neuroscout · yarikoptic · Jul 2, 2023 · Jun 16, 2023 · Jun 16, 2023 · Jun 16, 2023
diff --git a/.codespellrc b/.codespellrc
@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,*.pdf,*.svg,bibliography.json,yarn.lock,tslint.json,lunr.js
+# Mor - name
+ignore-words-list = mor,ser,pres
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
diff --git a/README.md b/README.md
@@ -26,7 +26,7 @@ and saving as `neuroscout/frontend/src/config.ts`.
 For single sign on using Google, a [sign-in project](https://developers.google.com/identity/sign-in/web/sign-in) is needed.
 
 
-## Initalizing backend
+## Initializing backend
 Build the containers and start services using the development configuration:
 
     docker-compose -f docker-compose.yml -f docker-compose.dev.yml build
@@ -36,7 +36,7 @@ The server should now be running at http://localhost/
 
 Next, initialize, migrate and upgrade the database migrations.
 If you have a database file, load it using `pg_restore`. Otherwise, delete the migrations folder,
-initalize the database and add a test user.
+initialize the database and add a test user.
 
     docker-compose exec neuroscout bash
     rm -rf /migrations/migrations

diff --git a/neuroscout/auth.py b/neuroscout/auth.py
@@ -104,7 +104,7 @@ def _find_create_google(ginfo):
 
 def authenticate(username, password):
     """ Authenticate user and password combination
-    Returns user object if succesful, otherwise None """
+    Returns user object if successful, otherwise None """
     if username == 'GOOGLE':
         ginfo = _authenticate_google(password)
         if ginfo:

diff --git a/neuroscout/config/feature_schema.json b/neuroscout/config/feature_schema.json
@@ -428,7 +428,7 @@
           "description": "Mean concreteness rating of spoken words."
         },
         "aoa.AoA_Kup": {
-          "description": "Age of aquisition of spoken words."
+          "description": "Age of acquisition of spoken words."
         },
         "massiveauditorylexicaldecision_IsWord": {
           "description": "Whether the item is a word or pseudo-word."

diff --git a/neuroscout/config/predictor_schema.json b/neuroscout/config/predictor_schema.json
@@ -16,7 +16,7 @@
     "source": "fmriprep"
   },
   "^framewise_displacement$": {
-    "description": "Esimated bulk-head motion",
+    "description": "Estimated bulk-head motion",
     "source": "fmriprep"
   },
   "^non_steady_state_outlier([0-9]{2,3})$": {

diff --git a/neuroscout/frontend/public/index.html b/neuroscout/frontend/public/index.html
@@ -15,6 +15,15 @@
     -->
     <title>Neuroscout</title>
     <script async src="https://w.appzi.io/w.js?token=9vQ1A"></script>
+    <!-- Google tag (gtag.js) -->
+    <script async src="https://www.googletagmanager.com/gtag/js?id=G-WHXN332J31"></script>
+    <script>
+      window.dataLayer = window.dataLayer || [];
+      function gtag(){dataLayer.push(arguments);}
+      gtag('js', new Date());
+
+      gtag('config', 'G-WHXN332J31');
+    </script>
     <script defer data-domain="neuroscout.org" src="https://plausible.io/js/plausible.js"></script>
   </head>
   <body>

diff --git a/neuroscout/frontend/src/HelperComponents.tsx b/neuroscout/frontend/src/HelperComponents.tsx
@@ -6,7 +6,7 @@ import { Link } from 'react-router-dom'
 import { predictorColor } from './utils'
 import { Predictor } from './coretypes'
 
-// Simple space component to seperate buttons, etc.
+// Simple space component to separate buttons, etc.
 // eslint-disable-next-line react/self-closing-comp
 export const Space = () => <span> </span>
 

diff --git a/neuroscout/frontend/src/analysis_builder/Builder.tsx b/neuroscout/frontend/src/analysis_builder/Builder.tsx
@@ -785,7 +785,7 @@ export default class AnalysisBuilder extends React.Component<
   }
 
