Merge pull request hed-standard#382 from hed-standard/develop

Created various broken links

.lycheeignore

@@ -1,5 +1,6 @@
 <!-- This file lists all links/regex to be ignored by lychee in the link checker -->
 https://www.sciencedirect.com/science/article/pii/S1053811921010387
 https://www.sciencedirect.com/science/article/pii/S0010945221001106
+https://www.sciencedirect.com/science/article/pii/S1388245717309069
 (_anchor|-anchor)
 

docs/source/BidsAnnotationQuickstart.md

@@ -363,6 +363,7 @@ Once you have a JSON sidecar template, you should edit in your event annotations
 The following is an edited version of the 
 JSON template from the previous step containing a minimal set of HED annotations.
 
+(excerpted-json-file-with-tags-anchor)=
 `````{admonition} JSON sidecar with completed annotation.
 :class: tip
 ```json
@@ -496,7 +497,7 @@ or in a tool such as Excel.
 You may save the edited spreadsheet in either `.tsv` or `.xslx` format.
 
 The following is the extracted spreadsheet corresponding to the
-[**edited JSON sidecar above**](excerpted-json-file-with-tags).
+[**edited JSON sidecar above**](excerpted-json-file-with-tags-anchor).
 
 ````{admonition} HED annotation table extracted from JSON sidecar template.
 | **column_name** | **column_value** | **description** | **HED** |

docs/source/HedMatlabTools.md

@@ -454,9 +454,8 @@ See [**MathWorks Python Compatibility Docs**](https://www.mathworks.com/support/
 
 The greatest difficulty for users who are unfamiliar with Python is
 getting Python connected to MATLAB.
-Once that is done, many of the standard `hedtools` functions have 
-[**MATLAB HED tool wrapper functions**](https://github.com/hed-standard/hed-matlab/tree/main/hedmat/hedtools_wrappers)
-that take MATLAB variables as arguments and return either MATLAB variables or opaque objects that
+Once that is done, many of the standard `hedtools` functions can be accessed through 
+method call that take MATLAB variables and return either MATLAB variables or opaque objects that
 can be passed to other MATLAB functions.
 
 Thus, once the setup is done, you don't have to learn any Python syntax to use the tools.
@@ -669,7 +668,6 @@ Using HEDTOOLS version: {'date': '2022-06-20T14:40:24-0500', 'dirty': False, 'er
 ```
 ````
 
-
 ### MATLAB functions for Python
 
 The following table lists the relevant MATLAB functions that are available.
@@ -727,8 +725,6 @@ The remodeling file used in this example can be found at
 See [**File remodeling quickstart**](FileRemodelingQuickstart.md)
 and [**File remodeling tools**](FileRemodelingTools.md) for
 additional information.
-The wrapper functions are available on GitHub in
-the [**hedtools_wrappers**](https://github.com/hed-standard/hed-examples/tree/develop/src/matlab_scripts/hedtools_wrappers) directory.
 
 (web-service-matlab-demos-anchor)=
 ### Web service MATLAB demos
@@ -745,16 +741,16 @@ directory of the [**hed-matlab**](https://github.com/hed-standard/hed-matlab) Gi
 
 The following MATLAB code demos are available to show how to access HED web services.
 
-| Target | MATLAB source  | Purpose |
-| ------ |-----------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
-| Overall | [**runAllDemos.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/runAllDemos.m)  | Harness for running all demos. |
-| Overall | [**demoGetServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoGetServices.m)  | List available services. |
-| Events | [**demoEventServices.m**](https://raw.githubusercontent.com/hed-standard/hed-examples/main/hedcode/matlab_scripts/web_services_demos/demoEventServices.m) | Validation, conversion, sidecar generation. |
-| Events | [**demoEventSearchServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoEventSearchServices.m)  | Search, assembly. |
-| Schema | *in progress*  | For schema library developers. |
-| Sidecars | [**demoSidecarServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoSidecarServices.m)  | Validation, conversion, extraction, merging. |
-| Spreadsheets | [**demoSpreadsheetServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoSpreadsheetServices.m)  | Validation, conversion. |
-| Strings | [**demoStringServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoStringServices.m)  | Validation, conversion. |
+| Target | MATLAB source | Purpose |
+| ------ |----------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
+| Overall | [**runAllDemos.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/runAllDemos.m) | Harness for running all demos. |
+| Overall | [**demoGetServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoGetServices.m) | List available services. |
+| Events | [**demoEventServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoEventServices.m) | Validation, conversion, sidecar generation. |
+| Events | [**demoEventSearchServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoEventSearchServices.m) | Search, assembly. |
+| Schema | *in progress* | For schema library developers. |
+| Sidecars | [**demoSidecarServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoSidecarServices.m) | Validation, conversion, extraction, merging. |
+| Spreadsheets | [**demoSpreadsheetServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoSpreadsheetServices.m) | Validation, conversion. |
+| Strings | [**demoStringServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoStringServices.m) | Validation, conversion. |
 
 
 The [**runAllDemos.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/runAllDemos.m)

docs/source/HedOnlineTools.md

@@ -560,7 +560,7 @@ JSON sidecars, BIDS-style events files, and spreadsheets in `.tsv` or `.xlsx` fo
 Support is also included for assembling the annotations for a BIDS-style 
 events file with a JSON sidecar and for generating a template of a JSON sidecar from a BIDS events file.
 
-The [**web_services**](https://github.com/hed-standard/hed-matlab/tree/main/hedmat/web_services) 
+The [**web_services_demos**](https://github.com/hed-standard/hed-matlab/tree/main/hedmat/web_services_demos) 
 directory in the `hed-examples` GitHub repository provides MATLAB examples of how to call these 
 services in MATLAB.
 

