Run pre-commit

.github/CODEOWNERS

@@ -1 +1 @@
-* @Sage-Bionetworks/python-client-developers
+* @Sage-Bionetworks/python-client-developers

.github/workflows/codeql-analysis.yml

@@ -48,11 +48,11 @@ jobs:
         # If you wish to specify custom queries, you can do so here or in a config file.
         # By default, queries listed here will override any specified in a config file.
         # Prefix the list here with "+" to use these queries and those in the config file.
-        
+
         # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
         # queries: security-extended,security-and-quality
 
-        
+
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
@@ -61,7 +61,7 @@ jobs:
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
 
-    #   If the Autobuild fails above, remove it and uncomment the following three lines. 
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
     #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
 
     # - run: |

.gitignore

@@ -20,4 +20,3 @@ docs/build/html/_sources/*
 build/*
 
 /venv
-

CONTRIBUTING.md

@@ -123,7 +123,7 @@ pytest -vs tests/integration/synapseclient/test_command_line_client.py::test_tab
 
 ### Code style
 
-The Synapse Python Client uses [`flake8`](https://pypi.org/project/flake8/) to enforce 
+The Synapse Python Client uses [`flake8`](https://pypi.org/project/flake8/) to enforce
 [`PEP8`](https://legacy.python.org/dev/peps/pep-0008/) style consistency and to check for possible errors.
 You can verify your code matches these expectations by running the **flake8** command from the project root directory:
 

Dockerfile

@@ -14,4 +14,3 @@ RUN pip3 install --upgrade pip
 COPY . /synapsePythonClient
 WORKDIR /synapsePythonClient
 RUN python3 setup.py install
-

ISSUE_TEMPLATE.md

@@ -32,4 +32,3 @@ A minimal reproducible example:
 ### Actual behavior
 
 *What actually happened? Provide output or error messages from the console, if applicable.*
-

README.md

@@ -6,7 +6,7 @@ Branch  | Build Status
 develop | [![Build Status develop branch](https://github.com/Sage-Bionetworks/synapsePythonClient/workflows/build/badge.svg?branch=develop)](https://github.com/Sage-Bionetworks/synapsePythonClient/actions?query=branch%3Adevelop)
 master  | [![Build Status master branch](https://github.com/Sage-Bionetworks/synapsePythonClient/workflows/build/badge.svg?branch=master)](https://github.com/Sage-Bionetworks/synapsePythonClient/actions?query=branch%3Amaster)
 
-[![Get the synapseclient from PyPI](https://img.shields.io/pypi/v/synapseclient.svg)](https://pypi.python.org/pypi/synapseclient/) [![Supported Python Versions](https://img.shields.io/pypi/pyversions/synapseclient.svg)](https://pypi.python.org/pypi/synapseclient/) 
+[![Get the synapseclient from PyPI](https://img.shields.io/pypi/v/synapseclient.svg)](https://pypi.python.org/pypi/synapseclient/) [![Supported Python Versions](https://img.shields.io/pypi/pyversions/synapseclient.svg)](https://pypi.python.org/pypi/synapseclient/)
 
 A Python client for [Sage Bionetworks'](https://www.sagebase.org) [Synapse](https://www.synapse.org/), a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate. The Python client can be used as a library for development of software that communicates with Synapse or as a command-line utility.
 
@@ -17,7 +17,7 @@ Documentation
 
 For more information about the Python client, see:
 
- * [Python client API docs](https://python-docs.synapse.org) 
+ * [Python client API docs](https://python-docs.synapse.org)
 
 For more information about interacting with Synapse, see:
 
@@ -154,10 +154,10 @@ The purpose of synapseutils is to create a space filled with convenience functio
     import synapseutils
     import synapseclient
     syn = synapseclient.login()
-    
+
     #COPY: copies all Synapse entities to a destination location
     synapseutils.copy(syn, "syn1234", destinationId = "syn2345")
-    
+
     #COPY WIKI: copies the wiki from the entity to a destination entity. Only a project can have sub wiki pages.
     synapseutils.copyWiki(syn, "syn1234", destinationId = "syn2345")
 
@@ -169,7 +169,7 @@ The purpose of synapseutils is to create a space filled with convenience functio
         print(dirpath)
         print(dirname)
         print(filename)
-        
+
 
