Updating higra and gpu install docs (#135)

* updated docs to higra conda and gpu acceleration

* testing docs CI

* fixing pydantic autodoc

* added missing deps

* updating autodoc pydantic version

* testing docs build

* removed docs build CI test

.github/workflows/docs.yml

@@ -38,6 +38,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install ".[docs]"
+          pip install "autodoc_pydantic==1.9.1"
       - name: Set environment
         run: |
           REPO_OWNER="${GITHUB_REPOSITORY%%/*}"

docs/source/install.rst

@@ -9,7 +9,7 @@ Once you have conda (mamba) installed, you should create an environment for ``ul
 
 .. code-block:: bash
 
-    conda create -n ultrack python=3.11 gurobi pytorch pyqt -c pytorch -c gurobi -c conda-forge
+    conda create -n ultrack python=3.11 higra gurobi pytorch pyqt -c pytorch -c gurobi -c conda-forge
 
 Then, you can activate the environment and install ``ultrack``:
 
@@ -18,21 +18,29 @@ Then, you can activate the environment and install ``ultrack``:
     conda activate ultrack
     pip install ultrack
 
-If you're using OSX you may need to install ``higra`` from source. You can do this by running the following commands:
+You can check if the installation was successful by running:
 
 .. code-block:: bash
 
-    conda activate ultrack
-    pip install numpy
-    pip install -vv git+https://github.com/higra/Higra
-    pip install ultrack
+    ultrack --help
 
-You can check if the installation was successful by running:
+
+GPU acceleration
+----------------
+
+Ultrack makes use of GPU for image processing operations.
+You can install the additional packages required for GPU acceleration by running (Linux and Windows only):
 
 .. code-block:: bash
 
-    ultrack --help
+    conda install pytorch-cuda -c pytorch -c nvidia
+    conda install cupy -c conda-forge
+    # linux only
+    conda install cucim -c rapidsai
+    # for windows, you can install cucim using pip
+    pip install git+https://github.com/rapidsai/cucim.git#egg=cucim&subdirectory=python/cucim"
 
+See the `PyTorch website <https://pytorch.org/get-started/locally/>`_ for more information on how to install PyTorch with GPU support.
 
 Gurobi setup
 ------------

docs/source/quickstart.rst

@@ -9,7 +9,7 @@ Installation
 
 If already have a working Python environment, you can install ``ultrack`` using pip.
 We recommend you use a conda environment to avoid any conflicts with your existing packages.
-For additional information on how to create a conda environment and install packages, see :doc:`install`.
+If you're using OSX or for additional information on how to create a conda environment and install packages, see :doc:`install`.
 
 .. code-block:: bash
 

pyproject.toml

@@ -51,7 +51,9 @@ dependencies = [
 
 [project.optional-dependencies]
 docs = [
-    "autodoc_pydantic >= 2.0.0",
+    "sphinx == 6.2.1",
+    "autodoc_pydantic",  # NOT WORKING, needs to install 'autodoc_pydantic==1.9.1' to build docs
+    "pydantic-settings",
     "furo",
     "myst-parser >= 2.0.0",
     "nbsphinx >= 0.9.3",