Merge pull request #341 from VisLab/develop

Fixed site broken links

docs/source/BidsAnnotationQuickstart.md

@@ -17,7 +17,7 @@ You will put the finished annotation file at the top level of your dataset.
 
 The approach that we will use is to create a template file from an `events.tsv` file
 in your BIDS dataset using the online tools available at
-[**hedtools.ucsd.edu/hed**](https://hedtools.ucsd.edu/hed).
+[**hedtools.org/hed**](https://hedtools.org/hed).
 
 You can then edit this JSON file directly using a text editor
 to insert data descriptions and HED annotations.
@@ -31,7 +31,7 @@ Although the HED web tools base the template on the information extracted from a
 `events.tsv` file, this will be sufficient to produce a good template for most datasets.
 
 For datasets with widely-varying event files, you should use the 
-[bids_validate_hed.ipynb](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids_processing/bids_generate_sidecar.ipynb)
+[validate_bids_dataset.ipynb](https://github.com/hed-standard/hed-examples/blob/develop/hedcode/jupyter_notebooks/bids/validate_bids_dataset.ipynb)
 Jupyter notebook version rather than the online tools.
 The Jupyter notebook consolidates information from all of the `events.tsv` files in the dataset
 to produce a comprehensive JSON sidecar template.
@@ -426,7 +426,7 @@ editing and then convert back to a JSON file afterwards.
 This tutorial assumes that you already have a JSON events sidecar
 or have [**extracted a JSON sidecar template**](create-a-json-template-anchor).
 
-Using the [**HED sidecar online tools**](https://hedtools.ucsd.edu/hed/sidecar),
+Using the [**HED sidecar online tools**](https://hedtools.org/hed/sidecars),
 the steps to create a template are:
 
 * [**Step 1: Select extract HED spreadsheet.**](step-1-select-extract-hed-spreadsheet-anchor)  

docs/source/DocumentationSummary.md

@@ -90,7 +90,7 @@ The following is a summary of the HED-related websites:
 * - HED Python tools
   - [https://github.com/hed-standard/hed-python](https://github.com/hed-standard/hed-python)
 * - HED Javascript code
-  - [https://github.com/hed-standard/hed-javascript](https://github.com/hed-standard/hed-javacript)
+  - [https://github.com/hed-standard/hed-javascript](https://github.com/hed-standard/hed-javascript)
 * - HED Matlab code and EEGLAB support
   - [https://github.com/hed-standard/hed-matlab](https://github.com/hed-standard/hed-matlab)
 * - HED web deployment

docs/source/HedGovernance.md

@@ -210,7 +210,7 @@ organization site as indicated in the following table.
 | Docs/examples         | [hed-examples](https://github.com/hed-standard/hed-examples/issues)           | Documentation corrections.<br/>Questions on examples.<br/>Help on annotation.                       |   
 | Specification | [hed-specification](https://github.com/hed-standard/hed-specification/issues) | Clarification/suggestions on the<br/>specification document and JSON tests.                         |
 | Python codebase | [hed-python](https://github.com/hed-standard/hed-python/issues)               | Bug reports and feature requests.                                                                   |  
-| JavaScript codebase | [hed-validator](https://github.com/hed-standard/hed-validator/issues)         | Bug reports and feature requests.                                                                   | 
+| JavaScript codebase | [hed-javascript](https://github.com/hed-standard/hed-javascript/issues)       | Bug reports and feature requests.                                                                   | 
 
 HED also has a HED discussion group. (Subscribe by emailing:
 [**[email protected]**](mailto:[email protected]).

docs/source/HedMatlabTools.md

@@ -479,7 +479,7 @@ reimplementing these operations in MATLAB.
 **Note:** For your reference, the source for `hedtools` is the 
 [**hed-python**](https://github.com/hed-standard/hed-python) GitHub repository.
 The code is fully open-source with an MIT license.
-The actual API documentation is available [**here**](https://hed-python.readthedocs.io/en/latest/api.html),
+The actual API documentation is available [**here**](https://hed-python.readthedocs.io/en/latest/api2.html),
 but the tutorials and tool documentation for `hedtools` on 
 [**HED Resources**](https://www.hed-resources.org/en/latest/index.html) provides more
 examples of use.

docs/source/HedOnlineTools.md

@@ -85,7 +85,7 @@ However, the tool only validates a single events file with an accompanying sidec
 The tool does not validate multiple events files at the same time,
 nor does the tool handle inherited sidecars.
 
