bertini2 2.0.2__cp313-cp313-win_amd64.whl

bertini/__init__.py

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+# This file is part of Bertini 2.
+# 
+# python/bertini/__init__.py is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# python/bertini/__init__.py is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with python/bertini/__init__.py.  If not, see <http://www.gnu.org/licenses/>.
+# 
+#  Copyright(C) Bertini2 Development Team
+# 
+#  See <http://www.gnu.org/licenses/> for a copy of the license, 
+#  as well as COPYING.  Bertini2 is provided with permitted 
+#  additional terms in the b2/licenses/ directory.
+
+#  individual authors of this file include:
+# 
+#  silviana amethyst
+#  UWEC
+#  Spring 2018
+#
+#  MPI-CBG 
+#  2025
+# 
+
+
+
+
+"""
+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 
+Bertini name.  See b2/licenses/ for a complete copy of the license,
+and the licenses of software upon which Bertini depends.
+
+See the source at https://github.com/bertiniteam/b2
+"""
+
+
+# start delvewheel patch
+def _delvewheel_patch_1_12_1():
+    import os
+    if os.path.isdir(libs_dir := os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'bertini2.libs'))):
+        os.add_dll_directory(libs_dir)
+
+
+_delvewheel_patch_1_12_1()
+del _delvewheel_patch_1_12_1
+# end delvewheel patch
+
+### this __init__.py is strongly inspired by that for GalSim 
+### https://github.com/GalSim-developers/GalSim
+
+from importlib.metadata import version
+__version__ = version("bertini2")
+
+import os
+import sys
+
+if sys.platform == "win32":
+    from .windows_dll_manager import get_dll_paths, build_directory_manager
+    _dll_manager = build_directory_manager()
+    _dll_manager.__enter__()
+    for p in get_dll_paths():
+        _dll_manager.add_dll_directory(p)
+
+# put stuff in the bertini namespace
+
+import bertini.function_tree as function_tree
+
+import bertini.system as system
+import bertini.tracking as tracking
+import bertini.endgame as endgame
+import bertini.parse as parse
+import bertini.container as container
+import bertini.logging as logging
+import bertini.nag_algorithm as nag_algorithm
+import bertini.random as random
+
+from bertini._pybertini import info
+
+import bertini.multiprec as multiprec
+
+# some convenience assignments
+Variable = function_tree.symbol.Variable
+VariableGroup = function_tree.VariableGroup
+System = system.System
+default_precision = multiprec.default_precision
+
+
+
+# https://stackoverflow.com/questions/44834/what-does-all-mean-in-python
+# "a list of strings defining what symbols in a module will be exported when from <module> import * is used on the module"
+__all__ = ['Variable','VariableGroup','system','System',
+           'nag_algorithm','container','default_precision',
+           'tracking','endgame','logging','function_tree','parse','multiprec','random']
+
+
+

bertini/algorithms/__init__.py

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+# This file is part of Bertini 2.
+# 
+# python/bertini/algorithms/__init__.py is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# python/bertini/algorithms/__init__.py is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with python/bertini/algorithms/__init__.py.  If not, see <http://www.gnu.org/licenses/>.
+# 
+#  Copyright(C) Bertini2 Development Team
+# 
+#  See <http://www.gnu.org/licenses/> for a copy of the license, 
+#  as well as COPYING.  Bertini2 is provided with permitted 
+#  additional terms in the b2/licenses/ directory.
+
+#  individual authors of this file include:
+# 
+#  silviana amethyst
+#  UWEC
+#  Spring 2018
+# 
+
+"""
+Various algorithms for numerical algebraic geometry, notable the zero dimensional algorithm, which is used all over the place.
+"""
+

bertini/algorithms/zerodim.py

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+# This file is part of Bertini 2.
+# 
+# python/bertini/algorithms/zerodim.py is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# python/bertini/algorithms/zerodim.py is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with python/bertini/algorithms/zerodim.py.  If not, see <http://www.gnu.org/licenses/>.
+# 
+#  Copyright(C) Bertini2 Development Team
+# 
+#  See <http://www.gnu.org/licenses/> for a copy of the license, 
+#  as well as COPYING.  Bertini2 is provided with permitted 
+#  additional terms in the b2/licenses/ directory.
+
+#  individual authors of this file include:
+# 
+#  silviana amethyst
+#  UWEC
+#  Spring 2018
+# 

