Exclude few files and apply pre-commit throughout (#412)

* Remove requirement for python 3.9 to be used in pre-commit

AFAIK this is entirely not needed and in general just complicates
use of pre-commit on systems which no longer (for years) have 3.9
readily available

* Exclude .map and .svg files from pre-commit consideration

* [DATALAD RUNCMD] Run pre-commit run --all (Closes #411)

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "pre-commit run --all || :",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

.pre-commit-config.yaml

@@ -1,3 +1,4 @@
+exclude: \.(map|svg)$
 repos:
   -   repo: https://github.com/pre-commit/pre-commit-hooks
       rev: v2.3.0

neuvue_project/.ebextensions/django.config

@@ -1,17 +1,17 @@
-option_settings: 
-  aws:elasticbeanstalk:application:environment: 
-    DJANGO_SETTINGS_MODULE: "neuvue.settings" 
+option_settings:
+  aws:elasticbeanstalk:application:environment:
+    DJANGO_SETTINGS_MODULE: "neuvue.settings"
     PYTHONPATH: "/var/app/current:$PYTHONPATH"
-  aws:elasticbeanstalk:container:python: 
-    WSGIPath: neuvue.wsgi:application 
-    NumProcesses: 3 
+  aws:elasticbeanstalk:container:python:
+    WSGIPath: neuvue.wsgi:application
+    NumProcesses: 3
     NumThreads: 20
   aws:elasticbeanstalk:environment:proxy:staticfiles:
     /static: static
-  
+
 container_commands:
   01_collectstatic:
     command: "source /var/app/venv/*/bin/activate && python3 manage.py collectstatic --noinput"
   02_migrate:
     command: "source /var/app/venv/*/bin/activate && python3 manage.py migrate"
-    leader_only: true
+    leader_only: true

neuvue_project/.ebextensions/https.config

@@ -18,4 +18,4 @@ Resources:
               StatusCode: HTTP_301
             Type: redirect
         Port: 80
-        Protocol: HTTP
+        Protocol: HTTP

neuvue_project/.ebextensions/packages.config

@@ -2,4 +2,4 @@ packages:
   yum:
     python3-devel: []
     mariadb105-devel.x86_64: []
-    graphviz: []
+    graphviz: []

neuvue_project/.platform/nginx.config

@@ -1,3 +1,3 @@
 container_commands:
   01_reload_nginx:
-    command: "service nginx reload"
+    command: "service nginx reload"

neuvue_project/.platform/nginx/conf.d/proxy.conf

@@ -4,4 +4,4 @@ client_body_timeout     300;
 send_timeout            300;
 proxy_connect_timeout   300;
 proxy_read_timeout      300;
-proxy_send_timeout      300;
+proxy_send_timeout      300;

neuvue_project/dashboard/views.py

@@ -325,10 +325,14 @@ def post(self, request, *args, **kwargs):
             sieve=sieve,
             select=["assignee", "status", "duration", "metadata", "closed", "opened"],
         )
-        task_df['n_operation_ids'] = task_df['metadata'].apply(lambda x: len(x.get('operation_ids')) if isinstance(x.get('operation_ids'), list) else 0)
-        task_has_edits = True if any(task_df['n_operation_ids'].to_list()) else False
+        task_df["n_operation_ids"] = task_df["metadata"].apply(
+            lambda x: len(x.get("operation_ids"))
+            if isinstance(x.get("operation_ids"), list)
+            else 0
+        )
+        task_has_edits = True if any(task_df["n_operation_ids"].to_list()) else False
 
-        if bool((namespace in decision_namespaces) & (len(task_df)>0)):
+        if bool((namespace in decision_namespaces) & (len(task_df) > 0)):
             import plotly.express as px
             from plotly.subplots import make_subplots
 
@@ -343,14 +347,20 @@ def post(self, request, *args, **kwargs):
                 horizontal_spacing=0.02,
             )
 
