Fix/minor 2.0.1

.github/workflows/build_and_test.yml

@@ -9,13 +9,15 @@ on:
       - 'doc_resources/**'
       - 'Doxyfile'
       - '**/*.md'
+      - '**/*.html'
       - '.github/workflows/build_docs.yml'
   pull_request:
     paths-ignore:
       - 'python/docs/**'
       - 'doc_resources/**'
       - 'Doxyfile'
       - '**/*.md'
+      - '**/*.html'
       - '.github/workflows/build_docs.yml'
   workflow_call:
     inputs:

doc_resources/landing/index.html

@@ -32,7 +32,7 @@ <h2>C++</h2>
     <footer>
       <p>
         <a href="https://github.com/bertiniteam/b2">GitHub repository</a> &middot;
-        <a href="https://pypi.org/project/bertini/">PyPI package</a> &middot;
+        <a href="https://pypi.org/project/bertini2/">PyPI package</a> &middot;
         Licensed under GPLv3 with additional terms.
       </p>
       <p class="build-info">

python/bertini/__init__.py

@@ -33,7 +33,7 @@
 
 
 """
-PyBertini -- Python bindings for Bertini2.
+bertini -- Python bindings for Bertini 2.
 
 This code is licensed under the GNU Public License, Version 3, with
 additional clauses under section 7 as permitted, to protect the 

python/docs/source/conf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 #
-# PyBertini documentation build configuration file, created by
+# Bertini 2 documentation build configuration file, created by
 # sphinx-quickstart on Wed Oct  4 23:28:46 2017.
 #
 # This file is execfile()d with the current directory set to its

python/docs/source/detailed/logging.rst

@@ -4,7 +4,7 @@
 Notes
 --------
 
-Logging is enabled for PyBertini through Bertini2's core logging facilities, in turn powered by Boost.Log.  
+Logging is enabled for through Bertini2's core logging facilities, in turn powered by Boost.Log.  
 
 They currently aren't fancy, but you have a few things you can do.
 

python/docs/source/index.rst

@@ -1,9 +1,9 @@
-.. PyBertini documentation master file, created by
+.. bertini2 documentation main file, created by
    sphinx-quickstart on Wed Oct  4 23:28:46 2017.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-PyBertini -- the Python bindings for Bertini
+The Python bindings for Bertini 2
 *************************************************
 
 

python/docs/source/tutorials/manual_endgame_usage.rst

@@ -12,7 +12,7 @@ So, if we can't track to a singular solution, but we still want to track to comp
 
 Endgames represent a way to finish a tracking of a path, when the endpoint is possibly singular.  Rather than track all the way to the endtime, you instead run an endgame that uses mathematical theory to compute the root.
 
-Endgames in PyBertini
+Endgames in Bertini 2
 ==========================
 
 An endgame is a computational tool that one does in the final stage of a path track to a possibly singular root.  There are two implemented endgames in Bertini:

python/docs/source/tutorials/tracking_nonsingular.rst

@@ -5,7 +5,7 @@
 
    import bertini
 
-PyBertini works by setting up systems, setting up algorithms to use those systems, and doing something with the output.
+Bertini works by setting up systems, setting up algorithms to use those systems, and doing something with the output.
 
 Forming a system
 =================
@@ -84,7 +84,7 @@ We can indeed do homotopy continuation with a non-algebraic systems.  What we ca
 Forming a start system
 =========================
 
-To solve our algebraic system ``sys``, we need a corresponding start system -- one with related structure, but that is actually solvable without too much trouble.  Bertini2 has several implemented options.  The most basic (easiest to form and solve) start system is the Total Degree (TD) start system.  It is implemented as a first-class object in Bertini and PyBertini.  It takes in a polynomial system as its argument, and self-forms.
+To solve our algebraic system ``sys``, we need a corresponding start system -- one with related structure, but that is actually solvable without too much trouble.  Bertini2 has several implemented options.  The most basic (easiest to form and solve) start system is the Total Degree (TD) start system.  It is implemented as a first-class object in Bertini.  It takes in a polynomial system as its argument, and self-forms.
 
