[docs] fixes and restructuring

Author: jgrewe

docs/source/api/nixio.rst

@@ -1,5 +1,5 @@
-nixio package
-=============
+Internal API
+============
 
 Subpackages
 -----------

docs/source/examples/singleROI.py

@@ -51,13 +51,15 @@ def plot_data(tag):
     ext = tuple(map(int, tag.extent))
     draw_rect(img_data, pos, ext)
     new_img = img.fromarray(img_data)
+
+    new_img.save("../images/single_roi.png")
     new_img.show()
 
 
 def main():
     img_data, channels = load_image()
     # create a new file overwriting any existing content
-    file_name = 'single_roi.h5'
+    file_name = 'single_roi.nix'
     f = nix.File.open(file_name, nix.FileMode.Overwrite)
 
     # create a 'Block' that represents a grouping object. Here, the recording session.

docs/source/genindex.rst

@@ -0,0 +1,4 @@
+.. This file is a placeholder and will be replaced
+
+Index
+#####

docs/source/getting_started.rst

@@ -1,21 +1,20 @@
 Tutorials
-=====================
+=========
 
 This introduction guides through the *NIX* data model and shows how to use it with the `nixio python library <https://github.com/g-node/nixpy>`__.
 
----------------
 
 In the following we provide an introduction to the general concepts of the *NIX* data model, try to illustrate its design principles and provide code examples showing the usage of the `python <https://github.com/g-node/nixpy>`__ library for reading and writing *NIX* files.
 
 Code examples use the python library but almost all functions have direct counterparts also in the `C++ library <https://github.com/g-node/nix>`__ or the language bindings to this for `Matlab <https://github.com/g-node/nix-mx>`__ and `java <https://github.com/g-node/nix-java>`__. 
 
-
-List of tutorials
------------------
+---------------
 
 Most code examples are standalone and you should be able to run them. The code is also available from the `project repository on GitHub <https://github.com/G-Node/nixpy/tree/master/docs/source/examples>`_.
 
 .. toctree::
+   :maxdepth: 1
+
    file_handling
    storing_data
    tagging
@@ -24,5 +23,4 @@ Most code examples are standalone and you should be able to run them. The code i
    sources
    finding_things
    image_data
-   spike_time_data
-   :maxdepth: 1
+   spike_time_data

docs/source/image_data.rst

@@ -1,7 +1,6 @@
 .. toctree::
     :maxdepth: 1
 
-.. _Image Data:
 
 Image data
 ==========
@@ -47,7 +46,7 @@ data. The same Tag can be applied to many references as long as
     :lines: 80-84
     :caption: A *Tag* is used to tag a a single region of interest. Most image data is 3D with the third dimension representing the color channels (:download:`singleROI.py <examples/singleROI.py>`).
 
-.. image:: examples/single_roi.png
+.. image:: images/single_roi.png
     :alt: single roi
     :width: 240
 

docs/source/images/single_roi.png

@@ -48,21 +48,6 @@ Support
 If you need help, want to get in touch, or have any other request
 `these <contact.html>`__ are your options.
 
-Contributing & Governance
-=========================
-
-Any kind of contribution is welcome! This includes reporting bugs and
-issues. If you want to contribute to code or documentation please refer
-to the `contributing
-guide <https://github.com/G-Node/nix/blob/master/CONTRIBUTING.md>`__.
-
-License
-=======
-
-This project is open source published under the BSD-3 license see
-`license file <https://github.com/G-Node/nix/blob/master/LICENSE>`__ for
-details.
-
 Citing
 ======
 
@@ -76,6 +61,8 @@ Neuroinform. Conference Abstract: Neuroinformatics 2014. doi:
 
 Referenced by
 =============
+-  Sinz et al. (2020)
+   `doi:10.1152/jn.00615.2019 <https://doi.org/10.1152/jn.00615.2019>`__
 -  Buccino et al. (2019)
    `doi:10.1101/796599 <https://www.biorxiv.org/content/10.1101/796599v1>`__
 -  Sprenger et al. (2019)
@@ -94,76 +81,52 @@ Referenced by
    `doi:10.1007/978-3-319-50862-7_5 <https://doi.org/doi:10.1007/978-3-319-50862-7_5>`__
 -  Teeters et al (2015)
    `doi:10.1016/j.neuron.2015.10.025 <https://doi.org/doi:10.1016/j.neuron.2015.10.025>`__
-   
-
---------------
 
 .. toctree::
+   :caption: Introduction
+   :maxdepth: 1
+
    basic_idea
    install
    standardization
-   :caption: Introduction
-
-   :maxdepth: 1
-   :caption: Getting started:
+   Use-cases <https://nixio.readthedocs.io/en/master/use_cases.html>
 
 .. toctree::
-   news
    :maxdepth: 1
    :caption: News
+   :hidden:
+
+   news
 
 .. toctree::
-   getting_started
    :maxdepth: 1
    :caption: Tutorials
 
+   getting_started
+
 .. toctree::
-   contact
-   faq
    :caption: Troubleshooting:
    :maxdepth: 1
+   :hidden:
 
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-
-
-
-High Level API Reference
-========================
-
-User API documentation for Data and Metadata
+   contact
+   faq
 
 .. toctree::
-   user_api
-   :maxdepth: 2
-   :caption: High Level API
-
-
-Advanced
-========
-
-Internal NIXIO API Developer Documentation
-------------------------------------------
-
-The API documentation of internal modules, for NIXPy developers.
+   :maxdepth: 1
+   :caption: API Reference
+   :hidden:
 
-.. toctree::
+   user_api
    api/nixio
-   :maxdepth: 2
-   :caption: Internal API
-
-Source code
-===========
-
-All sources are available under MIT open-souce license and is hosted on `GitHub <https://github.com/g-node/nixpy>`_.
 
 .. toctree::
-    Sources on GitHub <https://github.com/g-node/nixpy>
-    :maxdepth: 1
-    :caption: Source code
+   :caption: Appendix
+   :maxdepth: 1
+   :hidden:
+
+   genindex
+   py-modindex
+   Sources on GitHub <https://github.com/g-node/nixpy>
+   License <https://github.com/G-Node/nixpy/blob/master/LICENSE>
+   Contributing guide <https://github.com/G-Node/nix/blob/master/CONTRIBUTING.md>

docs/source/index.rst

@@ -0,0 +1,4 @@
+.. This file is a placeholder and will be replaced
+
+Module Index
+============