   // run any time we attempt to leave tab
-  // xform and contrast checks are more or less the same save validate funciton call...
+  // xform and contrast checks are more or less the same save validate function call...
   preTabChange = (nextTab: TabName): boolean => {
     let errors: string[] = []
     if (this.state.activeTab === 'transformations') {

diff --git a/neuroscout/frontend/src/analysis_builder/Overview.tsx b/neuroscout/frontend/src/analysis_builder/Overview.tsx
@@ -90,7 +90,7 @@ export class OverviewTab extends React.Component<
 
   applyFilter = (pagination, filters, sorter, extra): void => {
     /* If we have no set filters, but some selected subjects and we change pages then all subjects will
-     * be selected. To prevent this we return immediatly if no filters are set.
+     * be selected. To prevent this we return immediately if no filters are set.
      */
     if (
       Object.keys(filters)

diff --git a/neuroscout/frontend/src/analysis_builder/Transformations.tsx b/neuroscout/frontend/src/analysis_builder/Transformations.tsx
@@ -1,5 +1,5 @@
 /*
-This module comtains the following components:
+This module contains the following components:
  - XformsTab: parent component implementing the transformation tab of the analysis builder.
  - XformDisplay: component to display a single transformation
  - XformEditor: component to add/edit a transformtion
@@ -59,7 +59,7 @@ export function validateXform(xform: Transformation) {
   }
   if (xform.Name === 'Orthogonalize' && xform.Input !== undefined) {
     if (xform.Other === undefined || xform.Other.length < 1) {
-      errors.push('Must orthoganalize with respect to at least one predictor')
+      errors.push('Must orthogonalize with respect to at least one predictor')
     }
   }
 

diff --git a/neuroscout/frontend/src/browser/AnalysisList.tsx b/neuroscout/frontend/src/browser/AnalysisList.tsx
@@ -1,5 +1,5 @@
 /*
-Resuable AnalysisList component used for displaying a list of analyses, e.g. on
+Reusable AnalysisList component used for displaying a list of analyses, e.g. on
 the home page or on the 'browse public analysis' page
 */
 import * as React from 'react'

diff --git a/neuroscout/frontend/src/user.ts b/neuroscout/frontend/src/user.ts
@@ -319,7 +319,7 @@ export class UserStore {
         Modal.success({
           title: 'Account created!',
           content:
-            'Your account has been sucessfully created. \
+            'Your account has been successfully created. \
         You will receive a confirmation email shortly. Please follow the instructions to activate your account\
         and start using Neuroscout. ',
           okText: 'Okay',

diff --git a/neuroscout/frontend/src/utils/index.ts b/neuroscout/frontend/src/utils/index.ts
@@ -135,7 +135,7 @@ const _sortRuns = (keys, a, b) => {
   return 0
 }
 
-// Comparison functions to pass to sort for arrays of type Run by differnt keys
+// Comparison functions to pass to sort for arrays of type Run by different keys
 export const sortSub = _sortRuns.bind(null, ['subject', 'number', 'session'])
 export const sortNum = _sortRuns.bind(null, ['number', 'subject', 'session'])
 export const sortSes = _sortRuns.bind(null, ['session', 'subject', 'number'])

diff --git a/neuroscout/models/predictor.py b/neuroscout/models/predictor.py
@@ -51,7 +51,7 @@ def float_values(self):
 
 
     def get_top_bottom(self, bottom=False, limit=None):
-        """ Get the Stimuli associated with the top or botton N values for this Predictor """
+        """ Get the Stimuli associated with the top or bottom N values for this Predictor """
         try:
             val = cast(ExtractedEvent.value, Float)
             if bottom:

diff --git a/neuroscout/populate/annotate.py b/neuroscout/populate/annotate.py
@@ -21,7 +21,7 @@ def __init__(self, schema, add_all):
 
