Merge pull request #797 from yarikoptic/enh-codespell

codespell: workflow, config, some typos fixed

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,*.pdf,*.svg,*.min.js,xtk.js,*.min.map,*.css,*.pkl,papaya.js,ahba_data
+ignore-regex = \b(FWE|TE)\b
+# ignore-words-list = 

.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

README.md

@@ -34,7 +34,7 @@ After making changes to the code you need to restart the server (but just the uw
 ```
 docker-compose restart nginx django worker
 ```
-### Reseting the server
+### Resetting the server
 If you would like to reset the server and clean the database:
 ```
 docker-compose stop

neurovault/CELERY_README.md

@@ -1,6 +1,6 @@
 # Setting Up Celery for NeuroVault
 
-Celery requires a task server. They recommend rabbitmq (and I tested this for the virtual machine) however django (a database) can also be used (but it's not recommended). The other option is redis, but they don't recommend because it is "suseptible to data loss in event of power failures"  This is really just like a task database or queue. I was going to do rabbit, but Gabriel said do redis, so I will do redis. Celery is python based so we install from pip.
+Celery requires a task server. They recommend rabbitmq (and I tested this for the virtual machine) however django (a database) can also be used (but it's not recommended). The other option is redis, but they don't recommend because it is "susceptible to data loss in event of power failures"  This is really just like a task database or queue. I was going to do rabbit, but Gabriel said do redis, so I will do redis. Celery is python based so we install from pip.
 
      source /opt/nv_env/bin/activate
      pip install -U celery[redis]

neurovault/apps/main/templates/FAQ.html

@@ -49,7 +49,7 @@ <h4>2. Why would I submit anything?</h4>
                     decoded
                     using <a href="http://neurosynth.org">neurosynth.org</a>.
                 </p>
-            <h4 id="persistance">3. How do I know my data is safe and will be
+            <h4 id="persistence">3. How do I know my data is safe and will be
                 available
                 for the years to come?</h4>
                 <p> All of NeuroVault is backed up daily into off site storage.

neurovault/apps/statmaps/migrations/0001_initial.py

@@ -71,7 +71,7 @@ class Migration(migrations.Migration):
                 ('file', models.FileField(max_length=500, storage=neurovault.apps.statmaps.storage.DoubleExtensionStorage(), upload_to=neurovault.apps.statmaps.models.upload_img_to, verbose_name='File with the unthresholded volume map (.img, .nii, .nii.gz)')),
                 ('surface_left_file', models.FileField(blank=True, null=True, storage=neurovault.apps.statmaps.storage.DoubleExtensionStorage(), upload_to=neurovault.apps.statmaps.models.upload_img_to, verbose_name='File with the unthresholded LEFT hemisphere fsaverage surface map (.mgh, .curv, .gii)')),
                 ('surface_right_file', models.FileField(blank=True, null=True, storage=neurovault.apps.statmaps.storage.DoubleExtensionStorage(), upload_to=neurovault.apps.statmaps.models.upload_img_to, verbose_name='File with the unthresholded RIGHT hemisphere fsaverage surface map (.mgh, .curv, .gii)')),
-                ('data_origin', models.CharField(blank=True, choices=[('volume', 'volume'), ('surface', 'surface')], default='volume', help_text='Was this map originaly derived from volume or surface?', max_length=200, null=True, verbose_name='Data origin')),
+                ('data_origin', models.CharField(blank=True, choices=[('volume', 'volume'), ('surface', 'surface')], default='volume', help_text='Was this map originally derived from volume or surface?', max_length=200, null=True, verbose_name='Data origin')),
                 ('target_template_image', models.CharField(choices=[('GenericMNI', 'Human (Generic/Unknown MNI)'), ('Dorr2008', 'Mouse (Dorr 2008 space)'), ('NMT', 'Rhesus - macacca mulatta (NMT)'), ('MNI152NLin2009cAsym', 'Human (MNI152 NLin 2009c Asym)')], default='GenericMNI', help_text='Name of target template image', max_length=200, verbose_name='Target template image')),
                 ('subject_species', models.CharField(blank=True, default='homo sapiens', max_length=200, null=True)),
