https://github.com/janverschelde/PHCpack
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Tip revision: 4561a59f5e5c72a2c3603e60b15687cc482bae61 authored by Jan Verschelde on 30 September 2020, 21:42:23 UTC
added reference to the CAMPARY software in the documentation
Tip revision: 4561a59
UPDATES
Wed 30 Sep 2020 : added reference to SciPy 2019 paper to welcome.rst in
  the phcpy documentation.  In blackbox.rst, added descriptions on the
  options mvfocus, dictionary_output, and verbose_level of the solver.
  To welcome.rst, added the talk at the Python devroom at FOSDEM 2019.

Tue 29 Sep 2020 : updated files for version 1.0.7.

Mon 28 Sep 2020 : added the option mvfocus to the double precision solve()
  functions in the solver module of python2 and python3.

Thu 30 Jul 2020 : updated files for version 1.0.6.

Wed 29 Jul 2020 : to the blackbox solver functions, added added the parameter
  verbose_level for listing the called procedures during the solving.

Wed 1 Jul 2020 : added a function to the solver module to compute a
  condition report in double precision.  Updated files for version 1.0.5.

Fri 12 Jun 2020 : added the computation of condition tables to the
  solution modules of the python2 and python3 versions.
  Updated __init__.py, setup.py, and conf.py for version 1.0.4.

Wed 29 Apr 2020 : updated files for version 1.0.3 of phcpy.

Tue 28 Apr 2020 : commented out some print statements in the sweepers module
  of the python2 and python3 versions.

Thu 21 Oct 2019 : updated the documentation of phcpy to include the new
  module polynomials.  Added a couple of lines about the polynomials module
  to the __init__.py of both the python2 and the python3 versions of phcpy.
  Updates files for version 1.0.2 of phcpy.

Thu 3 Oct 2019 : updates files for version 1.0.1 of phcpy.

Sun 29 Sep 2019 : added the number of tasks to the solve() method in the
  class polynomials.

Sat 28 Sep 2019 : added the list of variables as a data attribute in the
  class polynomials.

Mon 23 Sep 2019 : modified the setup.py for python3 to include polynomials.py
  and did the same for the python2 version, after adding the polynomials.py.

Sun 22 Sep 2019 : start of a new module polynomials for the python3 version
  of phcpy which exports the class Polynomials.

Sat 21 Sep 2019 : extended the constructor of a Solution in solutions
  with the alternative dictionary argument, for python3.
  Did the same for the python2 version of the solutions module.

Wed 18 Sep 2019 : swapped the string representation for the dictionary
  in the definition of the class Solution.  Did the same for the python2
  version of the Solution class in the solutions module.

Tue 17 Sep 2019 : added to solutions.py in PHCpy3/phcpy a basic definition
  of the class Solution, and a test_class() function.  Also updated the
  python2 version of the module solutions with a basic Solution class.

Sun 8 Sep 2019 : to the interface.py module added functions to read solutions
  from file, given a file name, both for python2 and python3.

Sun 1 Sep 2019 : prepared files for version 1.0.0 of phcpy.

Sat 31 Aug 2019 : test on 2-homogenization and 1-homogenization in the
  curves module improved.

Fri 30 Aug 2019 : extended the curves module with a test on 2-homogenization.

Sun 25 Aug 2019 : extended the call to the tracking functions in the curves
  modules (both for python2 and python3) to include the m-homogenization
  value and the index representation of the partition of the variable set.

Tue 13 Aug 2019 : updated functions in the curves module to show also the
  pole step, estimated distance, and Hessian step; fixed initialization of
  the homotopy for the step-by-step with default 0 flag for homogeneous.
  The step-by-step trackers in curves support homogeneous coordinates.
  Prepared files for version 0.9.9 of phcpy.

Mon 12 Aug 2019 : fixed writing of homotopy parameters in curves, after the
  removal of the beta for the series step.

Sun 11 Aug 2019 : to the curves module, added default values for the new
  parameters in the track functions for Pade continuation.

Sun 28 Jul 2019 : updated random_system in the solver modules for python2
  and python3 so systems with double double and quad double precision can
  be generated.

Sat 27 Jul 2019 : updated random_system in the solver modules for python2
  and python3 so nonsquare systems can be generated.

Thu 25 Jul 2019 : prepared files for release 0.9.8.

Mon 15 Jul 2019 : updated the interface module for the python2 phcpy.

Sun 14 Jul 2019 : added test_tableau function to the interface module
  of the python3 version of phcpy.

Sat 13 Jul 2019 : prepared code for retrieval of tableau form in the
  interface module of the python3 version of phcpy.
  Completed first version of load tableau form in interface.py for python3.

Fri 12 Jul 2019 : fixed flattening of complex coefficients in the
  interface module for python3.  Update store_standard_tableau in the
  interface.py for python3 and python2.  Fixed the import inside the
  store_standard_tableau function of the interface.py for python2.

Thu 11 Jul 2019 : added the SciPy 2019 paper to the reference list in
  the file welcome.rst of the python2 and python3 documentation.
  Added to interface.py in PHCpy3/phcpy a function to store the
  tableau representation of a system.

Fri 5 Jul 2019 : updated files for version 0.9.7 of phcpy.

Thu 4 Jul 2019 : added functions to the curves module to return the various
  different step sizes.

Tue 25 Jun 2019 : extended the curves modules with functions to tune the
  multiplication factor for the curvature step control.

Fri 21 Jun 2019 : fixed copying of target solutions with zero coordinates
  for the solving of the random coefficient start system.
  Updates files for version 0.9.6 of phcpy.

Thu 20 Jun 2019 : additions to solver.py for zero coordinate solutions,
  both for python2 and python3.

Mon 17 Jun 2019 : updates in random_coefficient_system() functions in
  python2 and python3 for stable mixed volumes.

Sun 26 May 2019 : in the trackers module, replaced silent by verbose in
  the test_track(), both for python2 and python3.

Sat 25 May 2019 : replaced deprecated 'silent' option by 'verbose' in the
  solve() called in the tropism module, for both python2 and python3.

Fri 17 May 2019 : prepared files for version 0.9.5 of phcpy.
  Updated the step-by-step trackers in curves to print the previous
  t value with the printing of series, Pade approximants and poles.

Tue 14 May 2019 : extended the python2 version of the curves module with an
  interactive step-by-step loop on a parameter homotopy, tested on hyperbola.
  Also extended the python3 version of the curves module in a similar way.

Sat 11 May 2019 : prompted user for verbose option in the test_solve()
  of the factor module, both for python2 and python3.  Also added a prompt
  for verbose in test_run_cascade() in the cascades module.

Wed 8 May 2019 : improved the pylint score of the solutions module for
  the Python3 version.  Also imported the python2 solutions module and
  added the j = complex(0, 1) definition back in for the test().

Tue 9 Apr 2019 : to wilkinson.py added print of solutions at the end.

Sun 7 Apr 2019 : added the script wilkinson.py to the examples folder of
  PHCpy2, to run a polynomial homotopy on the Wilkinson polynomials.

Fri 29 Mar 2019 : prepared files for version 0.9.4 of phcpy.

Thu 28 Mar 2019 : added gamma constant as optional parameter to initialize
  the homotopies in the step-by-step path trackers in the trackers module,
  which changed the file tracker.py both in the PHCpy2 and PHCpy3 folders.

Sat 23 Mar 2019 : improved the make_solution function of the solutions
  module, adding also a function numerals.

Thu 21 Mar 2019 : added functions to the solutions module to return the
  coordinates in Python complex number string representations. 
  To the solve functions in the solver modules of python2 and python3
  added the dictionary_output option.

Wed 20 Mar 2019 : started adding the option dictionary_output to the
  solver module.

Tue 19 Mar 2019 : added the function formdictlist to the solutions modules
  in the PHCpy2 and PHCpy3 folders.

Thu 28 Feb 2019 : fixed errors in the documentation for the path trackers.
  Prepared files for version 0.9.3 of phcpy.

