From 732db51ef773dd815c2f22f6a393d40643ea8a1f Mon Sep 17 00:00:00 2001
From: Pierre-antoine Comby <pierre-antoine.comby@crans.org>
Date: Thu, 18 Jan 2024 14:33:18 +0100
Subject: [PATCH] docs: update getting started

---
 docs/getting_started.rst | 32 +++++++++++++++++++++++++-------
 docs/index.rst           |  9 ++++++++-
 docs/misc/related.rst    |  2 +-
 pyproject.toml           |  8 ++++++--
 4 files changed, 40 insertions(+), 11 deletions(-)

diff --git a/docs/getting_started.rst b/docs/getting_started.rst
index f6a85a8c..b4252d2c 100644
--- a/docs/getting_started.rst
+++ b/docs/getting_started.rst
@@ -41,8 +41,10 @@ finufft_             CPU          ✔                   single/double    numpy
 gpunufft_            GPU          ✔                   single/double    numpy
 tensorflow-nufft_    GPU (CUDA)   ✘                   single           tensorflow
 pynufft-cpu_         CPU          ✘                   single/double    numpy
-pynfft_ (*)          CPU          ✘                   singles/double   numpy
-stacked (**)         CPU/GPU      ✔                   single/double    numpy
+pynfft_              CPU          ✘                   single/double    numpy
+bart_                CPU/GPU      ✔                   single           numpy
+sigpy_               CPU          ✔                   single           numpy
+stacked (*)          CPU/GPU      ✔                   single/double    numpy
 ==================== ============ =================== ===============  =================
 
 
@@ -51,10 +53,11 @@ stacked (**)         CPU/GPU      ✔                   single/double    numpy
 .. _tensorflow-nufft: https://github.com/flatironinstitute/pynufft
 .. _gpunufft: https://github.com/chaithyagr/gpuNUFFT
 .. _pynufft-cpu: https://github.com/jyhmiinlin/pynufft
-.. _pynfft: https://github.com/ghisvail/pynfft
+.. _pynfft: https://github.com/pynfft/pynfft
+.. _bart: https://github.com/mrirecon/bart
+.. _sigpy: https://github.com/sigpy/sigpy
 
-- (*) PyNFFT is only working with Cython < 3.0.0 , and is not actively maintained (https://github.com/mind-inria/mri-nufft/issues/19)
-- (**) stacked-nufft allow to use any supported backend to perform a stack of 2D NUFFT and adds a z-axis FFT (using scipy or cupy)
+- (*) stacked-nufft allow to use any supported backend to perform a stack of 2D NUFFT and adds a z-axis FFT (using scipy or cupy)
 
 
 **The NUFFT operation is often not enough to provide good image quality by itself (even with density compensation)**.
@@ -72,7 +75,7 @@ To benefit the most from certain backend we recommend to use the following instr
 finufft / cufinufft
 ~~~~~~~~~~~~~~~~~~~
 
-Those are develop by the `flatiron-institute <https://github.com/flatironinstitute/finufft>` and are installable with `pip install finufft` and `pip install cufinufft`.
+Those are develop by the `flatiron-institute <https://github.com/flatironinstitute/finufft>`_ and are installable with `pip install finufft` and `pip install cufinufft`.
 
 .. warning::
 
@@ -81,7 +84,7 @@ Those are develop by the `flatiron-institute <https://github.com/flatironinstitu
 gpuNUFFT
 ~~~~~~~~
 
-an active gpuNUFFT fork is maintained by `chaithyagr <https://github.com/chaithyagr/gpunufft/>`.
+an active gpuNUFFT fork is maintained by `chaithyagr <https://github.com/chaithyagr/gpunufft/>`_.
 
 .. warning::
 
@@ -95,6 +98,21 @@ To install it use `pip install gpuNUFFT` or for local development.
     cd gpuNUFFT
     python setup.py install
 
+BART
+~~~~
+
+BART has to be installed separately and `bart` command needs to be runnable from your `PATH`.
+See `installation instructions <https://mrirecon.github.io/bart/installation.html>`_
+
+
+PyNFFT
+~~~~~~
+
+PyNFFT requires Cython<3.0.0 to work.  and can be installed using
+
+.. code-block:: sh
+
+    pip install cython<3.0.0 pynfft2
 
 Which backend to use
 --------------------
diff --git a/docs/index.rst b/docs/index.rst
index 9a79df16..53665bab 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -35,4 +35,11 @@
    misc/code_of_conduct
    misc/license
    misc/development
-   misc/related
+
+.. toctree::
+   :hidden:
+   :caption: Related Projects
+
+   PySAP <https://cea-cosmic.github.io/pysap>
+   ModOpt <https://cea-cosmic.github.io/ModOpt/>
+   Brainweb-dl <http://github.com/paquiteau/brainweb-dl>
diff --git a/docs/misc/related.rst b/docs/misc/related.rst
index e303af00..6b0b545f 100644
--- a/docs/misc/related.rst
+++ b/docs/misc/related.rst
@@ -5,6 +5,6 @@ Related Projects
 .. toctree::
    :maxdepth: 2
 
-    PySAP <https://python-pysap.readthedocs.io/en/latest/>
+    PySAP <https://cea-cosmic.github.io/pysap>
     ModOpt <https://cea-cosmic.github.io/ModOpt/>
     Brainweb-dl <http://github.com/paquiteau/brainweb-dl>
diff --git a/pyproject.toml b/pyproject.toml
index e6f407a0..8bc8d2aa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,10 +11,14 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 
-gpu = ["cupy-wheel"]
+gpunufft = ["gpunufft", "cupy-cuda11x"]
+cufinufft = ["cufinufft", "cupy-cuda11x"]
+finufft = ["finufft"]
+pynfft = ["pynfft2", "cython<3.0.0"]
+pynufft = ["pynufft"]
+
 test = ["pytest", "pytest-cov", "pytest-xdist", "pytest-sugar", "pytest-cases"]
 dev = ["black", "isort", "ruff"]
-
 doc = ["sphinx-book-theme","sphinx-copybutton", "sphinx-gallery", "matplotlib", "pooch", "brainweb-dl"]
 # pooch is for scipy.datasets