                 ('figure', models.CharField(blank=True, help_text='Which figure in the corresponding paper was this map displayed in?', max_length=200, null=True, verbose_name='Corresponding figure')),

neurovault/apps/statmaps/models.py

@@ -1000,7 +1000,7 @@ class Image(BaseCollectionItem):
         verbose_name="File with the unthresholded RIGHT hemisphere fsaverage surface map (.mgh, .curv, .gii)",
     )
     data_origin = models.CharField(
-        help_text=("Was this map originaly derived from volume or surface?"),
+        help_text=("Was this map originally derived from volume or surface?"),
         verbose_name="Data origin",
         default="volume",
         max_length=200,
@@ -1156,7 +1156,7 @@ def create(
         niftiFile = File(f)
         image.file.save(my_file_name, niftiFile)
 
-        # If a .img file was loaded then load the correspoding .hdr file as well
+        # If a .img file was loaded then load the corresponding .hdr file as well
         _, ext = os.path.splitext(my_file_name)
         print(ext)
         if ext in [".img"]:

neurovault/apps/statmaps/templates/pycortex/dataview.html

@@ -185,7 +185,7 @@
             <div class='opt_category'>
                 <fieldset id="viewopt_fieldset" class='subtable'>
                     <legend>View</legend>
-                    <div class='display_opt' title="Enable to show slice planes. Not available in flat view. (Hotkeys: Q/W move saggital plane, A/S move coronal plane, Z/X move axial plane)">
+                    <div class='display_opt' title="Enable to show slice planes. Not available in flat view. (Hotkeys: Q/W move sagittal plane, A/S move coronal plane, Z/X move axial plane)">
                         <input id='volvis' type='checkbox'><label for='volvis'>Volume slices visible</label>
                     </div>
                     <div class='display_opt' title="Enable to show left hemisphere surface">

neurovault/apps/statmaps/templates/statmaps/atlas_details.html

@@ -99,7 +99,7 @@ <h5>Regions</h5>
                      <table id="image-regions-datatable" class="table table-striped table-sm w-100">
                          <thead>
                             <tr>
-                                <th>Intesity</th>
+                                <th>Intensity</th>
                                 <th>Name</th>
                             </tr>
                          </thead>

neurovault/apps/statmaps/templates/statmaps/my_metaanalyses.html

@@ -35,7 +35,7 @@
     <h2>My metanalyses</h2>
     <p>Here you can create, activate, and finalize (run inference on) your metaanalyses.
 			When you will have an active metaanalysis an "Add to the active metaanalysis" button
-        become present on comaptible (group level T or Z) maps.</p>
+        become present on compatible (group level T or Z) maps.</p>
     <div class="table-responsive-md">
         <table id="collections-table" class="table table-striped table-sm table-hover">
             <thead>

neurovault/apps/statmaps/templates/statmaps/statisticmap_details.html

@@ -200,19 +200,19 @@ <h2>{{ image.name }}</h2>
             </button>
             <div class="dropdown-menu" aria-labelledby="btnGroupDropAnalysis">
                 {% if neurosynth_compatible %}
-                    <a class="dropdown-item" href="http://neurosynth.org/decode/?neurovault={{ api_cid }}" data-toggle="tooltip" title="Cognitive decoding using coordiante based data collected from thousands of papers.">
+                    <a class="dropdown-item" href="http://neurosynth.org/decode/?neurovault={{ api_cid }}" data-toggle="tooltip" title="Cognitive decoding using coordinate based data collected from thousands of papers.">
                         Cognitive decoding (neurosynth)
                     </a>
                 {% endif %}
                 {% if comparison_is_possible %}
-                    <a class="dropdown-item" href="{% url 'statmaps:find_similar' image.id %}" data-toggle="tooltip" title="Find maps with similar patters.">
+                    <a class="dropdown-item" href="{% url 'statmaps:find_similar' image.id %}" data-toggle="tooltip" title="Find maps with similar patterns.">
                         Similar maps search
                     </a>
                 {% else %}