Mon 21 Jan 2019 : added functions to the curves module to initialize
  a parameter homotopy for the step-by-step Pade continuation.
  Prepared files for version 0.9.2 of phcpy.
  In the __init__.py, added the import of the new module curves.

Fri 11 Jan 2019 : added the functions for a symbolic Pade vector to the
  curves module for python3.

Wed 9 Jan 2019 : to the curves module for python2, added a function to
  compute a symbolic representation of a Pade vector.

Fri 28 Dec 2018 : the curves module has functions to extract the coefficients
  of the power series and the Pade approximants.
  Extended the curves module with functions to return all poles.
  Prepared files for version 0.9.1 of phcpy.

Thu 27 Dec 2018 : extended the curves module with functions to return
  the t value, the step size, pole radius, and closest pole.

Tue 25 Dec 2018 : added the step-by-step run of the series-Pade tracker
  to the module curves, both for python2 and python3.

Mon 10 Dec 2018 : improved the track functions in curves.py.

Sun 9 Dec 2018 : prepared files for release 0.9.0 of phcpy.

Sat 8 Dec 2018 : to the module curves.py added extra function to document
  better each parameter, in the python2 version.  Updated for python3 too.

Thu 6 Dec 2018 : updated the documentation with a few words about the
  new module curves.

Wed 5 Dec 2018 : new module curves, to export Pade continuation,
  defines the tuning of the homotopy continuation parameters.
  Wrapped the path trackers in the new module curves.py.

Sun 11 Nov 2018 : prepare files setup.py, __init__.py, and conf.py, for
  version 0.8.9 of phcpy for python2 and python3.

Fri 9 Nov 2018 : to series.py, added the maximal degree bound, both
  for the Python2 and Python3 versions.

Sun 14 Oct 2018 : updated setup.py, __init__.py, conf.py for version 0.8.8
  in the PHCpy2 and PHCpy3 folders.

Thu 27 Sep 2018 : in factor.py in the PHCpy2/phcpy folder, replaced the
  import of phcpy2c3 by phcpy2c2.  Updated __init__.py, conf.py and setup.py
  in the PHCpy2 and PHCpy3 folders for version 0.8.7.

Fri 31 Aug 2018 : adjustment for version 0.8.6 of phcpy.

Tue 28 Aug 2018 : added the eacute definition to blackbox.rst to write
  the e in Bezout properly.  Added a wrapper to the polysys and laursys
  solve functions in factor.py, to wrap the precision levels.

Sun 26 Aug 2018 : added function for double double and quad double precision
  to the factor module of phcpy for python2.  Did the same for python3.

Sat 25 Aug 2018 : extended the factor module of PHCpy2 with the functions
  standard_polysys_solve and test_polysys_solve.  Added the corresponding
  function to the factor module of PHCpy3.

Tue 14 Aug 2018 : adjustments for version 0.8.5 of phcpy.

Sat 2 Jun 2018 : prepared files __init__.py, setup.py, conf.py for 0.8.4
  of python2 and python3.

Fri 1 Jun 2018 : extended mixed_volume_by_demics() with the stable option,
  to compute the stable mixed volume.

Wed 16 May 2018 : added mixed_volume_by_demics() to the solver module of phcpy,
  with an added test_mixed_volume() to compare with MixedVol.
  Updated the files welcome.rst and blackbox.rst to document the new function
  to compute mixed volumes by DEMiCs.  Updates files setup.py, __init__.py,
  and conf.py in the documentation for version 0.8.3.

Tue 1 May 2018 : updated blackbox.rst in the Python documentation with a
  small section on computing the multiplicity structure.
  Updates files for version 0.8.2.

Sun 29 Apr 2018 : extended solver.py in PHCpy2/phcpy with wrappers to compute
  the multiplicity structure and a test function.
  Extended the solver.py for python3 in PHCpy3/phcpy similarly.

Tue 10 Apr 2018 : improved test in sets.py in PHCpy2/phcpy and PHCpy3/phcpy,
  adding the number of tasks.  Prepared files for version 0.8.1,
  in PHCpy2 and PHCpy3: setup.py, conf.py (doc/source), __init__.py (phcpy).

Thu 5 Apr 2018 : extended sets.py for python2 and python3 with the parameter
  tasks in the functions for the homotopy membership tests.
  In sets.py, updated the calls to the C membership tests to take the
  number of tasks as the extra second parameter.

Mon 26 Mar 2018 : prepared files for version 0.8.0.

Tue 13 Mar 2018 : updated setup.py, __init__.py, and conf.py for 0.7.9.
  In the documentation string of solve() in solver.py, referred explicitly to
  the solve in the factor module for a numerical irreducible decomposition.

Mon 12 Mar 2018 : added a tolerance to the membership filters in sets.py
  to bypass the homotopy membership tests for regular solutions,
  modified cascades.py and factor.py in the Python2 version of phcpy.
  Made the similar updates to the Python3 version of phcpy.

Mon 5 Mar 2018 : added a checkin_newton_power_series_function() to check
  the input of the newton_power_series functions in the series.py module.
  Updated files setup.py, __init__.py, conf.py in the PHCpy2/PHCpy3,
  in the phcpy and doc/source directories for version 0.7.8.

Sun 4 Mar 2018 : added snippets.rst to the user manual, listing all code
  snippets for the Jupyter notebook extension in the documentation.

Thu 4 Jan 2018 : added comment lines to the __init__.py of phcpy to 
  suggest the init_cysignals() when using phcpy in SageMath.

Tue 2 Jan 2018 : replaced the silent=True option in the test() of series.py
  by verbose=False, when calling the blackbox solver solve().

Sat 30 Dec 2017 : added the work around of Marc Culler for the signals
  when importing phcpy in Sage session to the welcome.rst files.
  Updated setup.py, conf.py, and __init__.py for version 0.7.7 of phcpy.

Thu 19 Oct 2017 : added lower dimension to run_cascade of cascades.py.

Wed 18 Oct 2017 : in solutions.py, converted the value for t from a string
  to a complex number.  In solver.py, provided a checkin for mixed_volume.
  Also fixed the python3 version and returned -1 for nonsquare input.

Tue 17 Oct 2017 : fixed verbose option in appolonius.py files.
  In the __init__.py, added the import of the modules, so dir(phcpy)
  shows the modules and phcpy.solver.solve can be used directly
  and did the same for the __init__.py in the PHCpy2/phcpy folder.
  Fixed the example touchcircle.py for the updated options and the
  module diagonal, extracted out of the old sets.
  Fixed the tangents4spheres.sage and tangents4spheres.sws for the
  deprecated option silent of the blackbox solver.
  Fixed the documentation apollonius.rst, touchcircle.rst, and
  tangents4spheres.rst for the deprecated silent option and the
  diagonal module.  With the checkin option of the blackbox solver,
  the number of tasks is checked for being nonnegative.
  Prepared the __init__.py, conf.py, and setup.py for phcpy 0.7.6.

Mon 16 Oct 2017 : fixed bug in random_coefficient_system() by clearing the
  systems container for a subsequent mixed volume computation.
  Applied the same changes also to the python3 version.

Thu 28 Sep 2017 : prepared version 0.7.5 of phcpy.

Sun 24 Sep 2017 : added a short paragraph about nonlinear reduction in the
  documentation file blackbox.rst for python 2 and 3.

Sat 23 Sep 2017 : to the solver module for python2 and python3 added a
  function for nonlinear reduction, along with a simple test.

Wed 20 Sep 2017 : added wrapper function, linear_reduce, to the solver.py,
  wrote short section in the user manual to document linear_reduce.

Tue 19 Sep 2017 : added a simple linear reduction to the solver modules
  for python 2 and 3.  Added double double and quad double versions.

Wed 13 Sep 2017 : corrected the silent= option into the verbose= options into
  the calls to the solve function in cascades.py and factor.py.
  Fixed the test_factor function in the factor module.

Tue 12 Sep 2017 : extended the definition of the blackbox solver, in the
  source file blackbox.rst of the Sphinx documentation of python 2 and 3.
  Added an example to blackbox.rst to illustrate the value of rco.
  The start of the user manual chapter in userman.rst summarizes the
  inventory and the structure of the chapter.
  Updated setup.py, __init__.py, and conf.py for version 0.7.4 of phcpy.

