[MRG] Replace most RST with Markdown (#973)

* feat: change non-autogen content to use Markdown

* update spacing and fix broken link

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Co-authored-by: dylansdaniels <[email protected]>

README.md

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+# hnn-core
+
+[![tests](https://github.com/jonescompneurolab/hnn-core/actions/workflows/unix_unit_tests.yml/badge.svg?branch=master)](https://github.com/jonescompneurolab/hnn-core/actions/?query=branch:master+event:push)
+[![CircleCI](https://circleci.com/gh/jonescompneurolab/hnn-core.svg?style=svg)](https://circleci.com/gh/jonescompneurolab/hnn-core)
+[![Codecov](https://codecov.io/gh/jonescompneurolab/hnn-core/branch/master/graph/badge.svg)](https://codecov.io/gh/jonescompneurolab/hnn-core)
+[![PyPI](https://img.shields.io/pypi/dm/hnn-core.svg?label=PyPI%20downloads)](https://pypi.org/project/hnn-core/)
+[![Gitter](https://badges.gitter.im/jonescompneurolab/hnn_core.svg)](https://gitter.im/jonescompneurolab/hnn-core?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
+[![JOSS](https://joss.theoj.org/papers/10.21105/joss.05848/status.svg)](https://doi.org/10.21105/joss.05848)
+
+![HNN-GUI](https://raw.githubusercontent.com/jonescompneurolab/hnn-core/acbcc4a598610dc3be5d4b0b7c59f98251ea7690/.github/images/hnn_gui.png)
+
+## About
+
+This is a leaner and cleaner version of the code based off the [HNN
+repository](https://github.com/jonescompneurolab/hnn).
+
+The **Human Neocortical Neurosolver (HNN)** is an open-source neural modeling
+tool designed to help researchers/clinicians interpret human brain imaging
+data. Based off the original [HNN
+repository](https://github.com/jonescompneurolab/hnn), **HNN-core** provides a
+convenient way to run simulations of an anatomically and biophysically detailed
+dynamical system model of human thalamocortical brain circuits with only a few
+lines of code. Given its modular, object-oriented design, HNN-core makes it
+easy to generate and evaluate hypotheses on the mechanistic origin of signals
+measured with magnetoencephalography (MEG), electroencephalography (EEG), or
+intracranial electrocorticography (ECoG). A unique feature of the HNN model is
+that it accounts for the biophysics generating the primary electric currents
+underlying such data, so simulation results are directly comparable to source
+localized data (current dipoles in units of nano-Ampere-meters); this enables
+precise tuning of model parameters to match characteristics of recorded
+signals. Multimodal neurophysiology data such as local field potential (LFP),
+current-source density (CSD), and spiking dynamics can also be simulated
+simultaneously with current dipoles.
+
+While the HNN-core API is designed to be flexible and serve users with varying
+levels of coding expertise, the HNN-core GUI is designed to be useful to
+researchers with no formal computational neural modeling or coding experience.
+
+For more information visit <https://hnn.brown.edu>. There, we describe the use
+of HNN in studying the circuit-level origin of some of the most commonly
+measured MEG/EEG and ECoG signals: event related potentials (ERPs) and low
+frequency rhythms (alpha/beta/gamma).
+
+Contributors are very welcome. Please read our [contributing
+guide][] if you are interested.
+
+## Dependencies
+
+hnn-core requires Python (>=3.8) and the following packages:
+
+-   numpy
+-   scipy
+-   matplotlib
+-   Neuron (>=7.7)
+
+## Optional dependencies
+
+### GUI
+
+-   ipywidgets
+-   voila
+-   ipympl
+-   ipykernel
+
+*Note*: Please follow the **GUI installation** section to install the
+correct GUI dependency versions automatically.
+
+### Optimization
+
+-   scikit-learn
+
+### Parallel processing
+
+-   joblib (for simulating trials simultaneously)
+-   mpi4py (for simulating the cells in parallel for a single trial).
+    Also depends on:
+    -   openmpi or other mpi platform installed on system
+    -   psutil
+
+# Installation
+
+We recommend the [Anaconda Python