-            namespace_submission_method = Namespaces.objects.get(display_name=display_name).submission_method
-            decision_types = ForcedChoiceButton.objects.filter(set_name=namespace_submission_method).values_list('display_name','submission_value')
-
+            namespace_submission_method = Namespaces.objects.get(
+                display_name=display_name
+            ).submission_method
+            decision_types = ForcedChoiceButton.objects.filter(
+                set_name=namespace_submission_method
+            ).values_list("display_name", "submission_value")
+
             color_count = 0
             for namespace_display_name, submission_value in decision_types:
                 decision_counts = {}
                 for assignee in users:
-                    decision_counts[assignee] = len(task_df[task_df["decision"] == submission_value])
+                    decision_counts[assignee] = len(
+                        task_df[task_df["decision"] == submission_value]
+                    )
 
                 x = list(decision_counts.keys())
                 y = list(decision_counts.values())
@@ -388,7 +398,7 @@ def post(self, request, *args, **kwargs):
             "Username",
             "Total Duration (h)",
             "Avg Closed Duration (m)",
-            "Avg Duration (m)"
+            "Avg Duration (m)",
         ]
         if task_has_edits:
             columns.extend(["Average Edits", "Total Edits"])
@@ -453,7 +463,7 @@ def post(self, request, *args, **kwargs):
             "fig_time": fig_time.to_html(),
         }
 
-        if bool((namespace in decision_namespaces) & (len(task_df)>0)):
+        if bool((namespace in decision_namespaces) & (len(task_df) > 0)):
             context["fig_decision"] = fig_decision.to_html()
 
         return render(request, "report.html", context)

neuvue_project/neuvue/settings.py

@@ -204,7 +204,7 @@
 LOGIN_URL = "index"
 LOGIN_REDIRECT_URL = "/tasks"
 LOGOUT_REDIRECT_URL = "/"
-SOCIALACCOUNT_LOGIN_ON_GET = True 
+SOCIALACCOUNT_LOGIN_ON_GET = True
 
 # Needed for NeuroGlancer Popups
 SECURE_CROSS_ORIGIN_OPENER_POLICY = None

neuvue_project/requirements.txt

@@ -98,4 +98,4 @@ urllib3==1.26.18
 wcwidth==0.1.9
 webcolors==1.13
 zipp==3.18.1
-./deps/neuvue-client 
+./deps/neuvue-client

neuvue_project/requirements.txt.general

@@ -19,4 +19,4 @@ pandas
 Pillow
 plotly
 requests
-./deps/neuvue-client 
+./deps/neuvue-client

neuvue_project/requirements.txt.old

@@ -79,4 +79,4 @@ typing-extensions==3.10.0.2
 urllib3==1.26.7
 wcwidth==0.1.9
 websocket-client==0.59.0
-./deps/neuvue-client 
+./deps/neuvue-client

neuvue_project/templates/404.html

@@ -163,4 +163,4 @@
     canvas { outline: none; border: none; }
 </style>
 
-{% endblock %}
+{% endblock %}

neuvue_project/templates/about.html

@@ -9,7 +9,7 @@
         <h1 class="pt-5 pb-3" aria-level="1"> About Us </h1>
 
         <p>
-            We are a team of research scientists and engineers from the Johns Hopkins Applied Physics 
+            We are a team of research scientists and engineers from the Johns Hopkins Applied Physics
             Laboratory that developed NeuVue with the help of a friendly <em>axon</em>olotl!
         </p>
 
@@ -25,21 +25,21 @@ <h1 class="pt-5 pb-3" aria-level="1"> About Us </h1>
         </div>
 
         <p>
-            NeuVue is a software platform created for large-scale proofreading of machine segmentation and neural 
-            circuit reconstruction in high-resolution electron microscopy connectomics datasets. NeuVue provides an 
-            intuitive interface for proofreaders to collaboratively view, annotate, and edit segmentation and 
+            NeuVue is a software platform created for large-scale proofreading of machine segmentation and neural
+            circuit reconstruction in high-resolution electron microscopy connectomics datasets. NeuVue provides an
+            intuitive interface for proofreaders to collaboratively view, annotate, and edit segmentation and
             connectivity data.
-            
-            NeuVue has everything you need for a high-throughput proofreading workflow! Analytical dashboards, data 
-            visualization tools, and simple API enables stakeholders real-time access to proofreading progress at an 
-            individual proofreader level as well as global reconstruction quality insights. NeuVue is intentionally 
-            agnostic to the underlying data management backend and can be easily deployed in an AWS environment. 
-            Proofreaders can work with powerful streamlined tools for splitting and merging connectivity data in 
-            dense nano-scale reconstruction better than ever before. 
+
+            NeuVue has everything you need for a high-throughput proofreading workflow! Analytical dashboards, data
+            visualization tools, and simple API enables stakeholders real-time access to proofreading progress at an
+            individual proofreader level as well as global reconstruction quality insights. NeuVue is intentionally
+            agnostic to the underlying data management backend and can be easily deployed in an AWS environment.
+            Proofreaders can work with powerful streamlined tools for splitting and merging connectivity data in
+            dense nano-scale reconstruction better than ever before.
         </p>
 
