Tutorial Modifications and Extension (#204)

Tutorials updated and extended and a few other fixes

* rgb contrast and unsafe access fix

* experimental numpy fix

* fixes a lot of accumulated mypy problem

* rgb contrast and unsafe access fix

* experimental numpy fix

* fixes a lot of accumulated mypy problem

* first small adjustments

* class imbalance,  finetuning, & advanced tips

* refactoring tutorials

* unrelated small fix

* removing "step X" strings

* Zenodo release version update

Author: ChristopherKotthoff

docs/source/contributing.rst

@@ -317,7 +317,7 @@ The idea of Continuous integration (CI) is to frequently commit code to a shared
 
 Building and testing code requires a server. CI using GitHub actions offers workflows that can build the repository code and run tests. We can run on GitHub's own virtual machines (using GitHub-hosted runners), or on machines that we host ourselves (or on compute clusters). The latter is desirable as GitHub does not currently support access to GPU resources.
 
-Currently there are three files that steer workflows. The schedule is set at the top of the file. The workflows are found `here <https://github.com/PatBall1/detectree2/tree/master/.github/workflows>`_
+Currently there are three files that steer workflows. The schedule is set at the top of the file. The workflows are found `here <https://github.com/PatBall1/detectree2/tree/master/.github/workflows>`__
 
 - ``python-app.yml``: All style CI - builds the code on Ubuntu-20.04
 - ``dockertest.yml``: All style CI - uses docker image for dependencies and installs detectree2 using pip.

docs/source/index.rst

@@ -22,8 +22,6 @@ applications. Below is an example image of the predictions made by Detectree2.
    :alt: Prediction
    :align: center
 
-
-|
 Code developed by James Ball, Seb Hickman, Thomas Koay, Oscar Jiang, Luran Wang, Panagiotis Ioannou, James Hinton and Matthew Archer in the `Forest Ecology and Conservation Group <https://coomeslab.org/>`_ 
 at the University of Cambridge.  The Forest Ecology and Conservation Group is led by Professor David Coomes and is part of the University of Cambridge `Conservation Research Institute <https://www.conservation.cam.ac.uk/>`_.
 MRes project repo available `here <https://github.com/shmh40/detectreeRGB/>`_.
@@ -36,19 +34,16 @@ Accurate delineation of individual tree crowns in tropical forests from aerial R
 *Remote Sens Ecol Conserv*. `https://doi.org/10.1002/rse2.332 <https://doi.org/10.1002/rse2.332>`_
 
 .. toctree::
-   :numbered:
    :maxdepth: 2
    :caption: Contents:
 
    installation
-   tutorial
-   tutorial_multi
+   tutorials/index
    cluster
+   usage
    contributing
    using-git
    api
-   .. _notebooks/contributing_guide
-   .. _notebooks/trainingJB
 
 
 Indices and tables