bertini/container/__init__.py

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+# This file is part of Bertini 2.
+# 
+# python/bertini/container/__init__.py is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# python/bertini/container/__init__.py is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with python/bertini/container/__init__.py.  If not, see <http://www.gnu.org/licenses/>.
+# 
+#  Copyright(C) Bertini2 Development Team
+# 
+#  See <http://www.gnu.org/licenses/> for a copy of the license, 
+#  as well as COPYING.  Bertini2 is provided with permitted 
+#  additional terms in the b2/licenses/ directory.
+
+#  individual authors of this file include:
+# 
+#  silviana amethyst
+#  UWEC
+#  Spring 2018, 2023
+# 
+
+
+
+
+
+"""
+container types, coming from C++
+
+
+"""
+
+import bertini._pybertini.container
+
+from bertini._pybertini.container import *
+
+
+
+__all__ = [
+"ListOfEGBoundaryMetaData_DoublePrec",
+"ListOfJacobian",
+"ListOfVariableGroup",
+"ListOfEGBoundaryMetaData_MultiPrec",
+"ListOfRational",
+"ListOfVectorComplexDoublePrecision",
+"ListOfFunction",
+"ListOfSolutionMetaData_DoublePrec",
+"ListOfVectorComplexVariablePrecision",
+"ListOfInt",
+"ListOfSolutionMetaData_MultiPrec",
+"VariableGroup",
+"ListOfVectorComplexVariablePrecision", 
+"ListOfVectorComplexDoublePrecision"
+]
+

bertini/endgame/__init__.py

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+# This file is part of Bertini 2.
+# 
+# python/bertini/endgame/__init__.py is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# python/bertini/endgame/__init__.py is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with python/bertini/endgame/__init__.py.  If not, see <http://www.gnu.org/licenses/>.
+# 
+#  Copyright(C) Bertini2 Development Team
+# 
+#  See <http://www.gnu.org/licenses/> for a copy of the license, 
+#  as well as COPYING.  Bertini2 is provided with permitted 
+#  additional terms in the b2/licenses/ directory.
+
+#  individual authors of this file include:
+# 
+#  silviana amethyst
+#  UWEC
+#  Spring 2018
+# 
+
+"""
+Endgame-specific things -- endgames, configs
+***********************************************
+
+Endgames allow the computation of singular endpoints.  
+
+Flavors
+=========
+
+There are two basic flavors of endgame implemented:
+
+1. Power Series, commonly written PS or PSEG
+2. Cauchy
+
+Both estimate the cycle number and use it to compute a root at a time which is never tracked to.  PSEG uses Hermite interpolation and extrapolation, and Cauchy uses loops around the target time coupled with the `Cauchy integral formula <https://en.wikipedia.org/wiki/Cauchy%27s_integral_formula>`_.  Both continue until two successive approximations of the root match to a given tolerance (:py:attr:`bertini.endgame.config.Endgame.final_tolerance`).
+
+The implementations of the endgames go with a particular tracker, hence there are six provided endgame types.  Choose the one that goes with your selected tracker type.  Adaptive Multiple Precision is a good choice.
+
+
+Implementation reference
+=========================
+
+AMP Endgames
+-------------
+
+* :class:`~bertini.endgame.AMPCauchyEG`
+* :class:`~bertini.endgame.AMPPSEG`
+
+Fixed Double Precision Endgames
+---------------------------------
+
+* :class:`~bertini.endgame.FixedDoublePSEG`
+* :class:`~bertini.endgame.FixedDoublePSEG`
+
+Fixed Multiple Precision  Endgames
+-------------------------------------
+
+* :class:`~bertini.endgame.FixedMultiplePSEG`
+* :class:`~bertini.endgame.FixedMultiplePSEG`
+
+"""
+
+import bertini._pybertini.endgame
+
+from bertini._pybertini.endgame import *
+
+__all__ = ['AMPCauchyEG',
+ 'AMPPSEG',
+ 'FixedDoubleCauchyEG',
+ 'FixedDoublePSEG',
+ 'FixedMultipleCauchyEG',
+ 'FixedMultiplePSEG',
+ '__doc__',
+ '__loader__',
+ '__name__',
+ '__package__',
+ '__spec__',
+ 'config',
+ 'observers']

