Merge pull request #377 from VisLab/develop

Fixed bad links

CODE_OF_CONDUCT.md

@@ -46,4 +46,4 @@ Project maintainers who do not follow or enforce the Code of Conduct in good fai
 ## Attribution
 
 This Code of Conduct is adapted from the [**BIDS Code of Conduct**](https://github.com/bids-standard/bids-specification/blob/master/CODE_OF_CONDUCT.md) which is based on information from the
-[**Contributor Covenant**](http://contributor-covenant.org]).
+[**Contributor Covenant**](http://contributor-covenant.org).

README.md

@@ -14,7 +14,7 @@ Most of these datasets have complete versions available on
 [**openNeuro**](https://openneuro.org/).
 See [**datasets/README.md**](./datasets/README.md) for details.
 
-The [**src**](https://github.com/hed-standard/hed-examples/tree/main/hedcode)
+The [**src**](https://github.com/hed-standard/hed-examples/tree/main/src)
 subdirectory contains Python Jupyter notebooks demonstrating calls to HedTools.
 For MATLAB support for HED see the [**hed-matlab**](https://github.com/hed-standard/hed-matlab)
 GitHub repository.

docs/source/BidsAnnotationQuickstart.md

@@ -322,7 +322,6 @@ The [**sub-002_task-FacePerception_run-1_events.tsv**](./_static/data/sub-002_ta
 The following is a simplified excerpt of this template,
 which we will use to illustrate the rest of the annotation process.
 
-(simplified-json-template)=
 `````{admonition} JSON sidecar generated template.
 :class: tip
 ```json
@@ -362,10 +361,8 @@ when the annotation is assembled.
 
 Once you have a JSON sidecar template, you should edit in your event annotations.
 The following is an edited version of the 
-[**simplified template excerpt**](simplified-json-template)
-containing a minimal set of HED annotations.
+JSON template from the previous step containing a minimal set of HED annotations.
 
-(excerpted-json-file-with-tags)=
 `````{admonition} JSON sidecar with completed annotation.
 :class: tip
 ```json

docs/source/FileRemodelingTools.md

@@ -218,9 +218,8 @@ of these operations and how to use them.
 
 The remodeling command-line interface can be used from the command line,
 called from another Python program, or used in a Jupyter notebooks.
-Example notebooks can be found in the
-[**Jupyter notebooks**](https://github.com/hed-standard/hed-examples/tree/main/hedcode/jupyter_notebooks/remodeling)
- to support remodeling.
+Example Jupyter notebooks using the remodeling commands can be found 
+[**here**](https://github.com/hed-standard/hed-examples/tree/main/src/jupyter_notebooks/remodeling).
 
 
 (calling-remodel-tools-anchor)=
@@ -673,7 +672,7 @@ as the `PARAMS` property of the operation's class definition.
 The use of the JSON schema allows the remodeler to specify and validate requirements on most of an
 operation's parameters using standardized methods.
 
-The remodeler [**validator**](https://raw.githubusercontent.com/hed-standard/hed-python/develop/hed/tools/remodeling/validator.py)
+The [**remodeler_validator**](https://github.com/hed-standard/hed-python/blob/master/hed/tools/remodeling/remodeler_validator.py)
 compiles a JSON schema for the remodeler from individual operations and validates
 the remodel file against the compiled JSON schema. The validator should always before executing any remodel operations.
 

docs/source/HedMatlabTools.md

@@ -740,24 +740,24 @@ Alternatively, these services can be accessed through a locally-deployed docker
 See the [**hed-web**](https://hed-web.readthedocs.io/en/latest/index.html)
 GitHub repository documentation for additional information on the docker deployment.
 The MATLAB code to run demos of these services is available on the 
-[**hed-matlab**](https://github.com/hed-standard/hed-matlab/tree/main/hedmat/web_services)
-GitHub repository. 
+[**web_services_demo**](https://github.com/hed-standard/hed-matlab/tree/main/hedmat/web_services_demos)
+directory of the [**hed-matlab**](https://github.com/hed-standard/hed-matlab) GitHub repository. 
 