-The [bids_validate_hed.ipynb](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/bids_validate_dataset.ipynb)
+The [validate_bids_dataset.ipynb](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/validate_bids_dataset.ipynb)
 Python Jupyter notebook is available for validating all the events files
 in a BIDS dataset along with multiple sidecars.
 The Jupyter notebook handles validation with library schema.
@@ -141,7 +141,7 @@ The online generation tool is very useful for constructing a sidecar template fi
 but the template is based only on the particular events file used in the generation.
 For many BIDS datasets, this is sufficient for generating a complete template.
 However, for datasets that have many types of events files, you will want to use the
-[bids_generate_sidecar.ipynb](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/bids_generate_sidecar.ipynb)
+[extract_json_template.ipynb](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/extract_json_template.ipynb)
 to generate a JSON sidecar based on all the events files in a BIDS dataset.
 
 #### Execute remodel script
@@ -273,7 +273,7 @@ for a tutorial on how to use the resulting spreadsheet for annotation.
 If there are any errors, the tool returns a downloadable `.txt` file of error messages,
 otherwise the tool returns a downloadable `.tsv` spreadsheet.  
 ``````
-The [bids_sidecar_to_spreadsheet.ipynb](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/bids_sidecar_to_spreadsheet.ipynb) Python Jupyter notebook does the same operation.
+The [sidecar_to_spreadsheet.ipynb](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb) Python Jupyter notebook does the same operation.
 
 #### Merge a spreadsheet with a sidecar
 
@@ -302,7 +302,7 @@ for a tutorial on how this works in practice.
 If there are any errors, the tool returns a downloadable `.txt` file of error messages,
 otherwise the tool returns a downloadable merged `.json` file.  
 ``````
-The [bids_merge_sidecar.ipynb](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/bids_merge_sidecar.ipynb) Python Jupyter notebook does the same operation.
+The [bids_merge_spreadsheet_into_sidecar.ipynb](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/merge_spreadsheet_into_sidecar.ipynb) Python Jupyter notebook does the same operation.
 
