prep for pypi

Author: eltrompetero

README.md

@@ -30,7 +30,7 @@ source.  Download the latest release from GitHub. Make sure that you are running
 3.7 or higher.  Inside the top directory "coniii", you must run 
 ```bash
 $ cd dist
-$ pip install coniii-2.0.0-py3-none-any.whl 
+$ pip install coniii-2.1.1-py3-none-any.whl 
 ```
 or the appropriate wheel file version.  
 

RELEASE_NOTES

@@ -23,6 +23,14 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 
 
+v2.1.1 (Released 2019/11/29) 
+----------------------------------------------------
+- Added convenient multiplier transformation functions utils.vec2mat and
+  utils.mat2vec.
+- Output from ClusterExpansion.solve is of different order when
+  full_output=True. Now, entropy estimate comes second instead of first to
+  maintain consistency for when full_output=False.
+
 v2.1.0 (Released 2019/11/28) 
 ----------------------------------------------------
 - Fixed bug in Pseudo. It was using a non-standard algorithm for solving the

coniii/version.py

@@ -19,4 +19,4 @@
 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
-version = '2.1.0'
+version = '2.1.1'

dist/coniii-2.1.0-py3-none-any.whl dist/coniii-2.1.1-py3-none-any.whldist/coniii-2.1.0-py3-none-any.whl renamed to dist/coniii-2.1.1-py3-none-any.whl

@@ -121,25 +121,31 @@
 <dd><p>threshold : float
 meanFieldRef : bool, False</p>
 <blockquote>
-<div><p>Expand about mean-field reference</p>
+<div><p>Expand about mean-field reference.</p>
 </div></blockquote>
 <dl class="simple">
-<dt>independentRef<span class="classifier">bool, True</span></dt><dd><p>Expand about independent reference</p>
+<dt>independentRef<span class="classifier">bool, True</span></dt><dd><p>Expand about independent reference.</p>
 </dd>
-<dt>priorLmbda<span class="classifier">float, 0.</span></dt><dd><p>Strength of non-interacting prior</p>
+<dt>priorLmbda<span class="classifier">float, 0.</span></dt><dd><p>Strength of non-interacting prior.</p>
 </dd>
 <dt>meanFieldPriorLmbda<span class="classifier">float, None</span></dt><dd><p>Strength of non-interacting prior in mean field calculation (defaults to
-priorLmbda)</p>
+priorLmbda).</p>
 </dd>
 </dl>
 <dl class="simple">
-<dt>With full_output=False, returns</dt><dd><p>J           : Estimated interaction matrix</p>
+<dt>ndarray</dt><dd><p>Solved multipliers (parameters). For Ising problem, these can be converted
+into matrix format using utils.vec2mat.</p>
 </dd>
-<dt>With full_output=True, returns</dt><dd><p>ent         : Estimated entropy
-J           : Estimated interaction matrix
-clusters    : List of clusters
-deltaSdict  : 
-deltaJdict  :</p>
+<dt>float (optional, only if full_output=True)</dt><dd><p>Estimated entropy.</p>
+</dd>
+<dt>ndarray</dt><dd><p>Solved multipliers (parameters). For Ising problem, these can be converted
+into matrix format using utils.vec2mat.</p>
+</dd>
+<dt>list (optional, only if full_output=True)</dt><dd><p>List of clusters.</p>
+</dd>
+<dt>dict (optional, only if full_output=True)</dt><dd><p>deltaSdict</p>
+</dd>
+<dt>dict (optional, only if full_output=True)</dt><dd><p>deltaJdict</p>
 </dd>
 </dl>
 </dd></dl>
@@ -200,7 +206,8 @@
 </dd>
 </dl>
 <dl class="simple">
-<dt>ndarray</dt><dd><p>Solved multipliers (parameters).</p>
+<dt>ndarray</dt><dd><p>Solved multipliers (parameters). For Ising problem, these can be converted
+into matrix format using utils.vec2mat.</p>
 </dd>
 <dt>dict, optional</dt><dd><p>Output from scipy.optimize.root.</p>
 </dd>
@@ -301,7 +308,8 @@
 <p>learn_parameters_kwargs : dict, {‘maxdlamda’:1,’eta’:1}
 generate_kwargs : dict, {}</p>
 <dl class="simple">
-<dt>ndarray</dt><dd><p>Found solution to inverse problem.</p>
+<dt>ndarray</dt><dd><p>Solved multipliers (parameters). For Ising problem, these can be converted
+into matrix format using utils.vec2mat.</p>
 </dd>
 <dt>int</dt><dd><p>Error flag.
 0, converged within given criterion
@@ -507,7 +515,8 @@
 </dd>
 </dl>
 <dl class="simple">
-<dt>ndarray</dt><dd><p>Solution.</p>
+<dt>ndarray</dt><dd><p>Solved multipliers (parameters). For Ising problem, these can be converted
+into matrix format using utils.vec2mat.</p>
 </dd>
 <dt>dict (optional)</dt><dd><p>Output from scipy.optimize.minimize returned if full_output is True.</p>
 </dd>
@@ -601,7 +610,8 @@
 </dd>
 </dl>
 <dl class="simple">
-<dt>ndarray</dt><dd><p>multipliers</p>
+<dt>ndarray</dt><dd><p>Solved multipliers (parameters). For Ising problem, these can be converted
+into matrix format using utils.vec2mat.</p>
 </dd>
 </dl>
 </dd></dl>
@@ -646,7 +656,7 @@
 <dt>min_independent<span class="classifier">bool, True</span></dt><dd><p>** As of v1.0.3, min_independent is the only mode currently supported **
 Each &lt;xi&gt; and &lt;xi xj&gt; residual is treated as independent</p>
 </dd>
-<dt>cooc_cov<span class="classifier">ndarray,None</span></dt><dd><p>** As of v1.0.3, not currently supported **
+<dt>cooc_cov<span class="classifier">ndarray, None</span></dt><dd><p>** As of v1.0.3, not currently supported **
 Provide a covariance matrix for residuals.  Should typically be
 coocSampleCovariance(samples).  Only used if min_covariance and
 min_independent are False.</p>
@@ -655,6 +665,11 @@
 Strength of noninteracting prior.</p>
 </dd>
 </dl>
+<dl class="simple">
+<dt>ndarray</dt><dd><p>Solved multipliers (parameters). For Ising problem, these can be converted
+into matrix format using utils.vec2mat.</p>
+</dd>
+</dl>
 </dd></dl>
 
