Update Changelog and __init__ with new version

AdaptivePELE/__init__.py

@@ -1,2 +1,2 @@
-__version__ = "1.6"
+__version__ = "1.6.1"
 name = "AdaptivePELE"

AdaptivePELE/docs/Changelog.rst

@@ -6,20 +6,41 @@ All notable changes to this project will be documented in this file.
 
 The format is based on `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_.
 
-1.x - Unreleased
+
+XXX - Unreleased
 ----------------
 
+New features:
+.............
+
+    - Add possibility to generate cylinder box from pdb
+
+Bug fixes:
+..........
+
+
+Behaviour changes from previous version:
+........................................
+
+    - Allow PELE equilibration to run without a box
+
+1.6.1 - 2019-04-26
+------------------
+
 New features:
 .............
 
     - Add cylindrical box for MD
     - Add script to generate cylindrical box for visualization
+    - Introduce new postprocessing function for MD
 
 Bug fixes:
 ..........
 
     - Fix bug selecting topolgies for odd number of initial conditions
     - Fix bug extracting indexes from topology in MSMClustering
+    - Fix bug in atomset writing PDBs with gaps, now if there are residues with
+      a difference in more than one in the residue number a TER is written 
 
 
 Behaviour changes from previous version:

CHANGELOG.md

@@ -3,17 +3,34 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 
+
 ## [1.x] - Unreleased
 
+### New features:
+
+    - Add possibility to generate cylinder box from pdb
+
+### Bug fixes:
+
+
+### Behaviour changes from previous version:
+
+    - Allow PELE equilibration to run without a box
+
+## [1.6.1] - 2019-04-26
+
 ### New features:
 
     - Add cylindrical box for MD
     - Add script to generate cylindrical box for visualization
+    - Introduce new postprocessing function for MD
 
 ### Bug fixes:
 
     - Fix bug selecting topolgies for odd number of initial conditions
     - Fix bug extracting indexes from topology in MSMClustering
+    - Fix bug in atomset writing PDBs with gaps, now if there are residues with
+      a difference in more than one in the residue number a TER is written 
 
 ### Behaviour changes from previous version:
 

docs/AdaptivePELE.analysis.html

@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.6
+                v1.6.1
               </div>
 
 

docs/AdaptivePELE.atomset.html

@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.6
+                v1.6.1
               </div>
 
 

docs/AdaptivePELE.clustering.html

@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.6
+                v1.6.1
               </div>
 
 
@@ -90,8 +90,8 @@
 <li class="toctree-l1"><a class="reference internal" href="Examples.html">User Manual</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Problems.html">Frequently Asked Questions</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="AdaptivePELE.html">AdaptivePELE – Package Description</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#adaptivesampling-module"><code class="docutils literal"><span class="pre">adaptiveSampling</span></code> Module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#automateroundsadaptive-module"><code class="docutils literal"><span class="pre">automateRoundsAdaptive</span></code> Module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#module-AdaptivePELE.adaptiveSampling"><code class="docutils literal"><span class="pre">adaptiveSampling</span></code> Module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#module-AdaptivePELE.automateRoundsAdaptive"><code class="docutils literal"><span class="pre">automateRoundsAdaptive</span></code> Module</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="AdaptivePELE.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l3"><a class="reference internal" href="AdaptivePELE.analysis.html">analysis Package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="AdaptivePELE.atomset.html">atomset Package</a></li>
@@ -604,7 +604,7 @@ <h1>clustering Package<a class="headerlink" href="#clustering-package" title="Pe
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>simulationRunnerParams</strong> (<code class="xref py py-class docutils literal"><span class="pre">SimulationParameters</span></code>) – <code class="xref py py-class docutils literal"><span class="pre">SimulationParameters</span></code> Simulation parameters object</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>simulationRunnerParams</strong> (<a class="reference internal" href="AdaptivePELE.simulation.html#AdaptivePELE.simulation.simulationrunner.SimulationParameters" title="AdaptivePELE.simulation.simulationrunner.SimulationParameters"><code class="xref py py-class docutils literal"><span class="pre">SimulationParameters</span></code></a>) – <a class="reference internal" href="AdaptivePELE.simulation.html#AdaptivePELE.simulation.simulationrunner.SimulationParameters" title="AdaptivePELE.simulation.simulationrunner.SimulationParameters"><code class="xref py py-class docutils literal"><span class="pre">SimulationParameters</span></code></a> Simulation parameters object</td>
 </tr>
 <tr class="field-even field"><th class="field-name" colspan="2">Returns list, list:</th></tr>
 <tr class="field-even field"><td>&#160;</td><td class="field-body">– list of the filtered clusters, list of bools flagging wether the cluster is selected or not</td>
@@ -1244,7 +1244,7 @@ <h1>clustering Package<a class="headerlink" href="#clustering-package" title="Pe
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>simulationRunnerParams</strong> (<code class="xref py py-class docutils literal"><span class="pre">SimulationParameters</span></code>) – <code class="xref py py-class docutils literal"><span class="pre">SimulationParameters</span></code> Simulation parameters object</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>simulationRunnerParams</strong> (<a class="reference internal" href="AdaptivePELE.simulation.html#AdaptivePELE.simulation.simulationrunner.SimulationParameters" title="AdaptivePELE.simulation.simulationrunner.SimulationParameters"><code class="xref py py-class docutils literal"><span class="pre">SimulationParameters</span></code></a>) – <a class="reference internal" href="AdaptivePELE.simulation.html#AdaptivePELE.simulation.simulationrunner.SimulationParameters" title="AdaptivePELE.simulation.simulationrunner.SimulationParameters"><code class="xref py py-class docutils literal"><span class="pre">SimulationParameters</span></code></a> Simulation parameters object</td>
 </tr>
 <tr class="field-even field"><th class="field-name" colspan="2">Returns list, list:</th></tr>
 <tr class="field-even field"><td>&#160;</td><td class="field-body">– list of the filtered clusters, list of bools flagging wether the cluster is selected or not</td>