more consistent markup use, add toc to html docs (#64)

INM-6 · Jun 17, 2021 · c81d276 · c81d276
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diff --git a/README.md b/README.md
@@ -4,7 +4,6 @@ Python module implementing a hybrid scheme for predictions of
 extracellular potentials (local field potentials, LFPs) of spiking
 neuron network simulations.
 
-
 ## Project Status
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.45185.svg)](https://doi.org/10.5281/zenodo.45185)
@@ -13,34 +12,35 @@ neuron network simulations.
 [![Python pytest](https://github.com/INM-6/hybridLFPy/workflows/Python%20pytest/badge.svg)](https://github.com/INM-6/hybridLFPy/actions/workflows/python-pytest.yml)
 [![License](http://img.shields.io/:license-GPLv3+-green.svg)](http://www.gnu.org/licenses/gpl-3.0.html)
 
-
-##  Development
+## Development
 
 The module hybridLFPy was mainly developed in the Computational Neuroscience
-Group (http://compneuro.umb.no), Department of Mathemathical Sciences and
-Technology (http://www.nmbu.no/imt), at the Norwegian University of Life
-Sciences (http://www.nmbu.no), Aas, Norway, in collaboration with Institute of
+Group (<http://compneuro.umb.no>), Department of Mathemathical Sciences and
+Technology (<http://www.nmbu.no/imt>), at the Norwegian University of Life
+Sciences (<http://www.nmbu.no>), Aas, Norway, in collaboration with Institute of
 Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6),
 Juelich Research Centre and JARA, Juelich, Germany
-(http://www.fz-juelich.de/inm/inm-6/EN/).
-
+(<http://www.fz-juelich.de/inm/inm-6/EN/>).
 
 ## Citation
 
-Should you find `hybridLFPy` useful for your research, please cite the following paper:
+Should you find `hybridLFPy` useful for your research, please cite the
+following paper:
 
     Espen Hagen, David Dahmen, Maria L. Stavrinou, Henrik Lindén, Tom Tetzlaff,
     Sacha J. van Albada, Sonja Grün, Markus Diesmann, Gaute T. Einevoll;
     Hybrid Scheme for Modeling Local Field Potentials from Point-Neuron Networks,
     Cerebral Cortex, Volume 26, Issue 12, 1 December 2016, Pages 4461–4496,
     https://doi.org/10.1093/cercor/bhw237
 
-
 Bibtex source:
 
     @article{doi:10.1093/cercor/bhw237,
-    author = {Hagen, Espen and Dahmen, David and Stavrinou, Maria L. and Lindén, Henrik and Tetzlaff, Tom and van Albada, Sacha J. and Grün, Sonja and Diesmann, Markus and Einevoll, Gaute T.},
-    title = {Hybrid Scheme for Modeling Local Field Potentials from Point-Neuron Networks},
+    author = {Hagen, Espen and Dahmen, David and Stavrinou, Maria L. and Lindén,
+      Henrik and Tetzlaff, Tom and van Albada, Sacha J. and Grün, Sonja and
+      Diesmann, Markus and Einevoll, Gaute T.},
+    title = {Hybrid Scheme for Modeling Local Field Potentials from
+      Point-Neuron Networks},
     journal = {Cerebral Cortex},
     volume = {26},
     number = {12},
@@ -51,73 +51,68 @@ Bibtex source:
     eprint = {/oup/backfile/content_public/journal/cercor/26/12/10.1093_cercor_bhw237/2/bhw237.pdf}
     }
 
-
 ## License
 
-This software is released under the General Public License (see the [LICENSE](https://github.com/INM-6/hybridLFPy/blob/master/LICENSE) file).
-
+This software is released under the General Public License (see the
+  [LICENSE](https://github.com/INM-6/hybridLFPy/blob/master/LICENSE) file).
 
 ## Warranty
 
 This software comes without any form of warranty.
 
-
 ## Installation
 
 First download all the `hybridLFPy` source files using `git`
-(http://git-scm.com). Open a terminal window and type:
-
-    $ cd $HOME/where/to/put/hybridLFPy
-    $ git clone https://github.com/INM-6/hybridLFPy.git
+(<http://git-scm.com>). Open a terminal window and type:
 
+    cd $HOME/where/to/put/hybridLFPy
+    git clone https://github.com/INM-6/hybridLFPy.git
 
 To use `hybridLFPy` from any working folder without copying files, run:
-    $ (sudo) pip install -e . (--user)
 
+    (sudo) pip install -e . (--user)
 
 Installing it is also possible, but not recommended as things might change with
 future pulls from the repository:
 
-    $ (sudo) pip install . (--user)
-
+    (sudo) pip install . (--user)
 
 ### examples folder
 
 Some example script(s) on how to use this module
 
-
 ### docs folder
 
-Source files for autogenerated documentation using `Sphinx` (https://www.sphinx-doc.org).
+Source files for autogenerated documentation using `Sphinx`
+(<https://www.sphinx-doc.org>).
 