 </dd></dl>

docs/_build/html/coniii_rst/coniii.solvers.html

@@ -78,6 +78,11 @@
 <code class="sig-prename descclassname">coniii.test_utils.</code><code class="sig-name descname">test_sub_to_ind</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#coniii.test_utils.test_sub_to_ind" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
+<dl class="function">
+<dt id="coniii.test_utils.test_vec2mat">
+<code class="sig-prename descclassname">coniii.test_utils.</code><code class="sig-name descname">test_vec2mat</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#coniii.test_utils.test_vec2mat" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
 </div>
 
 

docs/_build/html/coniii_rst/coniii.test_utils.html

@@ -295,6 +295,21 @@
 </dl>
 </dd></dl>
 
+<dl class="function">
+<dt id="coniii.utils.mat2vec">
+<code class="sig-prename descclassname">coniii.utils.</code><code class="sig-name descname">mat2vec</code><span class="sig-paren">(</span><em class="sig-param">multipliers</em><span class="sig-paren">)</span><a class="headerlink" href="#coniii.utils.mat2vec" title="Permalink to this definition">¶</a></dt>
+<dd><p>Convert matrix form of Ising parameters to a vector.</p>
+<p>This is specific to the Ising model.</p>
+<dl class="simple">
+<dt>multipliers<span class="classifier">ndarray</span></dt><dd><p>Matrix of couplings with diagonal elements as fields.</p>
+</dd>
+</dl>
+<dl class="simple">
+<dt>ndarray</dt><dd><p>Vector of fields and couplings, respectively.</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="function">
 <dt id="coniii.utils.multinomial">
 <code class="sig-prename descclassname">coniii.utils.</code><code class="sig-name descname">multinomial</code><span class="sig-paren">(</span><em class="sig-param">*args</em><span class="sig-paren">)</span><a class="headerlink" href="#coniii.utils.multinomial" title="Permalink to this definition">¶</a></dt>
@@ -427,6 +442,27 @@
 </dl>
 </dd></dl>
 