-                    <a class="dropdown-item disabled" tabindex="-1" role="button" aria-disabled="true" href="#" data-toggle="tooltip" title="Find maps with similar patters. This function is only enabled for public group level unthresholded statistical maps.">
+                    <a class="dropdown-item disabled" tabindex="-1" role="button" aria-disabled="true" href="#" data-toggle="tooltip" title="Find maps with similar patterns. This function is only enabled for public group level unthresholded statistical maps.">
                         Similar maps search
                     </a>
-                    <a class="dropdown-item disabled" tabindex="-1" role="button" aria-disabled="true" href="#" data-toggle="tooltip" title="Find genes with similar expression patters. This function is only enabled for public group level unthresholded statistical maps.">
+                    <a class="dropdown-item disabled" tabindex="-1" role="button" aria-disabled="true" href="#" data-toggle="tooltip" title="Find genes with similar expression patterns. This function is only enabled for public group level unthresholded statistical maps.">
                         Gene expression decoding
                     </a>
                 {% endif %}

neurovault/apps/statmaps/tests/test_data/api/VentralFrontal_thr75_summaryimage_2mm.xml

@@ -3,7 +3,7 @@
   <header>
     <name>Neubert Ventral Frontal connectivity-based parcellation</name>
     <shortname>Ventral Frontal CBP</shortname>
-    <type>Probabalistic</type>
+    <type>Probabilistic</type>
     <images>
       <imagefile>/NeubertVentralFrontalParcellation/VentralFrontal_thr25_2mm</imagefile>
       <summaryimagefile>/NeubertVentralFrontalParcellation/VentralFrontal_thr75_summaryimage_2mm</summaryimagefile>

neurovault/apps/statmaps/tests/test_data/api/unordered_VentralFrontal_thr75_summaryimage_2mm.xml

@@ -3,7 +3,7 @@
   <header>
     <name>Neubert Ventral Frontal connectivity-based parcellation</name>
     <shortname>Ventral Frontal CBP</shortname>
-    <type>Probabalistic</type>
+    <type>Probabilistic</type>
     <images>
       <imagefile>/NeubertVentralFrontalParcellation/VentralFrontal_thr25_2mm</imagefile>
       <summaryimagefile>/NeubertVentralFrontalParcellation/VentralFrontal_thr75_summaryimage_2mm</summaryimagefile>

neurovault/apps/statmaps/views.py

@@ -1597,7 +1597,7 @@ class ImagesInCollectionJson(BaseDatatableView):
     order_columns = ["", "pk", "name", "polymorphic_ctype.name", ""]
 
     def get_initial_queryset(self):
-        # return queryset used as base for futher sorting/filtering
+        # return queryset used as base for further sorting/filtering
         # these are simply objects displayed in datatable
         # You should not filter data returned here by any filter values entered by user. This is because
         # we need some base queryset to count total number of records.
@@ -1715,7 +1715,7 @@ class AtlasesAndParcellationsJson(BaseDatatableView):
     order_columns = ["", "name", "polymorphic_ctype.name"]
 
     def get_initial_queryset(self):
-        # return queryset used as base for futher sorting/filtering
+        # return queryset used as base for further sorting/filtering
         # these are simply objects displayed in datatable
         # You should not filter data returned here by any filter values entered by user. This is because
         # we need some base queryset to count total number of records.
@@ -1766,7 +1766,7 @@ class PublicCollectionsJson(BaseDatatableView):
     order_columns = ["name", "", "description", ""]
 
     def get_initial_queryset(self):
-        # return queryset used as base for futher sorting/filtering
+        # return queryset used as base for further sorting/filtering
         # these are simply objects displayed in datatable
         # You should not filter data returned here by any filter values entered by user. This is because
         # we need some base queryset to count total number of records.

scripts/preparing_AHBA_data.py

@@ -41,7 +41,7 @@
     urllib.request.urlretrieve(url, os.path.join(download_dir, "donor%d.zip" % (i + 1)))
     zipfile.ZipFile(os.path.join(download_dir, "donor%d.zip" % (i + 1)))
 
-# Dowloading MNI coordinates
+# Downloading MNI coordinates
 urllib.request.urlretrieve(
     "https://raw.githubusercontent.com/chrisfilo/alleninf/master/alleninf/data/corrected_mni_coordinates.csv",
     os.path.join(download_dir, "corrected_mni_coordinates.csv"))