this headline"></a></h2>
+<section id="id44">
+<h3>Highlights<a class="headerlink" href="#id44" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>This version addresses an issue with downloads being retried unsuccessfully after encountering certain types of errors.</p></li>
 <li><p>A <a class="reference external" href="index.html#synapseclient.Synapse.create_snapshot_version">create_snapshot_version</a> function is added for making table and view snapshots.</p></li>
 </ul>
 </section>
-<section id="id42">
-<h3>Bug Fixes<a class="headerlink" href="#id42" title="Permalink to this headline"></a></h3>
+<section id="id45">
+<h3>Bug Fixes<a class="headerlink" href="#id45" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1096">SYNPY-1096</a>] -
 Fix link to Synapse on PyPI</p></li>
@@ -955,15 +978,15 @@ <h3>Bug Fixes<a class="headerlink" href="#id42" title="Permalink to this headlin
 downloaded files are reset when disk space exhausted</p></li>
 </ul>
 </section>
-<section id="id43">
-<h3>New Features<a class="headerlink" href="#id43" title="Permalink to this headline"></a></h3>
+<section id="id46">
+<h3>New Features<a class="headerlink" href="#id46" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1041">SYNPY-1041</a>] -
 Snapshot feature and programmatic clients</p></li>
 </ul>
 </section>
-<section id="id44">
-<h3>Improvements<a class="headerlink" href="#id44" title="Permalink to this headline"></a></h3>
+<section id="id47">
+<h3>Improvements<a class="headerlink" href="#id47" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1063">SYNPY-1063</a>] -
 Consolidate builds to GitHub Actions</p></li>
@@ -972,10 +995,10 @@ <h3>Improvements<a class="headerlink" href="#id44" title="Permalink to this head
 </ul>
 </section>
 </section>
-<section id="id45">
-<h2>2.2.0 (2020-08-31)<a class="headerlink" href="#id45" title="Permalink to this headline"></a></h2>
-<section id="id46">
-<h3>Highlights<a class="headerlink" href="#id46" title="Permalink to this headline"></a></h3>
+<section id="id48">
+<h2>2.2.0 (2020-08-31)<a class="headerlink" href="#id48" title="Permalink to this headline"></a></h2>
+<section id="id49">
+<h3>Highlights<a class="headerlink" href="#id49" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>Files that are part of
 <a class="reference external" href="https://python-docs.synapse.org/build/html/synapseutils.html#synapseutils.sync.syncFromSynapse">syncFromSynapse</a>
@@ -987,15 +1010,15 @@ <h3>Highlights<a class="headerlink" href="#id46" title="Permalink to this headli
 <li><p>Users can now pass their API key to <cite>synapse login</cite> in place of a password.</p></li>
 </ul>
 </section>
-<section id="id47">
-<h3>Bug Fixes<a class="headerlink" href="#id47" title="Permalink to this headline"></a></h3>
+<section id="id50">
+<h3>Bug Fixes<a class="headerlink" href="#id50" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1082">SYNPY-1082</a>] -
 Downloading entity linked to URL fails: module ‘urllib.parse’ has no attribute ‘urlretrieve’</p></li>
 </ul>
 </section>
-<section id="id48">
-<h3>Improvements<a class="headerlink" href="#id48" title="Permalink to this headline"></a></h3>
+<section id="id51">
+<h3>Improvements<a class="headerlink" href="#id51" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1072">SYNPY-1072</a>] -
 Improve throughput of multiple small file transfers</p></li>
@@ -1011,8 +1034,8 @@ <h3>Improvements<a class="headerlink" href="#id48" title="Permalink to this head
 Command line client does not support apikey</p></li>
 </ul>
 </section>
-<section id="id49">
-<h3>Tasks<a class="headerlink" href="#id49" title="Permalink to this headline"></a></h3>
+<section id="id52">
+<h3>Tasks<a class="headerlink" href="#id52" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1080">SYNPY-1080</a>] -
 Remove Versionable from SchemaBase</p></li>
@@ -1023,10 +1046,10 @@ <h3>Tasks<a class="headerlink" href="#id49" title="Permalink to this headline">
 </ul>
 </section>
 </section>
-<section id="id50">
-<h2>2.1.1 (2020-07-10)<a class="headerlink" href="#id50" title="Permalink to this headline"></a></h2>
-<section id="id51">
-<h3>Highlights<a class="headerlink" href="#id51" title="Permalink to this headline"></a></h3>
+<section id="id53">
+<h2>2.1.1 (2020-07-10)<a class="headerlink" href="#id53" title="Permalink to this headline"></a></h2>
+<section id="id54">
+<h3>Highlights<a class="headerlink" href="#id54" title="Permalink to this headline"></a></h3>
 <ul>
 <li><p>This version includes a performance improvement for
 <a class="reference external" href="https://python-docs.synapse.org/build/html/synapseutils.html#synapseutils.sync.syncFromSynapse">syncFromSynapse</a>
@@ -1045,8 +1068,8 @@ <h3>Highlights<a class="headerlink" href="#id51" title="Permalink to this headli
 </li>
 </ul>
 </section>
-<section id="id52">
-<h3>Bug Fixes<a class="headerlink" href="#id52" title="Permalink to this headline"></a></h3>
+<section id="id55">
+<h3>Bug Fixes<a class="headerlink" href="#id55" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1075">SYNPY-1075</a>] -
 Error in Python test (submission annotations)</p></li>
@@ -1054,8 +1077,8 @@ <h3>Bug Fixes<a class="headerlink" href="#id52" title="Permalink to this headlin
 Upgrade/fix Pandas dependency</p></li>
 </ul>
 </section>
-<section id="id53">
-<h3>Improvements<a class="headerlink" href="#id53" title="Permalink to this headline"></a></h3>
+<section id="id56">
+<h3>Improvements<a class="headerlink" href="#id56" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1070">SYNPY-1070</a>] -
 Add support for submission views</p></li>
@@ -1064,10 +1087,10 @@ <h3>Improvements<a class="headerlink" href="#id53" title="Permalink to this head
 </ul>
 </section>
 </section>
-<section id="id54">
-<h2>2.1.0 (2020-06-16)<a class="headerlink" href="#id54" title="Permalink to this headline"></a></h2>
-<section id="id55">
-<h3>Highlights<a class="headerlink" href="#id55" title="Permalink to this headline"></a></h3>
+<section id="id57">
+<h2>2.1.0 (2020-06-16)<a class="headerlink" href="#id57" title="Permalink to this headline"></a></h2>
+<section id="id58">
+<h3>Highlights<a class="headerlink" href="#id58" title="Permalink to this headline"></a></h3>
 <ul>
 <li><p>A <code class="code docutils literal notranslate"><span class="pre">max_threads</span></code> property of the Synapse object has been added to customize the number of concurrent threads
 that will be used during file transfers.</p>
@@ -1110,8 +1133,8 @@ <h3>Highlights<a class="headerlink" href="#id55" title="Permalink to this headli
 </ul>
 <p>A full list of issues addressed in this release are below.</p>
 </section>
-<section id="id56">
-<h3>Bug Fixes<a class="headerlink" href="#id56" title="Permalink to this headline"></a></h3>
+<section id="id59">
+<h3>Bug Fixes<a class="headerlink" href="#id59" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-913">SYNPY-913</a>] -
 Travis Build badge for develop branch is pointing to pull request</p></li>
@@ -1123,8 +1146,8 @@ <h3>Bug Fixes<a class="headerlink" href="#id56" title="Permalink to this headlin
 syn.getSubmissions fails due to new Annotation class in v2.1.0-rc</p></li>
 </ul>
 </section>
-<section id="id57">
-<h3>Improvements<a class="headerlink" href="#id57" title="Permalink to this headline"></a></h3>
+<section id="id60">
+<h3>Improvements<a class="headerlink" href="#id60" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1029">SYNPY-1036</a>] -
 Make upload speeds comparable to those of the AWS S3 CLI</p></li>
@@ -1132,19 +1155,19 @@ <h3>Improvements<a class="headerlink" href="#id57" title="Permalink to this head
 Expose STS-related APIs</p></li>
 </ul>
 </section>
-<section id="id58">
-<h3>Tasks<a class="headerlink" href="#id58" title="Permalink to this headline"></a></h3>
+<section id="id61">
+<h3>Tasks<a class="headerlink" href="#id61" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-1059">SYNPY-1059</a>] -
 Use collections.abc instead of collections</p></li>
 </ul>
 </section>
 </section>
-<section id="id59">
-<h2>2.0.0 (2020-03-23)<a class="headerlink" href="#id59" title="Permalink to this headline"></a></h2>
+<section id="id62">
+<h2>2.0.0 (2020-03-23)<a class="headerlink" href="#id62" title="Permalink to this headline"></a></h2>
 <p><strong>Python 2 is no longer supported as of this release.</strong> This release requires Python 3.6+.</p>
-<section id="id60">
-<h3>Highlights:<a class="headerlink" href="#id60" title="Permalink to this headline"></a></h3>
+<section id="id63">
+<h3>Highlights:<a class="headerlink" href="#id63" title="Permalink to this headline"></a></h3>
 <ul>
 <li><p>Multi-threaded download of files from Synapse can be enabled by setting <code class="code docutils literal notranslate"><span class="pre">syn.multi_threaded</span></code> to <code class="code docutils literal notranslate"><span class="pre">True</span></code> on a
 <code class="code docutils literal notranslate"><span class="pre">synapseclient.Synapse</span></code> object. This will become the default implementation in the future,
@@ -1186,8 +1209,8 @@ <h3>Bugs Fixes<a class="headerlink" href="#bugs-fixes" title="Permalink to this
 - Support new columnTypes defined in backend</p></li>
 </ul>
 </section>
-<section id="id61">
-<h3>Tasks<a class="headerlink" href="#id61" title="Permalink to this headline"></a></h3>
+<section id="id64">
+<h3>Tasks<a class="headerlink" href="#id64" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-999">SYNPY-999</a>] -
 Remove unsafe copy functions from client</p></li>
@@ -1196,8 +1219,8 @@ <h3>Tasks<a class="headerlink" href="#id61" title="Permalink to this headline">
 has DOWNLOAD access</p></li>
 </ul>
 </section>
-<section id="id62">
-<h3>Improvements<a class="headerlink" href="#id62" title="Permalink to this headline"></a></h3>
+<section id="id65">
+<h3>Improvements<a class="headerlink" href="#id65" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-389">SYNPY-389</a>] -
 submission of Docker repository</p></li>
@@ -1219,10 +1242,10 @@ <h3>Improvements<a class="headerlink" href="#id62" title="Permalink to this head
 </ul>
 </section>
 </section>
-<section id="id63">
-<h2>1.9.4 (2019-06-28)<a class="headerlink" href="#id63" title="Permalink to this headline"></a></h2>
-<section id="id64">
-<h3>Bug Fixes<a class="headerlink" href="#id64" title="Permalink to this headline"></a></h3>
+<section id="id66">
+<h2>1.9.4 (2019-06-28)<a class="headerlink" href="#id66" title="Permalink to this headline"></a></h2>
+<section id="id67">
+<h3>Bug Fixes<a class="headerlink" href="#id67" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-881">SYNPY-881</a>] -
 Synu.copy fails when copying a file with READ permissions</p></li>
@@ -1236,15 +1259,15 @@ <h3>Bug Fixes<a class="headerlink" href="#id64" title="Permalink to this headlin
 - Synu.copy shouldn’t copy any files with access restrictions</p></li>
 </ul>
 </section>
-<section id="id65">
-<h3>New Features<a class="headerlink" href="#id65" title="Permalink to this headline"></a></h3>
+<section id="id68">
+<h3>New Features<a class="headerlink" href="#id68" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-851">SYNPY-851</a>] -
 invite user or list of users to a team</p></li>
 </ul>
 </section>
-<section id="id66">
-<h3>Improvements<a class="headerlink" href="#id66" title="Permalink to this headline"></a></h3>
+<section id="id69">
+<h3>Improvements<a class="headerlink" href="#id69" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-608">SYNPY-608</a>] -
 Add how to contribute md to github project</p></li>
@@ -1262,10 +1285,10 @@ <h3>Improvements<a class="headerlink" href="#id66" title="Permalink to this head
 </ul>
 </section>
 </section>
-<section id="id67">
-<h2>1.9.3 (2019-06-28)<a class="headerlink" href="#id67" title="Permalink to this headline"></a></h2>
-<section id="id68">
-<h3>Bug Fixes<a class="headerlink" href="#id68" title="Permalink to this headline"></a></h3>
+<section id="id70">
+<h2>1.9.3 (2019-06-28)<a class="headerlink" href="#id70" title="Permalink to this headline"></a></h2>
+<section id="id71">
+<h3>Bug Fixes<a class="headerlink" href="#id71" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-993">SYNPY-993</a>] -
 Fix <cite>sendMessage</cite> function</p></li>
@@ -1274,8 +1297,8 @@ <h3>Bug Fixes<a class="headerlink" href="#id68" title="Permalink to this headlin
 </ul>
 </section>
 </section>
-<section id="id69">
-<h2>1.9.2 (2019-02-15)<a class="headerlink" href="#id69" title="Permalink to this headline"></a></h2>
+<section id="id72">
+<h2>1.9.2 (2019-02-15)<a class="headerlink" href="#id72" title="Permalink to this headline"></a></h2>
 <p>In version 1.9.2, we improved Views’ usability by exposing <cite>set_entity_types()</cite> function to change the entity types that will show up in a View:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">synapseclient</span>
 <span class="kn">from</span> <span class="nn">synapseclient.table</span> <span class="kn">import</span> <span class="n">EntityViewType</span>
@@ -1293,8 +1316,8 @@ <h3>Features<a class="headerlink" href="#features" title="Permalink to this head
 Expose a way to update entity types in a view using EntityViewType</p></li>
 </ul>
 </section>
-<section id="id70">
-<h3>Bug Fixes<a class="headerlink" href="#id70" title="Permalink to this headline"></a></h3>
+<section id="id73">
+<h3>Bug Fixes<a class="headerlink" href="#id73" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-855">SYNPY-855</a>] -
 Single thread uploading fails in Lambda python3.6 environment</p></li>
@@ -1304,8 +1327,8 @@ <h3>Bug Fixes<a class="headerlink" href="#id70" title="Permalink to this headlin
 Project View turned into File View after using syndccutils template</p></li>
 </ul>
 </section>
-<section id="id71">
-<h3>Tasks<a class="headerlink" href="#id71" title="Permalink to this headline"></a></h3>
+<section id="id74">
+<h3>Tasks<a class="headerlink" href="#id74" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-790">SYNPY-790</a>] -
 Pin to a fixed version of the request package</p></li>
@@ -1313,8 +1336,8 @@ <h3>Tasks<a class="headerlink" href="#id71" title="Permalink to this headline">
 Update Synapse logo in Python docs :)</p></li>
 </ul>
 </section>
-<section id="id72">
-<h3>Improvements<a class="headerlink" href="#id72" title="Permalink to this headline"></a></h3>
+<section id="id75">
+<h3>Improvements<a class="headerlink" href="#id75" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-783">SYNPY-783</a>] -
 typos in comments and in stdout</p></li>
@@ -1327,15 +1350,15 @@ <h3>Improvements<a class="headerlink" href="#id72" title="Permalink to this head
 </ul>
 </section>
 </section>
-<section id="id73">
-<h2>1.9.1 (2019-01-20)<a class="headerlink" href="#id73" title="Permalink to this headline"></a></h2>
+<section id="id76">
+<h2>1.9.1 (2019-01-20)<a class="headerlink" href="#id76" title="Permalink to this headline"></a></h2>
 <p>In version 1.9.1, we fix various bugs and added two new features:</p>
 <ul class="simple">
 <li><p>Python 3.7 is supported.</p></li>
 <li><p>Deprecation warnings are visible by default.</p></li>
 </ul>
-<section id="id74">
-<h3>Features<a class="headerlink" href="#id74" title="Permalink to this headline"></a></h3>
+<section id="id77">
+<h3>Features<a class="headerlink" href="#id77" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-802">SYNPY-802</a>] -
 Support Python 3.7</p></li>
@@ -1343,8 +1366,8 @@ <h3>Features<a class="headerlink" href="#id74" title="Permalink to this headline
 Add deprecation warning that isn’t filtered by Python</p></li>
 </ul>
 </section>
-<section id="id75">
-<h3>Bug Fixes<a class="headerlink" href="#id75" title="Permalink to this headline"></a></h3>
+<section id="id78">
+<h3>Bug Fixes<a class="headerlink" href="#id78" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-454">SYNPY-454</a>] -
 Some integration tests do not clean up after themselves</p></li>
@@ -1367,8 +1390,8 @@ <h3>Bug Fixes<a class="headerlink" href="#id75" title="Permalink to this headlin
 error if password stored in config file contains a ‘%’</p></li>
 </ul>
 </section>
-<section id="id76">
-<h3>Tasks<a class="headerlink" href="#id76" title="Permalink to this headline"></a></h3>
+<section id="id79">
+<h3>Tasks<a class="headerlink" href="#id79" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-491">SYNPY-491</a>] -
 Figure out custom release note fitlers</p></li>
@@ -1390,8 +1413,8 @@ <h3>Tasks<a class="headerlink" href="#id76" title="Permalink to this headline">
 consolidate integration testing to platform dev account</p></li>
 </ul>
 </section>
-<section id="id77">
-<h3>Improvements<a class="headerlink" href="#id77" title="Permalink to this headline"></a></h3>
+<section id="id80">
+<h3>Improvements<a class="headerlink" href="#id80" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p>[<a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-473">SYNPY-473</a>] -
 Change syn.list to no longer use deprecated function chunkedQuery</p></li>
@@ -1422,8 +1445,8 @@ <h3>Improvements<a class="headerlink" href="#id77" title="Permalink to this head
 </ul>
 </section>
 </section>
-<section id="id78">
-<h2>1.9.0 (2018-09-28)<a class="headerlink" href="#id78" title="Permalink to this headline"></a></h2>
+<section id="id81">
+<h2>1.9.0 (2018-09-28)<a class="headerlink" href="#id81" title="Permalink to this headline"></a></h2>
 <p>In version 1.9.0, we deprecated and removed <cite>query()</cite> and <cite>chunkedQuery()</cite>. These functions used the old query services which does not perform well. To query for entities filter by annotations, please use <cite>EntityViewSchema</cite>.</p>
 <p>We also deprecated the following functions and will remove them in Synapse Python client version 2.0.
 In the <cite>Activity</cite> object:</p>
@@ -1445,14 +1468,14 @@ <h2>1.9.0 (2018-09-28)<a class="headerlink" href="#id78" title="Permalink to thi
 <li><p><cite>downloadTableFile()</cite></p></li>
 </ul>
 <p>Please see our documentation for more details on how to migrate your code away from these functions.</p>
-<section id="id79">
-<h3>Features<a class="headerlink" href="#id79" title="Permalink to this headline"></a></h3>
+<section id="id82">
+<h3>Features<a class="headerlink" href="#id82" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-806">SYNPY-806</a> - Support Folders and Tables in View</p></li>
 </ul>
 </section>
-<section id="id80">
-<h3>Bug Fixes<a class="headerlink" href="#id80" title="Permalink to this headline"></a></h3>
+<section id="id83">
+<h3>Bug Fixes<a class="headerlink" href="#id83" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-195">SYNPY-195</a> - Dangerous exception handling</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-261">SYNPY-261</a> - error downloading data from synapse (python client)</p></li>
@@ -1461,16 +1484,16 @@ <h3>Bug Fixes<a class="headerlink" href="#id80" title="Permalink to this headlin
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-819">SYNPY-819</a> - command-line clients need to be updated to replace the EntityView ‘viewType’ with ‘viewTypeMask’</p></li>
 </ul>
 </section>
-<section id="id81">
-<h3>Tasks<a class="headerlink" href="#id81" title="Permalink to this headline"></a></h3>
+<section id="id84">
+<h3>Tasks<a class="headerlink" href="#id84" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-759">SYNPY-759</a> - Look for all functions that are documented as “Deprecated” and apply the deprecation syntax</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-812">SYNPY-812</a> - Add Github issue template</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-824">SYNPY-824</a> - Remove the deprecated function query() and chunkedQuery()</p></li>
 </ul>
 </section>
-<section id="id82">
-<h3>Improvements<a class="headerlink" href="#id82" title="Permalink to this headline"></a></h3>
+<section id="id85">
+<h3>Improvements<a class="headerlink" href="#id85" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-583">SYNPY-583</a> - Better error message for create Link object</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-810">SYNPY-810</a> - simplify docs for deleting rows</p></li>
@@ -1480,8 +1503,8 @@ <h3>Improvements<a class="headerlink" href="#id82" title="Permalink to this head
 </ul>
 </section>
 </section>
-<section id="id83">
-<h2>1.8.2 (2018-08-17)<a class="headerlink" href="#id83" title="Permalink to this headline"></a></h2>
+<section id="id86">
+<h2>1.8.2 (2018-08-17)<a class="headerlink" href="#id86" title="Permalink to this headline"></a></h2>