docs/source/HedPythonTools.md

@@ -43,7 +43,7 @@ and an online version of the tools.
 The [**Create a JSON template**](https://hed-examples.readthedocs.io/en/latest/BidsAnnotationQuickstart.html#create-a-json-template) tutorial provides a step-by-step tutorial for using the online tool 
 that creates a template based on the information in a single `events.tsv` file.
 For most datasets, this is sufficient.
-In contrast, the [**extract_json_template.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/extract_json_template.ipynb)
+In contrast, the [**extract_json_template.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/extract_json_template.ipynb)
 Jupyter notebook bases the extracted template on the entire dataset.
 
 To use this notebook, substitute the specifics of your BIDS

docs/source/HedSchemas.md

@@ -92,7 +92,7 @@ directory of the [**hed-schemas**](https://github.com/hed-standard/hed-schemas)
 
 ### The SCORE library
 
-The HED SCORE library is an implementation of the [**SCORE**](https://www.sciencedirect.com/science/article/pii/S1388245717309069?via%3Dihub) standard for clinical annotation of EEG by neurologists.
+The HED SCORE library is an implementation of the [**SCORE**](https://www.sciencedirect.com/science/article/pii/S1388245717309069) standard for clinical annotation of EEG by neurologists.
 For more information and the latest references see 
 [**HED SCORE schema**](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/README.md).
 

docs/source/HowCanYouUseHed.md

@@ -616,7 +616,7 @@ for more information on installation and use.
 The project source code is located in the [**CTagger**](https://github.com/hed-standard/ctagger) GitHub repository.
 <p></p>
 
-[*MATLAB HedTools**](https://www.hed-resources.org/en/latest/MatlabHedTools.md) explains how the 
+[*HED MATLAB Tools**](https://www.hed-resources.org/en/latest/HedMatlabTools.html) explains how the 
 users can use the HEDTools in MATLAB using one of three approaches: using MATLAB wrappers for the HED Python tools,
 using MATLAB wrappers for the HED web services, or by calling HED tools through EEGLAB.
 

docs/source/index.rst

@@ -86,7 +86,8 @@ San Diego (UCSD) under funding by The Swartz Foundation and by U.S. National Ins
 
 Further **HED (Gen 2, 4.0.0 <= version < 8.0.0)** development led by Kay Robbins
 of the University of Texas San Antonio was
-funded by The Cognition and Neuroergonomics Collaborative Technology Alliance (CaN CTA) program of U.S Army Research Laboratory (ARL) under Cooperative Agreement Number W911NF-10-2-0022.
+funded by The Cognition and Neuroergonomics Collaborative Technology Alliance (CaN CTA) program
+of U.S Army Research Laboratory (ARL) under Cooperative Agreement Number W911NF-10-2-0022.
 
 **HED (Gen 3, version >= 8.0.0)** is now maintained and further developed by the
 HED Working Group led by Kay Robbins and Scott Makeig with Dung Truong, Monique Denissen,

src/jupyter_notebooks/bids/README.md

@@ -5,16 +5,16 @@ validating, summarizing, and analyzing your BIDS datasets.
 
 **Table 1:** Useful Jupyter notebooks for processing BIDS datasets.
 
-| Notebooks  | Purpose | 
-|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------| 
-| [`extract_json_sidecar`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/extract_json_sidecar.ipynb)  | Creates a JSON sidecar based on all the event files in a dataset. |
-| [`find_event_combinations`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/find_event_combinations.ipynb)  | Creates a spreadsheet of unique combinations of event values. |
-| [`merge_spreadsheet_into_sidecar`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/bids_merge_sidecarmerge_spreadsheet_into_sidecar.ipynb) | Merges a spreadsheet version of a sidecar into a JSON sidecar. |
-| [`sidecar_to_spreadsheet`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb)  | Converts the HED portion of a JSON sidecar into a 4-column spreadsheet. |
-| [`summarize_events`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/summarize_events.ipynb)  | Summarizes the contents of the event files, including value counts. | 
-| [`validate_bids_dataset`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset.ipynb)  | Validates the HED annotations in a BIDS dataset. |
-| [`validate_bids_dataset_with_libraries`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset_with_libraries.ipynb)  | Demonstrates use of HED libraries in validation. | 
-| [`validate_bids_datasets`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_datasets.ipynb)  | Validates the HED annotations in a list of BIDS datasets. | 
+| Notebooks | Purpose | 
+|------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------| 
+| [`extract_json_template`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/extract_json_template.ipynb) | Creates a JSON sidecar based on all the event files in a dataset. |
+| [`find_event_combinations`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/find_event_combinations.ipynb) | Creates a spreadsheet of unique combinations of event values. |
+| [`merge_spreadsheet_into_sidecar`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/merge_spreadsheet_into_sidecar.ipynb)  | Merges a spreadsheet version of a sidecar into a JSON sidecar. |
+| [`sidecar_to_spreadsheet`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb) | Converts the HED portion of a JSON sidecar into a 4-column spreadsheet. |
+| [`summarize_events`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/summarize_events.ipynb) | Summarizes the contents of the event files, including value counts. | 
+| [`validate_bids_dataset`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset.ipynb) | Validates the HED annotations in a BIDS dataset. |
+| [`validate_bids_dataset_with_libraries`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset_with_libraries.ipynb) | Demonstrates use of HED libraries in validation. | 
+| [`validate_bids_datasets`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_datasets.ipynb) | Validates the HED annotations in a list of BIDS datasets. | 
 
 These notebooks require HEDTools, which can be installed using `pip` or directly.