bertini/endgame/config/__init__.py

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+# This file is part of Bertini 2.
+# 
+# python/bertini/endgame/config/__init__.py is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# python/bertini/endgame/config/__init__.py is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with python/bertini/endgame/config/__init__.py.  If not, see <http://www.gnu.org/licenses/>.
+# 
+#  Copyright(C) Bertini2 Development Team
+# 
+#  See <http://www.gnu.org/licenses/> for a copy of the license, 
+#  as well as COPYING.  Bertini2 is provided with permitted 
+#  additional terms in the b2/licenses/ directory.
+
+#  individual authors of this file include:
+# 
+#  silviana amethyst
+#  UWEC
+#  Spring 2018
+# 
+
+
+
+"""
+
+Configs for endgames
+
+"""
+
+import bertini._pybertini.endgame.config
+
+from bertini._pybertini.endgame.config import *
+
+__all__ = dir(bertini._pybertini.endgame.config)

bertini/function_tree/__init__.py

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+# This file is part of Bertini 2.
+# 
+# python/bertini/function_tree/__init__.py is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# python/bertini/function_tree/__init__.py is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with python/bertini/function_tree/__init__.py.  If not, see <http://www.gnu.org/licenses/>.
+# 
+#  Copyright(C) Bertini2 Development Team
+# 
+#  See <http://www.gnu.org/licenses/> for a copy of the license, 
+#  as well as COPYING.  Bertini2 is provided with permitted 
+#  additional terms in the b2/licenses/ directory.
+
+#  individual authors of this file include:
+# 
+#  silviana amethyst
+#  UWEC
+#  Spring 2018
+# 
+
+
+
+import bertini._pybertini
+import bertini._pybertini.function_tree
+
+# from bertini._pybertini import function_tree
+from bertini._pybertini.container import VariableGroup
+
+from bertini._pybertini.function_tree import *
+
+
+VariableGroup.__str__ = lambda vg: '[{}]'.format( ','.join([str(v) for v in vg]) )
+
+__all__ = dir(bertini._pybertini.function_tree)
+

bertini/function_tree/root/__init__.py

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+# This file is part of Bertini 2.
+# 
+# python/bertini/function_tree/root/__init__.py is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# python/bertini/function_tree/root/__init__.py is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with python/bertini/function_tree/root/__init__.py.  If not, see <http://www.gnu.org/licenses/>.
+# 
+#  Copyright(C) Bertini2 Development Team
+# 
+#  See <http://www.gnu.org/licenses/> for a copy of the license, 
+#  as well as COPYING.  Bertini2 is provided with permitted 
+#  additional terms in the b2/licenses/ directory.
+
+#  individual authors of this file include:
+# 
+#  silviana amethyst
+#  UWEC
+#  Spring 2018
+# 
+
+
+
+import bertini._pybertini
+import bertini._pybertini.function_tree.root
+
+from bertini._pybertini.function_tree.root import *
+
+__all__ = dir(bertini._pybertini.function_tree.root)
+

bertini/function_tree/symbol/__init__.py

@@ -0,0 +1,37 @@
+# This file is part of Bertini 2.
+# 
+# python/bertini/function_tree/symbol/__init__.py is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# python/bertini/function_tree/symbol/__init__.py is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with python/bertini/function_tree/symbol/__init__.py.  If not, see <http://www.gnu.org/licenses/>.
+# 
+#  Copyright(C) Bertini2 Development Team
+# 
+#  See <http://www.gnu.org/licenses/> for a copy of the license, 
+#  as well as COPYING.  Bertini2 is provided with permitted 
+#  additional terms in the b2/licenses/ directory.
+
+#  individual authors of this file include:
+# 
+#  silviana amethyst
+#  UWEC
+#  Spring 2018
+# 
+
+
+
+import bertini._pybertini
+import bertini._pybertini.function_tree.symbol
+
+from bertini._pybertini.function_tree.symbol import *
+
+__all__ = dir(bertini._pybertini.function_tree.symbol)
+

bertini/include/bertini2/bertini.hpp

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+//This file is part of Bertini 2.
+//
+//bertini.hpp is free software: you can redistribute it and/or modify
+//it under the terms of the GNU General Public License as published by
+//the Free Software Foundation, either version 3 of the License, or
+//(at your option) any later version.
+//
+//bertini.hpp is distributed in the hope that it will be useful,
+//but WITHOUT ANY WARRANTY; without even the implied warranty of
+//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+//GNU General Public License for more details.
+//
+//You should have received a copy of the GNU General Public License
+//along with bertini.hpp.  If not, see <http://www.gnu.org/licenses/>.
+//
+// Copyright(C) Bertini2 Development Team
+//
+// See <http://www.gnu.org/licenses/> for a copy of the license, 
+// as well as COPYING.  Bertini2 is provided with permitted 
+// additional terms in the b2/licenses/ directory.
+
+
+/**
+\file bertini.hpp 
+
+\brief The main file for including the entirety of Bertini's header files.
+*/
+
+#ifndef BERTINI_HPP
+#define BERTINI_HPP
+
+
+#include "bertini2/blackbox/argc_argv.hpp"
+#include "bertini2/blackbox/main_mode_switch.hpp"
+
+#include "bertini2/parallel.hpp"
+
+
+#endif
+
+

