fixes for v2.3.0

touched up readme for both PyPI and GH updated release notes updated doc updated usage guide checked that tests ran fine
eltrompetero · May 12, 2020 · 0d48825 · 0d48825
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diff --git a/README.md b/README.md
@@ -2,20 +2,20 @@
 
 # Convenient Interface to Inverse Ising
 
-**ConIII is now on version 2. Major interface updates may break code compatibility.  See
-[release notes](https://github.com/eltrompetero/coniii/blob/py3/RELEASE_NOTES "release
-notes").**
+**ConIII is now on version 2. Major interface updates may break code compatibility from
+version 1.  See [release
+notes](https://github.com/eltrompetero/coniii/blob/py3/RELEASE_NOTES "release notes").**
 
 ConIII is a Python package for solving maximum entropy problems with a focus on the
 pairwise maximum entropy model, also known as the inverse Ising problem. Support for
-Python 3.7.4 and higher only.
+Python 3.7.5 and higher.
 
 If you use ConIII for your research, please consider citing the following:
 > Lee, E.D. and Daniels, B.C., 2019. Convenient Interface to Inverse Ising (ConIII): A
 > Python 3 Package for Solving Ising-Type Maximum Entropy Models. Journal of Open Research
 > Software, 7(1), p.3. DOI: http://doi.org/10.5334/jors.217.
 
-The paper also contains an overview of the module. For code documentation, see
+The paper also contains an overview of the modules. For code documentation, see
 [here](https://eddielee.co/coniii/index.html "Documentation").
 
 ## Installation
@@ -27,9 +27,9 @@ $ pip install coniii
 We highly recommend the use of virtual environments as supported through Anaconda to
 manage this package and associated ones that need to be installed.
 
-If you have trouble using `pip` and PyPI, then you can always build this package from
+If you have trouble using `pip`, then you can always build this package from
 source.  Download the latest release from GitHub. Make sure that you are running Python
-3.7 or higher.  Inside the top directory "coniii", you must run 
+3.7.5 or higher.  Inside the top directory "coniii", you must run 
 ```bash
 $ ./pypi_compile.sh
 $ pip install dist/*.whl
@@ -66,7 +66,7 @@ variable to include this path. Alternatively, you can modify the environment pat
 variables LIBRARY_PATH and LD_LIBRARY_PATH. For a few more hints, see DEVREADME or open an
 issue!
 
-#### Setting up analytic solution for systems *N > 9*
+#### Setting up exact solution for systems *N > 9*
 If you would like to use the `Enumerate` solver for system sizes greater than 9 spins, you
 must run enumerate.py to write those files yourself. This can be run from the install
 directory.  If you do not know where the installation directory is, you can find it by
@@ -88,9 +88,9 @@ for the Ising model in the {0,1} basis. On the other hand,
 $ python enumerate.py [N] 1
 ```
 
-specifies that the system should be written for the {-1,1} basis. Note that the solver
-uses the {-1,1} basis. For more details, see the `__main__` block at the end of the file
-enumerate.py.
+specifies that the system should be written for the {-1,1} basis. Note that the package
+uses the {-1,1} basis by default. For more details, see the `__main__` block at the end of
+the file enumerate.py.
 
 ## Quick guide (with Jupyter notebook)
 
@@ -157,7 +157,7 @@ $ pip install matplotlib 'multiprocess>=0.70.5,<1' matplotlib scipy 'numpy>=1.15
 ## Troubleshooting
 
