Merge branch 'main' of https://github.com/CBICA/NiChart_Project

CBICA · Dec 13, 2024 · 506a5d9 · 506a5d9
2 parents 6f16c65 + d9bb3fc
commit 506a5d9
Show file tree

Hide file tree

Showing 19 changed files with 60 additions and 176 deletions.
diff --git a/.github/workflows/sphinx-docs.yml b/.github/workflows/sphinx-docs.yml
@@ -29,16 +29,16 @@ jobs:
           pip install sphinx sphinx_rtd_theme sphinx-tabs sphinx_toolbox
       - name: Sphinx build
         run: |
-          sphinx-apidoc -o docs2 src/
-          cd docs2/
+          sphinx-apidoc -o docs src/
+          cd docs/
           make html
           cd ..
 
       - name: Upload pages artifact
         uses: actions/upload-pages-artifact@v3
 
         with:
-          path: docs2/_build/html
+          path: docs/_build/html
           retention-days: 90
 
   deploy-docs:

diff --git a/docs/Makefile b/docs/Makefile
@@ -5,8 +5,8 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
-BUILDDIR      = build
+SOURCEDIR     = .
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:

diff --git a/docs2/README.rst → docs/README.rst b/docs2/README.rst → docs/README.rst
diff --git a/docs2/api.rst → docs/api.rst b/docs2/api.rst → docs/api.rst
diff --git a/docs2/components.rst → docs/components.rst b/docs2/components.rst → docs/components.rst
@@ -20,17 +20,16 @@ Neuroimaging pipeline for computing AI biomarkers of disease and aging from T1-w
 Segmentation
 ------------
 
-`DLMUSE <https://neuroimagingchart.com/components/#Image%20Processing>`: Rapid and accurate **brain anatomy segmentation**
+`DLMUSE <https://neuroimagingchart.com/components/#Image%20Processing>`_: Rapid and accurate **brain anatomy segmentation**
 
 .. image:: https://github.com/CBICA/NiChart_Project/blob/031d1cafc5091eb514511ee25af189d5f0b5ac56/resources/images/dlicv%2Bdlmuse_segmask.png
-   :target https://github.com/CBICA/NiChart_DLMUSE
    :alt: DLMUSE
 
 -------------
 Harmonization
 -------------
 
-`COMBAT <https://neuroimagingchart.com/components/#Harmonization>`: **Statistical data harmonization** of ROI volumes to `reference data <https://neuroimagingchart.com/components/#Reference%20Dataset>`
+`COMBAT <https://neuroimagingchart.com/components/#Harmonization>`_: **Statistical data harmonization** of ROI volumes to `reference data <https://neuroimagingchart.com/components/#Reference%20Dataset>`_
 
 .. image:: https://raw.githubusercontent.com/CBICA/NiChart_Project/refs/heads/ge-dev/resources/images/combat_agetrend.png
    :alt: COMBAT
@@ -39,13 +38,12 @@ Harmonization
 Supervised ML Biomarkers
 ------------------------
 
-`SPARE-AD and SPARE-Age indices <https://neuroimagingchart.com/components/##Machine%20Learning%20Models>`: AI biomarkers of **Alzheimer's Disease and Aging** related brain atrophy patterns
+`SPARE-AD and SPARE-Age indices <https://neuroimagingchart.com/components/##Machine%20Learning%20Models>`_: AI biomarkers of **Alzheimer's Disease and Aging** related brain atrophy patterns
 
 .. image:: https://raw.githubusercontent.com/CBICA/NiChart_Project/refs/heads/ge-dev/resources/images/sparead%2Bage.png
-  :target https://github.com/CBICA/spare_scores
   :alt: SPARE-AD and SPARE-Age indices
 
-`SPARE-CVR indices <https://alz-journals.onlinelibrary.wiley.com/doi/abs/10.1002/alz.067709>`: AI biomarkers of brain atrophy patterns associated with **Cardio-Vascular Risk Factors**
+`SPARE-CVR indices <https://alz-journals.onlinelibrary.wiley.com/doi/abs/10.1002/alz.067709>`_: AI biomarkers of brain atrophy patterns associated with **Cardio-Vascular Risk Factors**
 
 .. image:: https://raw.githubusercontent.com/CBICA/NiChart_Project/refs/heads/ge-dev/resources/images/sparecvr.png
   :alt: SPARE-CVR indices, Govindarajan, S.T., et. al., Nature Communications, 2024
@@ -54,7 +52,7 @@ Supervised ML Biomarkers
 Semi-supervised ML Biomarkers
 -----------------------------
 
- - `SurrealGAN indices <https://www.nature.com/articles/d41586-024-02692-z>`: Data-driven phenotyping of brain aging, **5 Brain Aging Subtypes**
+ - `SurrealGAN indices <https://www.nature.com/articles/d41586-024-02692-z>`_: Data-driven phenotyping of brain aging, **5 Brain Aging Subtypes**
 
 .. image:: https://raw.githubusercontent.com/CBICA/NiChart_Project/refs/heads/ge-dev/resources/images/sgan1.jpg
    :alt: SurrrealGAN indices
@@ -63,9 +61,9 @@ Semi-supervised ML Biomarkers
 2. WM Lesion Segmentation
 ====================================
 
-Neuroimaging pipeline for segmenting white matter lesions on FLAIR MRI scans. 
+Neuroimaging pipeline for segmenting white matter lesions on FLAIR MRI scans.
 