 <p>In this release, we have been performed some house-keeping on the code base. The two major changes are:</p>
 <blockquote>
 <div><ul>
@@ -1508,8 +1531,8 @@ <h2>1.8.2 (2018-08-17)<a class="headerlink" href="#id83" title="Permalink to thi
 </li>
 </ul>
 </div></blockquote>
-<section id="id84">
-<h3>Bug Fixes<a class="headerlink" href="#id84" title="Permalink to this headline"></a></h3>
+<section id="id87">
+<h3>Bug Fixes<a class="headerlink" href="#id87" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-535">SYNPY-535</a> - Synapse Table update: Connection Reset</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-603">SYNPY-603</a> - Python client and synapser cannot handle table column type LINK</p></li>
@@ -1523,42 +1546,42 @@ <h3>Bug Fixes<a class="headerlink" href="#id84" title="Permalink to this headlin
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-795">SYNPY-795</a> - Not recognizable column in query result</p></li>
 </ul>
 </section>
-<section id="id85">
-<h3>Features<a class="headerlink" href="#id85" title="Permalink to this headline"></a></h3>
+<section id="id88">
+<h3>Features<a class="headerlink" href="#id88" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-582">SYNPY-582</a> - move file or folder in the client</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-788">SYNPY-788</a> - Add option to use syn.store() without exercising multithreads</p></li>
 </ul>
 </section>
-<section id="id86">
-<h3>Tasks<a class="headerlink" href="#id86" title="Permalink to this headline"></a></h3>
+<section id="id89">
+<h3>Tasks<a class="headerlink" href="#id89" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-729">SYNPY-729</a> - Deprecate query() and chunkedQuery()</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-797">SYNPY-797</a> - Check Python client code base on using PLFM object model</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-798">SYNPY-798</a> - Using github.io to host documentation</p></li>
 </ul>
 </section>
-<section id="id87">
-<h3>Improvements<a class="headerlink" href="#id87" title="Permalink to this headline"></a></h3>
+<section id="id90">
+<h3>Improvements<a class="headerlink" href="#id90" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-646">SYNPY-646</a> - Error output of synGet is non-informative</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-743">SYNPY-743</a> - lint the entire python client code base</p></li>
 </ul>
 </section>
 </section>
-<section id="id88">
-<h2>1.8.1 (2018-05-17)<a class="headerlink" href="#id88" title="Permalink to this headline"></a></h2>
+<section id="id91">
+<h2>1.8.1 (2018-05-17)<a class="headerlink" href="#id91" title="Permalink to this headline"></a></h2>
 <p>This release is a hotfix for a bug.
 Please refer to 1.8.0 release notes for information about additional changes.</p>
-<section id="id89">
-<h3>Bug Fixes<a class="headerlink" href="#id89" title="Permalink to this headline"></a></h3>
+<section id="id92">
+<h3>Bug Fixes<a class="headerlink" href="#id92" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-706">SYNPY-706</a> - syn.username can cause attribute not found if user not logged in</p></li>
 </ul>
 </section>
 </section>
-<section id="id90">
-<h2>1.8.0 (2018-05-07)<a class="headerlink" href="#id90" title="Permalink to this headline"></a></h2>
+<section id="id93">
+<h2>1.8.0 (2018-05-07)<a class="headerlink" href="#id93" title="Permalink to this headline"></a></h2>
 <p>This release has 2 major changes:</p>
 <ul class="simple">
 <li><p>The client will no longer store your saved credentials in your synapse cache (<cite>~/synapseCache/.session</cite>). The python client now relies on <a class="reference external" href="https://pypi.org/project/keyring/">keyring</a> to handle credential storage of your Synapse credentials.</p></li>
@@ -1566,8 +1589,8 @@ <h2>1.8.0 (2018-05-07)<a class="headerlink" href="#id90" title="Permalink to thi
 </ul>
 <p>The remaining changes are bug fixes and cleanup of test code.</p>
 <p>Below are the full list of issues addressed by this release:</p>
-<section id="id91">
-<h3>Bug Fixes<a class="headerlink" href="#id91" title="Permalink to this headline"></a></h3>
+<section id="id94">
+<h3>Bug Fixes<a class="headerlink" href="#id94" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-654">SYNPY-654</a> - syn.getColumns does not terminate</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-658">SYNPY-658</a> - Security vunerability on clusters</p></li>
@@ -1576,28 +1599,28 @@ <h3>Bug Fixes<a class="headerlink" href="#id91" title="Permalink to this headlin
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-693">SYNPY-693</a> - synapseutils.sync.generateManifest() UnicodeEncodingError in python 2</p></li>
 </ul>
 </section>
-<section id="id92">
-<h3>Tasks<a class="headerlink" href="#id92" title="Permalink to this headline"></a></h3>
+<section id="id95">
+<h3>Tasks<a class="headerlink" href="#id95" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-617">SYNPY-617</a> - Remove use of deprecated service to delete table rows</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-673">SYNPY-673</a> - Fix Integration Tests being run on Appveyor</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-683">SYNPY-683</a> - Clean up print()s used in unit/integration tests</p></li>
 </ul>
 </section>
-<section id="id93">
-<h3>Improvements<a class="headerlink" href="#id93" title="Permalink to this headline"></a></h3>
+<section id="id96">
+<h3>Improvements<a class="headerlink" href="#id96" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-408">SYNPY-408</a> - Add bettter error messages when /filehandle/batch fails.</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-647">SYNPY-647</a> - Use connection pooling for Python client’s requests</p></li>
 </ul>
 </section>
 </section>
-<section id="id94">
-<h2>1.7.5 (2018-01-31)<a class="headerlink" href="#id94" title="Permalink to this headline"></a></h2>
+<section id="id97">
+<h2>1.7.5 (2018-01-31)<a class="headerlink" href="#id97" title="Permalink to this headline"></a></h2>
 <p>v1.7.4 release was broken for new users that installed from pip. v1.7.5 has the same changes as v1.7.4 but fixes the pip installation.</p>
 </section>
-<section id="id95">
-<h2>1.7.4 (2018-01-29)<a class="headerlink" href="#id95" title="Permalink to this headline"></a></h2>
+<section id="id98">
+<h2>1.7.4 (2018-01-29)<a class="headerlink" href="#id98" title="Permalink to this headline"></a></h2>
 <dl class="simple">
 <dt>This release mostly includes bugfixes and improvements for various Table classes:</dt><dd><ul class="simple">
 <li><p>Fixed bug where you couldn’t store a table converted to a <cite>pandas.Dataframe</cite> if it had a INTEGER column with some missing values.</p></li>
@@ -1612,15 +1635,15 @@ <h2>1.7.4 (2018-01-29)<a class="headerlink" href="#id95" title="Permalink to thi
 </dd>
 </dl>
 <p>Below are the full list of issues addressed by this release:</p>
-<section id="id96">
-<h3>Features<a class="headerlink" href="#id96" title="Permalink to this headline"></a></h3>
+<section id="id99">
+<h3>Features<a class="headerlink" href="#id99" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-506">SYNPY-506</a> - need convenience function for /entity/child</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-517">SYNPY-517</a> - sync command line</p></li>
 </ul>
 </section>
-<section id="id97">
-<h3>Improvements<a class="headerlink" href="#id97" title="Permalink to this headline"></a></h3>
+<section id="id100">
+<h3>Improvements<a class="headerlink" href="#id100" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-267">SYNPY-267</a> - Update Synapse tables for integer types</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-304">SYNPY-304</a> - Table objects should implement len()</p></li>
@@ -1633,8 +1656,8 @@ <h3>Improvements<a class="headerlink" href="#id97" title="Permalink to this head
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-539">SYNPY-539</a> - When creating table Schemas, enforce a limit on the number of columns that can be created.</p></li>
 </ul>
 </section>
-<section id="id98">
-<h3>Bug Fixes<a class="headerlink" href="#id98" title="Permalink to this headline"></a></h3>
+<section id="id101">
+<h3>Bug Fixes<a class="headerlink" href="#id101" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-235">SYNPY-235</a> - can’t print Row objects with dates in them</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-272">SYNPY-272</a> - bug syn.storing rowsets containing Python datetime objects</p></li>
@@ -1651,16 +1674,16 @@ <h3>Bug Fixes<a class="headerlink" href="#id98" title="Permalink to this headlin
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-605">SYNPY-605</a> - Update documentation for getUserProfile to include information about refreshing and memoization</p></li>
 </ul>
 </section>
-<section id="id99">
-<h3>Tasks<a class="headerlink" href="#id99" title="Permalink to this headline"></a></h3>
+<section id="id102">
+<h3>Tasks<a class="headerlink" href="#id102" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-451">SYNPY-451</a> - Add limit and offset for accessApproval and accessRequirement API calls and remove 0x400 flag default when calling GET /entity/{id}/bundle</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-546">SYNPY-546</a> - Change warning message when user does not DOWNLOAD permissions.</p></li>
 </ul>
 </section>
 </section>
-<section id="id100">
-<h2>1.7.3 (2017-12-08)<a class="headerlink" href="#id100" title="Permalink to this headline"></a></h2>
+<section id="id103">
+<h2>1.7.3 (2017-12-08)<a class="headerlink" href="#id103" title="Permalink to this headline"></a></h2>
 <p>Release 1.7.3 introduces fixes and quality of life changes to Tables and synapseutils:</p>
 <ul>
 <li><p>Changes to Tables:</p>
@@ -1682,8 +1705,8 @@ <h2>1.7.3 (2017-12-08)<a class="headerlink" href="#id100" title="Permalink to th
 </ul>
 <p>We also added improved debug logging and use Python’s builtin <cite>logging</cite> module instead of printing directly to <cite>sys.stderr</cite></p>
 <p>Below are the full list of issues addressed by this release:</p>
-<section id="id101">
-<h3>Bug Fixes<a class="headerlink" href="#id101" title="Permalink to this headline"></a></h3>
+<section id="id104">
+<h3>Bug Fixes<a class="headerlink" href="#id104" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-419">SYNPY-419</a> - support object store from client</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-499">SYNPY-499</a> - metadata manifest file name spelled wrong</p></li>
@@ -1694,8 +1717,8 @@ <h3>Bug Fixes<a class="headerlink" href="#id101" title="Permalink to this headli
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-572">SYNPY-572</a> - Users should only be prompted for updates if the first or second part of the version number is changed.</p></li>
 </ul>
 </section>
-<section id="id102">
-<h3>Features<a class="headerlink" href="#id102" title="Permalink to this headline"></a></h3>
+<section id="id105">
+<h3>Features<a class="headerlink" href="#id105" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-450">SYNPY-450</a> - Create convenience functions for synapse project settings</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-517">SYNPY-517</a> - sync command line</p></li>
@@ -1704,14 +1727,14 @@ <h3>Features<a class="headerlink" href="#id102" title="Permalink to this headlin
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-577">SYNPY-577</a> - Expose new view etags in command line clients</p></li>
 </ul>
 </section>
-<section id="id104">
-<h3>Tasks<a class="headerlink" href="#id104" title="Permalink to this headline"></a></h3>
+<section id="id107">
+<h3>Tasks<a class="headerlink" href="#id107" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-569">SYNPY-569</a> - ‘includeEntityEtag’ should be True for Async table csv query downloads</p></li>
 </ul>
 </section>
-<section id="id105">
-<h3>Improvements<a class="headerlink" href="#id105" title="Permalink to this headline"></a></h3>
+<section id="id108">
+<h3>Improvements<a class="headerlink" href="#id108" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-304">SYNPY-304</a> - Table objects should implement len()</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-511">SYNPY-511</a> - improve exception handling</p></li>
@@ -1721,8 +1744,8 @@ <h3>Improvements<a class="headerlink" href="#id105" title="Permalink to this hea
 </ul>
 </section>
 </section>
-<section id="id108">
-<h2>1.7.1 (2017-11-17)<a class="headerlink" href="#id108" title="Permalink to this headline"></a></h2>
+<section id="id111">
+<h2>1.7.1 (2017-11-17)<a class="headerlink" href="#id111" title="Permalink to this headline"></a></h2>
 <p>Release 1.7 is a large bugfix release with several new features. The main ones include:</p>
 <ul>
 <li><p>We have expanded the <a class="reference external" href="python-docs.synapse.org/build/html/synapseutils.html#module-synapseutils">synapseutils packages</a> to add the ability to:</p>
@@ -1746,8 +1769,8 @@ <h2>1.7.1 (2017-11-17)<a class="headerlink" href="#id108" title="Permalink to th
 </ul>
 <p>We also added a optional <cite>convert_to_datetime</cite> parameter to <cite>CsvFileTable.asDataFrame()</cite> that will automatically convert Synapse DATE columns into <cite>datetime</cite> objects instead of leaving them as <cite>long</cite> unix timestamps</p>
 <p>Below are the full list of bugs and issues addressed by this release:</p>
-<section id="id109">
-<h3>Features<a class="headerlink" href="#id109" title="Permalink to this headline"></a></h3>
+<section id="id112">
+<h3>Features<a class="headerlink" href="#id112" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-53">SYNPY-53</a> - support syn.get of external FTP links in py client</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-179">SYNPY-179</a> - Upload to user owned S3 bucket</p></li>
@@ -1760,8 +1783,8 @@ <h3>Features<a class="headerlink" href="#id109" title="Permalink to this headlin
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-442">SYNPY-442</a> - set config file path on command line</p></li>
 </ul>
 </section>
-<section id="id110">
-<h3>Improvements<a class="headerlink" href="#id110" title="Permalink to this headline"></a></h3>
+<section id="id113">
+<h3>Improvements<a class="headerlink" href="#id113" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-407">SYNPY-407</a> - support LARGETEXT in tables</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-360">SYNPY-360</a> - Duplicate file handles are removed from BulkFileDownloadRequest</p></li>
@@ -1779,8 +1802,8 @@ <h3>Improvements<a class="headerlink" href="#id110" title="Permalink to this hea
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-475">SYNPY-475</a> - Store Tables timeout error</p></li>
 </ul>
 </section>
-<section id="id111">
-<h3>Bug Fixes<a class="headerlink" href="#id111" title="Permalink to this headline"></a></h3>
+<section id="id114">
+<h3>Bug Fixes<a class="headerlink" href="#id114" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-190">SYNPY-190</a> - syn.login(‘asdfasdfasdf’) should fail</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-344">SYNPY-344</a> - weird cache directories</p></li>
@@ -1810,8 +1833,8 @@ <h3>Bug Fixes<a class="headerlink" href="#id111" title="Permalink to this headli
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-464">SYNPY-464</a> - synapse get syn4988808 KeyError: u’preSignedURL’</p></li>
 </ul>
 </section>
-<section id="id112">
-<h3>Tasks<a class="headerlink" href="#id112" title="Permalink to this headline"></a></h3>
+<section id="id115">
+<h3>Tasks<a class="headerlink" href="#id115" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-422">SYNPY-422</a> - reduce default page size for GET /evaluation/{evalId}/submission/bundle/all</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-437">SYNPY-437</a> - Remove tests for access restrictions on evaluations</p></li>
@@ -1819,8 +1842,8 @@ <h3>Tasks<a class="headerlink" href="#id112" title="Permalink to this headline">
 </ul>
 </section>
 </section>
-<section id="id113">
-<h2>1.6.1 (2016-11-02)<a class="headerlink" href="#id113" title="Permalink to this headline"></a></h2>
+<section id="id116">
+<h2>1.6.1 (2016-11-02)<a class="headerlink" href="#id116" title="Permalink to this headline"></a></h2>
 <section id="what-is-new">
 <h3>What is New<a class="headerlink" href="#what-is-new" title="Permalink to this headline"></a></h3>
 <p>In version 1.6 we introduce a new sub-module _synapseutils_ that
@@ -1834,8 +1857,8 @@ <h3>What is New<a class="headerlink" href="#what-is-new" title="Permalink to thi
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-371">SYNPY-371</a>  - Support paths in syn.onweb</p></li>
 </ul>
 </section>
-<section id="id114">
-<h3>Improvements<a class="headerlink" href="#id114" title="Permalink to this headline"></a></h3>
+<section id="id117">
+<h3>Improvements<a class="headerlink" href="#id117" title="Permalink to this headline"></a></h3>
 <p>We have improved download robustness and error checking, along with extensive recovery on failed operations. This includes the ability for the client to pause operation when Synapse is updated.</p>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-270">SYNPY-270</a>  - Synapse READ ONLY mode should cause pause in execution</p></li>
@@ -1849,8 +1872,8 @@ <h3>Improvements<a class="headerlink" href="#id114" title="Permalink to this hea
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-390">SYNPY-390</a>  - Move recursive download to Python client utils</p></li>
 </ul>
 </section>
-<section id="id115">
-<h3>Bug Fixes<a class="headerlink" href="#id115" title="Permalink to this headline"></a></h3>
+<section id="id118">
+<h3>Bug Fixes<a class="headerlink" href="#id118" title="Permalink to this headline"></a></h3>
 <ul class="simple">
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-154">SYNPY-154</a>  - 500 Server Error when storing new version of file from command line</p></li>
 <li><p><a class="reference external" href="https://sagebionetworks.jira.com/browse/SYNPY-168">SYNPY-168</a>  - Failure on login gives an ugly error message</p></li>
@@ -1889,7 +1912,7 @@ <h3>Bug Fixes<a class="headerlink" href="#id115" title="Permalink to this headli
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -1910,7 +1933,7 @@ <h3>Bug Fixes<a class="headerlink" href="#id115" title="Permalink to this headli
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
     </div>
     <script type="text/javascript">
diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv
index 09b78d8cb..197620499 100644
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diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html
index 5f2ae42c8..b0eb32134 100644
--- a/docs/build/html/py-modindex.html
+++ b/docs/build/html/py-modindex.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Python Module Index &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Python Module Index &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="_static/synapse_logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                3.1.0
+                3.1.1
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 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -227,7 +227,7 @@ <h1>Python Module Index</h1>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -248,7 +248,7 @@ <h1>Python Module Index</h1>
   </script>
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
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     <script type="text/javascript">
diff --git a/docs/build/html/search.html b/docs/build/html/search.html
index 268153a2e..f2fcae1f2 100644
--- a/docs/build/html/search.html
+++ b/docs/build/html/search.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Search &mdash; Synapse Python Client 3.1.0 documentation</title>
+  <title>Search &mdash; Synapse Python Client 3.1.1 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -37,7 +37,7 @@
               <img src="_static/synapse_logo.png" class="logo" alt="Logo"/>
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+                3.1.1
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   <form id="rtd-search-form" class="wy-form" action="#" method="get">
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     <p>&#169; Copyright 2012-2023, Sage Bionetworks.
-      <span class="lastupdated">Last updated on Oct 23, 2023.
+      <span class="lastupdated">Last updated on Oct 30, 2023.
       </span></p>
   </div>
 
