Merge pull request #313 from yarikoptic/enh-codespell

add codespell: config, workflow and have typos fixed

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,*.pdf,*.svg,versioneer.py,sub-*.json
+#
+ignore-words-list = covert

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+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

datasets/eeg_ds002893s_hed_attention_shift/README

@@ -58,7 +58,7 @@ between 200 and 800 ms.
 
 **Note 1**:  ERP measure results for the FA and FV conditions only were presented in Ceponiene, R., Westerfield, M., Torki, M. and Townsend, J., 2008. Modality-specificity of sensory aging in vision and audition: evidence from event-related potentials.?Brain research,?1215, pp.53-68. Some unpublished results by Christian Kothe and Scott Makeig on the SH condition may be available from the authors <[email protected]> <[email protected]>.
 
-**Note 2**: The code subdirectory has several auxilliary files that were produced during
+**Note 2**: The code subdirectory has several auxiliary files that were produced during
 the curation process. The curation was done using a series of Jupyter notebooks
 that are available as run in the code/curation_notebooks subdirectory.
 

datasets/fmri_ds002790s_hed_aomic/participants.json

@@ -34,7 +34,7 @@
     "Description": "Self-reported religious affiliation",
     "Levels": {
       "no": "No religious affiliation",
-      "yes": "Considers him/herself to be religous" 
+      "yes": "Considers him/herself to be religious" 
     }
   },
   "raven_score": {

docs/source/HedConditionsAndDesignMatrices.md

@@ -346,7 +346,7 @@ Example 9 shows the portion of the
 [**task-facePerception_events.json**](./_static/data/task-FacePerception_events.json)
 that encodes information about the *setup_right_sym* event found as the first event
 in the event file excerpt of Example 8.
-This excerpt only contains the relevent definition and the relevant annotation.
+This excerpt only contains the relevant definition and the relevant annotation.
 
 
 ````{admonition} Example 9: Excerpt of the JSON sidecar relevant to the *setup_right_sym* event.

docs/source/HedMatlabTools.md

@@ -329,7 +329,7 @@ in the *EEG.event* data structure in sufficient detail that anyone using the dat
 in the future will not need to find and read a separate, detailed description of the dataset
 or study to understand the recorded experimental events. 
 As demonstrated below, such annotation will allow us to extract epochs using meaningful
-HED tags instead of the alpha-numeric codes often associated with shared EEG data.
+HED tags instead of the alphanumeric codes often associated with shared EEG data.
 
 #### Launching EEGLAB HEDTools
 To add and view HED tags for the dataset, from EEGLAB menu, select:  
@@ -608,7 +608,7 @@ to indicate the command line version.
 
 Use the MATLAB `pyenv` function again without arguments to check that your installation is as expected.
 
-````{Admonition} Example response for pyenv all with no argments after setting environment.
+````{Admonition} Example response for pyenv all with no arguments after setting environment.
 
 ```matlab
  PythonEnvironment with properties:

docs/source/HedOnlineTools.md

@@ -406,7 +406,7 @@ The non-HED portions of the spreadsheet and the prefix-columns are the same as i
    