 class PredictorSerializer(Serializer):
     def __init__(self, add_all=True, include=None, exclude=None, TR=None):
-        """ Initalize serializer for ingested features.
+        """ Initialize serializer for ingested features.
         Args:
             add_all - Add all variables including those not in the schema
             include - List of variables to include
@@ -140,7 +140,7 @@ def _annotate_feature(self, pattern, schema, feat, extractor, sub_df,
             sub_df - df with ef values
             default_active - set to active by default?
         """
-        # If name is in schema, substitue regex patterns from schema pattern
+        # If name is in schema, substitute regex patterns from schema pattern
         # and fill in format strings from extractor_dict
         feat = feat.replace(',', '')  # Remove commas
         if 'name' in schema:

diff --git a/neuroscout/populate/extract.py b/neuroscout/populate/extract.py
@@ -77,7 +77,7 @@ def _extract_to_serial(graphs, stim_object, serializer):
     """ For a stim_object, load stim and apply graphs, and serialize """
     results = []
     for stim_obj, pliers_stim in _load_stim(stim_object):
-        # For each graph, check compatability, and then extract
+        # For each graph, check compatibility, and then extract
         for graph in graphs:
             ext = graph.roots[0].transformer
             if ext._stim_matches_input_types(pliers_stim):

diff --git a/neuroscout/populate/ingest.py b/neuroscout/populate/ingest.py
@@ -165,7 +165,7 @@ def add_task(task_name, dataset_name, local_path,
             include_predictors - set of predictors to ingest
             exclude_predictors - set of predictors to exclude from ingestions
             reingest - force reingesting even if dataset already exists
-            scan_length - default scan length in case it cant be found in image
+            scan_length - default scan length in case it can't be found in image
             summary - Task summary description,
             layout - Preinstantiated BIDSLayout
             kwargs - arguments to filter runs by

diff --git a/neuroscout/populate/setup.py b/neuroscout/populate/setup.py
@@ -218,7 +218,7 @@ def ingest_from_json(config_file, reingest=False, auto_fetch=False):
 
 def extract_from_json(extract_config, dataset_name=None, task_name=None):
     """ Applies JSON file specifying conversion and extractions to
-    specifed tasks.
+    specified tasks.
 
     Args:
         extract_config: JSON specifying the arguments to each step

diff --git a/neuroscout/populate/utils.py b/neuroscout/populate/utils.py
@@ -50,11 +50,11 @@ def hash_stim(stim, blocksize=65536):
         filename = stim.history.source_file \
                     if stim.history \
                     else stim.filename
-        with open(filename, 'rb') as afile:
-            buf = afile.read(blocksize)
+        with open(filename, 'rb') as f:
+            buf = f.read(blocksize)
             while len(buf) > 0:
                 hasher.update(buf)
-                buf = afile.read(blocksize)
+                buf = f.read(blocksize)
 
     return hasher.hexdigest()
 

diff --git a/neuroscout/resources/user.py b/neuroscout/resources/user.py
@@ -114,7 +114,7 @@ def post(self, **kwargs):
         else:
             user.password = kwargs['password']
             db.session.commit()
-            return {'message': 'Password reset succesfully.'}
+            return {'message': 'Password reset successfully.'}
 
 
 class UserPredictorListResource(MethodResource):

diff --git a/neuroscout/resources/utils.py b/neuroscout/resources/utils.py
@@ -62,7 +62,7 @@ def wrapper(*args, **kwargs):
 def owner_required(function):
     """ A JWT matching the user id of the analysis is required,
         assumes analysis id is second argument, and replaces id with
-        Analysis object if succesfull. """
+        Analysis object if successful. """
     @auth_required
     @fetch_analysis
     def wrapper(*args, **kwargs):