-`DLWMLS <https://neuroimagingchart.com/components/#Image%20Processing>`: Rapid and accurate **white matter lesion segmentation**
+`DLWMLS <https://neuroimagingchart.com/components/#Image%20Processing>`_: Rapid and accurate **white matter lesion segmentation**
 
 .. image:: https://github.com/CBICA/NiChart_Project/blob/031d1cafc5091eb514511ee25af189d5f0b5ac56/resources/images/dlwmls.png
    :target https://github.com/CBICA/NiChart_DLWMLS

diff --git a/docs2/conf.py → docs/conf.py b/docs2/conf.py → docs/conf.py
diff --git a/docs2/contributors.rst → docs/contributors.rst b/docs2/contributors.rst → docs/contributors.rst
diff --git a/docs2/help.rst → docs/help.rst b/docs2/help.rst → docs/help.rst
diff --git a/docs2/index.rst → docs/index.rst b/docs2/index.rst → docs/index.rst
diff --git a/docs2/installation.rst → docs/installation.rst b/docs2/installation.rst → docs/installation.rst
@@ -16,34 +16,32 @@ We release our latest stable version on PyPI; accordingly, **we strongly recomme
 .. warning::
     PyTorch and NumPy have known compatibility issues across different platforms. To avoid potential conflicts, please follow the installation instructions below.
 
-- After installing all other necessary packages, uninstall any existing Torch installations:   
-   
+- After installing all other necessary packages, uninstall any existing Torch installations: ::
+
    $ pip uninstall torch
 
 - Reinstall PyTorch:
 
     - **Linux:** PyTorch version 2.3.1
     - **Windows:** PyTorch version 2.5.1
-
-- Users can select the correct index URL for their CUDA version based on the `PyTorch getting started page <https://pytorch.org/get-started/locally>`
 
-**Example on a Linux x86 system:**
+- Users can select the correct index URL for their CUDA version based on the `PyTorch getting started page <https://pytorch.org/get-started/locally>`_
+
+**Example on a Linux x86 system:** ::
 
     $ pip install torch==2.3.1 --index-url https://download.pytorch.org/whl/cu121
 
 *************************
 Managing your environment
 *************************
 
-We recommend installing NiChart Project within a dedicated environment. Users can create an environment using Mamba (please see `Mamba Installation Guide <https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html>`).
+We recommend installing NiChart Project within a dedicated environment. Users can create an environment using Mamba (please see `Mamba Installation Guide <https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html>`_).
 
 **Example on a Linux x86 system:** ::
 
-    wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
-    bash Mambaforge-Linux-x86_64.sh
-    mamba create -c conda-forge -c bioconda -n NCP_env python=3.12 
-    mamba activate NCP_env
-    git clone https://github.com/CBICA/NiChart_Project.git
-    pip install -r requirements.txt
-
-
+    $ wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
+      bash Mambaforge-Linux-x86_64.sh
+      mamba create -c conda-forge -c bioconda -n NCP_env python=3.12
+      mamba activate NCP_env
+      git clone https://github.com/CBICA/NiChart_Project.git
+      pip install -r requirements.txt
diff --git a/docs2/license.rst → docs/license.rst b/docs2/license.rst → docs/license.rst
@@ -2,4 +2,4 @@
 License
 #######
 
-NiChart application, web site, the content and the logo of NiChart are intellectual property of CBICA, UPENN. For details, please see `the licence <https://github.com/CBICA/NiChart_Project/blob/main/LICENSE>`.
+NiChart application, web site, the content and the logo of NiChart are intellectual property of CBICA, UPENN. For details, please see `the licence <https://github.com/CBICA/NiChart_Project/blob/main/LICENSE>`_.
diff --git a/docs/make.bat b/docs/make.bat
@@ -1,35 +1,35 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/docs2/modules.rst → docs/modules.rst b/docs2/modules.rst → docs/modules.rst
diff --git a/docs/source/conf.py b/docs/source/conf.py
diff --git a/docs/source/index.rst b/docs/source/index.rst
diff --git a/docs/source/modules.rst b/docs/source/modules.rst
diff --git a/docs2/usage.rst → docs/usage.rst b/docs2/usage.rst → docs/usage.rst
diff --git a/docs2/Makefile b/docs2/Makefile
diff --git a/docs2/make.bat b/docs2/make.bat
-Original file line number
+Diff line change
@@ Expand Up / @@ -2,4 +2,4 @@ @@
     License
     #######
-    NiChart application, web site, the content and the logo of NiChart are intellectual property of CBICA, UPENN. For details, please see `the licence <https://github.com/CBICA/NiChart_Project/blob/main/LICENSE>`.
+    NiChart application, web site, the content and the logo of NiChart are intellectual property of CBICA, UPENN. For details, please see `the licence <https://github.com/CBICA/NiChart_Project/blob/main/LICENSE>`_.