Merge pull request #209 from VisLab/develop

Updated what's new 1/20/2023

docs/requirements.txt

@@ -1,17 +1,17 @@
 attrs>=21.4.0
-click==8.1.3
+click>=8.1.3
 coverage>=6.3.2
-defusedxml==0.7.1
-et-xmlfile==1.1.0
+defusedxml>=0.7.1
+et-xmlfile>=1.1.0
 Flask>=2.1.2
-Flask-WTF==1.0.1
+Flask-WTF>=1.0.1
 hedtools >= 0.1.0
 inflect>=5.5.2
-itsdangerous==2.1.2
-jdcal==1.4.1
+itsdangerous>=2.1.2
+jdcal>=1.4.1
 Jinja2>=3.0.0
-jupyter==1.0.0
-MarkupSafe==2.1.1
+jupyter>=1.0.0
+MarkupSafe>=2.1.1
 myst-parser>=0.18.1
 numpy>=1.20.3
 numpydoc>=1.3.1
@@ -22,11 +22,10 @@ Pygments>=2.12.0
 python-dateutil==2.8.2
 pytz>=2022.1
 semantic_version>=2.9.0
-six==1.16.0
-sphinx-tabs>=3.4.1
-Sphinx==5.2.2
-SphinxExtensions==0.2.0
-sphinx_rtd_theme==1.0.0
+six>=1.16.0
+Sphinx>=5.2.2
+SphinxExtensions>=0.2.0
+sphinx_rtd_theme>=1.0.0
 Werkzeug>=2.1.2
-WTForms==3.0.1
-xlrd==2.0.1
+WTForms>=3.0.1
+xlrd>=2.0.1

docs/source/HedMatlabTools.md

@@ -556,12 +556,14 @@ There are several likely places to look for Python on your system.
 
 **For Linux users**:
 
->Likely places for system-space installation are `/bin`, `/local/bin`, `/usr/bin`, `/usr/local/bin`, or `/opt/bin`. User-space installations are usually some where in your home directory such as `~/bin`. 
+>Likely places for system-space installation are `/bin`, `/local/bin`, `/usr/bin`, `/usr/local/bin`, or `/opt/bin`. User-space installations are usually your home directory in a subdirectory such as `~/bin`
+or `~/.local/bin`. 
 
 **For Windows users**:
 > Likely places for system-space installation are `C:\`, `C:\Python`, or `C:\Program Files`.
 User-space installations default to your personal account 
-in `C:\Users\yourname\AppData\Local\Programs\Python\python311` where `yourname` is your Windows accountname.
+in `C:\Users\yourname\AppData\Local\Programs\Python\python39` where `yourname` is your Windows account name
+and `python39` will be the particular version (in this case Python 3.9).
 
