deploy: 010f669

.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 34f960415cd8a980b220340501b8d8bc
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/index.rst.txt

@@ -0,0 +1,101 @@
+.. vbjax documentation master file, created by
+   sphinx-quickstart on Tue Dec  5 11:11:08 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+***********************************
+Welcome to vbjax's documentation!
+***********************************
+
+Introduction
+############
+`vbjax` is a Jax-based package for working with virtual brain style models.
+
+Installation
+############
+
+Installs with `pip install "vbjax"`, but you can use the source,
+
+.. code-block:: bash
+
+   git clone https://github.com/ins-amu/vbjax
+   cd vbjax
+   pip install .[dev]
+
+
+The primary additional dependency of vbjax is
+[JAX](github.com/google/jax), which itself depends only on
+NumPy, SciPy & opt-einsum, so it should be safe to add to your
+existing projects.
+
+gee pee you
+------------
+
+**CUDA**
+
+If you have a CUDA-enabled GPU, you install the requisite dependencies like so
+
+.. code-block:: bash
+
+   pip install --upgrade "jax[cuda11_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+
+
+**M1/M2** 🍎
+
+On newer Apple machines w/ M1 or M2 GPUs, JAX supports using the GPU experimentally
+by installing just two extra packages:
+
+.. code-block:: bash
+
+   pip install ml-dtypes==0.2.0 jax-metal
+
+
+About a third of vbjax tests fail due to absence of certain operations like n-dim
+scatter/gather & FFTs, and it may not be faster because these CPUs already have
+excellent memory bandwidth & latency hiding.
+
+**CUDA** 🐳 
+
+*BUT* because GPU software stack versions make aligning stars look like child's play,
+container images are available and auto-built w/
+[GitHub Actions](.github/workflows/docker-image.yml), so you can use w/ Docker
+
+.. code-block:: bash
+
+   docker run --rm -it ghcr.io/ins-amu/vbjax:main python3 -c 'import vbjax; print(vbjax.__version__)'
+
+
+The images are built on Nvidia runtime images, so `--gpus all` is enough
+for Jax to discover the GPU(s).
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+Tutorial
+########
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   tutorial
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+Modules
+########
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+

_sources/modules.rst.txt

@@ -0,0 +1,66 @@
+neural_mass 
+-----------
+
+.. automodule:: vbjax.neural_mass
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+monitor
+--------
+
+.. automodule:: vbjax.monitor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+loops 
+-----
+
+.. automodule:: vbjax.loops
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+connectome
+----------
+
+.. automodule:: vbjax.connectome
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+layers
+------
+
+.. automodule:: vbjax.layers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+sparse
+------
+
+.. automodule:: vbjax.sparse
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+util
+----
+
+.. automodule:: vbjax.util
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+shtlc
+-----
+
+.. automodule:: vbjax.shtlc
+   :members:
+   :undoc-members:
+   :show-inheritance:

_sources/tutorial.rst.txt

@@ -0,0 +1,7 @@
+Examples 
+========
+
+.. automodule:: 00_intro
+
+.. automodule:: 01_sweep
+