Merge pull request #355 from VisLab/develop

Fixed links broken due to matlab repo reorganization

Author: VisLab

docs/source/FileRemodelingQuickstart.md

@@ -488,7 +488,7 @@ Now you can try out the *split_rows* on the full dataset!
 ### Jupyter notebooks for remodeling
 
 Three Jupyter remodeling notebooks are available at 
-[**Jupyter notebooks for remodeling**](https://github.com/hed-standard/hed-examples/tree/main/hedcode/jupyter_notebooks/remodeling).
+[**Jupyter notebooks for remodeling**](https://github.com/hed-standard/hed-examples/tree/main/src/jupyter_notebooks/remodeling).
 
 These notebooks are wrappers that create the backup as well as run restructuring operations on data files.
 If you do not have access to a Jupyter notebook facility, the article

docs/source/HedMatlabTools.md

@@ -26,7 +26,7 @@ The following MATLAB code demos are available to show how to access HED web serv
 | ------ |-----------------|-----------|
 | 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/testEventServices.m)   | Validation, conversion, sidecar generation.  |
+| 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. |
@@ -503,7 +503,7 @@ installed on your machine.
 The most difficult part of the process 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 wrapper functions**](https://github.com/hed-standard/hed-examples/tree/main/hedcode/matlab_scripts/hedtools_wrappers),
+[**MATLAB HED tool wrapper functions**](https://github.com/hed-standard/hed-matlab/tree/main/hedmat/hedtools_wrappers),
 which take MATLAB variables as arguments and return MATLAB variables.
 Thus, once the setup is done, you don't have to learn any additional Python syntax to use the tools.
 You should only have to do this setup once, since MATLAB retains the setup information
@@ -713,7 +713,7 @@ Wrapper functions are provided to some of the more commonly used
 functions in the HEDTools suite.
 
 The following example shows the MATLAB wrapper function
-[**validateHedInBids.m**](https://raw.githubusercontent.com/hed-standard/hed-examples/main/hedcode/matlab_scripts/hedtools_wrappers/validateHedInBids.m),
+[**validateHedInBids.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/hedtools_wrappers/validateHedInBids.m),
 which contains the underlying calls to HEDTools Python BIDs validation.
 
 

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/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/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
-[extract_json_template.ipynb](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/extract_json_template.ipynb)
+[extract_json_template.ipynb](https://github.com/hed-standard/hed-examples/blob/main/src/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 [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.
+The [sidecar_to_spreadsheet.ipynb](https://github.com/hed-standard/hed-examples/blob/main/src/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_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.
+The [bids_merge_spreadsheet_into_sidecar.ipynb](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/merge_spreadsheet_into_sidecar.ipynb) Python Jupyter notebook does the same operation.
 
 
 (spreadsheets-online-tools-anchor)=
@@ -558,7 +558,7 @@ 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-examples/tree/main/hedcode/matlab_scripts/web_services) 
+The [**web_services**](https://github.com/hed-standard/hed-matlab/tree/main/hedmat/web_servicess) 
 directory in the `hed-examples` GitHub repository provides MATLAB examples of how to call these 
 services in MATLAB.
 

docs/source/HedPythonTools.md

@@ -70,7 +70,7 @@ All columns not designated as skip columns or value columns are considered to be
 (find-event-combinations-anchor)=
 ### Find event combinations
 
-The [**find_event_combinations.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/find_event_combinations.ipynb)
+The [**find_event_combinations.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/find_event_combinations.ipynb)
 Jupyter notebook extracts a spreadsheet containing the unique combination of values in the
 specified `key_columns`.
 The setup requires the following variables for your dataset:
@@ -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/hedcode/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/summarize_events.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.
@@ -215,7 +215,7 @@ It does not do a full BIDS validation.
 ### Validate BIDS dataset with libraries
 
 
-The [**validate_bids_dataset_with_libraries.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/validate_bids_dataset_with_libraries.ipynb)
+The [**validate_bids_dataset_with_libraries.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset_with_libraries.ipynb)
 Jupyter notebook validates HED in a BIDS dataset using the `validate` method of `BidsDataset`.
 The example uses three schemas and also illustrates how to manually override the
 schema specified in `dataset_description.json` with schemas from other places.
@@ -224,7 +224,7 @@ This is very useful for testing new schemas that are underdevelopment.
 (validate-bids-datasets-anchor)=
 ### Validate BIDS datasets
 
-The [**validate_bids_datasets.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/validate_bids_datasets.ipynb) is similar to the other validation notebooks, but it takes a list of datasets to validate as a convenience.
+The [**validate_bids_datasets.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_datasets.ipynb) is similar to the other validation notebooks, but it takes a list of datasets to validate as a convenience.
 
 
 (jupyter-curation-notebooks-anchor)=

docs/source/HedValidationGuide.md

@@ -214,7 +214,7 @@ directly using PIP.
 
 #### Jupyter notebooks for validation
 
-Several [**Jupyter notebooks**](https://github.com/hed-standard/hed-examples/tree/main/hedcode/jupyter_notebooks) are available 
+Several [**Jupyter notebooks**](https://github.com/hed-standard/hed-examples/tree/main/src/jupyter_notebooks) are available 
 as wrappers for calling various Python HED tools. 
 
 For example, the [**validate_bids_datasets.ipynb**](https://github.com/hed-standard/hed-examples/blob/develop/src/jupyter_notebooks/bids/validate_bids_datasets.ipynb) notebook shown in the following example validates an entire BIDS dataset