         <p class="fw-bold">
-            This research was enabled by the IARPA Machine Intelligence from Cortical Networks (MICrONS) program. 
+            This research was enabled by the IARPA Machine Intelligence from Cortical Networks (MICrONS) program.
             <a class="text-secondary-color-activated" href="https://www.iarpa.gov/research-programs/microns">Learn more about MICrONS.</a>
         </p>
 
@@ -88,4 +88,4 @@ <h2 class="pt-5 pb-3"> Contact Us </h2>
     </div>
 </div>
 <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/js/bootstrap.bundle.min.js" integrity="sha384-ka7Sk0Gln4gmtz2MlQnikT1wXgYsOg+OMhuP+IlRH9sENBO0LRn5q+8nbTov4+1p" crossorigin="anonymous"></script>
-{% endblock %}
+{% endblock %}

neuvue_project/templates/admin_dashboard/dashboard-namespace-view.html

@@ -40,7 +40,7 @@ <h3 class="d-flex flex-row bd-highlight mb-3 text-white">
               <div>
                 <div id="action-buttons" class="container-fluid">
                   <form id="taskPatchForm" action="" method="POST" class="form-inline float-start" >{% csrf_token %}
-                    
+
                     <input type="hidden" name="username" value="{{username}}" />
                     <input type="hidden" name="namespace" value="{{namespace}}" />
                     <label class="m-2"> Assign  </label>
@@ -64,13 +64,13 @@ <h3 class="d-flex flex-row bd-highlight mb-3 text-white">
                     <button type="button" id="distribute-button" form="taskPatchForm" name="selected_action" value="distribute" class="btn btn-primary" >
                       Distribute Tasks
                     </button>
-                    
+
                   </form>
                 </div>
                 <br><br>
-                <hr>  
+                <hr>
               </div>
-              
+
             {% endif %}
             <table id="summary-table" class="table table-striped table-hover">
               <thead>
@@ -130,7 +130,7 @@ <h3 class="d-flex flex-row bd-highlight mb-3 text-white">
     // Perform download
     $('#summary-table').table2csv('download', {'filename': filename});
 
-  }); 
+  });
     // button is clicked
     if ("{{group}}" === "unassigned") {
       const distributeButton = document.getElementById("distribute-button");

neuvue_project/templates/admin_dashboard/dashboard-user-view.html

@@ -119,13 +119,13 @@ <h3 class="d-flex flex-row bd-highlight mb-3 text-white">
                     <td>{{taskrow.closed}}</td>
                     <td>{{taskrow.duration}}</td>
                     {% if taskrow.tags %}
-                    <td class='userTags'> 
-                      <span 
-                        data-bs-toggle="tooltip" 
-                        data-bs-placement="right" 
+                    <td class='userTags'>
+                      <span
+                        data-bs-toggle="tooltip"
+                        data-bs-placement="right"
                         data-bs-html="true"
                         title="{{taskrow.tags|join:", "}}" >
-                        {{ taskrow.tags.0 }} 
+                        {{ taskrow.tags.0 }}
                       </span>
                       </td>
                       {% else %}
@@ -142,7 +142,7 @@ <h3 class="d-flex flex-row bd-highlight mb-3 text-white">
     </div>
 
   </div>
-  <div id="hiddenSelectedTable" style="visibility: none;"> 
+  <div id="hiddenSelectedTable" style="visibility: none;">
 </div>
 