 
 (spreadsheets-online-tools-anchor)=
@@ -581,11 +581,11 @@ web-based tools and services.
 * - Service
   - URL
 * - Online HED tools
-  - [https://hedtools.ucsd.edu/hed](https://hedtools.ucsd.edu/hed)
+  - [https://hedtools.org/hed](https://hedtools.org/hed)
 * - CSRF token access
-  - [https://hedtools.ucsd.edu/hed/services](https://hedtools.ucsd.edu/hed/services)  
+  - [https://hedtools.org/hed/services](https://hedtools.org/hed/services)  
 * - Service request
-  - [https://hedtools.ucsd.edu/hed/services_submit](https://hedtools.ucsd.edu/hed/services_submit)
+  - [https://hedtools.org/hed/services_submit](https://hedtools.org/hed/services_submit)
 `````
 
 ### Request format

docs/source/HedPythonTools.md

@@ -251,9 +251,6 @@ The example data curation scripts discussed in this section assume that two vers
 of each BIDS event file are present: `events.tsv` and a corresponding `events_temp.tsv` file.
 The example datasets that are using for these tutorials assume that the recordings
 are in EEG.set format.
-We used the [runEeglabEventsToFiles](https://raw.githubusercontent.com/hed-standard/hed-curation/main/src/curation/matlab_utility_scripts/hed_utilities/runEeglabEventsToFiles.m)
-MATLAB script to dump the events stored in the data.
-
 
 (calling-hed-tools-anchor)=
 ## Calling HED tools
@@ -381,10 +378,6 @@ If you choose the `name_indices` incorrectly, the keys for the event files
 will not be unique, and the notebook will throw a `HedFileError`.
 If this happens, modify your `name_indices` key choice to include more entity pairs.
 
-The Jupyter notebook
-[go_nogo_01_initial_summary.ipynb](https://raw.githubusercontent.com/hed-standard/hed-examples/main/hedcode/jupyter_notebooks/dataset_specific_processing/go_nogo/go_nogo_01_initial_summary.ipynb)
-illustrates using this dictionary in a larger context.
-
 For example, to compare the events stored in a recording file and the events
 in the `events.tsv` file associated with that recording,
 we might dump the recording events in files with the same name, but ending in `events_temp.tsv`.

docs/source/HedSchemaDevelopersGuide.md

@@ -15,7 +15,7 @@ The HED Working Group would be happy to give you technical guidance in getting s
 and working through the process to final release.
 
 More detailed information is available in
-the [**Library schemas**](https://https://hed-specification.readthedocs.io/en/latest/07_Library_schemas.html) chapter of
+the [**Library schemas**](https://https://https://hed-specification.readthedocs.io/en/latest/07_Library_schemas.html) chapter of
 the [**HED specification**](https://hed-specification.readthedocs.io/en/latest/index.html).
 
 Details about syntax are available in the 
@@ -343,7 +343,7 @@ Use the [**HED online tools**](https://hedtools.org) to convert as shown in the
 
 All HED schemas, including library schemas, adhere to [**semantic versioning**](https://semver.org/). 
 The rules for what constitutes major, minor and patch changes are given
-in the hed-schemas [**README**](https://github.com/hed-standard/hed-schemas/#hed-semantic-versioning).
+in the hed-schemas [**README.md**](https://github.com/hed-standard/hed-schemas/README.md#hed-semantic-versioning).
 
 ### Schema file names
 
@@ -450,8 +450,8 @@ Here is a brief summary of the development process.
 - Request a branch be created on [**hed-schemas**](https://github.com/hed-standard/hed-schemas) for your development.
 - Develop your schema:
   - Modify your prerelease `.mediawiki`.
-  - Validate the prerelease `.mediawiki` file using the [**HED online tools**](https://hedtools.org/hed/schema).
-  - Convert to the prerelease `.mediawiki` file to `.xml` using the [**HED online tools**](https://hedtools.org/hed/schema) and replace the existing prerelease `.xml`.
+  - Validate the prerelease `.mediawiki` file using the [**HED online tools**](https://hedtools.org/hed/schemas).
+  - Convert to the prerelease `.mediawiki` file to `.xml` using the [**HED online tools**](https://hedtools.org/hed/schemas) and replace the existing prerelease `.xml`.
   - Check the schema using [**HED Schema Viewer**](https://www.hedtags.org/display_hed.html).
   - Update your prerelease `CHANGES.md` and `PROPOSED.md` files.
   - Update your schema's `README.md`.

docs/source/HedTestDatasets.md

@@ -132,7 +132,7 @@ The dataset is used as a case study for the book chapter
 ## BIDS validation
 
 For general information on the `bids-validator`, including installation, configuration, and usage,
-see the [bids-validator README file](https://github.com/bids-standard/bids-validator#quickstart).
+see the [bids-validator README file](https://github.com/bids-standard/bids-validator/blob/master/README.md).
 
 **Example:** The following command validates the  `eeg_ds003645s_hed` dataset:
 

docs/source/HedValidationGuide.md

@@ -217,7 +217,7 @@ directly using PIP.
 Several [**Jupyter notebooks**](https://github.com/hed-standard/hed-examples/tree/main/hedcode/jupyter_notebooks) are available 
 as wrappers for calling various Python HED tools. 
 
-For example, the [**bids_validate_datasets.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/bids_validate_datasets.ipynb) notebook shown in the following example validates an entire BIDS dataset 
+For example, the [**validate_bids_datasets.ipynb**](https://github.com/hed-standard/hed-examples/blob/develop/hedcode/jupyter_notebooks/bids/validate_bids_datasets.ipynb) notebook shown in the following example validates an entire BIDS dataset 
 just give the path to the root directory of the dataset.
 
 `````{admonition} Python code to validate HED in a BIDS dataset.

docs/source/HowCanYouUseHed.md

@@ -242,7 +242,7 @@ in [**Software currently supporting BIDS**](https://bids.neuroimaging.io/benefit
 (learning-about-hed-anchor)=
 #### Learning about HED
 
-- The [**HED introduction**](https://www.hed-resources.org/en/latest/HedIntroduction.html)
+- The [**Introduction to HED**](https://www.hed-resources.org/en/latest/IntroductionToHed.html)
 gives a basic overview of HED's history and goals.   
 <p></p>
 
@@ -291,12 +291,9 @@ See [**BIDS annotation quickstart**](https://www.hed-resources.org/en/latest/Bid
 
 - The HED vocabulary is hierarchically organized as shown
 in the schema as viewed in the [**HED Schema Viewer**](https://www.hedtags.org/display_hed.html).
+Library schemas can also be viewed using this viewer.
 <p></p>
 
-- [**Schema viewers**](https://www.hed-resources.org/en/latest/HedSchemaViewers.html)
-gives links to different versions of the HED standard HED vocabularies as well as 
-library vocabularies.
-
 (basic-annotation-strategies-anchor)=
 #### Basic annotation strategies
 HED annotations come in variety of levels and complexity.
@@ -327,7 +324,7 @@ HED supports a number of advanced annotation concepts which are necessary for a
 description of the experiment. 
 