 
 Above, we formed a target system, ``sys``.  Now, let's make a start system ``td``.  Later, we will couple it to ``sys``.
@@ -133,7 +133,7 @@ as well as a few other incidentals which will be implicitly used, such as a path
 Tracking a single path
 ======================
 
-There are three basic trackers available in PyBertini:
+There are three basic trackers available in Bertini 2:
 
 
 #. Fixed double precision: :class:`~bertini.tracking.DoublePrecisionTracker`

python/docs/source/welcome.rst

@@ -1,7 +1,7 @@
-👋 Welcome to PyBertini
+👋 Welcome to Bertini 2
 ====================================
 
-Bertini is software for numerically solving systems of polynomials.  PyBertini is the Python provided for running Bertini.
+Bertini 2 is software for numerically solving systems of polynomials. 
 
 🗺 Mathematical overview
 ----------------------------------
@@ -17,7 +17,7 @@ The main algorithm for numerical algebraic geometry implemented in Bertini is ho
 
    Predictor-corrector methods with optional adaptive precision track paths from 1 to 0, solving :math:`f`.
 
-The definitive resource for Bertini 1 is the book :cite:`bertinibook`.  While the way we interact with Bertini changes from version 1 to version 2, particularly when using PyBertini, the algorithms remain fundamentally the same.  So do most of the ways to change settings for the path trackers, etc.  We believe that embracing the flexibility of Python3 with PyBertini allows for much greater flexibility.  It also will relieve the user from the burden of input and output file writing and parsing.  Instead, computed results are returned directly to the user.  
+The definitive resource for Bertini 1 is the book :cite:`bertinibook`.  While the way we interact with Bertini changes from version 1 to version 2, particularly when using the Python library, the algorithms remain fundamentally the same.  So do most of the ways to change settings for the path trackers, etc.  We believe that embracing the flexibility of Python allows for much greater flexibility.  It also will relieve the user from the burden of input and output file writing and parsing.  Instead, computed results are returned directly to the user.  
 
 Consider checking out the :ref:`🔦 Tutorials <tutorials>`.
 

python_bindings/src/containers.cpp

@@ -63,7 +63,7 @@ void ExportContainers()
 	current_scope.attr("container") = new_submodule;
 
 	scope new_submodule_scope = new_submodule;
-	new_submodule_scope.attr("__doc__") = "Various container types for PyBertini";
+	new_submodule_scope.attr("__doc__") = "Various container types";
 
 
 	boost::python::converter::registry::push_back(&pylist_converter<bertini::VariableGroup>::convertible

python_bindings/src/logging.cpp

@@ -68,7 +68,7 @@ void ExportLogging()
 
 	def("add_file", &bertini::logging::Logging::AddFile, 
 		((boost::python::arg("pattern")), boost::python::arg("format"), boost::python::arg("rotation_size")), 
-		"Add a file-name pattern to be written to, with a given formatting, and a threshold rotation size.  See Boost.Log for more information on these strings.  This part of PyBertini is a direct shunt to Boost.Log.");
+		"Add a file-name pattern to be written to, with a given formatting, and a threshold rotation size.  See Boost.Log for more information on these strings.  This part of Bertini is a direct shunt to Boost.Log.");
 
 
 

python_bindings/src/tracker_export.cpp

@@ -162,7 +162,7 @@ namespace bertini{
 			current_scope.attr("tracking") = new_submodule;
 
 			scope new_submodule_scope = new_submodule;
-			new_submodule_scope.attr("__doc__") = "Tracking things for PyBertini.  Includes the three fundamental trackers, and utility functions.";
+			new_submodule_scope.attr("__doc__") = "Tracking things.  Includes the three fundamental trackers, and utility functions.";
 
 			ExportConfigSettings();
 			ExportAMPTracker();

python_bindings/src/tracker_observers.cpp

@@ -70,7 +70,7 @@ void ExportTrackerObservers()
 	current_scope.attr("tracking") = new_submodule;
 
 	scope new_submodule_scope = new_submodule;
-	new_submodule_scope.attr("__doc__") = "Tracking things for PyBertini.  Includes the three fundamental trackers, and utility functions.";
+	new_submodule_scope.attr("__doc__") = "Observers for trackers.";
 
 	{
 	// this should be called in the tracking module namespace