 License and Copyright
 ---------------------

docs/Activity.rst

@@ -1 +1 @@
-.. automodule:: synapseclient.activity
+.. automodule:: synapseclient.activity

docs/Annotations.rst

@@ -1 +1 @@
-.. automodule:: synapseclient.annotations
+.. automodule:: synapseclient.annotations

docs/CNAME

@@ -1 +1 @@
-python-docs.synapse.org
+python-docs.synapse.org

docs/Client.rst

@@ -1 +1 @@
-.. automodule:: synapseclient.client
+.. automodule:: synapseclient.client

docs/Credentials.rst

@@ -103,4 +103,3 @@ The second time you login, you will not have to enter any arguments to :code:`lo
 
     import synapseclient
     syn = synapseclient.login()
-

docs/Evaluation.rst

@@ -1 +1 @@
-.. automodule:: synapseclient.evaluation
+.. automodule:: synapseclient.evaluation

docs/Team.rst

@@ -1,3 +1,2 @@
 .. automodule:: synapseclient.team
    :members:
-

docs/Views.rst

@@ -80,4 +80,4 @@ The change in annotations reflect in synGetAnnotations()::
 
     syn.getAnnotations(file2['id'])
 
-A View is a Table. Please visit `Tables <https://python-docs.synapse.org/build/html/Table.html#module-synapseclient.table>`_ to see how to change schema, update content, and other operations that can be done on View.
+A View is a Table. Please visit `Tables <https://python-docs.synapse.org/build/html/Table.html#module-synapseclient.table>`_ to see how to change schema, update content, and other operations that can be done on View.

docs/Wiki.rst

@@ -1 +1 @@
-.. automodule:: synapseclient.wiki
+.. automodule:: synapseclient.wiki

docs/_static/custom.css

@@ -25,4 +25,3 @@ div.header img {
 table.field-list th {
     word-break: normal;
 }
-

docs/build/html/Activity.html

@@ -9,7 +9,7 @@
     <title>Provenance &#8212; Synapse Python Client 2.7.2 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/custom.css" />
-    
+
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
     <script src="_static/jquery.js"></script>
     <script src="_static/underscore.js"></script>
@@ -46,15 +46,15 @@ <h3>Navigation</h3>
           <a href="Evaluation.html" title="Evaluations"
              accesskey="P">previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.7.2 documentation</a> &#187;</li>
-        <li class="nav-item nav-item-this"><a href="">Provenance</a></li> 
+        <li class="nav-item nav-item-this"><a href="">Provenance</a></li>
       </ul>
-    </div>  
+    </div>
 
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
           <div class="body" role="main">
-            
+
   <span class="target" id="module-synapseclient.activity"></span><div class="section" id="provenance">
 <h1>Provenance<a class="headerlink" href="#provenance" title="Permalink to this headline">¶</a></h1>
 <p>The Activity object represents the source of a data set or the data processing steps used to produce it. Using
@@ -247,7 +247,7 @@ <h3>Navigation</h3>
           <a href="Evaluation.html" title="Evaluations"
              >previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.7.2 documentation</a> &#187;</li>
-        <li class="nav-item nav-item-this"><a href="">Provenance</a></li> 
+        <li class="nav-item nav-item-this"><a href="">Provenance</a></li>
       </ul>
     </div>
     <div class="footer">
@@ -264,4 +264,4 @@ <h3>Navigation</h3>
       ga('send', 'pageview');
     </script>
   </body>
-</html>
+</html>

docs/build/html/Annotations.html

@@ -9,7 +9,7 @@
     <title>Annotations &#8212; Synapse Python Client 2.7.2 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/custom.css" />
-    
+
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
     <script src="_static/jquery.js"></script>
     <script src="_static/underscore.js"></script>
@@ -46,15 +46,15 @@ <h3>Navigation</h3>
           <a href="Activity.html" title="Provenance"
              accesskey="P">previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.7.2 documentation</a> &#187;</li>
-        <li class="nav-item nav-item-this"><a href="">Annotations</a></li> 
+        <li class="nav-item nav-item-this"><a href="">Annotations</a></li>
       </ul>
-    </div>  
+    </div>
 
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
           <div class="body" role="main">
-            
+
   <span class="target" id="module-synapseclient.annotations"></span><div class="section" id="annotations">
 <h1>Annotations<a class="headerlink" href="#annotations" title="Permalink to this headline">¶</a></h1>
 <p>Annotations are arbitrary metadata attached to Synapse entities. They can be accessed like ordinary object properties
@@ -203,7 +203,7 @@ <h3>Navigation</h3>
           <a href="Activity.html" title="Provenance"
              >previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.7.2 documentation</a> &#187;</li>
-        <li class="nav-item nav-item-this"><a href="">Annotations</a></li> 
+        <li class="nav-item nav-item-this"><a href="">Annotations</a></li>
       </ul>
     </div>
     <div class="footer">
@@ -220,4 +220,4 @@ <h3>Navigation</h3>
       ga('send', 'pageview');
     </script>
   </body>
-</html>
+</html>

docs/build/html/Client.html

@@ -9,7 +9,7 @@
     <title>Synapse Client &#8212; Synapse Python Client 2.7.2 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/custom.css" />
-    
+
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
     <script src="_static/jquery.js"></script>
     <script src="_static/underscore.js"></script>
@@ -46,15 +46,15 @@ <h3>Navigation</h3>
           <a href="reticulate.html" title="Using synapseclient with R through reticulate"
              accesskey="P">previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.7.2 documentation</a> &#187;</li>
-        <li class="nav-item nav-item-this"><a href="">Synapse Client</a></li> 
+        <li class="nav-item nav-item-this"><a href="">Synapse Client</a></li>
       </ul>
-    </div>  
+    </div>
 
