Add note of under development and update documentation

.github/workflows/docs_pages_workflow.yml

@@ -24,5 +24,7 @@ jobs:
     - name: Execute script to build our documentation and update pages
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: "docs/buildDocs.sh"
+      run: |
+        git reset --hard origin/$GITHUB_REF_NAME
+        docs/buildDocs.sh
       shell: bash

README.md

@@ -1,52 +1,65 @@
-# BrainChart Toolbox
+# [NiBAx] The neuro-imaging brain aging chart
 
-After proper installation, the tools can be used as follows
+**This software is under development!**
 
-```shell
-QtBrainChart
-```
-
-where `istaging.pkl.gz` and `MUSE_harmonization_model.pkl` are the data and
-harmonization models, respectively.
-
-#
-![](QtBrainChartGUI/resources/workflow.gif)
+![](NiBAx/resources/workflow.gif)
 
 
 ## Setup for development
-Install Python version 3.8.8 or newer. Verify with
+Install Python version 3.8.8 or newer.
+The exact procedure depends on the operating system and configuration.
+Verify the version with
 
 ```shell
 python --version # should be 3.8.8 or newer
 ```
 
 ### Prepare environment in Linux (CUBIC)
-Assuming current working directory is `BrainChart`.
+Assuming current working directory is `NiBAx` and containing the source code
+cloned from https://github.com/CBICA/NiBAx.git.
+
 ```shell
 python -m venv .env
 .env/bin/activate
 python -m pip install --upgrade pip
 ```
 
 ### Prepare environment in Windows 10 or Windows 11
-Assuming current working directory is `BrainChart`.
+Assuming current working directory is `NiBAx` and containing the source code
+cloned from https://github.com/CBICA/NiBAx.git.
+
 ```shell
 python -m venv .env
 & .env/Scripts/Activate.ps1
 python -m pip install --upgrade pip
 ```
 
-### Install BrainChart Toolbox
-To install the `BrainChart Toolbox`, do one of these after activating the
-virtual environment:
+### Install [NiBAx] Toolbox
+To install the [NiBAx], install it in a virtual environment. Depending on the
+desired version, use one of the following commands to install it.
 
 ```shell
-# Editable version for development
-python -m pip install -e . 
+# Editable version for development after cloning https://github.com/CBICA/NiBAx.git 
+python -m pip install -U -e . 
 
-# Version from pull request for testing proposed changes
-python -m pip install git+https://github.com/CBICA/iSTAGING-Tools.git@refs/pull/57/head
+# Version from pull request (#57 in this example) for testing proposed changes
+python -m pip install -U git+https://github.com/CBICA/NiBAx.git@refs/pull/57/head
+
+# Main version of toolbox
+python -m pip install -U git+https://github.com/CBICA/NiBAx.git
+```
 
-# Main version for testing of what users would get
-python -m pip install git+https://github.com/CBICA/iSTAGING-Tools.git
+
+## Useage
+After proper installation, the standalone graphical user interface can be launched
+in the terminal with:
+
+```shell
+NiBAx
+```
+
+The data file can be passed as command line argument `--data_file` as shown below.
+
+```shell
+NiBAx --data_file istaging.pkl.gz
 ```

docs/contents/datapreprocessing.md

@@ -6,5 +6,4 @@
 Data Pre-Processing
 ======================================
 
-contents go here
-
+**The documentation is under active development.**

docs/contents/development.md

@@ -6,5 +6,4 @@
 Development
 ======================================
 
-contents go here
-
+**The documentation is under active development.**

docs/contents/guiplugins.md

@@ -6,5 +6,4 @@
 GUI Plugins
 ======================================
 
-contents go here
-
+**The documentation is under active development.**

docs/contents/installation.md

@@ -6,5 +6,4 @@
 Installation
 ======================================
 
-contents go here
-
+**The documentation is under active development.**

docs/contents/quickstart.md

@@ -6,5 +6,4 @@
 QuickStart
 ======================================
 
-contents go here
-
+**The documentation is under active development.**

docs/contents/userguide.md

@@ -6,5 +6,4 @@
 User Guide
 ======================================
 
-contents go here
-
+**The documentation is under active development.**