 To compile documentation source files in this directory using sphinx, use:
 
-    $ sphinx-build -b html docs documentation
-
+    sphinx-build -b html docs documentation
 
 ### Dockerfile
 
 The provided `Dockerfile` provides a Docker container recipe for `x86_64` hosts
 with all dependencies required to run simulation files provided in `examples`.
-To build and run the container locally, get Docker from https://www.docker.com
+To build and run the container locally, get Docker from <https://www.docker.com>
 and issue the following (replace `<image-name>` with a name of your choosing):
 
-    $ docker build -t <image-name> -< Dockerfile
-    $ docker run -it -p 5000:5000 <image-name>:latest
-
+    docker build -t <image-name> -< Dockerfile
+    docker run -it -p 5000:5000 <image-name>:latest
 
-The `--mount` option can be used to mount a folder on the host to a target folder as:
+The `--mount` option can be used to mount a folder on the host to a target
+folder as:
 
-    $ docker run --mount type=bind,source="$(pwd)",target=/opt/hybridLFPy -it -p 5000:5000 <image-name>
+    docker run --mount type=bind,source="$(pwd)",target=/opt/hybridLFPy \
+    -it -p 5000:5000 <image-name>
 
 Then, code examples may be run as:
 
-    $ cd /opt/hybridLFPy/examples
-    $ nrnivmodl  # compile local .mod (NMODL) files
-    $ mpirun --allow-run-as-root python3 example_brunel.py
-
+    cd /opt/hybridLFPy/examples
+    nrnivmodl  # compile local .mod (NMODL) files
+    mpirun --allow-run-as-root python3 example_brunel.py
 
 ## Online documentation
 
 The sphinx-generated html documentation can be accessed at
-https://hybridLFPy.readthedocs.io
+<https://hybridLFPy.readthedocs.io>
diff --git a/docs/index.rst b/docs/index.rst
@@ -6,6 +6,10 @@
 Welcome to the documentation of **hybridLFPy**!
 ===============================================
 
+.. toctree::
+    :maxdepth: 20
+    :caption: Contents:
+
 
 .. include:: readme.md
 
@@ -28,82 +32,80 @@ exemplified by a benchmark based on the Brunel-network example scaled up to
 
 
 
-========================
 Module :mod:`hybridLFPy`
 ========================
-
 .. automodule:: hybridLFPy
     :members:
     :show-inheritance:
     :undoc-members:
 
 
-    class :class:`CachedNetwork`
-    ============================
-    .. autoclass:: hybridLFPy.CachedNetwork
-        :members:
-        :show-inheritance:
-        :undoc-members:
+class :class:`CachedNetwork`
+============================
+.. autoclass:: hybridLFPy.CachedNetwork
+    :members:
+    :show-inheritance:
+    :undoc-members:
 
 
-    class :class:`CachedNoiseNetwork`
-    =================================
-    .. autoclass:: hybridLFPy.CachedNoiseNetwork
-        :members:
-        :show-inheritance:
-        :undoc-members:
+class :class:`CachedNoiseNetwork`
+=================================
+.. autoclass:: hybridLFPy.CachedNoiseNetwork
+    :members:
+    :show-inheritance:
+    :undoc-members:
 
 
-    class :class:`CachedFixedSpikesNetwork`
-    =======================================
-    .. autoclass:: hybridLFPy.CachedFixedSpikesNetwork
-        :members:
-        :show-inheritance:
-        :undoc-members:
+class :class:`CachedFixedSpikesNetwork`
+=======================================
+.. autoclass:: hybridLFPy.CachedFixedSpikesNetwork
+    :members:
+    :show-inheritance:
+    :undoc-members:
 
 
-    class :class:`PopulationSuper`
-    ==============================
-    .. autoclass:: hybridLFPy.PopulationSuper
-        :members:
-        :show-inheritance:
-        :undoc-members:
+class :class:`PopulationSuper`
+==============================
+.. autoclass:: hybridLFPy.PopulationSuper
+    :members:
+    :show-inheritance:
+    :undoc-members:
 
 
-    class :class:`Population`
-    =========================
-    .. autoclass:: hybridLFPy.Population
-        :members:
-        :show-inheritance:
-        :undoc-members:
+class :class:`Population`
+=========================
+.. autoclass:: hybridLFPy.Population
+    :members:
+    :show-inheritance:
+    :undoc-members:
 
 
-    class :class:`PostProcess`
-    ==========================
-    .. autoclass:: hybridLFPy.PostProcess
-        :members:
-        :show-inheritance:
-        :undoc-members:
+class :class:`PostProcess`
+==========================
+.. autoclass:: hybridLFPy.PostProcess
+    :members:
+    :show-inheritance:
+    :undoc-members:
 
 
-    class :class:`GDF`
-    ==================
-    .. autoclass:: hybridLFPy.GDF
-        :members:
-        :show-inheritance:
-        :undoc-members:
+class :class:`GDF`
+==================
+.. autoclass:: hybridLFPy.GDF
+    :members:
+    :show-inheritance:
+    :undoc-members:
 
 
-    submodule :mod:`helpers`
-    ========================
-    .. automodule:: hybridLFPy.helpers
-        :members:
-        :undoc-members:
+submodule :mod:`helpers`
+========================
+.. automodule:: hybridLFPy.helpers
+    :members:
+    :undoc-members:
 
 
-    submodulue :mod:`test`
-    ======================
-    .. autofunction:: hybridLFPy.test
+submodulue :mod:`test`
+======================
+.. autofunction:: hybridLFPy.test
 
 
 Indices and tables

diff --git a/hybridLFPy/version.py b/hybridLFPy/version.py
@@ -1 +1 @@
-version = "0.2rc2"
+version = "0.2rc3"