 - **HED definitions**: allow users to define complex concepts.
-See [**HED definitions**](https://hed-specification.readthedocs.io/en/latest/05_Advanced_annotation.html#hed-definitions) for an overview and syntax.
+See [**Creating definitions**](https://hed-specification.readthedocs.io/en/develop/05_Advanced_annotation.html#creating-definitions) and [**Using definitions**](https://hed-specification.readthedocs.io/en/develop/05_Advanced_annotation.html#using-definitions) for an overview and syntax.
 <p></p>
 
 - **Temporal scope**: annotate event processes that extend over time and provide a context for
@@ -582,7 +579,7 @@ The code for HEDTools is in the [**hed-python**](https://github.com/hed-standard
 The latest stable release is available as [**hedtools**](https://pypi.org/project/hedtools/)
 on PyPI and can be installed using the regular `pip` install mechanism.
 
-The `develop` branch of [**hed-python**](https://github.com/hed-python) contains the latest
+The `develop` branch of [**hed-python**](https://github.com/hed-standard/hed-python) contains the latest
 versions of the tools and can be installed from GitHub using:
 
 ```bash
@@ -593,7 +590,7 @@ versions of the tools and can be installed from GitHub using:
 #### The HED JavaScript code base
 
 GitHub repository. The JavaScript tools focus on HED validation and its main client is the 
-[**Bids validator**](https://github.com/bids-standard/bids-javascript).
+[**Bids validator**](https://github.com/bids-standard/bids-validator).
 The code for this project is in the [**hed-javascript**](https://github.com/hed-standard/hed-javascript)
 
 The latest stable release is available as the [**hed-validator**](https://www.npmjs.com/package/hed-validator)

docs/source/WhatsNew.md

@@ -109,7 +109,7 @@ points in an ongoing event as well as partnered library schemas.
 
 **February 22, 2023**: **HED YouTube Channel goes live**<br/>
 > First video:  [**HED Tagging 101**](https://youtu.be/iRAWO-Fn6Bw)  
-> HED YouTube channel: [**https://www.youtube.com/@hedworkinggroup/videos**](https://www.youtube.com/@hedworkinggroup/videos)
+> HED YouTube channel: [**https://www.youtube.com/@HierarchicalEventDescriptors/playlists**](https://www.youtube.com/@HierarchicalEventDescriptors/playlists)
 
 **February 14, 2023**: **HEDTools 0.2.0 is released.**  
 - This release includes the HED remodeling tools.   
@@ -121,7 +121,7 @@ points in an ongoing event as well as partnered library schemas.
 > This library is based on the Standardized Computer-based Organized Reporting of EEG
 > ([**SCORE**](https://pubmed.ncbi.nlm.nih.gov/28838815/)) standard and adapted for
 > annotation using the HED infrastructure and requirements. 
-> For more information see the [**SCORE schema library**](https://hed-schemas.readthedocs.io/en/latest/hed_score_library.html) guide.
+> For more information see the [**SCORE schema library**](https://hed-schemas.readthedocs.io/en/latest/hed_score_schema.html) guide.
 
 **January 20, 2023**: **New preprint available**<br/>
 

docs/source/index.rst

@@ -91,7 +91,7 @@ funded by The Cognition and Neuroergonomics Collaborative Technology Alliance (C
 **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,
 Dora Hermes Miller, Tal Pal Attia, and Arnaud Delorme, with funding from NIH grant
-`RF1-MH126700 <https://braininitiative.nih.gov/funded-awards/brain-initiative-hierarchical-event-descriptors-hed-system-characterize-events>`_.
+`RF1-MH126700 <https://reporter.nih.gov/project-details/10480619>`_.
 
 HED is an open research community effort; others interested are invited to participate and contribute.
 Visit the `HED project homepage <https://github.com/hed-standard>`_ for links to the latest developments..