Updated What's New -- minor doc typo corrections

.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

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",

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/HedGovernance.md

@@ -1,4 +1,3 @@
--------------------DRAFT---------------------------------------------------
 # HED governance and decision-making
 
 Table of Contents

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

@@ -290,9 +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)=

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

docs/source/WhatsNew.md

@@ -1,6 +1,10 @@
 (whats-new-anchor)=
 # What's new?
 
+<span style="color: red; font-weight: bold;">Upcoming... </span> **Nov. 10-17, 2023 sFN (Society for Neuroscience)** in Washington D.C.:  
+> **Visit SCCN booth (#3031)** for help and information (or just to visit) about **NEMAR/OpenNeuro**, **EEGLAB**, **HED**, **LSL**, and **MoBI**.  
+
+
 **September 20, 2023 16:00 CEST**: **INCF Workshop on HED and BIDS**
 > <em>Event annotation in neuroimaging using HED: from experiment to analysis</em>  
 > Half-day workshop at [**INCF Assembly 2023**](https://neuroinformatics.incf.org/register).  

docs/source/index.rst

@@ -105,7 +105,7 @@ Visit the `HED project homepage <https://github.com/hed-standard>`_ for links to
    IntroductionToHed.md
    WhatsNew.md
    HowCanYouUseHed.md
-
+   HedGovernance.md
 
 
 .. toctree::
@@ -144,12 +144,6 @@ Visit the `HED project homepage <https://github.com/hed-standard>`_ for links to
    HedSchemas.md
    HedTestDatasets.md
 
-.. toctree::
-   :maxdepth: 3
-   :hidden:
-   :caption: Drafts:
-
-   HedGovernance.md
 
 Indices and tables
 ==================

hedcode/jupyter_notebooks/bids/validate_bids_dataset.ipynb

@@ -32,18 +32,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Using HEDTOOLS version: {'date': '2023-09-01T15:54:07-0500', 'dirty': True, 'error': None, 'full-revisionid': '15594c2afa770e08f3881f4a9de04d21b3113750', 'version': '0.3.0+128.g15594c2.dirty'}\n",
-      "HED Examples version: {'version': '0.2.0+131.gae61cba.dirty', 'full-revisionid': 'ae61cba59be07284460a7503b282640e031b5e1f', 'dirty': True, 'error': None, 'date': '2023-09-03T13:50:01-0500'}\n",
-      "No HED validation errors\n"
-     ]
-    }
-   ],
+   "execution_count": null,
+   "outputs": [],
    "source": [
     "from hed.errors import get_printable_issue_string\n",
     "from hed.tools import BidsDataset\n",
@@ -55,23 +45,24 @@
     "\n",
     "## Set the dataset location and the check_for_warnings flag\n",
     "check_for_warnings = False\n",
-    "dataset_path = '../../../datasets/eeg_ds003645s_hed_column'\n",
-    "\n",
+    "#dataset_path = '../../../datasets/eeg_ds003645s_hed_column'\n",
+    "#dataset_path = '../../../datasets/eeg_ds004105s_hed'\n",
+    "dataset_path = 't:/summaryTests/ds004105-download'\n",
+    "outfile = 't:/ds004105_errors.txt'\n",
     "## Validate the dataset\n",
     "bids = BidsDataset(dataset_path)\n",
     "issue_list = bids.validate(check_for_warnings=check_for_warnings)\n",
     "if issue_list:\n",
     "    issue_str = get_printable_issue_string(issue_list, \"HED validation errors: \", skip_filename=False)\n",
     "else:\n",
     "    issue_str = \"No HED validation errors\"\n",
-    "print(issue_str)"
+    "print(issue_str)\n",
+    "if outfile:\n",
+    "    with open(outfile, 'w') as fp:\n",
+    "        fp.write(issue_str)\n"
    ],
    "metadata": {
-    "collapsed": false,
-    "ExecuteTime": {
-     "end_time": "2023-09-03T20:15:04.777492900Z",
-     "start_time": "2023-09-03T20:14:59.038952100Z"
-    }
+    "collapsed": false
    }
   }
  ],

hedcode/jupyter_notebooks/bids/validate_bids_datasets.ipynb

@@ -36,8 +36,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Using HEDTOOLS version: {'date': '2023-09-01T15:54:07-0500', 'dirty': True, 'error': None, 'full-revisionid': '15594c2afa770e08f3881f4a9de04d21b3113750', 'version': '0.3.0+128.g15594c2.dirty'}\n",
-      "HED Examples version: {'version': '0.2.0+131.gae61cba.dirty', 'full-revisionid': 'ae61cba59be07284460a7503b282640e031b5e1f', 'dirty': True, 'error': None, 'date': '2023-09-03T13:50:01-0500'}\n",
+      "Using HEDTOOLS version: {'date': '2023-10-12T10:29:43-0500', 'dirty': False, 'error': None, 'full-revisionid': 'e9e63e39f6a99487c5e69ae96e653c4580045ec0', 'version': '0.3.0+164.ge9e63e3'}\n",
+      "HED Examples version: {'version': '0.2.0+168.g92a829c.dirty', 'full-revisionid': '92a829cb0336bd952db10f1890f23dde80aecd36', 'dirty': True, 'error': None, 'date': '2023-10-10T13:35:06-0500'}\n",
       "Validating eeg_ds003645s_hed\n",
       "No HED validation errors\n",
       "Validating eeg_ds003645s_hed_column\n",
@@ -93,8 +93,8 @@
      "name": "#%%\n"
     },
     "ExecuteTime": {
-     "end_time": "2023-09-03T20:21:08.429817700Z",
-     "start_time": "2023-09-03T20:20:39.090638800Z"
+     "end_time": "2023-10-17T12:11:03.224728400Z",
+     "start_time": "2023-10-17T12:10:21.630499700Z"
     }
    }
   }

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'