diff --git a/neuroscout/schemas/dataset.py b/neuroscout/schemas/dataset.py
@@ -13,13 +13,13 @@ class DatasetSchema(Schema):
     summary = fields.Str(
         description='Dataset summary description')
     url = fields.Str(
-        descrption='Link to external resources')
+        description='Link to external resources')
     mimetypes = fields.List(
         fields.Str(), description='Dataset mimetypes/modalities')
     mean_age = fields.Float(
-        descrption='Mean age in years of subjects')
+        description='Mean age in years of subjects')
     percent_female = fields.Float(
-        descrption='Percent female subjects')
+        description='Percent female subjects')
     runs = fields.Pluck(
         'RunSchema', 'id', many=True)
     tasks = fields.Nested(

diff --git a/neuroscout/tests/api/test_analyses.py b/neuroscout/tests/api/test_analyses.py
@@ -145,7 +145,7 @@ def test_post(auth_client, add_task, add_predictor):
     assert Analysis.query.filter_by(
         hash_id=rv_json['hash_id']).one().name == 'some analysis'
 
-    # Re post analysis, check that id is diffeent
+    # Re post analysis, check that id is different
     rv_2 = auth_client.post('/api/analyses', data=test_analysis)
     assert rv_2.status_code == 200
     assert decode_json(rv_2)['hash_id'] != decode_json(resp)['hash_id']

diff --git a/neuroscout/tests/api/test_dataset.py b/neuroscout/tests/api/test_dataset.py
@@ -22,6 +22,6 @@ def test_get_dataset(auth_client, add_local_task_json):
     assert dataset['summary'] == "A test dataset"
     assert dataset['url'] == "https://github.com/adelavega/bids_test"
 
-    # Try getting nonexistent datset
+    # Try getting nonexistent dataset
     resp = auth_client.get('/api/datasets/{}'.format('1324'))
     assert resp.status_code == 404
diff --git a/neuroscout/tests/conftest.py b/neuroscout/tests/conftest.py
@@ -11,7 +11,7 @@
 from .. import populate
 
 """
-Session / db managment tools
+Session / db management tools
 """
 
 

diff --git a/site/builder/transformations/index.html b/site/builder/transformations/index.html
@@ -181,7 +181,7 @@ <h1 id="add-transformations">Add Transformations</h1>
 <p>The next step in defining model is to transform the variables you've selected. This step is optional-- for many models you may not need to make any modifications to the input variables.</p>
 <p>To add a transformation, click <code>Add Transformation</code> and select an operation from the dropdown list.</p>
 <p><img alt="Add transformation" src="../img/transformation_add.png" /></p>
-<p>The transformations currently supported by Neuroscout are a subset of the complete set of transformations detailed in the <a href="https://docs.google.com/document/d/1bq5eNDHTb6Nkx3WUiOBgKvLNnaa5OMcGtD0AZ9yms2M/edit?usp=sharing">BIDS StatsModel specification</a> (in active development). As Neuroscout matures, the number of suppport transformations will grow.</p>
+<p>The transformations currently supported by Neuroscout are a subset of the complete set of transformations detailed in the <a href="https://docs.google.com/document/d/1bq5eNDHTb6Nkx3WUiOBgKvLNnaa5OMcGtD0AZ9yms2M/edit?usp=sharing">BIDS StatsModel specification</a> (in active development). As Neuroscout matures, the number of support transformations will grow.</p>
 <table>
 <thead>
 <tr>

diff --git a/site/css/theme_extra.css b/site/css/theme_extra.css
@@ -178,7 +178,7 @@ form .search-query {
 
 /*
  * Account for wide tables which go off the side.
- * Override borders to avoid wierdness on narrow tables.
+ * Override borders to avoid weirdness on narrow tables.
  *
  * https://github.com/mkdocs/mkdocs/issues/834
  * https://github.com/mkdocs/mkdocs/pull/1034

diff --git a/site/search/search_index.json b/site/search/search_index.json