 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/runAllDemos.m)   | Harness for running all demos.   |
-| Overall | [**demoGetServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services/demoGetServices.m)   | List available services.  |
-| Events | [**demoEventServices.m**](https://raw.githubusercontent.com/hed-standard/hed-examples/main/hedcode/matlab_scripts/web_services/demoEventServices.m)   | Validation, conversion, sidecar generation.  |
-| Events | [**demoEventSearchServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services/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/demoSidecarServices.m) | Validation, conversion, extraction, merging. |
-| Spreadsheets | [**demoSpreadsheetServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services/demoSpreadsheetServices.m) | Validation, conversion.  |
-| Strings | [**demoStringServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services/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-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.  |
 
 
-The [**runAllDemos.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services/runAllDemos.m)
+The [**runAllDemos.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/runAllDemos.m)
 script runs all the demo code and reports whether
 the demos run successfully.
 Before using the HED web services from MATLAB, 
@@ -767,7 +767,7 @@ that you have Internet access, and that the HED services are available.
 This script also demonstrates how to call the individual demo functions.
 Each demo function takes a host URL as a parameter and returns a list of errors.
 The demos all use demo data read by the 
-[**getDemoData**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services/getDemoData.m) 
+[**getDemoData**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/getDemoData.m) 
 function, which returns a MATLAB `struct` containing all needed test data.
 The individual demo scripts illustrate how to call each type of available web service.
 
@@ -788,7 +788,7 @@ to construct a fixed session header that can be used in subsequent requests in y
 #### Setting up a session from MATLAB
 
 The goal of the session setup is to construct a header that can be used in subsequent web requests.
-The first step is to call the [**getHostOptions.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services/getHostOptions.m).
+The first step is to call the [**getHostOptions.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/getHostOptions.m).
 
 (setting)=
 `````{admonition} Establish a session.
@@ -806,7 +806,7 @@ The `servicesURL` and the `options` can be used for all of your subsequent reque
 
 This function constructs the services URL from the host URL.
 The function also makes a service request to obtain a CSRF token and a cookie using
-[**getSessionInfo**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services/getSessionInfo.m).
+[**getSessionInfo**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/getSessionInfo.m).
 The function then constructs a header and calls the MATLAB `weboptions` function
 to get an options object suitable for use with the MATLAB `webwrite` function
 use in all of our examples.
@@ -917,7 +917,7 @@ and makes a request for validation using `HED8.2.0.xml`.
 The request indicates that validation warnings as well as errors should be included in the response.
 If you wish to exclude warnings, use `off` instead of `on` as the `check_for_warnings` field value.
 
-The [**demoSidecarServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services/demoSidecarServices.m)
+The [**demoSidecarServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoSidecarServices.m)
 function shows complete examples of the various HED services for JSON sidecars.
 
 (making-a-service-request-anchor)=
@@ -937,7 +937,7 @@ outputReport(response, 'Example: validate a JSON sidecar');
 ```
 `````
 
-The [**<code>outputReport.m</code>**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services/outputReport.m)
+The [**<code>outputReport.m</code>**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/outputReport.m)
 MATLAB script outputs the response in readable form with a user-provided table.
 
 If the web server is down or times out during a request,
@@ -993,4 +993,3 @@ For example, if a sidecar had validation errors,
 `results.msg_category` will be `warning` and the `results.data` value
 should be interpreted as a list of errors.
 If the sidecar had no errors, `results.data` will be an empty string.
-

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 [validate_bids_dataset.ipynb](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset.ipynb)
+The [validate_bids_dataset.ipynb](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_datasets.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.
@@ -203,7 +203,7 @@ dataset root directory, this is all that is needed.
 However, if the sidecar is part of an inheritance chain, some of its definitions
 are externally defined, or the sidecar contains tags from multiple HED schemas,
 you should use the 
-[validate_bids_dataset.ipynb](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/validate_bids_dataset.ipynb)
+[validate_bids_dataset.ipynb](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_datasets.ipynb)
 Python Jupyter notebook to validate the HED in your BIDS dataset.
 
 #### Convert sidecar to long
@@ -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_servicess) 
+The [**web_services**](https://github.com/hed-standard/hed-matlab/tree/main/hedmat/web_services) 
 directory in the `hed-examples` GitHub repository provides MATLAB examples of how to call these 
 services in MATLAB.
 

docs/source/HedPythonTools.md

@@ -100,7 +100,7 @@ For this reason, the HED tools offer the option of creating a 4-column spreadshe
 a BIDS JSON sidecar and using it to create annotations. The four columns are: 
 `column_name`, `column_value`, `description`, and `HED`. 
 See [**task-WorkingMemory_example_spreadsheet.tsv**](https://github.com/hed-standard/hed-examples/blob/main/docs/source/_static/data/task-WorkingMemory_example_spreadsheet.tsv)
-The [**sidecar_to_spreadsheet.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb)
+The [**sidecar_to_spreadsheet.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb)
 
 ```{admonition} Variables to set in the extract_json_template.ipynb Jupyter notebook.
 :class: tip
@@ -121,7 +121,7 @@ spreadsheet rather than working with the JSON file directly as explained in the
 [**Spreadsheet templates**](https://hed-examples.readthedocs.io/en/latest/BidsAnnotationQuickstart.html#spreadsheet-templates-anchor)
 tutorial.
 