Mon 11 Sep 2017 : added documentation about the four computed root counts
  of the blackbox solver.

Sun 10 Sep 2017 : the solve functions in the solver module print the root
  counter output strings, both for the python 2 and 3 versions.
  In solver.py, the solver should not print empty strings for special cases.
  Instead of calling a function to write the set structure, a function is
  called which returns the set structure string in solver.py; replaced the
  silent argument by verbose in solver.py.

Fri 8 Sep 2017 : replaced the silent option of the solve function in the
  solver module by a verbose option.  Updated the documentation.

Tue 5 Sep 2017 : added two code snippets to custom.js to illustrate the use
  of multitasking in the solver and the path tracker.  Removed the GPU snippet
  from the path trackers in the file custom.js, as not ready for production.
  Prepared __init__.py, setup.py, and conf.py for version 0.7.3 of phcpy,
  in both the PHCpy2 and PHCpy3 folders.

Mon 4 Sep 2017 : fixed the code in the documentation blocks for the
  Pieri homotopies in the file numschub.rst in the PHCpy2 and PHCpy3 folders.
  Fixed snippets for the Schubert calculus and the extension module,
  in the file Jupyter/custom.js.  Correct the use of get_seed and set_seed
  in the file blackbox.rst in PHCpy2 and PHCpy3 folders.  All snippets in
  the blackbox solver work.  Fixed import phcpy.series in newtopes.rst.
  Updated diagonal.py for the drop_coordinate_ and drop_variable_ functions.
  In custom.js, fixed all snippets for the solution sets menu.
  Updated snippets in custom.js for the path trackers.

Sun 3 Sep 2017 : added a new folder Jupyter into the src/Python directory,
  with the custom.js file to define the menu Jupyter notebook extension.
  Fixed the blackbox coding blocks in custom.js.  Corrected the blackbox.rst
  in the PHCpy2 and PHCpy3, fixing the "from solver import deflate" into
  "from solver import standard_deflate"; fixed the call standard_deflate().
  In custom.js, added titles to 12 titles in the sub-menus.

Thu 31 Aug 2017 : fixed a bug in the a documentation block in newtopes.rst,
  both in the source of the python2 and python3 documentation.
  Improved the documentation string of the mixed_volume function in the
  polytopes module, with two examples.  Fixed another documentation block
  in newtopes.rst with an example of a volume computation.
  For Sage, forced the type of the values in make_solution in blackbox.rst.

Sun 20 Aug 2017 : extended the examples.py module in PHCpy2/phcpy with
  the special sevenbar example, added new functions, refactoring the main
  test function.  In the interface module, when storing a solution fails,
  the failure should not cause a break out of the loop.  Replaced the break
  in interface.py with an error message.  Updates the examples modules for
  the Python 2 and 3 versions of phcpy.  Added references to the sevenbar()
  documentation string in the examples module.  Adjusted setup.py, conf.py,
  and __init__.py for version 0.7.2 of phcpy.

Sun 13 Aug 2017 : updated setup.py, __init__.py, and conf.py for version
  0.7.1 of phcpy for python2 and python3.

Sat 12 Aug 2017 : added a solve() to factor.py in the PHCpy2/phcpy folder,
  and did the same addition to factor.py for the python3 version of phcpy.
  Bug fixed in the run_cascade() functions of the cascades module.
  Rearranged documentation strings in the *top_cascade() functions in the
  cascades module, because of complaint of sphinx.
  Many fixes in the factor module.  In the interface module, initialized the
  failure code in the store_* functions, so storing nothing does not crash.
  Passed the verbose flag properly in the top_cascade routines so the
  split_filter() remains silent if verbose is set to False.

Fri 11 Aug 2017 : added parameters to the run_cascade() function in the
  python2 and python3 cascades modules.  Added a decompose() function to
  the factor module in the PHCpy2 and PHCpy3 folders.  Augmented the
  run_cascade() with an islaurent option for python 2 and 3.

Thu 10 Aug 2017 : the ismember() tests return a tuple of booleans, in order
  to filter also the end points of diverging paths, with are junk points;
  updated the sets modules, both for python2 and python3.
  Used the filters in the sevenbar.py in the examples of PHCpy2 and PHCpy3.
  Added a run_cascade function and a test to cascades.py in PHCpy2/phcpy.
  Updated the python3 version of cascades.py with a run_cascade().

Wed 9 Aug 2017 : added ismember_filter() functions to the sets module in
  the PHCpy2 folder, tested in the illusex2.py script.  Did the same for
  the python3 versions, updating sets.py and the illusex3.py script.
  Added laurent_cascade_filter to the cascades module for python2 and 3.
  Bug fixed in laurent_ismember_filter() functions in the sets module.

Tue 8 Aug 2017 : added top_cascade() to the cascades module for python2 and 3,
  developed in the illustrated example illusex.py.  Added a cascade_filter()
  function in cascades.py in PHCpy2 and PHCpy3, updated illusex.py.
  The function laurent_top_cascade() is tested on the sevenbar.py example.

Mon 7 Aug 2017 : bug fix in sets.py for python2.  Added an illustrative
  example for the witness generate, illusex.py, to the examples in PHCpy2.
  Added a split_filter function to the cascades modules for python2 and 3.

Sun 6 Aug 2017 : to the module sets in the PHCpy2 and PHCpy3 folders,
  added functions to run the homotopy membership test for Laurent systems,
  with the test point given in the symbolic representation of a solution.
  Added functions to the module sets for python2 and python3, to drop
  a variable from a Laurent system.

Sat 5 Aug 2017 : extended the python2 module sets with membership tests
  and extended the python3 module sets as well.

Fri 4 Aug 2017 : added a function ismember to the module sets, a function
  which takes the test points as a PHCpack solution string.

Thu 3 Aug 2017 : used store-witness-set functions in the cascades module,
  both in the python2 and python3 versions.  Updated the documentation of
  the cascade_step in posdimsols.rst for the extra dimension parameter.

Wed 2 Aug 2017 : added six functions to the python2 interface module to store
  witness sets, with the swapping of the symbols for the slack variables.
  Did the same additions to the python3 interface module.
  Used the store-witness-set functions in the factor modules for python2
  and python3.  Also used these functions in the sets modules.

Mon 31 Jul 2017 : added function to make a witness set of a hypersurface
  defined by a Laurent polynomial to sets.py in the PHCpy2 and PHCpy3 folders.
  Updated the files setup.py, __init__.py, and conf.py for version 0.7.0.

Tue 18 Jul 2017 : prepared files for version 0.6.9 of phcpy, adjusting
  setup.py, __init__.py, and conf.py in the PHCpy2 and PHCpy3 folders.
  Corrected the documentation for the new modules, factor, cascades,
  and diagonal.

Mon 17 Jul 2017 : to the function in the factor module, stored the embedded
  system before the initialization of the monodromy breakup sampler.

Sun 16 Jul 2017 : to sets added functions to drop variables and coordinates
  in double double and quad double precision.  This changed cascades.
  Extended the functions in factor.py to decompose witness sets defined
  by a Laurent system.  Updated the sevenbar.py in the examples folder
  in the PHCpy2 directory.

Sat 15 Jul 2017 : moved the cascade homotopies from the sets module into
  the new module cascades.p, extended __init__.py and modified setup.py,
  all for Python 2.  Did the same for Python 3 in PHCpy3.
  Added the autodoc for the new cascade module to refman.rst in the
  source of the documentation in the PHCpy2 and PHCpy3 folders.
  Likewise, made a new module factor with code from sets.py,
  and also from sets.py extracted the code for the diagonal homotopies.

Fri 14 Jul 2017 : in sets.py, added a parameter to the calls to the
  functions *_track_paths(), to take into account the islaurent flag.

Mon 11 Jul 2017 : added homotopy membership tests for witness sets defined
  by Laurent systems in sets.py of PHCpy2 and PHCpy3.