@@ -151,7 +151,7 @@
 
     <div class="footer">
     &copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
-      Last updated on Oct 23, 2023.
+      Last updated on Oct 30, 2023.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.
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     <script type="text/javascript">
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index fabbbb30b..49279259a 100644
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Notes"],titleterms:{"0":24,"01":24,"02":24,"03":24,"04":24,"05":24,"06":24,"07":24,"08":24,"09":24,"1":24,"10":24,"11":24,"12":24,"13":24,"15":24,"16":24,"17":24,"18":24,"19":24,"2":24,"20":24,"2016":24,"2017":24,"2018":24,"2019":24,"2020":24,"2021":24,"2022":24,"2023":24,"23":24,"28":24,"29":24,"3":24,"30":24,"31":24,"4":24,"5":24,"6":24,"7":24,"8":24,"9":24,"class":[1,9],"function":10,"import":0,"new":[11,24],One:21,access:[12,15,16,20],activ:0,add:13,an:[0,14],annot:[1,3,8,11,13,16,19,20],api:12,app:16,argument:13,associ:13,attach:6,authent:[20,21],automat:14,awscli:14,boto3:14,bug:24,cat:13,chang:[3,6,11],client:[2,13,14,23],column:6,command:[13,14,23],config:13,configur:14,content:16,control:15,copi:17,core:10,cp:13,creat:[0,8,9,13,14,19],credenti:[14,16],data:[0,1,6,14,16,20],dataset:6,delet:[6,13],describ:17,detail:[1,3],dockerrepositori:3,document:23,download:[11,13],embed:9,enabl:14,encod:13,entiti:[0,3,16,20],environ:21,evalu:[4,16],exampl:6,extern:14,featur:[14,24],file:[3,6,11,20],fix:24,folder:[3,14],from:[14,16],get:13,highlight:24,imag:9,implement:[1,3],improv:24,inform:[2,20],instal:[14,16,22],json:[5,19],level:6,line:[13,14,23],link:3,list:13,local:22,locat:14,login:[13,21],manag:20,manifest:13,method:[6,9],migrat:[13,14,17],modul:6,monitor:17,more:[2,20],multipart:10,mv:13,name:3,note:24,object:0,onweb:13,option:13,organ:19,overview:17,panda:6,posit:13,programmat:14,project:[3,20],properti:3,proven:[0,11,13,16,20],pypi:22,python:[14,16,23],queri:[6,13],r:16,record:0,releas:24,reticul:16,row:6,rowset:6,s3:14,schema:[3,5,6,19],set:[11,13],sftp:14,share:16,shini:16,show:13,sourc:[0,1],specif:11,st:[13,14],statu:4,storag:14,store:[0,13],stori:24,structur:6,sub:13,submiss:4,submit:13,synaps:[2,16,17,20,23],synapsecli:[14,16],synapseconfig:21,sync:[13,17],tabl:[3,6,13,16,18],task:24,team:7,test:13,through:16,time:21,token:13,transfer:14,tutori:20,unix:14,updat:[8,9,11],upload:[10,11],us:[8,14,16,21],usag:[13,16],util:[10,17],valid:19,variabl:21,variant:14,version:[10,11,20],view:[3,8,16,20],walk:17,what:24,whole:6,wiki:[9,16],window:14,without:11,your:14}})
diff --git a/docs/news.rst b/docs/news.rst
index ec9a4f9b5..ce8dbdc31 100644
--- a/docs/news.rst
+++ b/docs/news.rst
@@ -2,6 +2,20 @@
 Release Notes
 =============
 