 **Returns:**  
 If there are any errors, the tool returns a downloadable `.txt` file of error messages,
-otherise the tool returns a downloadable spreadsheet with the HED tags converted to short.  
+otherwise the tool returns a downloadable spreadsheet with the HED tags converted to short.  
 ``````
 
 (strings-online-tools-anchor)=

docs/source/HedPythonTools.md

@@ -290,10 +290,6 @@ file_list = get_file_list(bids_root_path, extensions=[ ".json", ".tsv"], name_su
 
 The HED tools provide both generic and BIDS-specific classes for dictionaries of filenames.
 
-
-The 
-Many of the HED data processing tools make extensive use of dictionaries specif
-
 #### BIDS-specific dictionaries of files
 
 Files in BIDS have unique names that indicate not only what the file represents, 
@@ -436,7 +432,7 @@ and then to log each processing step using the file's key.
 This allows a processing step to be applied to all the relevant files in the dataset.
 After all the processing is complete, the `print_log` method
 outputs the logged messages by key, thus showing all the
-processing steps that hav been applied to each file
+processing steps that have been applied to each file
 as shown in the [**previous example**](example-output-hed-logger-anchor).
 
 (using-hed-logger-example-anchor)=

docs/source/HedSchemaDevelopersGuide.md

@@ -310,7 +310,7 @@ Drive has tags of interest to driving experiments.
 ```
 ````
 
-Notice that this schema does not include any auxilliary sections --- these are inherited
+Notice that this schema does not include any auxiliary sections --- these are inherited
 from the standard schema.
 
 This schema would be saved in a MediaWiki file called `HED_drive_0.0.1.mediawiki`.

docs/source/HedSearchGuide.md

@@ -127,7 +127,7 @@ The tag short forms are used for the matching to assure consistency.
 Matching using a tag prefix with the `*` wildcard, matches the starting portion of the tag.
 Thus, <em>Age/3*</em> matches *Age/3* as well as *Age/34*.
 
-Notice that the query <em>Age*</em> matches a myraid of tags including *Agent*, *Agent-state*,
+Notice that the query <em>Age*</em> matches a myriad of tags including *Agent*, *Agent-state*,
 and *Agent-property*.
 
 ### Logical queries

hedcode/data/schema_data/HED7.2.0.xml

@@ -280,7 +280,7 @@ From version 2.2, HED adheres to http://semver.org/ versioning. </prologue>
       </node>
       <node>
          <name>Object</name>
-         <description>Visually discernable objects. This item excludes sounds that are Items but not objects</description>
+         <description>Visually discernible objects. This item excludes sounds that are Items but not objects</description>
          <node>
             <name>Vehicle</name>
             <node>
@@ -3645,7 +3645,7 @@ From version 2.2, HED adheres to http://semver.org/ versioning. </prologue>
          <name>Pyramids and palm trees task</name>
       </node>
       <node>
-         <name>Rapid automatized naming test</name>
+         <name>Rapid automated naming test</name>
       </node>
       <node>
          <name>Rapid serial object transformation</name>

hedcode/data/schema_data/HED8.0.0.mediawiki

@@ -170,7 +170,7 @@ This schema is the first official release that includes an xsd and requires unit
 ** Learn <nowiki>[Adaptively change behavior as the result of experience.]</nowiki>
 ** Memorize <nowiki>[Adaptively change behavior as the result of experience.]</nowiki>
 ** Plan <nowiki>[Think about the activities required to achieve a desired goal. ]</nowiki>
-** Predict <nowiki>[Say or estimate that something will happen or will be a consequence of something without having exact informaton.]</nowiki>
+** Predict <nowiki>[Say or estimate that something will happen or will be a consequence of something without having exact information.]</nowiki>
 ** Recognize <nowiki>[Identify someone or something from having encountered them before.]</nowiki>
 ** Respond <nowiki>[React to something such as a treatment or a stimulus.]</nowiki>
 ** Recall <nowiki>[Remember information by mental effort.]</nowiki>
@@ -324,7 +324,7 @@ This schema is the first official release that includes an xsd and requires unit
 ***** Clock <nowiki>[A device designed to indicate the time of day or to measure the time duration of an event or action.]</nowiki>
 ****** Clock-face <nowiki>[A location identifier based on clockface numbering or anatomic subregion.]</nowiki>
 **** Robot <nowiki>[A mechanical device that sometimes resembles a living animal and is capable of performing a variety of often complex human tasks on command or by being programmed in advance.]</nowiki>
-**** Tool <nowiki>[A component that is not part of a device but is designed to support its assemby or operation.]</nowiki>