 <!-- Confirm action modals -->
@@ -213,13 +213,13 @@ <h3 class="d-flex flex-row bd-highlight mb-3 text-white">
         $('#summary-table input[name=selected_tasks]').each(function(){
           if ($(this).is(':checkbox') && !$(this).is(":checked")) {
             $(this).prop( "checked", true );
-          } 
+          }
         })
       } else {
         $('#summary-table input[name=selected_tasks]').each(function(ele){
           if ($(this).is(':checkbox') && $(this).is(":checked")) {
             $(this).prop( "checked", false );
-          } 
+          }
         })
       }
     });
@@ -239,7 +239,7 @@ <h3 class="d-flex flex-row bd-highlight mb-3 text-white">
       // Otherwise, download only the tasks that were selected
       } else {
         let filteredTable = $('#summary-table').clone()[0] // make a copy of the visible table to edit and export
-        filteredTable.id = 'userSelectedTable'; 
+        filteredTable.id = 'userSelectedTable';
         const selectedRows = $( '#summary-table' ).find( 'tbody' ) // select table body and
             .find( 'tr' ) // select all rows that has
             .has( 'input[type=checkbox]:checked' ); // checked checkbox element

neuvue_project/templates/admin_dashboard/dashboard.html

@@ -37,25 +37,25 @@ <h3 class="text-white"> Admin Dashboard</h3>
                         </select>
 
                     </div>
-                    
+
                     <div class="form-group my-3">
                         <label class="text-white" for="groupSelect">Group</label>
                         <select name="group" class="form-select" id="groupSelect" placeholder="Select one" required="true">
                             <option value="" selected disabled>Please select</option>
                             {% for group_opt in all_groups %}
                             <option>{{group_opt}} </option>
                             {% endfor %}
-                        </select> 
+                        </select>
                     </div>
 
                     <div class="form-group d-flex my-4">
                         <input type="submit" class="btn btn-primary" value="Submit">
                         <div id="submit-spinner-tab1" class="text-white ms-3 mt-2"></div>
-                        
+
                         {% if error %}
                         <small id="errormessage" class="form-text text-danger"> {{error}} </small>
                         {% endif %}
-                    
+
                     </div>
                 </form>
             </div>
@@ -70,17 +70,17 @@ <h3 class="text-white"> Admin Dashboard</h3>
                             {% for user_opt in all_users %}
                             <option>{{user_opt}} </option>
                             {% endfor %}
-                        </select> 
+                        </select>
                     </div>
 
                     <div class="form-group d-flex my-4">
                         <input type="submit" class="btn btn-primary" value="Submit">
                         <div id="submit-spinner-tab2" class="text-white ms-3 mt-2"></div>
-                        
+
                         {% if error %}
                         <small id="errormessage" class="form-text text-danger"> {{error}} </small>
                         {% endif %}
-                    
+
                     </div>
                 </form>
             </div>
@@ -106,4 +106,3 @@ <h3 class="text-white"> Admin Dashboard</h3>
 
 </script>
 {% endblock %}
-

neuvue_project/templates/base.html

@@ -14,7 +14,7 @@
     <link rel="preconnect" href="https://fonts.googleapis.com">
     <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
     <link href="https://fonts.googleapis.com/css2?family=Fira+Mono:wght@400;500&family=Montserrat:wght@500;700&family=Open+Sans:wght@400;600&display=swap" rel="stylesheet">
-    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/all.min.css"/>   
+    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/all.min.css"/>
     <link rel="apple-touch-icon" sizes="180x180" href="{% static 'favicon/apple-touch-icon.png' %}">
     <link rel="icon" type="image/png" sizes="32x32" href="{% static 'favicon/favicon-32x32.png' %}">
     <link rel="icon" type="image/png" sizes="16x16" href="{% static 'favicon/favicon-16x16.png' %}">
@@ -50,7 +50,7 @@
             </li>
 
             {% endif%}
-          
+
             {% if request.user|in_group:"AuthorizedUsers"%}
 
             <li class="nav-item">

neuvue_project/templates/getting-started.html

@@ -48,9 +48,9 @@
             var scrollLocation = headers[headerIndex]
         } else {
             var scrollLocation = document.getElementsByClassName('getting-started-content')[0];
-        } 
+        }
         scrollLocation.scrollIntoView({behavior: "smooth", block: "start", inline: "nearest"});
     }
 
 </script>
-{% endblock %}
+{% endblock %}

neuvue_project/templates/index.html

@@ -43,7 +43,7 @@ <h1 class="index-title-text mt-4 my-1">Welcome to NeuVue</h1>
               </div>
             </div>
           </div>
-        <div class="index-card-column">        
+        <div class="index-card-column">
         </div>
       </div>
     </div>