+<dl class="function">
+<dt id="coniii.utils.vec2mat">
+<code class="sig-prename descclassname">coniii.utils.</code><code class="sig-name descname">vec2mat</code><span class="sig-paren">(</span><em class="sig-param">multipliers</em>, <em class="sig-param">separate_fields=False</em><span class="sig-paren">)</span><a class="headerlink" href="#coniii.utils.vec2mat" title="Permalink to this definition">¶</a></dt>
+<dd><p>Convert vector of parameters containing fields and couplings to a matrix where the
+diagonal elements are the fields and the remaining elements are the couplings. Fields
+can be returned separately with the separate_fields keyword argument.</p>
+<p>This is specific to the Ising model.</p>
+<dl class="simple">
+<dt>multipliers<span class="classifier">ndarray</span></dt><dd><p>Vector of fields and couplings.</p>
+</dd>
+</dl>
+<p>separate_fields : bool, False</p>
+<dl class="simple">
+<dt>ndarray</dt><dd><p>n x n matrix. Diagonal elements are fields <em>unless</em> separate_fields keyword
+argument is True, in which case the diagonal elements are 0.</p>
+</dd>
+<dt>ndarray (optional)</dt><dd><p>Fields if separate_fields keyword argument is True.</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="function">
 <dt id="coniii.utils.xbin_states">
 <code class="sig-prename descclassname">coniii.utils.</code><code class="sig-name descname">xbin_states</code><span class="sig-paren">(</span><em class="sig-param">n</em>, <em class="sig-param">sym=False</em><span class="sig-paren">)</span><a class="headerlink" href="#coniii.utils.xbin_states" title="Permalink to this definition">¶</a></dt>

docs/_build/html/coniii_rst/coniii.utils.html

@@ -54,6 +54,7 @@ <h1 id="index">Index</h1>
  | <a href="#S"><strong>S</strong></a>
  | <a href="#T"><strong>T</strong></a>
  | <a href="#U"><strong>U</strong></a>
+ | <a href="#V"><strong>V</strong></a>
  | <a href="#W"><strong>W</strong></a>
  | <a href="#X"><strong>X</strong></a>
  | <a href="#Z"><strong>Z</strong></a>
@@ -409,6 +410,8 @@ <h2 id="M">M</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="coniii_rst/coniii.mean_field_ising.html#coniii.mean_field_ising.m">m() (in module coniii.mean_field_ising)</a>
+</li>
+      <li><a href="coniii_rst/coniii.utils.html#coniii.utils.mat2vec">mat2vec() (in module coniii.utils)</a>
 </li>
       <li><a href="coniii_rst/coniii.solvers.html#coniii.solvers.MCH">MCH (class in coniii.solvers)</a>
 </li>
@@ -617,6 +620,8 @@ <h2 id="T">T</h2>
       <li><a href="coniii_rst/coniii.test_utils.html#coniii.test_utils.test_sub_to_ind">test_sub_to_ind() (in module coniii.test_utils)</a>
 </li>
       <li><a href="coniii_rst/coniii.test_samplers.html#coniii.test_samplers.test_test_sample_ising">test_test_sample_ising() (in module coniii.test_samplers)</a>
+</li>
+      <li><a href="coniii_rst/coniii.test_utils.html#coniii.test_utils.test_vec2mat">test_vec2mat() (in module coniii.test_utils)</a>
 </li>
       <li><a href="coniii_rst/coniii.pseudo_inverse_ising.html#coniii.pseudo_inverse_ising.testDerivatives">testDerivatives() (in module coniii.pseudo_inverse_ising)</a>
 </li>
@@ -655,6 +660,14 @@ <h2 id="U">U</h2>
   </ul></td>
 </tr></table>
 
+<h2 id="V">V</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="coniii_rst/coniii.utils.html#coniii.utils.vec2mat">vec2mat() (in module coniii.utils)</a>
+</li>
+  </ul></td>
+</tr></table>
+
 <h2 id="W">W</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>