Add more documentation for Network._extractnetwork()

[jGaboardi]

This PR:

• addresses Clarify the Network._extractnetwork() creation procedure #533
• adds a section to the Caveats notebooks about Clarify the Network._extractnetwork() creation procedure #533
• fixes a matplotlib deprecation warning in several notebooks
• .... other?

[jGaboardi]

Two issues here:

• there is an issue with fiona upstream causing failures

=========================== short test summary info ===========================
542 ERROR spaghetti/__init__.py - AttributeError: module 'fiona' has no attribute...
543 ERROR spaghetti/network.py - AttributeError: module 'fiona' has no attribute ...
544 ERROR spaghetti/util.py - AttributeError: module 'fiona' has no attribute '_l...
545 ERROR spaghetti/tests/__init__.py - AttributeError: module 'fiona' has no att...
546 ERROR spaghetti/tests/network_unittest_classes.py - AttributeError: module 'f...
547 ERROR spaghetti/tests/test_api_network.py - AttributeError: module 'fiona' ha...
548 ERROR spaghetti/tests/test_api_network.py - AttributeError: module 'fiona' ha...
549 ERROR spaghetti/tests/test_dev_network.py - AttributeError: module 'fiona' ha...
550 ERROR spaghetti/tests/test_dev_network.py - AttributeError: module 'fiona' ha...
551 !!!!!!!!!!!!!!!!!!! Interrupted: 9 errors during collection !!!!!!!!!!!!!!!!!!!
============================== 9 errors in 4.23s ==============================

• the new https://numpy.org/doc/stable/ seems to be down, so docs can't be rebuilt

WARNING: failed to reach any of the inventories with the following issues:
intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to 
<class 'requests.exceptions.ConnectionError'>: 
('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))

[jGaboardi]

Going ahead with merge due to failure caused by fiona.