+**** Tool <nowiki>[A component that is not part of a device but is designed to support its assembly or operation.]</nowiki>
 ***	Document <nowiki>[A physical object, or electronic counterpart, that is characterized by containing writing which is meant to be human-readable.]</nowiki>
 **** Letter <nowiki>[A written message addressed to a person or organization.]</nowiki>
 **** Note <nowiki>[A brief written record.]</nowiki>
@@ -370,7 +370,7 @@ This schema is the first official release that includes an xsd and requires unit
 **** Cart <nowiki>[A cart is a vehicle which has two wheels and is designed to transport human passengers or cargo.]</nowiki>
 **** Tractor <nowiki>[A mobile machine specifically designed to deliver a high tractive effort at slow speeds, and mainly used for the purposes of hauling a trailer or machinery used in agriculture or construction.]</nowiki>
 **** Train <nowiki>[A connected line of railroad cars with or without a locomotive.]</nowiki>
-**** Truck <nowiki>[A motor vehicle which, as its primary funcion, transports cargo rather than human passangers.]</nowiki>
+**** Truck <nowiki>[A motor vehicle which, as its primary function, transports cargo rather than human passangers.]</nowiki>
 ** Natural-object <nowiki>[Something that exists in or is produced by nature, and is not artificial or man-made.]</nowiki>
 *** Mineral <nowiki>[A solid, homogeneous, inorganic substance occurring in nature and having a definite chemical composition.]</nowiki>
 *** Natural-feature <nowiki>[A feature that occurs in nature. A prominent or identifiable aspect, region, or site of interest.]</nowiki>
@@ -380,7 +380,7 @@ This schema is the first official release that includes an xsd and requires unit
 **** River <nowiki>[A natural freshwater surface stream of considerable volume and a permanent or seasonal flow, moving in a definite channel toward a sea, lake, or another river.]</nowiki>
 **** Waterfall <nowiki>[A sudden descent of water over a step or ledge in the bed of a river.]</nowiki>
 * Sound <nowiki>[Mechanical vibrations transmitted by an elastic medium. Something that can be heard.]</nowiki>
-** Environmental-sound<nowiki>[Sounds occuring in the environment. An accumulation of noise pollution that occurs outside. This noise can be caused by transport, industrial, and recreational activities.]</nowiki>
+** Environmental-sound<nowiki>[Sounds occurring in the environment. An accumulation of noise pollution that occurs outside. This noise can be caused by transport, industrial, and recreational activities.]</nowiki>
 *** Crowd-sound <nowiki>[Noise produced by a mixture of sounds from a large group of people.]</nowiki>
 *** Signal-noise <nowiki>[Any part of a signal that is not the true or original signal but is introduced by the communication mechanism.]</nowiki>
 ** Musical-sound <nowiki>[Sound produced by continuous and regular vibrations, as opposed to noise.]</nowiki>
@@ -581,7 +581,7 @@ This schema is the first official release that includes an xsd and requires unit
 **** Weight <nowiki>[The relative mass or the quantity of matter contained by something.]</nowiki>
 ***** <nowiki># {takesValue, valueClass=numericClass, unitClass=weightUnits}</nowiki>
 *** Quantitative-value <nowiki>[Something capable of being estimated or expressed with numeric values.] </nowiki> 
-**** Fraction <nowiki>[A numerical value betwee 0 and 1.]</nowiki>
+**** Fraction <nowiki>[A numerical value between 0 and 1.]</nowiki>
 ***** <nowiki># {takesValue, valueClass=numericClass}</nowiki>
 **** Item-count <nowiki>[The integer count of something which is usually grouped with the entity it is counting. (Item-count/3, A) indicates that 3 of A have occurred up to this point.]</nowiki>
 ***** <nowiki># {takesValue, valueClass=numericClass}</nowiki>  
@@ -608,7 +608,7 @@ This schema is the first official release that includes an xsd and requires unit
 ***** <nowiki># {takesValue, valueClass=numericClass}</nowiki> 
 **** Statistical-precision <nowiki>[A quantitative representation of the degree of accuracy necessary for or associated with a particular action.]</nowiki>
 ***** <nowiki># {takesValue, valueClass=numericClass}</nowiki> 
-**** Statistical-recall <nowiki>[Sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1.]</nowiki>
+**** Statistical-recall <nowiki>[Sensitivity is a measurement datum qualifying a binary classification test and is computed by subtracting the false negative rate to the integral numeral 1.]</nowiki>
 ***** <nowiki># {takesValue, valueClass=numericClass}</nowiki> 
 **** Statistical-uncertainty <nowiki> [A measure of the inherent variability of repeated observation measurements of a quantity including quantities evaluated by statistical methods and by other means.]</nowiki>
 ***** <nowiki># {takesValue, valueClass=numericClass}</nowiki>
@@ -689,7 +689,7 @@ This schema is the first official release that includes an xsd and requires unit