+3.1.1 (2023-10-30)
+==================
+
+Highlights
+----------
+- A fix to dowloads when file names match but content does not when `ifcollision=overwrite.local`
+
+Bug Fixes
+---------
+-  [`SYNPY-1316 <https://sagebionetworks.jira.com/browse/SYNPY-1316>`__] -
+   Calling `syn.get` with `ifcollision='overwrite.local` does not always overwrite previous file
+-  [`SYNPY-1298 <https://sagebionetworks.jira.com/browse/SYNPY-1298>`__] -
+   Resolve unstable integration tests
+
 3.1.0 (2023-10-20)
 ==================
 
diff --git a/docs/requirements.txt b/docs/requirements.txt
index c3939eb97..91ff9bd45 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,4 +1,3 @@
 sphinx
 sphinx-argparse
 sphinx_rtd_theme
--e .
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
index 7a631910d..1bde2727f 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -43,17 +43,6 @@ zip_safe = False
 include_package_data = True
 packages = find:
 python_requires = >=3.8
-# on Linux specify a cryptography dependency that will not
-# require a Rust compiler to compile from source (< 3.4).
-# on Linux cryptography is a transitive dependency
-# (keyring -> SecretStorage -> cryptography)
-# SecretStorage doesn't pin a version so otherwise if cryptography
-# is not already installed the dependency will resolve to the latest
-# and will require Rust if a precompiled wheel cannot be used
-# (e.g. old version of pip or no wheel available for an architecture).
-# if a newer version of cryptography is already installed that is
-# fine we don't want to trigger a downgrade, hence the conditional
-# addition of the versioned dependency.
 install_requires =
     # "requests>=2.22.0,<2.30.0; python_version<'3.10'",
     requests>=2.22.0,<3.0
@@ -61,28 +50,33 @@ install_requires =
     # "urllib3>=2; python_version>='3.10'",
     keyring>=15,<23.5
     keyrings.alt==3.1; sys_platform == "linux"
-    cryptography<3.4; sys_platform == "linux"
     deprecated>=1.2.4,<2.0
 tests_require =
-    pytest>=5.0.0,<7.0
+    pytest>=6.0.0,<7.0
     pytest-mock>=3.0,<4.0
     flake8>=3.7.0,<4.0
     pytest-xdist[psutil]>=2.2,<3.0.0
+    pytest-rerunfailures~=12.0
+    func-timeout~=4.3
 
 [options.extras_require]
 dev =
-    pytest>=5.0.0,<7.0
+    pytest>=6.0.0,<7.0
     pytest-mock>=3.0,<4.0
     flake8>=3.7.0,<4.0
     pytest-xdist[psutil]>=2.2,<3.0.0
+    pytest-rerunfailures~=12.0
+    func-timeout~=4.3
     black
     pre-commit
 
 tests =
-    pytest>=5.0.0,<7.0
+    pytest>=6.0.0,<7.0
     pytest-mock>=3.0,<4.0
     flake8>=3.7.0,<4.0
     pytest-xdist[psutil]>=2.2,<3.0.0
+    pytest-rerunfailures~=12.0
+    func-timeout~=4.3
 
 pandas =
     pandas>=1.5,<2.1
diff --git a/synapseclient/client.py b/synapseclient/client.py
index 8988c555a..a7a57a7cd 100644
--- a/synapseclient/client.py
+++ b/synapseclient/client.py
@@ -1035,7 +1035,11 @@ def _getWithEntityBundle(self, entityBundle, entity=None, **kwargs):
             if downloadFile:
                 if file_handle:
                     self._download_file_entity(
-                        downloadLocation, entity, ifcollision, submission
+                        downloadLocation,
+                        entity,
+                        ifcollision,
+                        submission,
+                        file_handle.get("contentMd5", None),
                     )
                 else:  # no filehandle means that we do not have DOWNLOAD permission
                     warning_message = (
@@ -1062,7 +1066,12 @@ def _ensure_download_location_is_directory(self, downloadLocation):
         return download_dir
 
     def _download_file_entity(
-        self, downloadLocation: str, entity: Entity, ifcollision: str, submission: str
+        self,
+        downloadLocation: str,
+        entity: Entity,
+        ifcollision: str,
+        submission: str,
+        expected_md5: typing.Union[str, None],
     ):
         # set the initial local state
         entity.path = None
@@ -1074,6 +1083,15 @@ def _download_file_entity(
         # downloaded the file
         cached_file_path = self.cache.get(entity.dataFileHandleId, downloadLocation)
 
+        # This is to handle for cases where the names of the files in the cache and the
+        # requested file name match - But there is a difference in content.
+        if (
+            expected_md5 is not None
+            and cached_file_path is not None
+            and utils.md5_for_file(cached_file_path).hexdigest() != expected_md5
+        ):
+            cached_file_path = None
+
         # location in .synapseCache where the file would be corresponding to its FileHandleId
         synapseCache_location = self.cache.get_cache_dir(entity.dataFileHandleId)
 
@@ -1437,7 +1455,9 @@ def store(
             self._createAccessRequirementIfNone(properties)
 
         # Update annotations
-        if not bundle or check_annotations_changed(bundle["annotations"], annotations):
+        if (not bundle and annotations) or (
+            bundle and check_annotations_changed(bundle["annotations"], annotations)
+        ):
             annotations = self.set_annotations(
                 Annotations(properties["id"], properties["etag"], annotations)
             )
diff --git a/synapseclient/core/upload/multipart_upload.py b/synapseclient/core/upload/multipart_upload.py
index aa64c803a..68ba0eb03 100644
--- a/synapseclient/core/upload/multipart_upload.py
+++ b/synapseclient/core/upload/multipart_upload.py
@@ -10,7 +10,6 @@
 
 import concurrent.futures
 from contextlib import contextmanager
-import hashlib
 import json
 import math
 import mimetypes
@@ -30,7 +29,7 @@
     SynapseUploadAbortedException,
     SynapseUploadFailedException,
 )
-from synapseclient.core.utils import md5_for_file, MB, Spinner
+from synapseclient.core.utils import md5_fn, md5_for_file, MB, Spinner
 
 # AWS limits
 MAX_NUMBER_OF_PARTS = 10000
@@ -345,7 +344,6 @@ def _upload_parts(self, part_count, remaining_part_numbers):
 
                 if isinstance(cause, KeyboardInterrupt):
                     raise SynapseUploadAbortedException("User interrupted upload")
-
                 raise SynapseUploadFailedException("Part upload failed") from cause
 
     def _complete_upload(self):
@@ -479,11 +477,6 @@ def multipart_upload_file(
     def part_fn(part_number):
         return _get_file_chunk(file_path, part_number, part_size)
 
-    def md5_fn(part, _):
-        md5 = hashlib.md5()
-        md5.update(part)
-        return md5.hexdigest()
-
     return _multipart_upload(
         syn,
         dest_file_name,
@@ -533,7 +526,7 @@ def multipart_upload_string(
 
     data = text.encode("utf-8")
     file_size = len(data)
-    md5_hex = hashlib.md5(data).hexdigest()
+    md5_hex = md5_fn(data, None)
 
     if not dest_file_name:
         dest_file_name = "message.txt"
@@ -557,11 +550,6 @@ def multipart_upload_string(
     def part_fn(part_number):
         return _get_data_chunk(data, part_number, part_size)
 
-    def md5_fn(part, _):
-        md5 = hashlib.md5()
-        md5.update(part)
-        return md5.hexdigest()
-
     part_size = _get_part_size(part_size, file_size)
     return _multipart_upload(
         syn,
diff --git a/synapseclient/core/utils.py b/synapseclient/core/utils.py
index 6b0fbd7b5..699581b87 100644
--- a/synapseclient/core/utils.py
+++ b/synapseclient/core/utils.py
@@ -57,6 +57,18 @@ def md5_for_file(filename, block_size=2 * MB, callback=None):
     return md5
 
 
+def md5_fn(part, _):
+    """Calculate the MD5 of a file-like object.
+
+    :part -- A file-like object to read from.
+
+    :returns: The MD5
+    """
+    md5 = hashlib.new("md5", usedforsecurity=False)
+    md5.update(part)
+    return md5.hexdigest()
+
+
 def download_file(url, localFilepath=None):
     """
     Downloads a remote file.
diff --git a/synapseclient/synapsePythonClient b/synapseclient/synapsePythonClient
index 17ffb7796..0144124ff 100644
--- a/synapseclient/synapsePythonClient
+++ b/synapseclient/synapsePythonClient
@@ -1,6 +1,6 @@
 {
   "client":"synapsePythonClient",
-  "latestVersion":"3.1.0",
+  "latestVersion":"3.1.1",
   "blacklist":["0.0.0", "0.4.1", "0.4.0", "0.3.0", "0.2.1", "0.2.0", "0.1.4"],
   "releaseNotes":"https://python-docs.synapse.org/build/html/news.html"
 }
diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py
index d7a691306..45b8c10e7 100644
--- a/tests/integration/conftest.py
+++ b/tests/integration/conftest.py
@@ -20,6 +20,7 @@
 def syn():
     """
     Create a logged in Synapse instance that can be shared by all tests in the session.
+    If xdist is being used a syn is created for each worker node.
     """
     print("Python version:", sys.version)
 
@@ -38,7 +39,8 @@ def syn():
 @pytest.fixture(scope="session")
 def project(request, syn):
     """
-    Create a project to be shared by all tests in the session.
+    Create a project to be shared by all tests in the session. If xdist is being used
+    a project is created for each worker node.
     """
 
     # Make one project for all the tests to use
diff --git a/tests/integration/synapseclient/core/test_caching.py b/tests/integration/synapseclient/core/test_caching.py
index 94c78ae6f..440c335a6 100644
--- a/tests/integration/synapseclient/core/test_caching.py
+++ b/tests/integration/synapseclient/core/test_caching.py
@@ -13,7 +13,8 @@
 
 import synapseclient.core.utils as utils
 from synapseclient.core.exceptions import SynapseError, SynapseHTTPError
-from synapseclient import File, Project
+from synapseclient import File, Project, Synapse, Entity
+from func_timeout import FunctionTimedOut, func_set_timeout
 
 
 @pytest.fixture(scope="module")
@@ -40,7 +41,8 @@ def syn_state(syn):
     del syn.test_threadsRunning
 
 
-def test_threaded_access(syn, project, schedule_for_cleanup):
+@pytest.mark.flaky(reruns=6)
+def test_threaded_access(syn: Synapse, project: Project, schedule_for_cleanup):
     """Starts multiple threads to perform store and get calls randomly."""
     # Doesn't this test look like a DOS attack on Synapse?
     # Maybe it should be called explicity...
@@ -60,16 +62,16 @@ def test_threaded_access(syn, project, schedule_for_cleanup):
     update_thread = wrap_function_as_child_thread(
         syn, thread_get_and_update_file_from_Project, syn, project, schedule_for_cleanup
     )
+    # thread.start_new_thread(store_thread, ())
+    # thread.start_new_thread(store_thread, ())
     thread.start_new_thread(store_thread, ())
     thread.start_new_thread(store_thread, ())
-    thread.start_new_thread(store_thread, ())
-    thread.start_new_thread(store_thread, ())
-    thread.start_new_thread(get_thread, ())
     thread.start_new_thread(get_thread, ())
     thread.start_new_thread(get_thread, ())
+    # thread.start_new_thread(get_thread, ())
     thread.start_new_thread(update_thread, ())
     thread.start_new_thread(update_thread, ())
-    thread.start_new_thread(update_thread, ())
+    # thread.start_new_thread(update_thread, ())
 
     # Give the threads some time to wreak havoc on the cache
     time.sleep(20)
@@ -89,7 +91,7 @@ def test_threaded_access(syn, project, schedule_for_cleanup):
 #############
 
 
-def wrap_function_as_child_thread(syn, function, *args, **kwargs):
+def wrap_function_as_child_thread(syn: Synapse, function, *args, **kwargs):
     """Wraps the given function so that it ties into the main thread."""
 
     def child_thread():
@@ -109,7 +111,7 @@ def child_thread():
     return child_thread
 
 
-def collect_errors_and_fail(syn):
+def collect_errors_and_fail(syn: Synapse):
     """Pulls error traces from the error queue and fails if the queue is not empty."""
     failures = []
     for i in range(syn.test_errors.qsize()):
@@ -123,7 +125,7 @@ def collect_errors_and_fail(syn):
 ######################
 
 
-def thread_keep_storing_one_File(syn, project, schedule_for_cleanup):
+def thread_keep_storing_one_File(syn: Synapse, project: Project, schedule_for_cleanup):
     """Makes one file and stores it over and over again."""
 