+distribution](https://www.anaconda.com/products/individual). To install
+`hnn-core`, simply do:
+
+    $ pip install hnn_core
+
+and it will install `hnn-core` along with the dependencies which are not
+already installed.
+
+Note that if you installed Neuron using the traditional installer
+package, it is recommended to remove it first and unset `PYTHONPATH` and
+`PYTHONHOME` if they were set. This is because the pip installer works
+better with virtual environments such as the ones provided by `conda`.
+
+If you want to track the latest developments of `hnn-core`, you can
+install the current version of the code (nightly) with:
+
+    $ pip install --upgrade https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master
+
+To check if everything worked fine, you can do:
+
+    $ python -c 'import hnn_core'
+
+and it should not give any error messages.
+
+**Installing optimization dependencies**
+
+If you are using bayesian optimization, then scikit-learn is required.
+Install hnn-core with scikit-learn using the following command:
+
+    $ pip install hnn_core[opt]
+
+**GUI installation**
+
+To install the GUI dependencies along with `hnn-core`, a simple tweak to
+the above command is needed:
+
+    $ pip install hnn_core[gui]
+
+Note if you are zsh in macOS the command is:
+
+    $ pip install hnn_core'[gui]'
+
+To start the GUI, please do:
+
+    $ hnn-gui
+
+**Parallel backends**
+
+For further instructions on installation and usage of parallel backends
+for using more than one CPU core, refer to our [parallel backend
+guide](https://jonescompneurolab.github.io/hnn-core/stable/parallel.html).
+
+**Note for Windows users**
+
+Install Neuron using the [precompiled
+installers](https://nrn.readthedocs.io/en/latest/) **before** installing
+`hnn-core`. Make sure that:
+
+    $ python -c 'import neuron;'
+
+does not throw any errors before running the install command. If you
+encounter errors, please get help from [NEURON
+forum](https://www.neuron.yale.edu/phpbb/). Finally, do:
+
+    $ pip install hnn_core[gui]
+
+# Documentation and examples
+
+Once you have tested that `hnn_core` and its dependencies were
+installed, we recommend downloading and executing the [example
+scripts](https://jonescompneurolab.github.io/hnn-core/stable/auto_examples/index.html)
+provided on the [documentation
+pages](https://jonescompneurolab.github.io/hnn-core/) (as well as in the
+[GitHub repository](https://github.com/jonescompneurolab/hnn-core)).
+
+Note that `python` plots are by default non-interactive (blocking): each
+plot must thus be closed before the code execution continues. We
+recommend using and 'interactive' python interpreter such as
+`ipython`:
+
+    $ ipython --matplotlib
+
+and executing the scripts using the `%run`-magic:
+
+    %run plot_simulate_evoked.py
+
+When executed in this manner, the scripts will execute entirely, after
+which all plots will be shown. For an even more interactive experience,
+in which you execute code and interrogate plots in sequential blocks, we
+recommend editors such as [VS Code](https://code.visualstudio.com) and
+[Spyder](https://docs.spyder-ide.org/current/index.html).
+
+# Bug reports
+
+Use the [github issue
+tracker](https://github.com/jonescompneurolab/hnn-core/issues) to report
+bugs. For user questions and scientific discussions, please see our
+[GitHub Discussions
+page](https://github.com/jonescompneurolab/hnn-core/discussions).
+
+# Interested in Contributing?
+
+Read our [contributing guide][].
+
+# Governance Structure
+
+Read our [governance
+structure](https://jonescompneurolab.github.io/hnn-core/stable/governance.html).
+
+# Citing
+
+If you use HNN-core in your work, please cite our [publication in
+JOSS](https://doi.org/10.21105/joss.05848):
+
+> Jas et al., (2023). HNN-core: A Python software for cellular and
+> circuit-level interpretation of human MEG/EEG. *Journal of Open Source
+> Software*, 8(92), 5848, <https://doi.org/10.21105/joss.05848>
+
+[contributing guide]: https://jonescompneurolab.github.io/hnn-core/stable/contributing.html