More things should be done:

1. remove nbsphinx from environment.yml
   

   pygmt/environment.yml

   Line 26 in 0fd514e

   - nbsphinx

2. If you look at the old documentation (https://www.pygmt.org/0.0.1a0/tutorials/plot-data-points.html), you will see a "Download notebook" button at the top right. That was added by the template, and we no longer need it. So the following lines should be safe to remove. (These lines check if the suffix of the source file is .ipynb. If yes, then add the download button).

and the top comments should also be updated accordingly:

More things should be done:

1. remove `nbsphinx` from `environment.yml`
   https://github.com/GenericMappingTools/pygmt/blob/0fd514e03c4e87515967140e8c3c47234380511a/environment.yml#L26

2. If you look at the old documentation (https://www.pygmt.org/0.0.1a0/tutorials/plot-data-points.html), you will see a "Download notebook" button at the top right. That was added by the template, and we no longer need it. So the following lines should be safe to remove. (These lines check if the suffix of the source file is `.ipynb`. If yes, then add the download button).

pygmt/doc/_templates/breadcrumbs.html

Lines 29 to 32 in 0fd514e

	{% if suffix == ".ipynb" %}
	<a href="https://github.com/{{ github_repo }}/raw/{{ github_version }}/{{ doc_path }}/{{ pagename }}{{ suffix }}"
	class="fa fa-download"> Download notebook</a>
	{% endif %}

and the top comments should also be updated accordingly:

pygmt/doc/_templates/breadcrumbs.html

Lines 1 to 2 in 0fd514e

	{# Extend the RTD template to include "Edit on GitHub" and option to download
	notebook generated pages from nbsphinx #}

Thanks, I made those changes.