Thu 6 Jul 2017 : to sets.py in PHCpy2 and PHCpy3, added functions to run
  one step of a cascade homotopy for Laurent polynomial systems.
  Added main laurent_cascade_step() function to sets.py.

Wed 5 Jul 2017 : prepared files for release 0.6.8.

Fri 30 Jun 2017 : shortened the code to embed systems in sets.py of PHCpy2
  and PHCpy3, using functions of the interface module.
  Applied the deallocation methods in trackers.py of PHCpy2 and PHCpy3.
  Added embedding of Laurent systems to sets.py in PHCpy2 and PHCpy3.

Sun 11 Jun 2017 : added functions for the crude trackers to the trackers
  module of phcpy in PHCpy2 and PHCpy3.

Wed 7 Jun 2017 : updated files, setup.py, __init__.py, and conf.py in
  the folders PHCpy2 and PHCpy3 to prepare release 0.6.7.

Sun 4 Jun 2017 : added functions to the series module for Python 3,
  to compute the Pade approximants for the regular case.
  Fixed the precision in the example test for Pade approximants.

Sat 3 Jun 2017 : made a start extending the series module for Python 2;
  adjusted the routines for double double and quad double precision.

Wed 17 May 2017 : prepared files for version 0.6.6, after introduction of
  a new use case: all tangent lines to four given spheres.

Fri 14 Apr 2017 : fixed bug in the run_pieri_homotopies of the schubert
  module which occurred with repeated calls to the function.
  Add the verbose as a last keyword argument.

Tue 11 Apr 2017 : added check_mixture() function to the polytopes module
  to check the input format because wrong input crashed python.

Tue 21 Mar 2017 : adjusted solver.py in PHCpy2/phcpy and PHCpy3/phcpy
  for the normalized name to call the blackbox solver in standard precision.

Sun 19 Feb 2017 : added tuned versions of the path trackers with AD to the
  trackers module of phcpy in PHCpy2; also did this addition to PHCpy3.
  Prepared files for version 0.6.5 of phcpy.

Sat 18 Feb 2017 : to tuning.py in PHCpy2 and PHCpy3 added function to get
  the default values for the path parameters, to write and tune them.

Fri 17 Feb 2017 : to interface.py in PHCpy2 and PHCpy3 added function to
  read a system and a list of solutions from file.

Thu 16 Feb 2017 : added functions to the interface module to read
  polynomial systems directly from file.

Tue 7 Feb 2017 : prepared files for version 0.6.4 of phcpy.

Fri 3 Feb 2017 : added tests on the algorithmic differentiation path trackers
  in trackers.py, both in PHCpy2/phcpy and PHCpy3/phcpy.

Thu 5 Jan 2017 : prepared for version 0.6.2 of phcpy, with updated conf.py
  in doc/source, updated __init__.py and setup.py, in PHCpy2 and PHCpy3.

Wed 4 Jan 2017 : added instructions to welcome.rst of the documentation for
  phcpy to extend Sage with phcpy.

Sun 1 Jan 2017 : fixed a bug in the writing of a power series, in the
  module series.py of PHCpy2 and of PHCpy3.

Fri 30 Dec 2016 : prepared for release 0.6.1 in PHCpy2 and PHCpy3.

Fri 23 Dec 2016 : added g48big.py as test script to the examples folder
  in the PHCpy2 and PHCpy3 directories.

Tue 20 Dec 2016 : added apollonius as a test to the series module,
  for both python2 and python3.  Adjusted the setup.py, __init__.py,
  and the conf.py in the doc/source for version 0.6.0 of phcpy,
  both for python2 and python3.

Mon 19 Dec 2016 : updated series.py in both PHCpy2 and PHCpy3 with three
  methods to compute power series starting at more than one term,
  using a lower triangular echelon form in Newton's method.

Sat 3 Dec 2016 : added cite() function to the __init__.py of python2
  and python3 versions of phcpy.

Thu 1 Dec 2016 : simplified the structure in welcome.rst, calling the
  chapter Getting Started.

Wed 30 Nov 2016 : prepared release 0.5.9 of phcpy.

Mon 28 Nov 2016 : in PHCpy2/doc/source and PHCpy3/doc/source reorganized
  the documentation chapters into one larger chapter, the User Manual.

Sun 20 Nov 2016 : improved the documentation, adding an example of the
  computation of a power series solution.  Prepared release 0.5.8 of phcpy.

Mon 31 Oct 2016 : prepared files for release 0.5.7 of phcpy.

Thu 27 Oct 2016 : restructured text added in the documentation strings
  of maps of PHCpy3 and of the modules tuning and series of PHCpy2.
  For Python2 modules trackers, sweepers, and tropisms, added documentation
  strings to have a better reference manual.

Wed 26 Oct 2016 : added restructured text in the documentation strings of
  the module interface.  For Python3, improved the documentation strings
  for the modules tuning and sets with restructured text and did the same
  for the Python3 modules polytopes, tropisms, and series.

Tue 25 Oct 2016 : used raw strings in the solver.py documentation strings
  which turns out better in the generated Sphinx documentation.
  Added restructured text is the documentation strings for solver.py.
  To blackbox.rst, added an illustration of make_solution.
  The documentation strings in solutions.py use restructured text.
  Also made the reference manual a bit better with restructured text
  in schubert.py, trackers.py, sweepers.py (the latter two only for Python3).

Sun 23 Oct 2016 : added paragraph in newtopes.rst about the alternative to
  mixed_volume, about the integer_mixed_cells function.

Sun 16 Oct 2016 : added writing of mixed cell configuration to polytopes.py,
  started adding a function to retrieve all data of a mixed cell.
  The function integer_mixed_cell in the module polytopes.py returns all 
  data of a mixed cell in a regular subdivision induced by an integer lifting.
  Prepared release files for version 0.5.6 of phcpy.

Sat 15 Oct 2016 : added to polytopes.py in PHCpy2/phcpy and PHCpy3/phcpy
  a function to compute the mixed cells in a regular subdivision induced
  by an integer value lifting function.

Tue 20 Sep 2016 : added checkin parameters to the start system constructors
  in solver.py to test whether the input system is square.
  Updated the __init__.py, conf.py, and setup.py for version 0.5.5.

Mon 1 Sep 2016 : renamed the phcwulf.py module to server.py in PHCpy2
  and also in PHCpy3.

Wed 31 Aug 2016 : prepared release 0.5.4, with the setup.py, conf.py, and
  the __init__.py files for Python 2 and 3.

Tue 30 Aug 2016 : added line in refman.rst concerning the sets module.

Mon 29 Aug 2016 : one more update in refman.rst in the doc folder of PHCpy3.

Sun 28 Aug 2016 : still some more updates in refman.rst in PHCpy3/doc.

Sat 27 Aug 2016 : more updates in refman.rst in PHCpy3/doc.

Fri 26 Aug 2016 : more text added to refman.rst for Python 3.

Thu 25 Aug 2016 : added text to the end of the reference manual of phcpy,
  both for Python 2 and Python 3.

Wed 24 Aug 2016 : corrected the refman.rst in the PHCpy2/doc/source and
  applied proper chapter headings for the Python 2 version.

Tue 23 Aug 2016 : used proper chapter headings for the phcpy documentation,
  as needed to restructure the reference manual.

Mon 22 Aug 2016 : moved the autogenerated module documentation for phcpy
  to the new reference manual chapter.

Sun 21 Aug 2016 : updated the documentation fourlines.rst and figfourlines.png
  so that the intersection points are marked on the plot.
  Updated the fourlines.py scripts in PHCpy2/examples and PHCpy3/examples.
  Extended in the documentation the introduction to the use cases,
  as the new use case applies numpy for the verification of the conditions.

Sat 20 Aug 2016 : added matplotlib plots to show the four given lines
  and the two lines that meet them, added to the fourlines.py scripts
  in the PHCpy2/examples and PHCpy3/examples directories.
  Extended the Sphinx documentation with a figure and text in fourlines.rst.