 ** Urban <nowiki>[Relating to, located in, or characteristic of a city or densely populated area.]</nowiki>
 ** Rural <nowiki>[Of or pertaining to the country as opposed to the city.]</nowiki>
 ** Terrain <nowiki>[Characterization of the physical features of a tract of land.]</nowiki>
-*** Composite-terrain <nowiki>[Tracts of land characterized by a mixure of physical features.]</nowiki>
+*** Composite-terrain <nowiki>[Tracts of land characterized by a mixture of physical features.]</nowiki>
 *** Dirt-terrain <nowiki>[Tracts of land characterized by a soil surface and lack of vegetation.]</nowiki>
 *** Grassy-terrain <nowiki>[Tracts of land covered by grass.]</nowiki>
 *** Gravel-terrain <nowiki>[Tracts of land covered by a surface consisting a loose aggregation of small water-worn or pounded stones.]</nowiki>

hedcode/data/schema_data/HED8.0.0.xml

@@ -770,7 +770,7 @@
             </node>
             <node>
                <name>Predict</name>
-               <description>Say or estimate that something will happen or will be a consequence of something without having exact informaton.</description>
+               <description>Say or estimate that something will happen or will be a consequence of something without having exact information.</description>
             </node>
             <node>
                <name>Recognize</name>
@@ -1397,7 +1397,7 @@
                   </node>
                   <node>
                      <name>Tool</name>
-                     <description>A component that is not part of a device but is designed to support its assemby or operation.</description>
+                     <description>A component that is not part of a device but is designed to support its assembly or operation.</description>
                   </node>
                </node>
                <node>
@@ -1581,7 +1581,7 @@
                   </node>
                   <node>
                      <name>Truck</name>
-                     <description>A motor vehicle which, as its primary funcion, transports cargo rather than human passangers.</description>
+                     <description>A motor vehicle which, as its primary function, transports cargo rather than human passangers.</description>
                   </node>
                </node>
             </node>
@@ -1623,7 +1623,7 @@
             <description>Mechanical vibrations transmitted by an elastic medium. Something that can be heard.</description>
             <node>
                <name>Environmental-sound</name>
-               <description>Sounds occuring in the environment. An accumulation of noise pollution that occurs outside. This noise can be caused by transport, industrial, and recreational activities.</description>
+               <description>Sounds occurring in the environment. An accumulation of noise pollution that occurs outside. This noise can be caused by transport, industrial, and recreational activities.</description>
                <node>
                   <name>Crowd-sound</name>
                   <description>Noise produced by a mixture of sounds from a large group of people.</description>
@@ -2751,7 +2751,7 @@
                   <description>Something capable of being estimated or expressed with numeric values.</description>
                   <node>
                      <name>Fraction</name>
-                     <description>A numerical value betwee 0 and 1.</description>
+                     <description>A numerical value between 0 and 1.</description>
                      <node>
                         <name>#</name>
                         <attribute>
@@ -2940,7 +2940,7 @@
                   </node>
                   <node>
                      <name>Statistical-recall</name>
-                     <description>Sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1.</description>
+                     <description>Sensitivity is a measurement datum qualifying a binary classification test and is computed by subtracting the false negative rate to the integral numeral 1.</description>
                      <node>
                         <name>#</name>
                         <attribute>
@@ -3526,7 +3526,7 @@
                <description>Characterization of the physical features of a tract of land.</description>
                <node>
                   <name>Composite-terrain</name>
-                  <description>Tracts of land characterized by a mixure of physical features.</description>
+                  <description>Tracts of land characterized by a mixture of physical features.</description>
                </node>
                <node>
                   <name>Dirt-terrain</name>