 If you don't have any success finding a Python executable,
 you will need to install Python as described in 
@@ -601,7 +603,7 @@ as illustrated by the following example.
 ````
 
 Be sure to substitute the path of the Python that you have found.
-Notice that the executable listed in Step 1 was pythonw.exe, but we have used python.exe here
+Notice that the executable listed in Step 1 was `pythonw.exe`, but we have used `python.exe` here
 to indicate the command line version.
 
 Use the MATLAB `pyenv` function again without arguments to check that your installation is as expected.

docs/source/HedSchemaDevelopmentGuide.md

@@ -17,6 +17,17 @@ or creating an entirely new one.
 
 ## Setting up for schema development
 
+Although schema developers work with HED schema in `.mediawiki` format for ease in editing,
+HED tools generally use XML versions of the HED schema. 
+
+````{admonition} **Standard development process for XML schema.**
+:class: tip
+
+1. Create or modify a `.mediawiki` file containing the schema.
+2. Validate the `.mediawiki` file using the [**HED online tools**](https://hedtools.ucsd.edu/hed/schema).
+2. Convert to `.xml` using the [**HED online tools**](https://hedtools.ucsd.edu/hed/schema).
+3. View in the [**expandable schema viewer**](https://www.hedtags.org/display_hed.html) to verify.
+````
 
 ## Design principles for schema
 

docs/source/HedSearchGuide.md

@@ -59,11 +59,15 @@ Notes: If you're searching many strings for the same expression, make sure you c
 
 ## Query types
 
-| Token      | Meaning                       | Example        | Example Meaning                                                                             |
-|------------|-------------------------------|----------------|-----------------------------------|
-| Single term | Searches matches the term <br/>or any of its children.<br/>No values or extensions are considered.| *Event*          | Matches string containing *Event*<br/>tag, or any child tag of Event. |
-| Tag path<br/> with slash | A tag with extension or value | Def/Def1       | Find strings that contain the exact tag Def/Def1.                                           |
-| ,          | and                           | A, B           | Find strings or groups with both A and B                                                    |
+### Single term queries
+
+
+
+| Query form     | Meaning                       | Example query        | Matches | Does not match |
+|------------|-------------------------------|----------------| --------------- | ---------------- |
+| Single term | Match the term or any of its children.<br/>Don't consider values or extensions.| *Event* | *Event*<br/>*Sensory-event*<br/>*Event/New-event*<br/>*Event/Sensory-event*|
+| Tag path<br/>with slash | Match the exact tag with extension or value | Def/Def1       | Find strings that contain the exact tag Def/Def1.                                           |
+| A, B         | Match both A and B. | *Event*, *Sensory-event* |               |    |
 | and        | and                           | A and B        | Find strings or groups with both A and B                                                    |
 | or         | or                            | A or B         | Find strings or groups with either A or B                                                   |
 | [[         | Exact group start             | [[A, B]]       | Find a group that contains both A and B.                                                    |
@@ -208,12 +212,12 @@ Meaning: Find a group containing a direct child group that does not contain Even
                      
     Note: Wildcards should be as late in a search as possible for efficency.  eg "A and ?" rather than "? and A"
 
-#### Wildcards
+### Wildcards
     Wildcards are supported under the new system.  They mostly make sense in containing groups.  They can be mixed and matched,
     e.g: [[A or B and ??? and ??]]
     Meaning: Find a group containing tag A or tag B, while also containing another unrelated tag and another unrelated group.
 
-#### Search Term Wildcards
+### Search Term Wildcards
 Term search - Checks all parent terms in the tags searched as well, does not interact with extensions of values in any way.
 Tag search - Finds tags where the short form IS the indicated search string, unless it has a wildcard.(any search term with a "/" or a "*" or wrapped in double quotes turns it into a tag search)
 
@@ -229,11 +233,11 @@ Examples:
 ### Updated search:
 Query: Event and Sensory-event<br>
 String being searched: Sensory-event<br>
-##### Old System
+#### Old System
     In the old system this would match.  It would first find an Event tag, matching Sensory-event.  It would then find a Sensory-event tag, also matching Sensory-event.
     It did not care it was matching the same tag twice.
 
-##### New System
+#### New System
     Once it matches a tag, it "consumes" the tag and marks it as used.  
     So it would find Event, then be unable to match Sensory-event as there were no tags left.
 

docs/source/WhatsNew.md

@@ -1,10 +1,18 @@
 (whats-new-anchor)=
 # What's new?
 
+**January 20, 2023**: **New preprint available**<br/>
+
+> **Actionable event annotation and analysis in fMRI** [**preprint**](https://osf.io/h7puk)<br/>
+> *Monique Denissen*, *Fabio Richlan*, *Jürgen Birkibauer*, *Mateusz Pawlik*, *Anna Ravenschlag*, *Nicole Himmelstoß*, *Florian Hutzler*, *Kay Robbins*</br>
+> Supporting materials and data are available at [** https://osf.io/93km8/**]( https://osf.io/93km8/)
+> to appear in the book *Methods for analyzing large neuroimaging datasets*
+edited by Robert Whelan and Herve Lemaitre
+
 **January 4, 2023**: **New preprint available**<br/>
 
-> **End-to-end processing of M/EEG data with BIDS, HED, and EEGLAB** [**preprint**](https://osf.io/uxah2)<br/>
-> by Dung Truong, Kay Robbins, Arnaud Delorme, and Scott Makeig</br>
+> **End-to-end processing of M/EEG data with BIDS, HED, and EEGLAB** [**preprint**](https://osf.io/h7puk)<br/>
+> *Dung Truong*, *Kay Robbins*, *Arnaud Delorme*, and *Scott Makeig*</br>
 > Supporting materials and data are available at [**https://osf.io/8brgv/**](https://osf.io/8brgv/)
 > to appear in the book *Methods for analyzing large neuroimaging datasets*
 edited by Robert Whelan and Herve Lemaitre

requirements.txt

@@ -9,8 +9,7 @@ portalocker>=2.4.0
 semantic_version>=2.9.0
 Werkzeug>=2.1.2
 flake8>=4.0.1
-importlib-metadata<3.8.0
-sphinx-tabs>=3.4.1
+importlib-metadata>=3.8.0
 sphinx>=4.5.0
 SphinxExtensions>=0.2.0
 attrs>=21.4.0