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Update docs
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‎docs/buildDocs.sh‎

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<!DOCTYPE html>
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<html>
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<head>
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<title>NiBAx Docs</title>
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<title>niCHART Docs</title>
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<meta http-equiv = "refresh" content="0; url='/${REPO_NAME}/en/main/'" />
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</head>
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<body>
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If you are looking for documentation, please see:
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* https://cbica.github.io/NiBAx/
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* https://cbica.github.io/niCHART/
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EOF
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# copy the resulting html pages built from sphinx above to our new git repo

‎docs/contents/datapreprocessing.rst‎

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.. code-block:: shell
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GIT_LFS_SKIP_SMUDGE=1 git clone https://github.com/CBICA/NiBAx/
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cd NiBAx/Image_Processing/sMRI
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GIT_LFS_SKIP_SMUDGE=1 git clone https://github.com/CBICA/niCHART/
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cd niCHART/Image_Processing/sMRI
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git lfs pull --include example
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git lfs pull --include sMRI_ProcessingPipeline
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‎docs/contents/development.rst‎

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/usr/bin/python --version
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It is recommended to install **[NiBAx]** in a virtual Python environment.
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It is recommended to install **[niCHART]** in a virtual Python environment.
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Shown below is an installation into the folder `.env` in the current working
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directory.
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.. code-block:: shell
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python -m venv .env
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source .env/bin/activate
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python -m pip install https://github.com/CBICA/NiBAx
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python -m pip install https://github.com/CBICA/niCHART
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Once installed, the GUI is accesible as command `NiBAx`.
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Once installed, the GUI is accesible as command `niCHART`.
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.. code-block:: shell
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# Typing NiBAx in an activated virtual environment
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# Typing niCHART in an activated virtual environment
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# will launch the graphical user interface.
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NiBAx
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niCHART
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***************************
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Build documentation locally

‎docs/contents/userguide.rst‎

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The easiest method to install the toolbox is via the binary installers for Windows, macOS, and Linux.
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Alternate releases of **[NiBAχ]** can be found `here <https://github.com/CBICA/NiBAx/tags>`_.
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Alternate releases of **[niCHART]** can be found `here <https://github.com/CBICA/niCHART/tags>`_.
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Until one-click installation packages are available, we recommend to install
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/usr/bin/python --version
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It is recommended to install **[NiBAx]** in a virtual Python environment.
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It is recommended to install **[niCHART]** in a virtual Python environment.
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Shown below is an installation into the folder `.env` in the current working
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directory.
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.. code-block:: shell
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python -m venv .env
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source .env/bin/activate
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python -m pip install https://github.com/CBICA/NiBAx
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python -m pip install https://github.com/CBICA/niCHART
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Once installed, the GUI is accesible as command `NiBAx`.
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Once installed, the GUI is accesible as command `niCHART`.
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.. code-block:: shell
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# Typing NiBAx in an activated virtual environment
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# Typing niCHART in an activated virtual environment
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# will launch the graphical user interface.
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NiBAx
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niCHART
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*********
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.. code-tab:: text PowerShell (Windows 10/11)
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& .env/Scripts/Activate.ps1
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NiBAx.exe
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niCHART.exe
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.. code-tab:: shell Bash (Linux and macOS)
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source /path/to/.env/bin/activate
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NiBAx
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niCHART
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This will launch the GUI.

‎docs/index.rst‎

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*****
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About
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*****
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By using NiBAx, the user agrees to the following license:
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By using niCHART, the user agrees to the following license:
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https://www.med.upenn.edu/cbica/software-agreement-non-commercial.html
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For more information and support, please post on the `Discussions <https://github.com/CBICA/NiBAx/discussions>`_
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For more information and support, please post on the `Discussions <https://github.com/CBICA/niCHART/discussions>`_
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section or contact `CBICA Software <[email protected]>`_.

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