Fri 19 Aug 2016 : extracted the points from the lines in fourlines.py
  and computed the range of the coordinates needed for the plot.

Thu 18 Aug 2016 : verification of the four lines problem with determinants
  on numpy matrices, updated fourlines.py scripts for python 2 and 3.
  Added a verbose option to the run_pieri_homotopies function of schubert.
  Extended the fourlines.py with the solution of a real instance.
  Started the restructured text documentation of the use case.

Wed 17 Aug 2016 : fixed bug in schubert.py of PHCpy2/phcpy and PHCpy3/phcpy,
  the pieri_root_count must return the root_count; added verbose option.
  Added the start of another use case in the examples folders.

Tue 16 Aug 2016 : added an introductory paragraph to the use cases.

Sat 13 Aug 2016 : extended the documentation for the use case on computing
  tangent lines to a circle.  Made corrections to the touchcircle.py scripts
  in the PHCpy2/examples and PHCpy3/examples folders.
  Completed the documentation for this use case.  Prepared setup.py,
  phcpy/__init__.py and doc/source/conf.py for version 0.5.3, in the
  PHCpy2 and PHCpy3 folders.

Fri 12 Aug 2016 : added is_vanishing() and filter_vanishing() functions
  to the solutions module.  The diagonal solver in the module sets is
  extended with a multi staged cascade.  Updated the touchcircle?.py
  scripts in the examples folders of PHCpy2 and PHCpy3.
  Started the description of the documentation of this new use case.

Wed 10 Aug 2016 : added names_of_variables() function to the solver module.
  To the module sets, fixed a bug in the python3 version for the membership
  test, added a wrapper to the membertest to given points as solutions.
  New scripts touchcircle.py in PHCpy2/examples and PHCpy3/examples.

Tue 9 Aug 2016 : fixed numbering of the figures in appolonius.rst and
  fourbar.rst to correspond better to LaTeX conventions.
  Also fixed the numbering of figures in dashboard.rst, in pathtrack.rst,
  and in the modphcpy2c2.rst, modphcpy2c3.rst documentation files.

Mon 8 Aug 2016 : merged the use cases into one chapter in the Sphinx doc.

Sun 7 Aug 2016 : added a picture with the complete coupler curve of the
  straight line 4-bar mechanism to the PHCpy2 and PHCpy3 documentation.
  Updated the scripts fourbar.py in PHCpy2/examples and PHCpy3/examples.
  Adjusted the documentation is fourbar.rst in PHCpy2/doc and PHCpy3/doc.

Sat 6 Aug 2016 : added reference to the script appolonius.py in the examples
  folders in PHCpy2 and PHCpy3.

Fri 5 Aug 2016 : added a picture of part of the coupler curve for the
  straight line 4-bar mechanism.  Added matplotlib code to the fourbar.py
  scripts in the PHCpy2/examples and PHCpy3/examples directories.

Thu 4 Aug 2016 : added a picture of a straight line 4-bar design to the
  documentation, to introduce the design problem.  Added more text to
  the fourbar.rst files, with an extra section about the straight line.
  Added the matplotlib visualization to the fourbar.py scripts in the
  PHCpy2/examples and PHCpy3/examples directories.

Wed 3 Aug 2016 : start of postprocessing in the python2 fourbar.py script.

Tue 2 Aug 2016 : refactored the fourbar.py scripts, with functions.
  Fixed the toctree of the PHCpy2 Sphinx documentation source, in index.rst.
  Added a mathematical description of the equations to fourbar.rst.
  Corrected in mistake in the fourbar.py scripts and added a special case.

Mon 1 Aug 2016 : added fourbar.py to PHCpy2/examples and PHCpy3/examples
  to prepare another use case, to design a 4-bar mechanism.
  Made a first version of fourbar.rst in the Sphinx documentation.

Sun 31 Jul 2016 : prepared setup.py, __init__.py, and conf.py for version
  0.5.2 of phcpy for python2 and python3.

Fri 29 Jul 2016 : more symmetric perturbed instance in appolonius.py,
  in the examples folders of PHCpy2 and PHCpy3.  In the doc/source folders
  of PHCpy, added the circle problem of Appolonius as a use case.

Thu 28 Jul 2016 : updated appolonius.py in PHCpy2 with a special case,
  with more refactoring and generalized setup.
  Added in PHCpy3 the appolonius.py script for version 3 of Python.
  Add to appolonius.py a perturbed instance of the special configuration,
  in the PHCpy2 and PHCpy3 folders.

Wed 27 Jul 2016 : refactored appolonius.py scripts in PHCpy2 and PHCpy3.
  Fixed a bug in the storing the second coordinate of each center.
  Added matplotlib code to the appolonius.py scripts.

Tue 26 Jul 2016 : added appolonius.py to PHCpy2/examples and the version for
  Python 3 of appolonius.py in PHCpy3/examples.

Fri 22 Jul 2016 : prepared version 0.5.1 for python2 and python3.

Fri 1 Jul 2016 : new module series.py in PHCpy2 and PHCpy3, prepared setup.py
  and __init__.py for version 0.5.0.

Wed 15 Jun 2016 : updated setup.py, __init__.py, and conf.py for both PHCpy2
  and PHCpy3 to prepare for version 0.4.9 of phcpy.

Sun 5 Jun 2016 : improved dashboard.rst with figure (instead of image),
  with captions and references.

Sat 4 Jun 2016 : improved the documentation string of solutions.coordinates.
  Add a coordinate plot to the dashboard.py.  Improved and augmented the
  documentation in dashboard.rst, with a coordinate plot for cyclic 5-roots.

Fri 3 Jun 2016 : added a SolveButton to PHCpy3/phcpy/dashboard.py, which 
  provides a very basic GUI to the blackbox solver.  Updated for python2.
  Added documentation about the GUI to the blackbox solver, with screen shot.
  Updated setup.py, __init__.py, and conf.py for version 0.4.8.

Thu 2 Jun 2016 : new module dashboard.py for GUI in PHCpy3, updated setup.py;
  did the same for PHCpy2, the python2 version of phcpy.
  Added on section in the Sphinx documentation.

Thu 26 May 2016 : prepared version 0.4.7 of phcpy.

Sun 22 May 2016 : added lrhomprob.py to the PHCpy3/examples directory.

Fri 20 May 2016 : improved interface to Littlewood-Richardson homotopies
  in python2 version, the file schubert.py in PHCpy2/phcpy.
  Also fixed the corresponding schubert.py in PHCpy3/phcpy.
  Prepared version 0.4.6 updating conf.py in doc, __init__.py in phcpy,
  and setup.py in PHCpy2 and PHCpy3.

Sat 30 Apr 2016 : added is_real and filter_real function to the solutions
  module in PHCpy2 and PHCpy3, with better documentation in welcome.rst
  and blackbox.rst.  Prepared version 0.4.4 of phcpy.

Tue 29 Mar 2016 : updated the documentation of the deflate in blackbox.rst
  of both PHCpy2 and PHCpy3 to illustrate the tolerance of the rank.

Sat 26 Mar 2016 : updated the deflate functions in the solver module for
  the additional parameters and tolerances, both in PHCpy2 and PHCpy3.

Fri 25 Mar 2016 : extended the newton_step function in the solver module
  so it should work for overdetermined polynomial systems.
  Made updates to the interface module for overdetermined Laurent systems.

Thu 24 Mar 2016 : extended the deflate functions in the solver module
  to work for overdetermined polynomial systems.

Fri 18 Mar 2016 : updates for version 0.4.2, setup.py, __init__.py and conf.py
  in the documentation.

Tue 23 Feb 2016 : added detailed installation instructions to welcome.rst
  in PHCpy2/doc/source and PHCpy3/doc/source.

Fri 19 Feb 2016 : updated setup.py, __init__.py, and conf.py for 0.4.1
  of phcpy, both for python2 and python3.

Wed 17 Feb 2016 : wrote a checkin function for the blackbox solver,
  for both the python2 and python3 versions.

Tue 16 Feb 2016 : added functions to the solver module of PHCpy2 and PHCpy3
  to determine if a polynomial system is square or not.

