update docs

aliby/baby_client.py

+"""
+Underlying methods for different neural network deployments.
+"""
 import collections
 import itertools
 import json

aliby/haystack.py

+"""
+Neural network initialisation.
+"""
 import numpy as np
 from time import perf_counter
 from pathlib import Path

aliby/io/__init__.py

+"""
+Methods and classes to fetch image data and metadata.
+"""

aliby/multiexperiment.py

+"""Experimental methods to deal with multiple experiments and data aggregation."""
 from pathos.multiprocessing import Pool
 
 from aliby.pipeline import PipelineParameters, Pipeline

aliby/tile/__init__.py

+"""
+Select regions from a larger image for efficient processing.
+"""

aliby/timelapse.py

+"""
+Classes to handle multidimensional images, both remotely and local.
+"""
 import itertools
 import logging
 

aliby/utils/__init__.py

+"""Additional tools to fetch and handle datasets programatically.
+"""

docs/source/index.rst

@@ -5,22 +5,28 @@
 
 ALIBY's guides and documentation
 =================================
+.. toctree::
+   :maxdepth: 3
 
-Summary
-=======
+.. include:: ../../README.md
+   :parser: myst_parser.sphinx_
 
+
+Contributing
+============
+.. toctree::
+   :maxdepth: 2
+
+.. include:: ../../CONTRIBUTING.md
+   :parser: myst_parser.sphinx_
+
+
+API Reference
+============
+.. toctree::
 .. autosummary::
-   :toctree: _autosummary
    :template: custom-module-template.rst
    :recursive:
 
    aliby
    extraction
-
-================
-Readme File
-================
-
-```{literalinclude} ../../README.md
-:language: md
-```