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
           <div class="body" role="main">
-            
+
   <span class="target" id="module-synapseclient.client"></span><div class="section" id="synapse-client">
 <h1>Synapse Client<a class="headerlink" href="#synapse-client" title="Permalink to this headline">¶</a></h1>
 <p>The <cite>Synapse</cite> object encapsulates a connection to the Synapse service and is used for building projects, uploading and
@@ -1631,7 +1631,7 @@ <h3>Navigation</h3>
           <a href="reticulate.html" title="Using synapseclient with R through reticulate"
              >previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.7.2 documentation</a> &#187;</li>
-        <li class="nav-item nav-item-this"><a href="">Synapse Client</a></li> 
+        <li class="nav-item nav-item-this"><a href="">Synapse Client</a></li>
       </ul>
     </div>
     <div class="footer">
@@ -1648,4 +1648,4 @@ <h3>Navigation</h3>
       ga('send', 'pageview');
     </script>
   </body>
-</html>
+</html>

docs/build/html/CommandLineClient.html

@@ -9,7 +9,7 @@
     <title>Synapse command line client &#8212; Synapse Python Client 2.7.2 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/custom.css" />
-    
+
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
     <script src="_static/jquery.js"></script>
     <script src="_static/underscore.js"></script>
@@ -46,15 +46,15 @@ <h3>Navigation</h3>
           <a href="Versions.html" title="Version Functions"
              accesskey="P">previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.7.2 documentation</a> &#187;</li>
-        <li class="nav-item nav-item-this"><a href="">Synapse command line client</a></li> 
+        <li class="nav-item nav-item-this"><a href="">Synapse command line client</a></li>
       </ul>
-    </div>  
+    </div>
 
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
           <div class="body" role="main">
-            
+
   <div class="section" id="synapse-command-line-client">
 <h1>Synapse command line client<a class="headerlink" href="#synapse-command-line-client" title="Permalink to this headline">¶</a></h1>
 <p>The Synapse Python Client can be used from the command line via the <strong>synapse</strong> command.</p>
@@ -1115,7 +1115,7 @@ <h3>Navigation</h3>
           <a href="Versions.html" title="Version Functions"
              >previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.7.2 documentation</a> &#187;</li>
-        <li class="nav-item nav-item-this"><a href="">Synapse command line client</a></li> 
+        <li class="nav-item nav-item-this"><a href="">Synapse command line client</a></li>
       </ul>
     </div>
     <div class="footer">
@@ -1132,4 +1132,4 @@ <h3>Navigation</h3>
       ga('send', 'pageview');
     </script>
   </body>
-</html>
+</html>

docs/build/html/Credentials.html

@@ -9,7 +9,7 @@
     <title>Manage Synapse Credentials &#8212; Synapse Python Client 2.7.2 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/custom.css" />
-    
+
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
     <script src="_static/jquery.js"></script>
     <script src="_static/underscore.js"></script>
@@ -46,15 +46,15 @@ <h3>Navigation</h3>
           <a href="index.html" title="Synapse Python Client Documentation"
              accesskey="P">previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.7.2 documentation</a> &#187;</li>
-        <li class="nav-item nav-item-this"><a href="">Manage Synapse Credentials</a></li> 
+        <li class="nav-item nav-item-this"><a href="">Manage Synapse Credentials</a></li>
       </ul>
-    </div>  
+    </div>
 
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
           <div class="body" role="main">
-            
+
   <div class="section" id="manage-synapse-credentials">
 <h1>Manage Synapse Credentials<a class="headerlink" href="#manage-synapse-credentials" title="Permalink to this headline">¶</a></h1>
 <p>There are multiple ways one can login to Synapse. We recommend users to choose the method that fits their workflow.</p>
@@ -208,7 +208,7 @@ <h3>Navigation</h3>
           <a href="index.html" title="Synapse Python Client Documentation"
              >previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.7.2 documentation</a> &#187;</li>
-        <li class="nav-item nav-item-this"><a href="">Manage Synapse Credentials</a></li> 
+        <li class="nav-item nav-item-this"><a href="">Manage Synapse Credentials</a></li>
       </ul>
     </div>
     <div class="footer">
@@ -225,4 +225,4 @@ <h3>Navigation</h3>
       ga('send', 'pageview');
     </script>
   </body>
-</html>
+</html>