Fri 12 Feb 2016 : updated __init__.py and setup.py, both in PHCpy2 and
  PHCpy3 for version 0.4.0 of phcpy.

Thu 11 Feb 2016 : updated the tropisms.py in PHCpy2/phcpy for python2.

Wed 10 Feb 2016 : updated test in tropisms.py for 'dd' and 'qd'.

Tue 9 Feb 2016 : random_coefficient_system in solver.py had no branch for
  the quad double precision.  Added test function to tropisms.py that runs
  a polyhedral end game.

Fri 5 Feb 2016 : testing for quaddobl versions of tropisms.py in python3.

Thu 4 Feb 2016 : dobldobl and quaddobl versions of functions in tropisms,
  tested for double double precision with python3.

Tue 2 Feb 2016 : updated tropisms.py with a new function to change the values
  of a stored tropism.

Sun 31 Jan 2016 : added python 2 version of tropisms.py.

Sat 30 Jan 2016 : start of code in a new module tropisms.py.

Sun 17 Jan 2016 : changed setup.py and MANIFEST.in in PHCpy2, with also most
  of the .py files in PHCpy2/phcpy.  Updated setup.py, __init__.py, and
  conf.py for both python2 and python3 versions of phcpy to 0.3.9.

Sat 16 Jan 2016 : Copied the new wrappers in tuning.py for python2,
  in PHCpy2/phcpy.

Fri 15 Jan 2016 : extended the tuning module with wrappers for the parameters
  and settings for the predictor and the corrector in PHCpy3/phcpy.
  Completed the wrappers in tuning.py for python3.

Thu 14 Jan 2016 : new module tuning with the wrappers from trackers
  to tune the parameters of the continuation in PHCpy2 and PHCpy3.
  Fixed bug in trackers, caused by standard making of names.
  Added auto documentation of the functions in the tuning module
  as an extra section to pathtrack.rst, in PHCpy3/doc.

Wed 13 Jan 2016 : started the extension of trackers in PHCpy3/phcpy with
  wrappers to get and set values of the continuation parameters.
  Did the same thing in the trackers module of PHCpy2/phcpy.

Sat 2 Jan 2016 : renamed the directory PHCpy into PHCpy2.  Prepared setup.py,
  __init__.py, and conf.py for version 0.3.8 of phcpy.

Fri 1 Jan 2016 : minor formatting changes in solutions.py both for PHCpy/phcpy
  and PHCpy3/phcpy.  As recommended by pylint, used ast.literal_eval() in
  the module solutions.py.  New documentation in PHCpy/doc with sphinx-1.3.3,
  processed with Python 3.5.

Thu 31 Dec 2015 : new directory PHCpy3 with the version of phcpy for
  Python 3.5.

Mon 28 Dec 2015 : made the tolerances in the membertest in sets.py
  explicit arguments with large default values.  Improved posdimsols.rst,
  modified about.rst, conf.py, __init__.py, and setup.py for 0.3.7.

Sun 27 Dec 2015 : added functions for membership tests to sets.py.
  Fixed type error in the test_member() function of sets.py.
  Started the documentation in posdimsols.rst a section on the
  homotopy membership test.

Thu 24 Dec 2015 : changes in sets.py for renamed functions in phcpy2c.
  More changes in sets.py for muting the monodromy breakup.
  Still more changes in sets.py for making the monodromy breakup verbose.
  Added a paragraph to posdimsols.rst about the factor method in
  double double and quad double precision, updated conf.py, __init__.py,
  and setup.py for version 0.3.6 of phcpy.

Wed 23 Dec 2015 : extended functionality of the monodromy breakup in sets.py
  Made some small change for the verbosity.  Added the reporting of the
  trace grid diagnostics in the monodromy breakup method.

Tue 22 Dec 2015 : improved tests on the monodromy in sets.py.

Mon 21 Dec 2015 : added functions to sets.py to run the monodromy_breakup
  in double double and quad double precision.

Sun 13 Dec 2015 : added functions to sets.py to embed systems with coefficients
  in double double and quad double precision.

Sat 12 Dec 2015 : added factor method to sets.py, which calls the
  methods monodromy_breakup and decomposition, tested by test_factor().
  In the phcpy documentation, added a subsection to posdimsols.rst

Fri 11 Dec 2015 : for version 0.3.5, adjusted setup.py, __init__.py and
  the conf.py in the documentation.

Sat 28 Nov 2015 : adjusted the checkout function for the convex hulls of
  polytopes in polytopes.py for points that are not vertices.
  Added a function to collect the edges of the facets.
  For 3-dimensional polytopes, the test computes the Euler characteristic.

Thu 26 Nov 2015 : added a checkout function to polytopes.py to check the
  correctness of the computed inner normals to the facets.

Wed 25 Nov 2015 : a checkout function is added to check the correctness of
  the planar convex hull function, in polytopes.py.  Added dim as argument
  to the test_convex_hull().  Also added parameters for the number of points
  and the range of the values for the coordinates.

Tue 24 Nov 2015 : added a function to polytopes.py to check the input type
  of the arguments to the convex hull function.  Fixed errors in polytopes.py
  reported by pylint and added a function 'initial_support'.

Mon 23 Nov 2015 : for version 0.3.4, updated setup.py, __init__.py and the
  conf.py in the documentation.

Sun 22 Nov 2015 : updated the documentation of positive dimensional solutions
  with a simple illustration of diagonal homotopies.  Added a picture about
  the design of phcpy to modphcpy2c.rst.  Documentation about the interface
  module is moved towards the description of the module phcpy2c.
  Integrated the documentation for the interesting example with the
  families into one restructured text chapter.

Sat 21 Nov 2015 : added an illustration of cascade_step to posdimsols.rst,
  on the illustrative example of a sphere, twisted cubic, and a point.

Fri 20 Nov 2015 : modified the diagonal solvers in sets.py to use the top
  dimension as needed in the collapsing of the diagonal.

Thu 12 Nov 2015 : updated witness_set_of_hypersurface in sets.py with an
  extra argument to select the precision.

Tue 10 Nov 2015 : extended sets.py with function to define the diagonal
  homotopies in double double and quad double precision.
  Versions of the diagonal solver in sets.py are available for double double
  and quad double precision.

Mon 9 Nov 2015 : modified sets.py for py2c_standard_diagonal_homotopy,
  renamed from the old py2c_create_diagonal_homotopy.

Sun 8 Nov 2015 : added the function standard_diagonal_solver to sets.py.

Sat 7 Nov 2015 : fixed bugs in sets.py with the standard_double_cascade_steps
  and started introduction of diagonal homotopies.

Fri 6 Nov 2015 : updated __init__.py, setup.py, and conf.py for version 0.3.3
  of phcpy.

Thu 5 Nov 2015 : extended sweepers.py with tests on the real sweep,
  and with double double and quad double versions for the real sweep.
  Started writing documentation on the sweepers module, with a new
  sweep.rst and a picture in circles.png.

Wed 4 Nov 2015 : in sweepers.py adjusted the names to the calls of the 
  functions that run the sweep, as they got changed in phcpy2c.
  Extended sweepers.py with functions to do a real parameter sweep.

Mon 2 Nov 2015 : in interface.py, added an optional argument nbvar to store
  systems that are not square with the parameter number of variables, in case
  that is different from the number of equations.  Adjusted sweepers.py
  so no trick is needed when storing the family of polynomial systems.

Sun 1 Nov 2015 : added skeleton for a new module sweepers.py, updating
  setup.py, to track paths defined by a sweep homotopy.
  Provided routines for a sweep in the module sweepers.py.

Fri 23 Oct 2015 : in schubert.py, changed parameter verify into vrfcnd
  for pylint warnings; improved random_trinomials() in solver.py.
  Some small changes in trackers.py for pylint warnings.

Thu 22 Oct 2015 : extended schubert.py to run L-R homotopies in double double
  and quad double precision.  
  For version 0.3.2, updated setup.py, __init__.py, and conf.py.

