build: Migrate notebooks directory (#186)

Part of a process to breakout the notebooks directory into a
separate branch for easier maintainence.
All subsequent notebook PRs should be made against the notebooks branch.

This PR removes notebooks, updates the binderhub link to reference
the new layout and updates the documentation.

Author: yangchoo

CHANGELOG.rst

@@ -10,6 +10,11 @@ Added
 
 - isort for automatic import sorting
 
+Updated
+~~~~~~~
+
+- Remove notebooks directory as we break it out into a `separate repository <https://github.com/open-strateos/txpy_jupyter_notebooks>`_
+
 Fixed
 ~~~~~
 

CONTRIBUTING.rst

@@ -32,7 +32,7 @@ Version Compatibility
 ---------------------
 
 TxPy is written with Python 3.6+ compatibility in mind. Python 2 is no
-longer officialy supported.
+longer officially supported.
 
 General Setup
 -------------

Dockerfile

@@ -28,8 +28,9 @@ RUN mkdir /pip_cache && \
 ENV XDG_CONFIG_HOME /pip_cache
 ENV PYTHON_EGG_CACHE /python_eggs
 
-# Install Jupyter
-RUN pip install --no-cache-dir notebook==5.*
+# Install Jupyter, nbgitpuller for separate notebook/environment
+RUN pip install --no-cache-dir notebook==5.* && \
+    pip install nbgitpuller
 
 # Install TxPy
 RUN pip install 'transcriptic[jupyter, analysis]'

README.rst

@@ -106,11 +106,23 @@ Here’s an example script for installing it on a bash shell in your
 Documentation
 -------------
 
+CLI
+~~~
+
 See the `Transcriptic Developer
 Documentation <https://developers.transcriptic.com/docs/getting-started-with-the-cli>`__
 for detailed information about how to use this package, including
 learning about how to package protocols and build releases.
 
+Jupyter
+~~~~~~~
+
+Click on the |Binder| icon to open an interactive notebook environment
+for using the library.
+
+Developer
+~~~~~~~~~
+
 View `Developer Specific
 Documentation <http://transcriptic.readthedocs.io/en/latest/>`__
 
@@ -137,4 +149,4 @@ Read `Contributing <http://transcriptic.readthedocs.io/en/latest/contributing.ht
 .. |Downloads| image:: https://img.shields.io/pypi/dm/transcriptic?logo=pypi
    :target: https://transcriptic.readthedocs.io/en/latest
 .. |Binder| image:: https://mybinder.org/badge_logo.svg
-  :target: https://mybinder.org/v2/gh/strateos/transcriptic/master
+   :target: https://mybinder.org/v2/gh/strateos/transcriptic/master?urlpath=git-pull%3Frepo%3Dhttps%253A%252F%252Fgithub.com%252Fopen-strateos%252Ftxpy_jupyter_notebooks%26urlpath%3Dtree%252Ftxpy_jupyter_notebooks%252Findex.ipynb%26branch%3Dmain