     # Make a local file to continuously store
@@ -134,7 +136,14 @@ def thread_keep_storing_one_File(syn, project, schedule_for_cleanup):
     )
 
     while syn.test_keepRunning:
-        stored = store_catch_412_HTTPError(syn, myPrecious)
+        stored = None
+        try:
+            stored = store_catch_412_HTTPError(syn, myPrecious)
+        except FunctionTimedOut:
+            syn.logger.warning(
+                f"thread_keep_storing_one_File()::store_catch_412_HTTPError timed out, [Path: {myPrecious.path}]"
+            )
+
         if stored is not None:
             myPrecious = stored
         elif "id" in myPrecious:
@@ -145,22 +154,35 @@ def thread_keep_storing_one_File(syn, project, schedule_for_cleanup):
         sleep_for_a_bit()
 
 
-def thread_get_files_from_Project(syn, project):
+def thread_get_files_from_Project(syn: Synapse, project: Project):
     """Continually polls and fetches items from the Project."""
 
     while syn.test_keepRunning:
-        for id in get_all_ids_from_Project(syn, project):
-            pass
+        try:
+            get_all_ids_from_Project(syn, project)
+        except FunctionTimedOut:
+            syn.logger.warning(
+                f"thread_get_files_from_Project()::get_all_ids_from_Project timed out, [Project: {project.id}]"
+            )
 
         sleep_for_a_bit()
 
 
-def thread_get_and_update_file_from_Project(syn, project, schedule_for_cleanup):
+def thread_get_and_update_file_from_Project(
+    syn: Synapse, project: Project, schedule_for_cleanup
+):
     """Fetches one item from the Project and updates it with a new file."""
 
     while syn.test_keepRunning:
-        id = get_all_ids_from_Project(syn, project)
-        if len(id) <= 0:
+        id = []
+        try:
+            id = get_all_ids_from_Project(syn, project)
+        except FunctionTimedOut:
+            syn.logger.warning(
+                f"thread_get_and_update_file_from_Project()::get_all_ids_from_Project timed out, [project: {project.id}]"
+            )
+        if len(id) == 0:
+            sleep_for_a_bit()
             continue
 
         id = id[random.randrange(len(id))]
@@ -170,7 +192,12 @@ def thread_get_and_update_file_from_Project(syn, project, schedule_for_cleanup):
         path = utils.make_bogus_data_file()
         schedule_for_cleanup(path)
         entity.path = path
-        entity = store_catch_412_HTTPError(syn, entity)
+        try:
+            entity = store_catch_412_HTTPError(syn, entity)
+        except FunctionTimedOut:
+            syn.logger.warning(
+                f"thread_get_and_update_file_from_Project()::store_catch_412_HTTPError timed out, [project: {project.id}, path: {entity.path}]"
+            )
         if entity is not None:
             assert os.stat(entity.path) == os.stat(path)
 
@@ -182,18 +209,23 @@ def thread_get_and_update_file_from_Project(syn, project, schedule_for_cleanup):
 ####################
 
 
-def sleep_for_a_bit():
+def sleep_for_a_bit() -> int:
     """Sleeps for a random amount of seconds between 1 and 5 inclusive."""
-
-    time.sleep(random.randint(1, 5))
+    time_to_sleep = random.randint(1, 5)
+    time.sleep(time_to_sleep)
+    return time_to_sleep
 
 
-def get_all_ids_from_Project(syn, project):
+# When running with multiple threads it can lock up and do nothing until pipeline is killed at 6hrs
+@func_set_timeout(20)
+def get_all_ids_from_Project(syn: Synapse, project: Project):
     """Fetches all currently available Synapse IDs from the parent Project."""
     return [result["id"] for result in syn.getChildren(project.id)]
 
 
-def store_catch_412_HTTPError(syn, entity):
+# When running with multiple threads it can lock up and do nothing until pipeline is killed at 6hrs
+@func_set_timeout(20)
+def store_catch_412_HTTPError(syn: Synapse, entity: Entity):
     """Returns the stored Entity if the function succeeds or None if the 412 is caught."""
     try:
         return syn.store(entity)
diff --git a/tests/integration/synapseclient/core/test_download.py b/tests/integration/synapseclient/core/test_download.py
index e14ecd577..858fc9aa4 100644
--- a/tests/integration/synapseclient/core/test_download.py
+++ b/tests/integration/synapseclient/core/test_download.py
@@ -27,6 +27,7 @@ def test_download_check_md5(syn, project, schedule_for_cleanup):
     )
 
 
+@pytest.mark.flaky(reruns=3)
 def test_resume_partial_download(syn, project, schedule_for_cleanup):
     original_file = utils.make_bogus_data_file(40000)
 
diff --git a/tests/integration/synapseclient/core/test_external_storage.py b/tests/integration/synapseclient/core/test_external_storage.py
index 13a838e5f..f32c043df 100644
--- a/tests/integration/synapseclient/core/test_external_storage.py
+++ b/tests/integration/synapseclient/core/test_external_storage.py
@@ -3,7 +3,7 @@
 import tempfile
 import uuid
 
-from synapseclient import File
+from synapseclient import File, Synapse, Project
 from synapseclient.core.retry import with_retry
 
 import pytest
@@ -48,11 +48,11 @@ def get_aws_env():
 @unittest.skipIf(*check_test_preconditions())
 class ExernalStorageTest(unittest.TestCase):
     @pytest.fixture(autouse=True)
-    def _syn(self, syn):
+    def _syn(self, syn: Synapse):
         self.syn = syn
 
     @pytest.fixture(autouse=True)
-    def _project(self, project):
+    def _project(self, project: Project):
         self.project = project
 
     @classmethod
diff --git a/tests/integration/synapseclient/core/upload/test_multipart_upload.py b/tests/integration/synapseclient/core/upload/test_multipart_upload.py
index 13531c66a..43d708bf6 100644
--- a/tests/integration/synapseclient/core/upload/test_multipart_upload.py
+++ b/tests/integration/synapseclient/core/upload/test_multipart_upload.py
@@ -2,6 +2,7 @@
 import hashlib
 import os
 import random
+import pytest
 import requests
 import string
 import tempfile
@@ -11,7 +12,7 @@
 
 from unittest import mock, skip
 
-from synapseclient import File
+from synapseclient import File, Project, Synapse
 import synapseclient.core.config
 import synapseclient.core.utils as utils
 from synapseclient.core.upload.multipart_upload import (
@@ -22,7 +23,8 @@
 )
 
 
-def test_round_trip(syn, project, schedule_for_cleanup):
+@pytest.mark.flaky(reruns=3, only_rerun=["SynapseHTTPError"])
+def test_round_trip(syn: Synapse, project: Project, schedule_for_cleanup):
     fhid = None
     filepath = utils.make_bogus_binary_file(MIN_PART_SIZE + 777771)
     try:
@@ -49,7 +51,7 @@ def test_round_trip(syn, project, schedule_for_cleanup):
             print(traceback.format_exc())
 
 
-def test_single_thread_upload(syn):
+def test_single_thread_upload(syn: Synapse):
     synapseclient.core.config.single_threaded = True
     try:
         filepath = utils.make_bogus_binary_file(MIN_PART_SIZE * 2 + 1)
@@ -58,7 +60,7 @@ def test_single_thread_upload(syn):
         synapseclient.core.config.single_threaded = False
 
 
-def test_randomly_failing_parts(syn, project, schedule_for_cleanup):
+def test_randomly_failing_parts(syn: Synapse, project: Project, schedule_for_cleanup):
     """Verify that we can recover gracefully with some randomly inserted errors
     while uploading parts."""
 
@@ -115,7 +117,9 @@ def _put_chunk_or_fail_randomly(self, url, *args, **kwargs):
                 print(traceback.format_exc())
 
 
-def test_multipart_upload_big_string(syn, project, schedule_for_cleanup):
+def test_multipart_upload_big_string(
+    syn: Synapse, project: Project, schedule_for_cleanup
+):
     cities = [
         "Seattle",
         "Portland",
@@ -174,7 +178,9 @@ def test_multipart_upload_big_string(syn, project, schedule_for_cleanup):
     assert retrieved_text == text
 
 
-def _multipart_copy_test(syn, project, schedule_for_cleanup, part_size):
+def _multipart_copy_test(
+    syn: Synapse, project: Project, schedule_for_cleanup, part_size: int
+):
     import logging
 
     logging.basicConfig()
@@ -257,11 +263,14 @@ def _multipart_copy_test(syn, project, schedule_for_cleanup, part_size):
     assert file_content == dest_file_content
 
 
-def test_multipart_copy(syn, project, schedule_for_cleanup):
+@pytest.mark.flaky(reruns=3, only_rerun=["SynapseHTTPError"])
+def test_multipart_copy(syn: Synapse, project: Project, schedule_for_cleanup):
     """Test multi part copy using the minimum part size."""
     _multipart_copy_test(syn, project, schedule_for_cleanup, MIN_PART_SIZE)
 
 
 @skip("Skip in normal testing because the large size makes it slow")
-def test_multipart_copy__big_parts(syn, project, schedule_for_cleanup):
+def test_multipart_copy__big_parts(
+    syn: Synapse, project: Project, schedule_for_cleanup
+):
     _multipart_copy_test(syn, project, schedule_for_cleanup, 100 * utils.MB)
diff --git a/tests/integration/synapseclient/integration_test.py b/tests/integration/synapseclient/integration_test.py
index 44fbbf243..571b91959 100644
--- a/tests/integration/synapseclient/integration_test.py
+++ b/tests/integration/synapseclient/integration_test.py
@@ -9,8 +9,9 @@
 import pytest
 from unittest.mock import patch
 
-from synapseclient import Entity, Team, UserProfile, client
+from synapseclient import Entity, Team, UserProfile, client, Synapse
 from synapseclient import Activity, Annotations, File, Folder, login, Project, Synapse
+import synapseclient
 from synapseclient.core.credentials import credential_provider
 from synapseclient.core.exceptions import (
     SynapseAuthenticationError,
@@ -122,6 +123,7 @@ def testCustomConfigFile(syn, schedule_for_cleanup):
         )
 
 
+@pytest.mark.flaky(reruns=3, only_rerun=["SynapseHTTPError"])
 def test_entity_version(syn, project, schedule_for_cleanup):
     # Make an Entity and make sure the version is one
     entity = File(parent=project["id"])
@@ -220,6 +222,7 @@ def test_uploadFile_given_dictionary(syn, project, schedule_for_cleanup):
     syn.get(entity["id"])
 
 
+@pytest.mark.flaky(reruns=3, only_rerun=["SynapseHTTPError"])
 def test_uploadFileEntity(syn, project, schedule_for_cleanup):
     # Create a FileEntity
     # Dictionaries default to FileEntity as a type
@@ -416,6 +419,61 @@ def test_annotations(syn, project, schedule_for_cleanup):
     assert annotation["maybe"] == [True, False]
 
 
+def test_annotations_on_file_during_create_no_annotations(
+    syn: Synapse, project: Project, schedule_for_cleanup
+):
+    # GIVEN a bogus file
+    path = utils.make_bogus_data_file()
+    schedule_for_cleanup(path)
+    file = File(path, parent=project["id"], description="test_annotations_on_file")
+
+    # AND the file is stored
+    with patch.object(syn, "set_annotations") as mock_set_annotations:
+        entity = syn.store(file)
+    schedule_for_cleanup(entity.id)
+
+    # WHEN I get the annotations
+    annotations = syn.get_annotations(entity)
+
+    # THEN I expect the annotations to be empty
+    assert hasattr(annotations, "id")
+    assert hasattr(annotations, "etag")
+    assert annotations.id == entity.id
+    assert annotations.etag == entity.etag
+    assert len(annotations) == 0
+
+    # AND set_annotations has not been called
+    assert not mock_set_annotations.called
+
+
+def test_annotations_on_file_during_create_with_annotations(
+    syn: Synapse, project: Project, schedule_for_cleanup
+):
+    # GIVEN a bogus file
+    path = utils.make_bogus_data_file()
+    schedule_for_cleanup(path)
+
+    # AND annotations have been set on the file
+    file = File(
+        path,
+        parent=project["id"],
+        description="test_annotations_on_file",
+        annotations={"label_1": "value_1", "label_2": "value_2"},
+    )
+
+    # AND the file is stored
+    entity = syn.store(file)
+    schedule_for_cleanup(entity.id)
+
+    # WHEN I get the annotations
+    annotations = syn.get_annotations(entity)
+
+    # THEN I expect the annotations to have been set
+    assert annotations["label_1"] == ["value_1"]
+    assert annotations["label_2"] == ["value_2"]
+    assert len(annotations) == 2
+
+
 def test_get_user_profile(syn):
     p1 = syn.getUserProfile()
 
diff --git a/tests/integration/synapseclient/integration_test_Entity.py b/tests/integration/synapseclient/integration_test_Entity.py
index 261a99616..a165e28b8 100644
--- a/tests/integration/synapseclient/integration_test_Entity.py
+++ b/tests/integration/synapseclient/integration_test_Entity.py
@@ -7,13 +7,24 @@
 import pytest
 from unittest.mock import patch
 
+from pytest_mock import MockerFixture
+
+
 from synapseclient.core.upload.upload_functions import create_external_file_handle
-from synapseclient import Activity, DockerRepository, File, Folder, Link, Project
+from synapseclient import (
+    Activity,
+    DockerRepository,
+    File,
+    Folder,
+    Link,
+    Project,
+    Synapse,
+)
 from synapseclient.core.exceptions import SynapseError, SynapseHTTPError
 import synapseclient.core.utils as utils
 
 
-def test_Entity(syn, project, schedule_for_cleanup):
+def test_Entity(syn: Synapse, project: Project, schedule_for_cleanup):
     # Update the project
     project_name = str(uuid.uuid4())
     project = Project(name=project_name)
@@ -77,7 +88,11 @@ def test_Entity(syn, project, schedule_for_cleanup):
     a_file = syn.get(a_file)
     assert filecmp.cmp(path, a_file.path)
 
-    b_file = File(name="blah", parent=folder, dataFileHandleId=a_file.dataFileHandleId)
+    b_file = File(
+        name="blah" + str(uuid.uuid4()),
+        parent=folder,
+        dataFileHandleId=a_file.dataFileHandleId,
+    )
     b_file = syn.store(b_file)
 
     assert b_file.dataFileHandleId == a_file.dataFileHandleId
@@ -152,7 +167,7 @@ def test_Entity(syn, project, schedule_for_cleanup):
     assert os.path.basename(a_file_cached.path) == os.path.basename(a_file.path)
 
 
-def test_special_characters(syn, project, schedule_for_cleanup):
+def test_special_characters(syn: Synapse, project: Project):
     folder = syn.store(
         Folder(
             "Special Characters Here",
@@ -174,7 +189,7 @@ def test_special_characters(syn, project, schedule_for_cleanup):
     assert folder.russian_annotation[0] == "Обезьяна прикладом"
 