 This package is only maintained for Python 3 as of v1.0.2 and has only been tested for
-Python 3.7.4 and 3.7.5. Check which version of Python you are running in your terminal
+Python 3.7.5. Check which version of Python you are running in your terminal
 with 
 ```bash
 $ python --version
@@ -167,9 +167,6 @@ ConIII has been tested on the following systems
 * Ubuntu 18.04.1
 * Mac OS X 10.15 (Catalina)
 
-multiprocess module problems: `n_cpus` kwarg can be set to 0 or 1 when the algorithm class
-instance is declared.  This will disable the parallel computing functionality.
-
 ### Support
 
 Please file an issue on the GitHub if you have any problems or feature requests. Provide a

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
@@ -23,7 +23,7 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 
 
-v2.3.0 (Scheduled release 2020/04)
+v2.3.0 (Released 2020/05)
 ----------------------------------------------------
 - Sped up Metropolis sampling using Boost C++ extension. Up to 1000x speedup
   achievable compared to Python version. This must be compiled separately and is

diff --git a/coniii/models.py b/coniii/models.py
@@ -54,7 +54,7 @@ def setup_sampler(self,
 
         self.sampleSize = sample_size
 
-        if sample_method=='metropolis' and type(self) is Ising:
+        if sample_method=='metropolis' and (type(self) is Ising or type(self) is Triplet):
             self.sampleMethod = sample_method
             self.sampler = Metropolis( self.n, self.multipliers, self.calc_e,
                                        n_cpus=self.nCpus,

diff --git a/coniii/samplers.py b/coniii/samplers.py
@@ -1613,7 +1613,7 @@ def sample_metropolis(self, sample0, E0,
                           rng=None,
                           flip_site=None,
                           calc_e=None):
-        """Metropolis sampling given an arbitrary sampling function.
+        """Metropolis sampling given an arbitrary energy function.
 
         Parameters
         ----------

diff --git a/coniii/utils.py b/coniii/utils.py
@@ -1175,7 +1175,7 @@ def calc_observables(X, k=k):
         Y = np.zeros((len(X), n*k+n*(n-1)//2), dtype=np.int8)
 
         # average orientation (magnetization)
-        # note that fields for the third state are set to 0 by default
+        # note that fields for the third state are often set to 0
         counter = 0
         for i in range(k):
             for j in range(n):

diff --git a/coniii/version.py b/coniii/version.py
@@ -1,6 +1,6 @@
 # MIT License
 # 
-# Copyright (c) 2019 Edward D. Lee, Bryan C. Daniels
+# Copyright (c) 2020 Edward D. Lee, Bryan C. Daniels
 # 
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

diff --git a/docs/_build/html/coniii_rst/coniii.enumerate.html b/docs/_build/html/coniii_rst/coniii.enumerate.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
     <title>coniii.enumerate module &#8212; ConIII 1.1.9 documentation</title>
@@ -250,7 +250,7 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2018, Edward D. Lee, Bryan C. Daniels.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.3</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
       |

diff --git a/docs/_build/html/coniii_rst/coniii.general_model_rmc.html b/docs/_build/html/coniii_rst/coniii.general_model_rmc.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
     <title>coniii.general_model_rmc module &#8212; ConIII 1.1.9 documentation</title>
@@ -94,7 +94,7 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2018, Edward D. Lee, Bryan C. Daniels.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.3</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
       |

diff --git a/docs/_build/html/coniii_rst/coniii.html b/docs/_build/html/coniii_rst/coniii.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
     <title>coniii package &#8212; ConIII 1.1.9 documentation</title>
@@ -140,7 +140,7 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2018, Edward D. Lee, Bryan C. Daniels.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.3</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
       |

diff --git a/docs/_build/html/coniii_rst/coniii.ising.automaton.html b/docs/_build/html/coniii_rst/coniii.ising.automaton.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
     <title>coniii.ising.automaton module &#8212; ConIII 1.1.9 documentation</title>
@@ -142,7 +142,7 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2018, Edward D. Lee, Bryan C. Daniels.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.3</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
       |

diff --git a/docs/_build/html/coniii_rst/coniii.ising.html b/docs/_build/html/coniii_rst/coniii.ising.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
     <title>coniii.ising package &#8212; ConIII 1.1.9 documentation</title>
@@ -114,7 +114,7 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2018, Edward D. Lee, Bryan C. Daniels.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.3</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
       |

diff --git a/docs/_build/html/coniii_rst/coniii.ising.test_automaton.html b/docs/_build/html/coniii_rst/coniii.ising.test_automaton.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
     <title>coniii.ising.test_automaton module &#8212; ConIII 1.1.9 documentation</title>
@@ -104,7 +104,7 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2018, Edward D. Lee, Bryan C. Daniels.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.3</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