bertini/include/bertini2/blackbox/algorithm_builder.hpp

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+//This file is part of Bertini 2.
+//
+//bertini2/blackbox/algorithm_builder.hpp is free software: you can redistribute it and/or modify
+//it under the terms of the GNU General Public License as published by
+//the Free Software Foundation, either version 3 of the License, or
+//(at your option) any later version.
+//
+//bertini2/blackbox/algorithm_builder.hpp is distributed in the hope that it will be useful,
+//but WITHOUT ANY WARRANTY; without even the implied warranty of
+//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+//GNU General Public License for more details.
+//
+//You should have received a copy of the GNU General Public License
+//along with bertini2/blackbox/algorithm_builder.hpp.  If not, see <http://www.gnu.org/licenses/>.
+//
+// Copyright(C) Bertini2 Development Team
+//
+// See <http://www.gnu.org/licenses/> for a copy of the license, 
+// as well as COPYING.  Bertini2 is provided with permitted 
+// additional terms in the b2/licenses/ directory.
+//
+// individual authors of this file include 
+//
+// silviana amethyst, university of wisconsin-eau claire
+
+/**
+\file include/bertini2/blackbox/algorithm_builder.hpp 
+
+\brief A type which determines which algorithms etc, to run, and sets them up.
+*/
+
+
+
+#pragma once
+
+#include "bertini2/io/file_utilities.hpp"
+
+namespace bertini {
+namespace blackbox {
+
+
+/**
+\brief A de-serializer, whose responsibility it is to construct runnable objects based on input files.
+
+This class is inspired by the SimBuilder class from Hythem Sidky's SAPHRON package for molecular dynamics.
+*/
+class AlgoBuilder
+{
+	
+public:
+	AlgoBuilder() = default;
+
+	/**
+	\brief Method for constructing an algorithm from a bertini classic input file
+	*/
+	int ClassicBuild(boost::filesystem::path const& input_file);
+
+	/**
+	\brief Returns a non-owning pointer to the built algorithm
+	*/
+	AnyAlgorithm* GetAlg()
+	{
+		return alg_.get();
+	}
+
+private:
+	std::unique_ptr<AnyAlgorithm> alg_;
+};
+
+
+
+} // blackbox
+} //namespace bertini
+

bertini/include/bertini2/blackbox/argc_argv.hpp

@@ -0,0 +1,41 @@
+//This file is part of Bertini 2.
+//
+//bertini2/blackbox/argc_argv.hpp is free software: you can redistribute it and/or modify
+//it under the terms of the GNU General Public License as published by
+//the Free Software Foundation, either version 3 of the License, or
+//(at your option) any later version.
+//
+//bertini2/blackbox/argc_argv.hpp is distributed in the hope that it will be useful,
+//but WITHOUT ANY WARRANTY; without even the implied warranty of
+//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+//GNU General Public License for more details.
+//
+//You should have received a copy of the GNU General Public License
+//along with bertini2/blackbox/argc_argv.hpp.  If not, see <http://www.gnu.org/licenses/>.
+//
+// Copyright(C) Bertini2 Development Team
+//
+// See <http://www.gnu.org/licenses/> for a copy of the license, 
+// as well as COPYING.  Bertini2 is provided with permitted 
+// additional terms in the b2/licenses/ directory.
+
+
+/**
+\file bertini2/blackbox/argc_argv.hpp 
+
+\brief Provides the methods for parsing the command-line arguments.
+*/
+
+#pragma once
+
+namespace bertini{
+
+/**
+Main initial function for doing stuff to interpret the command-line arguments for invokation of the program.
+
+\param argc The number of arguments to the program.  Must be at least one.
+\param argv array of character arrays, the arguments to the program when called.
+*/
+void ParseArgcArgv(int argc, char** argv);
+
+} //namespace bertini