 
-def test_get_local_file(syn, project, schedule_for_cleanup):
+def test_get_local_file(syn: Synapse, project: Project, schedule_for_cleanup):
     new_path = utils.make_bogus_data_file()
     schedule_for_cleanup(new_path)
     folder = Folder(
@@ -204,7 +219,7 @@ def test_get_local_file(syn, project, schedule_for_cleanup):
     pytest.raises(SynapseError, syn.get, new_path, limitSearch="syn1")
 
 
-def test_store_with_flags(syn, project, schedule_for_cleanup):
+def test_store_with_flags(syn: Synapse, project: Project, schedule_for_cleanup):
     # -- CreateOrUpdate flag for Projects --
     # If we store a project with the same name, it should become an update
     projUpdate = Project(project.name)
@@ -216,7 +231,8 @@ def test_store_with_flags(syn, project, schedule_for_cleanup):
     # Store a File
     filepath = utils.make_bogus_binary_file()
     schedule_for_cleanup(filepath)
-    origBogus = File(filepath, name="Bogus Test File", parent=project)
+    file_name = "Bogus Test File" + str(uuid.uuid4())
+    origBogus = File(filepath, name=file_name, parent=project)
     origBogus = syn.store(origBogus, createOrUpdate=True)
     assert origBogus.versionNumber == 1
 
@@ -248,7 +264,7 @@ def test_store_with_flags(syn, project, schedule_for_cleanup):
     # This should be ignored because contents (and md5) are different
     different_filepath = utils.make_bogus_binary_file()
     schedule_for_cleanup(different_filepath)
-    mutaBogus = File(different_filepath, name="Bogus Test File", parent=project)
+    mutaBogus = File(different_filepath, name=file_name, parent=project)
     mutaBogus = syn.store(mutaBogus, forceVersion=False)
     assert mutaBogus.versionNumber == 3
 
@@ -273,7 +289,7 @@ def test_store_with_flags(syn, project, schedule_for_cleanup):
     # Expected behavior is raising an exception with a 409 error
     newer_filepath = utils.make_bogus_binary_file()
     schedule_for_cleanup(newer_filepath)
-    badBogus = File(newer_filepath, name="Bogus Test File", parent=project)
+    badBogus = File(newer_filepath, name=file_name, parent=project)
     pytest.raises(SynapseHTTPError, syn.store, badBogus, createOrUpdate=False)
 
     # -- Storing after syn.get(..., downloadFile=False) --
@@ -287,11 +303,14 @@ def test_store_with_flags(syn, project, schedule_for_cleanup):
     assert ephemeralBogus.shoe_size == [11.5]
 
 
-def test_get_with_downloadLocation_and_ifcollision(syn, project, schedule_for_cleanup):
+def test_get_with_downloadLocation_and_ifcollision(
+    syn: Synapse, project: Project, schedule_for_cleanup
+):
     # Store a File and delete it locally
     filepath = utils.make_bogus_binary_file()
-    bogus = File(filepath, name="Bogus Test File", parent=project)
+    bogus = File(filepath, name="Bogus Test File" + str(uuid.uuid4()), parent=project)
     bogus = syn.store(bogus)
+    schedule_for_cleanup(bogus)
     os.remove(filepath)
 
     # Compare stuff to this one
@@ -339,13 +358,77 @@ def test_get_with_downloadLocation_and_ifcollision(syn, project, schedule_for_cl
     os.remove(renamedBogus.path)
 
 
-def test_store_activity(syn, project, schedule_for_cleanup):
+def test_get_with_cache_hit_and_miss_with_ifcollision(
+    syn: Synapse, project: Project, schedule_for_cleanup, mocker: MockerFixture
+):
+    download_file_function = mocker.spy(obj=syn, name="_downloadFileHandle")
+    # GIVEN a File that is stored in Synapse - and removed from the local machine
+    filepath = utils.make_bogus_binary_file()
+    original_file_md5 = utils.md5_for_file(filepath).hexdigest()
+    bogus_file = File(
+        filepath,
+        name="a_name_that_will_show_up_in_cache" + str(uuid.uuid4()),
+        parent=project,
+    )
+    bogus_file = syn.store(bogus_file)
+    schedule_for_cleanup(bogus_file)
+    os.remove(filepath)
+
+    # WHEN I get the File from synapse
+    unmodified_file_from_server = syn.get(
+        bogus_file,
+        downloadLocation=os.path.dirname(filepath),
+        ifcollision="overwrite.local",
+    )
+
+    # THEN I expect the file to have been downloaded and match the original files MD5
+    assert download_file_function.call_count == 1
+    assert unmodified_file_from_server._file_handle["contentMd5"] == original_file_md5
+    assert utils.md5_for_file(filepath).hexdigest() == original_file_md5
+
+    # AND I expect the file to be in the cache and match the original files MD5
+    copy_of_file_from_server = syn.get(
+        bogus_file,
+        downloadLocation=os.path.dirname(filepath),
+        ifcollision="overwrite.local",
+    )
+    assert copy_of_file_from_server.id == unmodified_file_from_server.id
+    assert filecmp.cmp(copy_of_file_from_server.path, unmodified_file_from_server.path)
+    assert download_file_function.call_count == 1
+    assert copy_of_file_from_server._file_handle["contentMd5"] == original_file_md5
+    assert utils.md5_for_file(filepath).hexdigest() == original_file_md5
+
+    # GIVEN another bogus file with the same name and non matching MD5 data
+    new_bogus_file = utils.make_bogus_binary_file()
+    os.remove(filepath)
+    os.rename(new_bogus_file, filepath)
+    assert utils.md5_for_file(filepath).hexdigest() != original_file_md5
+
+    # WHEN I get the File from synapse
+    copy_of_file_from_server = syn.get(
+        bogus_file,
+        downloadLocation=os.path.dirname(filepath),
+        ifcollision="overwrite.local",
+    )
+
+    # THEN I expect the file to have been downloaded and overwrite the file on my machine with the same name
+    assert copy_of_file_from_server._file_handle["contentMd5"] == original_file_md5
+    assert utils.md5_for_file(filepath).hexdigest() == original_file_md5
+    assert download_file_function.call_count == 2
+
+    os.remove(filepath)
+
+
+def test_store_activity(syn: Synapse, project: Project, schedule_for_cleanup):
     # Create a File and an Activity
     path = utils.make_bogus_binary_file()
     schedule_for_cleanup(path)
-    entity = File(path, name="Hinkle horn honking holes", parent=project)
+    entity = File(
+        path, name="Hinkle horn honking holes" + str(uuid.uuid4()), parent=project
+    )
+    activity_name = "Hinkle horn honking" + str(uuid.uuid4())
     honking = Activity(
-        name="Hinkle horn honking",
+        name=activity_name,
         description="Nettlebed Cave is a limestone cave located on the South Island of New Zealand.",
     )
     honking.used("http://www.flickr.com/photos/bevanbfree/3482259379/")
@@ -358,7 +441,7 @@ def test_store_activity(syn, project, schedule_for_cleanup):
     honking = syn.getProvenance(entity.id)
 
     # Verify the Activity
-    assert honking["name"] == "Hinkle horn honking"
+    assert honking["name"] == activity_name
     assert len(honking["used"]) == 2
     assert (
         honking["used"][0]["concreteType"]
@@ -377,7 +460,7 @@ def test_store_activity(syn, project, schedule_for_cleanup):
     # Store another Entity with the same Activity
     entity = File(
         "http://en.wikipedia.org/wiki/File:Nettlebed_cave.jpg",
-        name="Nettlebed Cave",
+        name="Nettlebed Cave" + str(uuid.uuid4()),
         parent=project,
         synapseStore=False,
     )
@@ -388,11 +471,11 @@ def test_store_activity(syn, project, schedule_for_cleanup):
     assert honking["id"] == honking2["id"]
 
 
-def test_store_isRestricted_flag(syn, project, schedule_for_cleanup):
+def test_store_isRestricted_flag(syn: Synapse, project: Project, schedule_for_cleanup):
     # Store a file with access requirements
     path = utils.make_bogus_binary_file()
     schedule_for_cleanup(path)
-    entity = File(path, name="Secret human data", parent=project)
+    entity = File(path, name="Secret human data" + str(uuid.uuid4()), parent=project)
 
     # We don't want to spam ACT with test emails
     with patch(
@@ -402,7 +485,7 @@ def test_store_isRestricted_flag(syn, project, schedule_for_cleanup):
         assert intercepted.called
 
 
-def test_ExternalFileHandle(syn, project, schedule_for_cleanup):
+def test_ExternalFileHandle(syn: Synapse, project: Project):
     # Tests shouldn't have external dependencies, but this is a pretty picture of Singapore
     singapore_url = "http://upload.wikimedia.org/wikipedia/commons/thumb/3/3e/1_singapore_city_skyline_dusk_panorama_2011.jpg/1280px-1_singapore_city_skyline_dusk_panorama_2011.jpg"  # noqa
     singapore = File(singapore_url, parent=project, synapseStore=False)
@@ -432,16 +515,22 @@ def test_ExternalFileHandle(syn, project, schedule_for_cleanup):
     assert s2.externalURL == singapore_2_url
 
 
-def test_synapseStore_flag(syn, project, schedule_for_cleanup):
+def test_synapseStore_flag(syn: Synapse, project: Project, schedule_for_cleanup):
     # Store a path to a local file
     path = utils.make_bogus_data_file()
     schedule_for_cleanup(path)
-    bogus = File(path, name="Totally bogus data", parent=project, synapseStore=False)
+    file_name = "Totally bogus data" + str(uuid.uuid4())
+    bogus = File(
+        path,
+        name=file_name,
+        parent=project,
+        synapseStore=False,
+    )
     bogus = syn.store(bogus)
 
     # Verify the thing can be downloaded as a URL
     bogus = syn.get(bogus, downloadFile=False)
-    assert bogus.name == "Totally bogus data"
+    assert bogus.name == file_name
     assert bogus.path == path, "Path: %s\nExpected: %s" % (bogus.path, path)
     assert not bogus.synapseStore
 
@@ -474,7 +563,7 @@ def test_synapseStore_flag(syn, project, schedule_for_cleanup):
     assert not bogus.synapseStore
 
 
-def test_create_or_update_project(syn, project, schedule_for_cleanup):
+def test_create_or_update_project(syn: Synapse, project: Project, schedule_for_cleanup):
     name = str(uuid.uuid4())
 
     project = Project(name, a=1, b=2)
@@ -498,14 +587,15 @@ def test_create_or_update_project(syn, project, schedule_for_cleanup):
     pytest.raises(Exception, syn.store, project, createOrUpdate=False)
 
 
-def test_download_file_false(syn, project, schedule_for_cleanup):
-    RENAME_SUFFIX = "blah"
+def test_download_file_false(syn: Synapse, project: Project, schedule_for_cleanup):
+    RENAME_SUFFIX = "blah" + str(uuid.uuid4())
 
     # Upload a file
     filepath = utils.make_bogus_binary_file()
     schedule_for_cleanup(filepath)
     schedule_for_cleanup(filepath + RENAME_SUFFIX)
-    file = File(filepath, name="SYNR 619", parent=project)
+    file_name = "SYNR-619-" + str(uuid.uuid4())
+    file = File(filepath, name=file_name, parent=project)
     file = syn.store(file)
 
     # Now hide the file from the cache and download with downloadFile=False
@@ -513,7 +603,7 @@ def test_download_file_false(syn, project, schedule_for_cleanup):
     file = syn.get(file.id, downloadFile=False)
 
     # Change something and reupload the file's metadata
-    file.name = "Only change the name, not the file"
+    file.name = "Only change the name, not the file" + str(uuid.uuid4())
     reupload = syn.store(file)
     assert reupload.path is None, "Path field should be null: %s" % reupload.path
 
@@ -523,7 +613,7 @@ def test_download_file_false(syn, project, schedule_for_cleanup):
     assert reupload.name == file.name
 
 
-def test_download_file_URL_false(syn, project, schedule_for_cleanup):
+def test_download_file_URL_false(syn: Synapse, project: Project):
     # Upload an external file handle
     fileThatExists = "http://dev-versions.synapse.sagebase.org/synapsePythonClient"
     reupload = File(fileThatExists, synapseStore=False, parent=project)
@@ -554,7 +644,9 @@ def test_download_file_URL_false(syn, project, schedule_for_cleanup):
 
 
 # SYNPY-366
-def test_download_local_file_URL_path(syn, project, schedule_for_cleanup):
+def test_download_local_file_URL_path(
+    syn: Synapse, project: Project, schedule_for_cleanup
+):
     path = utils.make_bogus_data_file()
     schedule_for_cleanup(path)
 
@@ -566,7 +658,9 @@ def test_download_local_file_URL_path(syn, project, schedule_for_cleanup):
 
 
 # SYNPY-424
-def test_store_file_handle_update_metadata(syn, project, schedule_for_cleanup):
+def test_store_file_handle_update_metadata(
+    syn: Synapse, project: Project, schedule_for_cleanup
+):
     original_file_path = utils.make_bogus_data_file()
     schedule_for_cleanup(original_file_path)
 
@@ -593,7 +687,7 @@ def test_store_file_handle_update_metadata(syn, project, schedule_for_cleanup):
     assert [os.path.basename(replacement_file_path)] == new_entity.files
 
 
-def test_store_DockerRepository(syn, project, schedule_for_cleanup):
+def test_store_DockerRepository(syn: Synapse, project: Project):
     repo_name = "some/repository/path"
     docker_repo = syn.store(DockerRepository(repo_name, parent=project))
     assert isinstance(docker_repo, DockerRepository)
@@ -601,11 +695,14 @@ def test_store_DockerRepository(syn, project, schedule_for_cleanup):
     assert repo_name == docker_repo.repositoryName
 
 
+@pytest.mark.flaky(reruns=3, only_rerun=["SynapseHTTPError"])
 def test_store__changing_externalURL_by_changing_path(
-    syn, project, schedule_for_cleanup
+    syn: Synapse, project: Project, schedule_for_cleanup
 ):
     url = "https://www.synapse.org/Portal/clear.cache.gif"
-    ext = syn.store(File(url, name="test", parent=project, synapseStore=False))
+    ext = syn.store(
+        File(url, name="test" + str(uuid.uuid4()), parent=project, synapseStore=False)
+    )
 
