ENH: Add optional and groups dependencies in pyproject.toml

GettingStarted.md

@@ -1,5 +1,4 @@
-Getting started
-===============
+# Getting started
 
 Here are suggested steps for the RTK beginner.
 

INSTALLATION.md

@@ -1,8 +1,6 @@
-RTK installation
-================
+# RTK installation
 
-Configuration, compilation and installation with ITK
-----------------------------------------------------
+## Configuration, compilation and installation with ITK
 RTK is a module of [ITK](https://www.itk.org), the Insight Toolkit. Follow the instructions of the [ITK software guide](https://itk.org/ITKSoftwareGuide/html) ([chapter 2](https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch2.html) mainly) for configuring and compiling ITK. The following CMake options are RTK specific:
 
 * `Module_RTK`: Activates RTK download and compilation. Default is `OFF`. Turn it `ON` to activate RTK or compile RTK independently (see below).
@@ -15,8 +13,7 @@ RTK is a module of [ITK](https://www.itk.org), the Insight Toolkit. Follow the i
 
 RTK will automatically be installed when installing ITK.
 
-Independent configuration and compilation
------------------------------------------
+## Independent configuration and compilation
 For RTK developpers, it may be useful to compile RTK independently from ITK. This is possible, simply:
 * Compile ITK with `Module_RTK=OFF`.
 * If you want to use CUDA, also activate `Module_CudaCommon` or compile it separately as RTK in the following two bullet points (cloning its [GitHub repository](https://github.com/RTKConsortium/ITKCudaCommon) or downloading it as a [zip package](https://codeload.github.com/RTKConsortium/ITKCudaCommon/zip/main)).
@@ -25,8 +22,7 @@ For RTK developpers, it may be useful to compile RTK independently from ITK. Thi
 
 Installation is currently not supported for independent RTK compilations.
 
-Pre-compiled binaries
----------------------
+## Python pre-compiled binaries
 We only provide pre-compiled binaries for the Python package which depends on ITK. Use the following commands to install the RTK module with `pip`.
 ```
 python -m pip install --upgrade pip
@@ -42,6 +38,40 @@ python -m pip install itk-rtk-cuda124
 python -m pip install itk-rtk-cuda124
 ```
 
-Getting started
----------------
+### GUI tools
+Some RTK command-line tools, such as `rtkshowgeometry`, require graphical visualization capabilities. To use these tools, install the GUI optional dependencies:
+```
+python -m pip install itk-rtk[gui]
+```
+
+This installs:
+* `pyvista` - for 3D visualization
+* `matplotlib` - for additional graphics support
+
+### Testing
+To run RTK Python tests with pytest, install the test dependencies from the directory containing `pyproject.toml`:
+
+```
+pip install --group test
+```
+
+This installs:
+* `pytest>=7.0` - for running Python unit tests
+* `matplotlib` - for visualization in tests
+
+After installing, run the tests with:
+```
+pytest test/
+```
+
+### Documentation
+To build the RTK documentation, install the documentation dependencies from the directory containing `pyproject.toml`:
+
+```
+pip install --group doc
+```
+
+This installs Sphinx and related tools for documentation generation.
+
+## Getting started
 See [GettingStarted.md](GettingStarted.md). Your `CMakeLists.txt` can now use RTK when importing ITK as shown in the [FirstReconstruction's CMakeLists.txt](https://github.com/RTKConsortium/RTK/blob/main/examples/FirstReconstruction/CMakeLists.txt#L7).

README.md

@@ -1,5 +1,4 @@
-RTK: The Reconstruction ToolKit
-===============================
+# RTK: The Reconstruction ToolKit
 
 [![GitHub release](https://img.shields.io/github/release/RTKConsortium/RTK.svg)](https://github.com/RTKConsortium/RTK/releases/latest)
 [![PyPI](https://img.shields.io/pypi/v/itk-rtk.svg)](https://pypi.python.org/pypi/itk-rtk)
@@ -11,8 +10,7 @@ RTK: The Reconstruction ToolKit
 [gha-link]: https://github.com/RTKConsortium/RTK/actions/workflows/build-test-package.yml
 
 
-Links
------
+## Links
 
 * [Homepage](https://www.openrtk.org)
 * [Download](https://www.openrtk.org/RTK/resources/software.html)
@@ -22,8 +20,7 @@ Links
 * [Issue tracking](https://github.com/RTKConsortium/RTK/issues)
 
 
-Copyright RTK Consortium
-------------------------
+## Copyright RTK Consortium
 
   Licensed under the Apache License, Version 2.0 (the
   "[License](https://www.apache.org/licenses/LICENSE-2.0.txt)"); you may not use

applications/rtkshowgeometry/README.md

@@ -4,6 +4,16 @@
 
 ![geom](../../documentation/docs/ExternalData/ShowGeometry.png){w=800 alt="Show Geometry"}
 
+## Installation
+
+`rtkshowgeometry` requires the GUI optional dependencies. Install RTK with GUI support using:
+
+```bash
+pip install itk-rtk[gui]
+```
+
+## Usage
+
 All geometries described in the [documentation](../../documentation/docs/Geometry.md) are supported: cone-beam and parallel (`SDD = 0`), flat and cylindrical (`RadiusCylindricalDetector > 0`) detectors. If no projections are given, the detector size defaults to 40% of the Source-to-Isocenter Distance (SID) and is centered around point `(u,v)=(0,0)`.
 
 ```{literalinclude} showgeometry.sh

examples/README.md

@@ -1,5 +1,4 @@
-C++ / Python examples
-========
+# C++ / Python examples
 
 This section provides a collection of C++ and Python code examples
 to demonstrate how to effectively use RTK in various applications.

index.md

@@ -1,5 +1,4 @@
-The Reconstruction Toolkit (RTK)
-================================
+# The Reconstruction Toolkit (RTK)
 
 RTK is an open-source and cross-platform software for fast circular cone-beam CT reconstruction based on the Insight Toolkit (ITK). RTK is developed by the RTK consortium.
 

pyproject.toml

@@ -40,6 +40,12 @@ dependencies = [
     "itk == 5.4.*",
 ]
 
+[project.optional-dependencies]
+gui = [
+    "pyvista",
+    "matplotlib"
+]
+
 [project.scripts]
 rtkadmmtotalvariation = "itk.rtkadmmtotalvariation:main"
 rtkadmmwavelets = "itk.rtkadmmwavelets:main"
@@ -152,3 +158,13 @@ minimum-version = "0.8.2"
 
 # The build directory. Defaults to a temporary directory, but can be set.
 build-dir = "build/{wheel_tag}"
+
+[dependency-groups]
+test = ["pytest>=7.0", "matplotlib"]
+doc = [
+    "furo",
+    "myst-parser[linkify]",
+    "sphinx>=7.2.6",
+    "sphinx-copybutton",
+    "sphinx-design",
+]