Merge pull request #324 from IanCa/develop

Add codespell/fix typos
hed-standard · Oct 17, 2023 · 91e52ef · 91e52ef
2 parents 92a829c + 9c0b91f
commit 91e52ef
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diff --git a/.github/workflows/codespell.yaml b/.github/workflows/codespell.yaml
@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [develop]
+  pull_request:
+    branches: [develop]
+
+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/docs/source/FileRemodelingTools.md b/docs/source/FileRemodelingTools.md
@@ -849,8 +849,8 @@ The resulting columns are called *stopped* and *stop_failed*, respectively.
 
 ```json
 [{ 
-    "operation": "factor_column"
-    "description": "Create factors for the succesful_stop and unsuccesful_stop values."
+    "operation": "factor_column",
+    "description": "Create factors for the succesful_stop and unsuccesful_stop values.",
     "parameters": {
         "column_name": "trial_type",
         "factor_values": ["succesful_stop", "unsuccesful_stop"],
@@ -923,12 +923,12 @@ The resulting factor columns are named *correct* and *incorrect*, respectively.
 
 ```json
 [{ 
-    "operation": "factor_hed_tags"
-    "description": "Create factors based on whether the event represented a correct or incorrect action.",
+    "operation": "factor_hed_tags",
+    "description": "Create factors based on whether the event represented a correct or incorrect action.",,
     "parameters": {
         "queries": ["correct-action", "incorrect-action"],
-        "query-names": ["correct", "incorrect"],
-        "remove-types": [],
+        "query_names": ["correct", "incorrect"],
+        "remove_types": [],
         "expand_context": false
     }
 }]
@@ -995,8 +995,8 @@ applies and 0's otherwise.
 
 ```json
 [{ 
-    "operation": "factor_hed_type"
-    "description": "Factor based on the sex of the images being presented."
+    "operation": "factor_hed_type",
+    "description": "Factor based on the sex of the images being presented.",
     "parameters": {
         "type_tag": "Condition-variable",
         "type_values": []
@@ -1075,8 +1075,8 @@ have the same values to be merged into a single event.
 
 ```json
 [{ 
-    "operation": "merge_consecutive"
-    "description": "Merge consecutive *succesful_stop* events that match the *match_columns."
+    "operation": "merge_consecutive",
+    "description": "Merge consecutive *succesful_stop* events that match the *match_columns.",
     "parameters": {
         "column_name": "trial_type",
         "event_code": "succesful_stop",

diff --git a/docs/source/HedConditionsAndDesignMatrices.md b/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.

diff --git a/docs/source/HedMatlabTools.md b/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:

diff --git a/docs/source/HedOnlineTools.md b/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)=

diff --git a/docs/source/HedPythonTools.md b/docs/source/HedPythonTools.md
@@ -290,9 +290,7 @@ 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
+Many of the HED data processing tools make extensive use of dictionaries specifying both data and format.
 
 #### BIDS-specific dictionaries of files
 
@@ -436,7 +434,7 @@ 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)=

diff --git a/docs/source/HedSchemaDevelopersGuide.md b/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`.

diff --git a/docs/source/HedSearchGuide.md b/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

diff --git a/setup.cfg b/setup.cfg
@@ -57,4 +57,8 @@ style = pep440
 versionfile_source = hedcode/_version.py
 versionfile_build = hedcode/_version.py
 tag_prefix =
-parentdir_prefix = hedcode-
+parentdir_prefix = hedcode-
+
+[codespell]
+skip = '*.git,*.pdf,*.xml,*.mediawiki,*.svg,versioneer.py,venv*,*.tsv,*.yaml,*.yml,*.json,*.rdf,*.jsonld,datasets*,'
+ignore-words-list = 'te,parms'