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diff --git a/docs/_build/html/coniii_rst/coniii.mc_hist.html b/docs/_build/html/coniii_rst/coniii.mc_hist.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
     <title>coniii.mc_hist module &#8212; ConIII 1.1.9 documentation</title>
@@ -94,7 +94,7 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2018, Edward D. Lee, Bryan C. Daniels.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.3</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
       |

diff --git a/docs/_build/html/coniii_rst/coniii.mean_field_ising.html b/docs/_build/html/coniii_rst/coniii.mean_field_ising.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
     <title>coniii.mean_field_ising module &#8212; ConIII 1.1.9 documentation</title>
@@ -329,7 +329,7 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2018, Edward D. Lee, Bryan C. Daniels.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.3</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
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diff --git a/docs/_build/html/coniii_rst/coniii.pseudo_inverse_ising.html b/docs/_build/html/coniii_rst/coniii.pseudo_inverse_ising.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
     <title>coniii.pseudo_inverse_ising module &#8212; ConIII 1.1.9 documentation</title>
@@ -158,7 +158,7 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2018, Edward D. Lee, Bryan C. Daniels.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.3</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
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diff --git a/docs/_build/html/coniii_rst/coniii.samplers.html b/docs/_build/html/coniii_rst/coniii.samplers.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
     <title>coniii.samplers module &#8212; ConIII 1.1.9 documentation</title>
@@ -85,7 +85,7 @@
 
 <dl class="py method">
 <dt id="coniii.samplers.Heisenberg3DSampler.sample_energy_min">
-<code class="sig-name descname">sample_energy_min</code><span class="sig-paren">(</span><em class="sig-param">nFixed=0</em>, <em class="sig-param">rng=RandomState(MT19937) at 0x7FDE1722E5A0</em>, <em class="sig-param">initialState=None</em>, <em class="sig-param">method='powell'</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#coniii.samplers.Heisenberg3DSampler.sample_energy_min" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">sample_energy_min</code><span class="sig-paren">(</span><em class="sig-param">nFixed=0</em>, <em class="sig-param">rng=RandomState(MT19937) at 0x7F4DCC0E07C0</em>, <em class="sig-param">initialState=None</em>, <em class="sig-param">method='powell'</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#coniii.samplers.Heisenberg3DSampler.sample_energy_min" title="Permalink to this definition">¶</a></dt>
 <dd><p>Find local energy minimum given state in angular form. Angular representation
 makes it easy to be explicit about constraints on the vectors.</p>
 <dl class="simple">
@@ -791,7 +791,7 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2018, Edward D. Lee, Bryan C. Daniels.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.3</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
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diff --git a/docs/_build/html/coniii_rst/coniii.solvers.html b/docs/_build/html/coniii_rst/coniii.solvers.html
@@ -1,7 +1,7 @@
 
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-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
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     <meta charset="utf-8" />
     <title>coniii.solvers module &#8212; ConIII 1.1.9 documentation</title>
@@ -781,7 +781,7 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2018, Edward D. Lee, Bryan C. Daniels.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.3</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
       |

diff --git a/docs/_build/html/coniii_rst/coniii.test_samplers.html b/docs/_build/html/coniii_rst/coniii.test_samplers.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
     <title>coniii.test_samplers module &#8212; ConIII 1.1.9 documentation</title>
@@ -119,7 +119,7 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2018, Edward D. Lee, Bryan C. Daniels.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.3</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
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diff --git a/docs/_build/html/coniii_rst/coniii.test_solvers.html b/docs/_build/html/coniii_rst/coniii.test_solvers.html
@@ -1,7 +1,7 @@
 
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-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
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     <meta charset="utf-8" />
     <title>coniii.test_solvers module &#8212; ConIII 1.1.9 documentation</title>
@@ -121,7 +121,7 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2018, Edward D. Lee, Bryan C. Daniels.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.3</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
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diff --git a/docs/_build/html/coniii_rst/coniii.test_utils.html b/docs/_build/html/coniii_rst/coniii.test_utils.html
@@ -1,7 +1,7 @@
 
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-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
     <title>coniii.test_utils module &#8212; ConIII 1.1.9 documentation</title>
@@ -145,7 +145,7 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2018, Edward D. Lee, Bryan C. Daniels.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.3</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
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