Wed 7 Oct 2015 : updated setup.py, __init__.py, and conf.py for version 0.3.1.

Sun 27 Sep 2015 : to solver.py extended the solve() with an extra option
  to set the working precision, to double, double double, or quad double.

Thu 24 Sep 2015 : in preparation for 0.3.0, updated setup.py, __init__.py,
  and conf.py, added reference to GPU paper in references.rst.

Mon 31 Aug 2015 : updated setup.py, __init__.py and conf.py for 0.2.9.
  Added a sentence to the history.rst to note that 0.2.9 coincides with
  release 2.4 of PHCpack.  Added the content of the runcyc10d.py of the
  examples directory to the documentation in pathtrack.rst.

Sun 30 Aug 2015 : extended ade_double_track in trackers.py with gamma option,
  added gpu_double_track to trackers.py, and created versions for double
  double and quad double precision.

Thu 27 Aug 2015 : fixed an error in the standard_double_track of trackers
  and added a function (with a test) to trackers that calls ade_manypaths_d
  to use algorithmic differentiation in the trackers in double precision.

Fri 31 Jul 2015 : updated setup.py and __init__.py for version 0.2.8.
  Replace input by raw_input in schubert.py.  Changed solutions.py
  for a pylint warning (unused variables).  Replaced fixedGamma by
  fixedgamma in trackers.py, also because of a pylint complaint.
  Added scaling.py to the demo folder in PHCpy.
  Updated the conf.py and blackbox.rst in the documentation.

Thu 30 Jul 2015 : test_scale() in solver.py works.

Wed 29 Jul 2015 : extended solver.py with a function to scale a polynomial
  system with standard double precision arithmetic.

Tue 28 Jul 2015 : changes in trackers.py for name changes in py2c functions.
  Also made changes to interface.py, solver.py, schubert.py, and sets.py
  for changed py2c_clear_solutions into py2c_clear_standard_solutions,
  and other name changes involving standard double precision.
  Also maps.py changed for later name changes in py2c functions.

Mon 20 Jul 2015 : added demo directory to the PHCpy distribution.

Wed 8 Jul 2015 : fixed bug in the test of sets.py, because the 
  py2c_solve_by_standard_homotopy_continuation() now requires the
  number of tasks as input parameter.  Fixed spelling error in the
  documentation, in posdimsols.rst.

Tue 7 Jul 2015 : added extra input parameter to the solve in solver.py.

Thu 25 Jun 2015 : updated __init__.py, setup.py for version 0.2.7.
  Then added one paragraph to the documentation for the py2c_get_seed
  and updated the version number of the documentation.

Wed 24 Jun 2015 : interface.py has faster load_*_solutions functions.

Fri 22 May 2015 : updated PHCpy for version 0.2.6.

Thu 21 May 2015 : improved Sphinx documentation with proper use of toctree
  and splitted index.rst into more meaningful subtitles.

Thu 26 Mar 2015 : new function initial_form in polytopes.py to compute the
  initial form of a Laurent polynomial system.

Wed 25 Mar 2015 : added support function to polytopes.py to compute the
  support of a Laurent polynomial.

Wed 25 Feb 2015 : updated trackers.py with next_varbprec_solution.

Tue 24 Feb 2015 : add initialization with solution for the variable precision
  path tracker with a generator.

Mon 23 Feb 2015 : initializer for variable precision tracker with generator
  added to trackers.py.

Tue 23 Dec 2014 : added more benchmark test cases to the degree computation
  list of backelin.py.

Sun 21 Dec 2014 : extended backelin.py with the degree computation of a list
  of benchmark systems.

Sat 20 Dec 2014 : extended backelin.py with degree computation.

Fri 19 Dec 2014 : linear instead of double indexing in pierisystems.py
  and generation of pairs of systems of hypersurface Pieri conditions.

Thu 18 Dec 2014 : updated pierisystems.py with path tracking between
  systems in a sequence of Pieri conditions.

Wed 17 Dec 2014 : updated pierisystems.py with computation of solutions
  and special plane to start the Pieri homotopy.

Tue 16 Dec 2014 : new script pierisystems.py in examples directory of PHCpy.

Mon 15 Dec 2014 : updated script backelin.py to generate generic points
  on the components of cyclic n-roots as defined by the tropical version
  of Backelin's Lemma, with one sampled point in a witness set.

Thu 27 Nov 2014 : fixed bug in documentation regarding refactoring of the
  solver module to the interface module, moving an example of a session
  to the documentation section on the interface module.

Wed 26 Nov 2014 : in solver.py took the failure codes into account
  when storing polynomials or solutions and computing the mixed_volume.
  New module interface.py with routines factored out from solver,
  which caused changes in sets.py, trackers.py, schubert.py, __init__.py,
  and updated setup.py for version 0.2.5.

Tue 25 Nov 2014 : minor changes in solver.py and schubert.py 
  for pylint warnings.  Fixed bugs in sets.py, found by pylint.

Mon 24 Nov 2014 : added Newton_steps function to solver.py.

Fri 31 Oct 2014 : updated __init__.py, setup.py for version 0.2.4.

Tue 16 Sep 2014 : forgot to clear the solutions container in the running
  of the Littlewood-Richardson homotopy function in the file schubert.py.
  Updated the Sphinx documentation with example sessions.

Fri 12 Sep 2014 : added mixed volume function to polytopes with test.
  Adjusted setup.py, __init__.py, and conf.py for version 0.2.3 of phcpy.

Mon 8 Sep 2014 : extended polytopes with function to compute the
  convex hull in 3-space and in 4-space, with a test function.

Thu 4 Sep 2014 : new Python package polytopes, updated setup.py.

Sun 31 Aug 2014 : updated READ_ME, __init__.py, setup.py, and conf.py
  for version 0.2.2 of phcpy.

Sat 30 Aug 2014 : extended solver.py with usolve functions to compute all
  roots of a univariate polynomial at various precision levels.

Sun 10 Aug 2014 : updated __init__.py, setup.py, and conf.py for 0.2.1
  version of phcpy.

Fri 8 Aug 2014 : upgraded the solver.py with deflate operations in
  double double and quad double precision and extended test_deflate.

Wed 30 Jul 2014 : added newton_laurent_step in solver.py with test routines
  for Newton's method on ordinary polynomial and Laurent polynomial systems.
  Upgraded READ_ME, __init__.py and setup.py to version 0.2.0.
  Upgraded conf.py in doc/source to version 0.2.0.

Tue 29 Jul 2014 : renaming of Newton_step into standard_Newton_step caused
  changes in the module solver.py of phcpy.

Mon 28 Jul 2014 : added store/load operations for systems of Laurent
  polynomials with multiprecision coefficients.

Thu 24 Jul 2014 : new store/load operations for Laurent systems to solver.

Tue 22 Jul 2014 : added permute operations to solver.py for systems with
  coefficients in double double and quad double precision.

Fri 18 Jul 2014 : extended solver.py with polyhedral homotopies in 
  double double and quad double precision.

Mon 30 Jun 2014 : updates in __init__.py, setup.py for version 0.1.9.

Sat 28 Jun 2014 : new directory "examples" in PHCpy directory with the
  randlrhom.py module.

Wed 25 Jun 2014 : modified seed constant in examples.py
  and added random_system function solver.py.

Thu 5 Jun 2014 : schubert.py now also shows the coordinates of the flags
  and adjusted __init__.py for the version number 0.1.8.
  Updated setup.py and README.txt for version 0.1.8.

Wed 4 Jun 2014 : added littlewood_richardson_homotopies to schubert.py,
  and a simple test function test_lrhom.

Fri 23 May 2014 : added resolve_schubert_conditions to schubert.py.

Thu 27 Mar 2014 : fixed_gamma option added to trackers.py.

Thu 6 Mar 2014 : added multitasking to trackers.py, the test script is in
  Tests/testpoco.py.

Mon 23 Dec 2013 : renamed phcsols, phcsets, phcmaps into solutions, sets,
  and maps respectively, changing schubert.py.  Also updated __init__.py,
  the documentation in doc/source and conf.py (for version 0.1.7).
  Updated PHCpy/setup.py.  Added nbodyeqs to families.py.