-The [**sidecar_to_spreadsheet.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb)
+The [**sidecar_to_spreadsheet.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb)
 notebook demonstrates how to extract the pertinent
 HED annotation to a 4-column spreadsheet (Pandas dataframe) corresponding
 to the HED content of a JSON sidecar.
@@ -154,7 +154,7 @@ Sometimes event files include unexpected or incorrect codes.
 It is a good idea to find out what is actually in the dataset
 event files and whether the information is consistent before starting the annotation process.
 
-The [**summarize_events.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/summarize_events.ipynb) finds the dataset event files and outputs
+The [**summarize_events.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb) finds the dataset event files and outputs
 the column names and number of events for each event file.
 You can visually inspect the output to make sure that the event file column names
 are consistent across the dataset.
@@ -189,7 +189,7 @@ faster to debug.
 The [**HED validation guide**](https://hed-examples.readthedocs.io/en/latest/HedValidationGuide.html)
 discusses various HED validation issues and how to fix them.
 
-The [**validate_bids_dataset.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/validate_bids_dataset.ipynb)
+The [**validate_bids_dataset.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb)
 Jupyter notebook validates HED in a BIDS dataset using the `validate` method
 of `BidsDataset`.
 The method first  gathers all the relevant JSON sidecars for each event file

docs/source/HedSchemas.md

@@ -92,31 +92,24 @@ 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://hed-schemas.readthedocs.io/en/latest/hed_lisa_schema.html) 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?via%3Dihub) standard for clinical annotation of EEG by neurologists.
 For more information and the latest references see 
-[**HED SCORE schema**](https://hed-schemas.readthedocs.io/en/latest/hed_score_schema.html).
+[**HED SCORE schema**](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/README.md).
 
 | Format     | Type | Use | 
 |------------| ---- | ---- | 
-| XML        |  [**Raw**](https://raw.githubusercontent.com/hed-standard/hed-schemas/main/library_schemas/score/hedxml/HED_score_1.0.0.xml) | Accessed by tools for validation and analysis. |  
-|            | [**Formatted**](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/hedxml/HED_score_1.0.0.xml) | Readable display. |
-| MediaWiki  | [**Raw**](https://raw.githubusercontent.com/hed-standard/hed-schemas/main/library_schemas/score/hedwiki/HED_score_1.0.0.mediawiki) | Edited to create a new schema. |  
-|            | [**Formatted**](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/hedwiki/HED_score_1.0.0.mediawiki) |  Readable display for editing. |
+| XML        |  [**Raw**](https://raw.githubusercontent.com/hed-standard/hed-schemas/main/library_schemas/score/hedxml/HED_score_1.1.0.xml) | Accessed by tools for validation and analysis. |  
+|            | [**Formatted**](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/hedxml/HED_score_1.1.0.xml) | Readable display. |
+| MediaWiki  | [**Raw**](https://raw.githubusercontent.com/hed-standard/hed-schemas/main/library_schemas/score/hedwiki/HED_score_1.1.0.mediawiki) | Edited to create a new schema. |  
+|            | [**Formatted**](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/hedwiki/HED_score_1.1.0.mediawiki) |  Readable display for editing. |
 | Prerelease | [**Directory**](https://github.com/hed-standard/hed-schemas/tree/main/library_schemas/score/prerelease) |  Working directory for developing the prerelease. |
 
-### The LISA library
+### The LANG library
 
-The HED LISA library represents a vocabulary for annotating linguistic stimuli in language and other
+The HED LANG library represents a vocabulary for annotating linguistic stimuli in language and other
 types of experiments.
 For more information and the latest references see 
-[**HED LISA schema**](https://hed-schemas.readthedocs.io/en/latest/hed_lisa_schema.html).
-The LISA library is under development and is only available in prerelease format.
-
-| Format     | Type | Use | 
-|------------| ---- | ---- | 
-| XML        | **Raw** | Accessed by tools for validation and analysis. |  
-|            | [**Formatted**] | Readable display. |
-| MediaWiki  | [**Raw**] | Edited to create a new schema. |  
-|            | [**Formatted**] |  Readable display for editing. |
-| Prerelease | [**Directory**](https://github.com/hed-standard/hed-schemas/tree/main/library_schemas/lisa/prerelease) |  Working directory for developing the prerelease. |
+[**HED LANG schema**](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/lang/README.md).
+The LANG library is under development and is only available in 
+[**prerelease**](https://github.com/hed-standard/hed-schemas/tree/main/library_schemas/lang/prerelease) format.