     # perform a syn.get so the filename changes
     ext = syn.get(ext)
@@ -627,8 +724,9 @@ def test_store__changing_externalURL_by_changing_path(
     assert not ext.synapseStore
 
 
+@pytest.mark.flaky(reruns=3, only_rerun=["SynapseHTTPError"])
 def test_store__changing_from_Synapse_to_externalURL_by_changing_path(
-    syn, project, schedule_for_cleanup
+    syn: Synapse, project: Project, schedule_for_cleanup
 ):
     # create a temp file
     temp_path = utils.make_bogus_data_file()
diff --git a/tests/integration/synapseclient/test_command_line_client.py b/tests/integration/synapseclient/test_command_line_client.py
index f58943bab..7ec2426cb 100644
--- a/tests/integration/synapseclient/test_command_line_client.py
+++ b/tests/integration/synapseclient/test_command_line_client.py
@@ -31,8 +31,8 @@
 from io import StringIO
 
 
-@pytest.fixture(scope="module")
-def test_state(syn, project, schedule_for_cleanup):
+@pytest.fixture(scope="function")
+def test_state(syn: Synapse, project: Project, schedule_for_cleanup):
     class State:
         def __init__(self):
             self.syn = syn
@@ -614,7 +614,11 @@ def test_command_get_recursive_and_query(test_state):
     cols = [Column(name="id", columnType="ENTITYID")]
 
     schema1 = test_state.syn.store(
-        Schema(name="Foo Table", columns=cols, parent=project_entity)
+        Schema(
+            name=str(uuid.uuid4()),
+            columns=cols,
+            parent=project_entity,
+        )
     )
     test_state.schedule_for_cleanup(schema1.id)
 
@@ -1165,7 +1169,7 @@ def test_create__same_project_name(test_state):
 
 
 @patch.object(utils.sys.stdin, "isatty")
-def test_storeTable__csv(mock_sys, test_state):
+def test_storeTable_csv(mock_sys, test_state):
     # when running on windows os with multiple CPU, the sys.stdin.isatty will return True
     # Thus we mock the utils.sys.stdin.
     mock_sys.return_value = False
diff --git a/tests/integration/synapseclient/test_tables.py b/tests/integration/synapseclient/test_tables.py
index 4a0efaee1..2b6db0c5a 100644
--- a/tests/integration/synapseclient/test_tables.py
+++ b/tests/integration/synapseclient/test_tables.py
@@ -27,6 +27,8 @@
     Schema,
     Table,
     Dataset,
+    Project,
+    Synapse,
 )
 import synapseclient.core.utils as utils
 
@@ -44,7 +46,10 @@ def revert_timeout():
     request.addfinalizer(revert_timeout)
 
 
-def test_create_and_update_file_view(syn, project, schedule_for_cleanup):
+@pytest.mark.flaky(reruns=3)
+def test_create_and_update_file_view(
+    syn: Synapse, project: Project, schedule_for_cleanup
+):
     # Create a folder
     folder = Folder(
         str(uuid.uuid4()), parent=project, description="creating a file-view"
@@ -225,7 +230,9 @@ def test_rowset_tables(syn, project):
         Column(name="description", columnType="LARGETEXT"),
     ]
 
-    schema1 = syn.store(Schema(name="Foo Table", columns=cols, parent=project))
+    schema1 = syn.store(
+        Schema(name="Foo Table_test_rowset_tables", columns=cols, parent=project)
+    )
 
     data1 = [
         ["Chris", "bar", 11.23, 45, False, "a"],
@@ -321,6 +328,7 @@ def test_dataset(syn, project):
     assert all(dataset_df.columns == ["id", "name"])
 
 
+@pytest.mark.flaky(reruns=3)
 def test_tables_csv(syn, project):
     # Define schema
     cols = [
@@ -358,6 +366,7 @@ def test_tables_csv(syn, project):
         assert expected_row == row, "expected %s but got %s" % (expected_row, row)
 
 
+@pytest.mark.flaky(reruns=3)
 def test_tables_pandas(syn, project):
     # create a pandas DataFrame
     df = pd.DataFrame(
diff --git a/tests/integration/synapseclient/test_wikis.py b/tests/integration/synapseclient/test_wikis.py
index 370cea734..0a16574cc 100644
--- a/tests/integration/synapseclient/test_wikis.py
+++ b/tests/integration/synapseclient/test_wikis.py
@@ -3,13 +3,13 @@
 
 import pytest
 
-from synapseclient import Project, Wiki
+from synapseclient import Project, Wiki, Synapse
 from synapseclient.core.exceptions import SynapseHTTPError
 from synapseclient.core.upload.upload_functions import upload_synapse_s3
 import synapseclient.core.utils as utils
 
 
-def test_wikiAttachment(syn, project, schedule_for_cleanup):
+def test_wikiAttachment(syn: Synapse, project: Project, schedule_for_cleanup):
     # Upload a file to be attached to a Wiki
     filename = utils.make_bogus_data_file()
     attachname = utils.make_bogus_data_file()
@@ -36,7 +36,10 @@ def test_wikiAttachment(syn, project, schedule_for_cleanup):
 
     # Create a Wiki sub-page
     subwiki = Wiki(
-        owner=project, title="A sub-wiki", markdown="nothing", parentWikiId=wiki.id
+        owner=project,
+        title="A sub-wiki",
+        markdown="nothing",
+        parentWikiId=wiki.id,
     )
     subwiki = syn.store(subwiki)
 
diff --git a/tests/integration/synapseutils/test_synapseutils_copy.py b/tests/integration/synapseutils/test_synapseutils_copy.py
index 5a4853f7c..b9b483286 100644
--- a/tests/integration/synapseutils/test_synapseutils_copy.py
+++ b/tests/integration/synapseutils/test_synapseutils_copy.py
@@ -2,6 +2,7 @@
 import time
 import re
 import json
+from func_timeout import FunctionTimedOut, func_set_timeout
 
 import pytest
 
@@ -18,6 +19,7 @@
     RowSet,
     Schema,
     Wiki,
+    Synapse,
 )
 import synapseclient.core.utils as utils
 import synapseutils
@@ -25,7 +27,18 @@
 
 # Add Test for UPDATE
 # Add test for existing provenance but the orig doesn't have provenance
-def test_copy(syn, schedule_for_cleanup):
+@pytest.mark.flaky(reruns=10)
+def test_copy(syn: Synapse, schedule_for_cleanup):
+    try:
+        execute_test_copy(syn, schedule_for_cleanup)
+    except FunctionTimedOut:
+        syn.logger.warning("test_copy timed out")
+        pytest.fail("test_copy timed out")
+
+
+# When running with multiple threads it can lock up and do nothing until pipeline is killed at 6hrs
+@func_set_timeout(120)
+def execute_test_copy(syn: Synapse, schedule_for_cleanup):
     """Tests the copy function"""
     # Create a Project
     project_entity = syn.store(Project(name=str(uuid.uuid4())))
diff --git a/tests/integration/synapseutils/test_synapseutils_migrate.py b/tests/integration/synapseutils/test_synapseutils_migrate.py
index c9b16aa9c..73770a4ae 100644
--- a/tests/integration/synapseutils/test_synapseutils_migrate.py
+++ b/tests/integration/synapseutils/test_synapseutils_migrate.py
@@ -5,6 +5,7 @@
 import uuid
 
 import synapseclient
+from synapseclient import Synapse
 from synapseclient.core.constants import concrete_types
 import synapseclient.core.utils as utils
 import synapseutils
@@ -12,7 +13,7 @@
 
 
 @pytest.fixture(scope="module")
-def storage_location_id(syn, project):
+def storage_location_id(syn: Synapse):
     storage_location_setting = syn.restPOST(
         "/storageLocation",
         json.dumps(
@@ -52,7 +53,9 @@ def _assert_storage_location(file_handles, storage_location_id):
         assert fh["storageLocationId"] == storage_location_id
 
 
-def test_migrate_project(request, syn, schedule_for_cleanup, storage_location_id):
+def test_migrate_project(
+    request, syn: Synapse, schedule_for_cleanup, storage_location_id
+):
     test_name = request.node.name
     project_name = "{}-{}".format(test_name, uuid.uuid4())
     project = synapseclient.Project(name=project_name)
diff --git a/tests/integration/synapseutils/test_synapseutils_sync.py b/tests/integration/synapseutils/test_synapseutils_sync.py
index 9b3556841..d8e38c7da 100644
--- a/tests/integration/synapseutils/test_synapseutils_sync.py
+++ b/tests/integration/synapseutils/test_synapseutils_sync.py
@@ -2,20 +2,21 @@
 import os
 import time
 import tempfile
+from func_timeout import FunctionTimedOut, func_set_timeout
 import pandas as pd
 
 import pytest
 
 from synapseclient.core.exceptions import SynapseHTTPError
-from synapseclient import Entity, File, Folder, Link, Project, Schema
+from synapseclient import Entity, File, Folder, Link, Project, Schema, Synapse
 import synapseclient.core.utils as utils
 import synapseutils
 
 from tests.integration import QUERY_TIMEOUT_SEC
 
 
-@pytest.fixture(scope="module", autouse=True)
-def test_state(syn, schedule_for_cleanup):
+@pytest.fixture(scope="function", autouse=True)
+def test_state(syn: Synapse, schedule_for_cleanup):
     class TestState:
         def __init__(self):
             self.syn = syn
@@ -102,6 +103,7 @@ def test_readManifest(test_state):
     pytest.raises(IOError, synapseutils.sync.readManifestFile, test_state.syn, manifest)
 
 
+@pytest.mark.flaky(reruns=3)
 def test_syncToSynapse(test_state):
     # Test upload of accurate manifest
     manifest = _makeManifest(
@@ -116,7 +118,11 @@ def test_syncToSynapse(test_state):
     # Download using syncFromSynapse
     tmpdir = tempfile.mkdtemp()
     test_state.schedule_for_cleanup(tmpdir)
-    synapseutils.syncFromSynapse(test_state.syn, test_state.project, path=tmpdir)
+    try:
+        execute_sync_from_synapse(test_state.syn, test_state.project, path=tmpdir)
+    except FunctionTimedOut:
+        test_state.syn.logger.warning("test_syncToSynapse timed out")
+        pytest.fail("test_syncToSynapse timed out")
 
     orig_df = pd.read_csv(manifest, sep="\t")
     orig_df.index = [os.path.basename(p) for p in orig_df.path]
@@ -168,6 +174,7 @@ def test_syncToSynapse(test_state):
                 assert set(orig_list) == set(new_list)
 
 
+@pytest.mark.flaky(reruns=3)
 def test_syncFromSynapse(test_state):
     """This function tests recursive download as defined in syncFromSynapse
     most of the functionality of this function are already tested in the
@@ -205,14 +212,19 @@ def test_syncFromSynapse(test_state):
         time.sleep(2)
 
     # Test recursive get
-    output = synapseutils.syncFromSynapse(test_state.syn, project_entity)
+    try:
+        output = execute_sync_from_synapse(test_state.syn, project_entity)
+    except FunctionTimedOut:
+        test_state.syn.logger.warning("test_syncFromSynapse timed out")
+        pytest.fail("test_syncFromSynapse timed out")
 
     assert len(output) == len(uploaded_paths)
     for f in output:
         assert utils.normalize_path(f.path) in uploaded_paths
 
 
-def test_syncFromSynapse__children_contain_non_file(test_state):
+@pytest.mark.flaky(reruns=3)
+def test_syncFromSynapse_children_contain_non_file(test_state):
     proj = test_state.syn.store(
         Project(name="test_syncFromSynapse_children_non_file" + str(uuid.uuid4()))
     )
@@ -233,11 +245,18 @@ def test_syncFromSynapse__children_contain_non_file(test_state):
     temp_folder = tempfile.mkdtemp()
     test_state.schedule_for_cleanup(temp_folder)
 
-    files_list = synapseutils.syncFromSynapse(test_state.syn, proj, temp_folder)
+    try:
+        files_list = execute_sync_from_synapse(test_state.syn, proj, temp_folder)
+    except FunctionTimedOut:
+        test_state.syn.logger.warning(
+            "test_syncFromSynapse_children_contain_non_file timed out"
+        )
+        pytest.fail("test_syncFromSynapse_children_contain_non_file timed out")
     assert 1 == len(files_list)
     assert file_entity == files_list[0]
 
 
+@pytest.mark.flaky(reruns=3)
 def test_syncFromSynapse_Links(test_state):
     """This function tests recursive download of links as defined in syncFromSynapse
     most of the functionality of this function are already tested in the
@@ -280,9 +299,13 @@ def test_syncFromSynapse_Links(test_state):
     test_state.syn.store(Link(file_entity.id, parent=inner_folder_entity))
 
     # Test recursive get
-    output = synapseutils.syncFromSynapse(
-        test_state.syn, folder_entity, followLink=True
-    )
+    try:
+        output = execute_sync_from_synapse(
+            test_state.syn, folder_entity, followLink=True
+        )
+    except FunctionTimedOut:
+        test_state.syn.logger.warning("test_syncFromSynapse_Links timed out")
+        pytest.fail("test_syncFromSynapse_Links timed out")
 
     assert len(output) == len(uploaded_paths)
     for f in output:
@@ -307,7 +330,8 @@ def test_write_manifest_data__unicode_characters_in_rows(test_state):
         assert datarow["col_B"] == dfrow.col_B
 