Thu 19 Dec 2013 : updated documentation and schubert.py.

Wed 18 Dec 2013 : documentation day!  The extra module trackers.py created
  severe inconsistencies in the index.rst in the PHCpy/doc/source directory.
  Modified solver.py and trackers.py for inserting _standard_ into the
  load and store operations for systems and solutions.

Tue 17 Dec 2013 : added three functions to solver.py to compute m-homogeneous
  Bezout numbers and construct m-homogeneous start systems.
  Separate module trackers.py (with code taken from solver.py).
  Updated setup.py for the trackers.py and the version number: 0.1.6.
  Also modified schubert.py and __init__.py.
  Added the chandra function to the families.py, modified the documentation.

Fri 6 Dec 2013 : changed almost all .py files so that localized run works,
  removing the "import phcpy" and "from phcpy import" constructions.

Wed 4 Dec 2013 : the auto tuning of the continuation parameters for the
  multiprecision tracker needs the number of decimal places.
  Added next() for multiprecision to solver.py.  Added to families.py
  the function Pieri_problem() to generate Pieri intersection problems,
  after extending schubert.py with the function random_complex_matrices.

Tue 3 Dec 2013 : added first version of multiprecision_track to solver.py.

Thu 28 Nov 2013 : extended solver.py with multiprecision operations on
  systems, solutions, and a newton_step in arbitrary precision.

Wed 25 Sep 2013 : fixed a bug in phcsols.py and updated documentation
  string in families.py.  Documented generators in the index.rst and
  adjusted conf.py in the Sphinx documentation for version 0.1.4.

Tue 24 Sep 2013 : added routines to phcpy.solver for path trackers with
  a generator, tested by test_next_track(), __init__.py ready for 0.1.4.

Wed 18 Sep 2013 : moved all test scripts into the directory Tests.
  Touched phcmaps.py for chasing a bug.

Tue 17 Sep 2013 : added references to families.py.  Added puretopdim as
  option to the solver in phcmaps.py; upgraded version number to 0.1.3
  in setup.py and __init__.py.

Thu 5 Sep 2013 : improved phcmaps.py with pylint and functions to return
  string representations of monomial maps.  Updated the index.rst in doc,
  ready for release 0.1.2, scheduled for tomorrow...

Wed 4 Sep 2013 : more adjustments in phcmaps.py, added two lines of
  documentation in __init__.py; added adjacent minors to families.py.

Tue 3 Sep 2013 : new module phcmaps.py, __init__.py has version 0.1.2.

Fri 30 Aug 2013 : updated schubert.py, phcsets.py, phcwulf.py, and
  solver.py so pylint gives almost no warnings.
  The rating of pylint *py has now increased to 9.73/10.

Thu 29 Aug 2013 : updated solver.py and __init__.py to get a global rating
  of 9.14/10.  Also updated phcsets.py.

Wed 28 Aug 2013 : modified schubert.py to raise the score to 8.41/10
  and improved phcsets.py and phcwulf.py as well.

Tue 27 Aug 2013 : modified solver.py so the code has pylint score of 8.77/10
  and examples.py now has an almost perfect pylint score of 9.93.
  Modified __init__.py, solver.py, phcwulf.py and schubert.py so that
  pylint *py gives a global score of 7.52/10.

Mon 26 Aug 2013 : to improve the pylint score for phcsols.py, lengthened
  the names of some of the variables, e.g.: "sol" instead of "s".
  Modified solver.py so its pylint score is now positive.

Sat 24 Aug 2013 : running pylint on setup.py warns for docstring and I put
  the comments previously preceded by # into a docstring.
  On families.py raised the pylint score to 5+ from a negative score.
  Also edited phcsols.py, schubert.py, and phcsets.py.

Wed 21 Aug 2013 : added __version__ to __init__.py of phcpy

Thu 8 Aug 2013 : made directory PHCpy to prepare for packaged distribution.

Wed 20 Feb 2013 : added witness_set_of_hypersurface function to phcsets.py.
  Added function noon to families.py.

Tue 19 Feb 2013 : new families.py exports the function cyclic.

Fri 15 Feb 2013 : added drop functions to phcsets.py and test_cascade.

Thu 14 Feb 2013 : added filters to phcsols.py and cascade_step to phcsets.py,
  made a change in phcpy.py.

Wed 13 Feb 2013 : added a session on the use of embed on twisted cubic.

Tue 12 Feb 2013 : extended the track functions in phcpy.py with the
  optional gamma constant.

Sun 10 Feb 2013 : added a deflate() and test_deflate() to phcpy.py.
  Function total_degree_start_system() added to phcpy.py.
  Used this function to solve the "mickey" system in the documentation.
  Added make_solution function to phcsols.py.

Thu 7 Feb 2013 : added total degree to phcpy.py and added one interactive
  session illustrating the root counts to the documentation.
  Fixed some typos in examples.py and updated the documentation.
  Added tune_track_parameters function to phcpy.py.

Wed 6 Feb 2013 : extended phcpy.py with double double and quad double track.

Fri 1 Feb 2013 : added {store,load}_{dobl,quad}dobl_solutions,
  store_{dobl,quad}dobl_system to phcpy.py, for a newton_step
  with double double and quad double arithmetic.

Sun 27 Jan 2013 : adding clears at the start of test_polyhedral_homotopy
  in phcpy.py allows for successful consecutive runs.

Tue 15 Jan 2013 : added linear_product_root_count function to phcpy.py,
  and a random_linear_product_system.

Fri 28 Dec 2012 : phcsets.py has the same functionality as lib_factor.c.

Thu 27 Dec 2012 : added monodromy_breakup to phcsets.py.

Wed 19 Dec 2012 : added Newton_step to phcpy.py and changed schubert.py.
  Wrapping of celcon led to random_coefficient_system in phcpy.py.

Tue 18 Dec 2012 : updates in schubert.py

Thu 13 Dec 2012 : the run_pieri_homotopies gets system and solutions
  from the containers which can then be tested with phcsols.

Wed 12 Dec 2012 : random input data is generated by schubert.py
  and passed to the run_Pieri_homotopies method.

Tue 11 Dec 2012 : new schubert.py exports Pieri root count.

Sun 9 Dec 2012 : new phcsets.py to manipulate algebraic sets.

Wed 5 Dec 2012 : extended phcpy.py with test_track, improved phcsols.py.

Tue 4 Dec 2012 : updates in phcpy.py and examples.py.
  Added a silent flag to phcpy.solve and stable flag to phcpy.mixed_volume.

Sun 2 Dec 2012 : added banners to the tests in examples.py.

Sat 1 Dec 2012 : added "binomials", "d1", "game4two", katsura6", "noon3",
  "rps10", and "tangents" to examples.py, so now there are 10 examples.

Fri 30 Nov 2012 : added "stewgou40" to examples.py and then discovered
  that this example no longer works!

Thu 29 Nov 2012 : added "test" function to phcpy.p and fixed phcwulf.py
  on dezon: closing the server before all handler threads are finished
  is a very bad thing to do!  Replaced "remove_padding" by "strip".
  Added examples.py and the doc directory to generate documentation
  with sphinx.

Wed 28 Nov 2012 : updated makefile_unix so the python interface works
  on Redhat 6.3 with python2.6 and GNAT GPL 2012.  New module phcsols.py
  to convert solutions in PHCpack string format to dictionaries.

Tue 6 Sep 2011 : updated makefile_mac so the python interface works
  on MacOS X!

Wed 30 Jul 2008 : added line to print number of solutions client sends
  in phcwulf.py to track down a bug.

Thu 5 Jun 2008 : random_trinomials() added to phcpy.py and used in
  the server in phcwulf.py.  Extended phcwulf.py with multithreading.

Tue 3 Jun 2008 : added a basic track function to phcpy.py.

Mon 2 Jun 2008 : phcwulf.py export basic client/server routines to solve
  many polynomial systems in a distributed manner.
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