 
-def test_syncFromSynapse__given_file_id(test_state):
+@pytest.mark.flaky(reruns=3)
+def test_syncFromSynapse_given_file_id(test_state):
     file_path = utils.make_bogus_data_file()
     test_state.schedule_for_cleanup(file_path)
     file = test_state.syn.store(
@@ -318,6 +342,17 @@ def test_syncFromSynapse__given_file_id(test_state):
             synapseStore=False,
         )
     )
-    all_files = synapseutils.syncFromSynapse(test_state.syn, file.id)
+    try:
+        all_files = execute_sync_from_synapse(test_state.syn, file.id)
+    except FunctionTimedOut:
+        test_state.syn.logger.warning("test_syncFromSynapse_given_file_id timed out")
+        pytest.fail("test_syncFromSynapse_given_file_id timed out")
+
     assert 1 == len(all_files)
     assert file == all_files[0]
+
+
+# When running with multiple threads it can lock up and do nothing until pipeline is killed at 6hrs
+@func_set_timeout(120)
+def execute_sync_from_synapse(*args, **kwargs):
+    return synapseutils.syncFromSynapse(*args, **kwargs)
diff --git a/tests/integration/synapseutils/test_synapseutils_walk.py b/tests/integration/synapseutils/test_synapseutils_walk.py
index fbe482b09..151d7f097 100644
--- a/tests/integration/synapseutils/test_synapseutils_walk.py
+++ b/tests/integration/synapseutils/test_synapseutils_walk.py
@@ -1,12 +1,26 @@
 import uuid
 import os
+from func_timeout import FunctionTimedOut, func_set_timeout
+
+import pytest
 
 from synapseclient import File, Folder, Project
 import synapseclient.core.utils as utils
 import synapseutils
 
 
+@pytest.mark.flaky(reruns=3)
 def test_walk(syn, schedule_for_cleanup):
+    try:
+        execute_test_walk(syn, schedule_for_cleanup)
+    except FunctionTimedOut:
+        syn.logger.warning("test_walk timed out")
+        pytest.fail("test_walk timed out")
+
+
+# When running with multiple threads it can lock up and do nothing until pipeline is killed at 6hrs
+@func_set_timeout(120)
+def execute_test_walk(syn, schedule_for_cleanup):
     walked = []
     firstfile = utils.make_bogus_data_file()
     schedule_for_cleanup(firstfile)
diff --git a/tests/unit/synapseclient/core/unit_test_Cache.py b/tests/unit/synapseclient/core/unit_test_Cache.py
index c8e7dd49e..b33b6405b 100644
--- a/tests/unit/synapseclient/core/unit_test_Cache.py
+++ b/tests/unit/synapseclient/core/unit_test_Cache.py
@@ -30,6 +30,7 @@ def add_file_to_cache(i, cache_root_dir):
         my_cache.add(file_handle_id, file_path)
 
 
+@pytest.mark.flaky(reruns=3)
 def test_cache_concurrent_access():
     cache_root_dir = tempfile.mkdtemp()
     processes = [
diff --git a/tests/unit/synapseclient/core/unit_test_download.py b/tests/unit/synapseclient/core/unit_test_download.py
index cb7561481..7543f3fd9 100644
--- a/tests/unit/synapseclient/core/unit_test_download.py
+++ b/tests/unit/synapseclient/core/unit_test_download.py
@@ -122,7 +122,7 @@ def mock_generate_headers(self, headers=None):
     return {}
 
 
-def test_mock_download(syn):
+def test_mock_download(syn: Synapse):
     temp_dir = tempfile.gettempdir()
 
     fileHandleId = "42"
@@ -388,7 +388,7 @@ def test_mock_download(syn):
 
 class Test__downloadFileHandle(unittest.TestCase):
     @pytest.fixture(autouse=True, scope="function")
-    def init_syn(self, syn):
+    def init_syn(self, syn: Synapse):
         self.syn = syn
 
     def tearDown(self) -> None:
@@ -506,7 +506,7 @@ def test_multithread_false__S3_fileHandle(self):
 
 class Test_download_from_url_multi_threaded:
     @pytest.fixture(autouse=True, scope="function")
-    def init_syn(self, syn):
+    def init_syn(self, syn: Synapse):
         self.syn = syn
 
     def test_md5_mismatch(self):
@@ -564,7 +564,7 @@ def test_md5_match(self):
             )
 
 
-def test_download_end_early_retry(syn):
+def test_download_end_early_retry(syn: Synapse):
     """
     -------Test to ensure download retry even if connection ends early--------
     """
@@ -645,7 +645,7 @@ def test_download_end_early_retry(syn):
         mocked_move.assert_called_once_with(temp_destination, destination)
 
 
-def test_download_md5_mismatch__not_local_file(syn):
+def test_download_md5_mismatch__not_local_file(syn: Synapse):
     """
     --------Test to ensure file gets removed on md5 mismatch--------
     """
@@ -712,7 +712,7 @@ def test_download_md5_mismatch__not_local_file(syn):
         mocked_remove.assert_called_once_with(destination)
 
 
-def test_download_md5_mismatch_local_file(syn):
+def test_download_md5_mismatch_local_file(syn: Synapse):
     """
     --------Test to ensure file gets removed on md5 mismatch--------
     """
@@ -743,7 +743,7 @@ def test_download_md5_mismatch_local_file(syn):
         assert not mocked_remove.called
 
 
-def test_download_file_entity__correct_local_state(syn):
+def test_download_file_entity__correct_local_state(syn: Synapse):
     mock_cache_path = utils.normalize_path("/i/will/show/you/the/path/yi.txt")
     file_entity = File(parentId="syn123")
     file_entity.dataFileHandleId = 123
@@ -753,6 +753,7 @@ def test_download_file_entity__correct_local_state(syn):
             entity=file_entity,
             ifcollision="overwrite.local",
             submission=None,
+            expected_md5=None,
         )
         assert mock_cache_path == utils.normalize_path(file_entity.path)
         assert os.path.dirname(mock_cache_path) == file_entity.cacheDir
@@ -760,7 +761,7 @@ def test_download_file_entity__correct_local_state(syn):
         assert os.path.basename(mock_cache_path) == file_entity.files[0]
 
 
-def test_getFileHandleDownload__error_UNAUTHORIZED(syn):
+def test_getFileHandleDownload__error_UNAUTHORIZED(syn: Synapse):
     ret_val = {
         "requestedFiles": [
             {
@@ -772,7 +773,7 @@ def test_getFileHandleDownload__error_UNAUTHORIZED(syn):
         pytest.raises(SynapseError, syn._getFileHandleDownload, "123", "syn456")
 
 
-def test_getFileHandleDownload__error_NOT_FOUND(syn):
+def test_getFileHandleDownload__error_NOT_FOUND(syn: Synapse):
     ret_val = {
         "requestedFiles": [
             {
diff --git a/tests/unit/synapseclient/core/upload/unit_test_multipart_upload.py b/tests/unit/synapseclient/core/upload/unit_test_multipart_upload.py
index 408b9b090..9ea7ee4af 100644
--- a/tests/unit/synapseclient/core/upload/unit_test_multipart_upload.py
+++ b/tests/unit/synapseclient/core/upload/unit_test_multipart_upload.py
@@ -23,6 +23,7 @@
     pool_provider,
     UploadAttempt,
 )
+from synapseclient.core.utils import md5_fn
 
 
 class TestUploadAttempt:
@@ -49,11 +50,6 @@ def _init_upload_attempt(self, syn):
         def part_request_body_provider_fn(part_number):
             return (f"{part_number}" * self.part_size).encode("utf-8")
 
-        def md5_fn(part, _):
-            md5 = hashlib.md5()
-            md5.update(part)
-            return md5.hexdigest()
-
         max_threads = 8
         force_restart = True
 
@@ -310,7 +306,7 @@ def _handle_part_success_test(
     ):
         mock_session = mock.Mock()
 
-        md5_hex = hashlib.md5(chunk).hexdigest()
+        md5_hex = md5_fn(chunk, None)
 
         with mock.patch.object(
             multipart_upload, "_get_file_chunk"
@@ -797,7 +793,7 @@ def test_multipart_upload_string(self):
             "_multipart_upload",
         ) as mock_multipart_upload:
             encoded = upload_text.encode("utf-8")
-            md5_hex = hashlib.md5(encoded).hexdigest()
+            md5_hex = md5_fn(encoded, None)
 
             # call w/ default args
             multipart_upload_string(
diff --git a/tests/unit/synapseutils/unit_test_synapseutils_sync.py b/tests/unit/synapseutils/unit_test_synapseutils_sync.py
index ae8068eb6..a2104ec17 100644
--- a/tests/unit/synapseutils/unit_test_synapseutils_sync.py
+++ b/tests/unit/synapseutils/unit_test_synapseutils_sync.py
@@ -26,7 +26,7 @@
 from synapseclient.core.pool_provider import get_executor
 
 
-def test_readManifest__sync_order_with_home_directory(syn):
+def test_readManifest__sync_order_with_home_directory(syn: Synapse):
     """SYNPY-508"""
 
     # row1's file depends on row2's file but is listed first
@@ -63,7 +63,7 @@ def test_readManifest__sync_order_with_home_directory(syn):
         )
 
 
-def test_readManifestFile__synapseStore_values_not_set(syn):
+def test_readManifestFile__synapseStore_values_not_set(syn: Synapse):
     project_id = "syn123"
     header = "path\tparent\n"
     path1 = os.path.abspath(os.path.expanduser("~/file1.txt"))
@@ -89,7 +89,7 @@ def test_readManifestFile__synapseStore_values_not_set(syn):
         assert expected_synapseStore == actual_synapseStore
 
 
-def test_readManifestFile__synapseStore_values_are_set(syn):
+def test_readManifestFile__synapseStore_values_are_set(syn: Synapse):
     project_id = "syn123"
     header = "path\tparent\tsynapseStore\n"
     path1 = os.path.abspath(os.path.expanduser("~/file1.txt"))
@@ -129,7 +129,7 @@ def test_readManifestFile__synapseStore_values_are_set(syn):
         assert expected_synapseStore == actual_synapseStore
 
 
-def test_syncFromSynapse__non_file_entity(syn):
+def test_syncFromSynapse__non_file_entity(syn: Synapse):
     table_schema = "syn12345"
     with patch.object(syn, "getChildren", return_value=[]), patch.object(
         syn, "get", return_value=Schema(name="asssdfa", parent="whatever")
@@ -137,7 +137,7 @@ def test_syncFromSynapse__non_file_entity(syn):
         pytest.raises(ValueError, synapseutils.syncFromSynapse, syn, table_schema)
 
 
-def test_syncFromSynapse__empty_folder(syn):
+def test_syncFromSynapse__empty_folder(syn: Synapse):
     folder = Folder(name="the folder", parent="whatever", id="syn123")
     with patch.object(syn, "getChildren", return_value=[]), patch.object(
         syn, "get", return_value=Folder(name="asssdfa", parent="whatever")
@@ -145,7 +145,7 @@ def test_syncFromSynapse__empty_folder(syn):
         assert list() == synapseutils.syncFromSynapse(syn, folder)
 
 
-def test_syncFromSynapse__file_entity(syn):
+def test_syncFromSynapse__file_entity(syn: Synapse):
     file = File(name="a file", parent="some parent", id="syn456")
     with patch.object(
         syn, "getChildren", return_value=[file]
@@ -154,7 +154,7 @@ def test_syncFromSynapse__file_entity(syn):
         patch_syn_get_children.assert_not_called()
 
 
-def test_syncFromSynapse__folder_contains_one_file(syn):
+def test_syncFromSynapse__folder_contains_one_file(syn: Synapse):
     folder = Folder(name="the folder", parent="whatever", id="syn123")
     file = File(name="a file", parent=folder, id="syn456")
     with patch.object(
@@ -164,7 +164,7 @@ def test_syncFromSynapse__folder_contains_one_file(syn):
         patch_syn_get_children.called_with(folder["id"])
 
 
-def test_syncFromSynapse__project_contains_empty_folder(syn):
+def test_syncFromSynapse__project_contains_empty_folder(syn: Synapse):
     project = Project(name="the project", parent="whatever", id="syn123")
     file = File(name="a file", parent=project, id="syn456")
     folder = Folder(name="a folder", parent=project, id="syn789")
@@ -194,7 +194,7 @@ def syn_get_side_effect(entity, *args, **kwargs):
         )
 
 
-def test_syncFromSynapse__downloadFile_is_false(syn):
+def test_syncFromSynapse__downloadFile_is_false(syn: Synapse):
     """
     Verify when passing the argument downloadFile is equal to False,
     syncFromSynapse won't download the file to clients' local end.
@@ -228,7 +228,7 @@ def syn_get_side_effect(entity, *args, **kwargs):
 @patch.object(synapseutils.sync, "generateManifest")
 @patch.object(synapseutils.sync, "_get_file_entity_provenance_dict")
 def test_syncFromSynapse__manifest_is_all(
-    mock__get_file_entity_provenance_dict, mock_generateManifest, syn
+    mock__get_file_entity_provenance_dict, mock_generateManifest, syn: Synapse
 ):
     """
     Verify manifest argument equal to "all" that pass in to syncFromSynapse, it will create root_manifest and all
@@ -297,7 +297,7 @@ def syn_get_side_effect(entity, *args, **kwargs):
 @patch.object(synapseutils.sync, "generateManifest")
 @patch.object(synapseutils.sync, "_get_file_entity_provenance_dict")
 def test_syncFromSynapse__manifest_is_root(
-    mock__get_file_entity_provenance_dict, mock_generateManifest, syn
+    mock__get_file_entity_provenance_dict, mock_generateManifest, syn: Synapse
 ):
     """
     Verify manifest argument equal to "root" that pass in to syncFromSynapse, it will create root_manifest file only.
@@ -359,7 +359,7 @@ def syn_get_side_effect(entity, *args, **kwargs):
 @patch.object(synapseutils.sync, "generateManifest")
 @patch.object(synapseutils.sync, "_get_file_entity_provenance_dict")
 def test_syncFromSynapse__manifest_is_suppress(
-    mock__get_file_entity_provenance_dict, mock_generateManifest, syn
+    mock__get_file_entity_provenance_dict, mock_generateManifest, syn: Synapse
 ):
     """
     Verify manifest argument equal to "suppress" that pass in to syncFromSynapse, it won't create any manifest file.
@@ -981,7 +981,8 @@ def test_abort(self):
         assert cm_ex.value.__cause__ == ex
         future_3.cancel.assert_called_once_with()
 
-    def test_upload__error(self, syn):
+    @pytest.mark.flaky(reruns=3, only_rerun=["AssertionError"])
+    def test_upload_error(self, syn):
         """Verify that if an item upload fails the error is raised in the main thread
         and any running Futures are cancelled"""