Merge branch 'release-v2.0.0-rc5'

# Conflicts:
#	PyPWA/__init__.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/GUI_alpha_main.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/GUI_gamp_main.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/GUI_subPyNormInt.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/PWA_GUI
#	bugfixed-isobar/pythonPWA/batchFarmServices/__init__.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/dataSimulatorNPY.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/farmCheck.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/fast_like.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/getImax.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/graphicHelp.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/graphicPlot
#	bugfixed-isobar/pythonPWA/batchFarmServices/graphicPlotSim
#	bugfixed-isobar/pythonPWA/batchFarmServices/gui_submit
#	bugfixed-isobar/pythonPWA/batchFarmServices/likelihoodTest.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/massBinner.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/massBinner2.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/mvBAMP_GUI
#	bugfixed-isobar/pythonPWA/batchFarmServices/pwa_SIM.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/pwa_controls
#	bugfixed-isobar/pythonPWA/batchFarmServices/resonances.txt
#	bugfixed-isobar/pythonPWA/batchFarmServices/rhoAA.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/simulation_Install
#	bugfixed-isobar/pythonPWA/batchFarmServices/simulatorMain.py
#	bugfixed-isobar/pythonPWA/batchFarmServices/subLikelihood
#	bugfixed-isobar/pythonPWA/batchFarmServices/subSimulator
#	bugfixed-isobar/pythonPWA/batchFarmServices/subWalkNTrue
#	bugfixed-isobar/pythonPWA/batchFarmServices/walkingNTrue.py
#	bugfixed-isobar/pythonPWA/pythonPWA/__init__.py
#	bugfixed-isobar/pythonPWA/pythonPWA/fileHandlers/__init__.py
#	bugfixed-isobar/pythonPWA/pythonPWA/fileHandlers/getWavesGen.py
#	bugfixed-isobar/pythonPWA/pythonPWA/model/__init__.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/DeltaPhis.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/LorentzTransform.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/OHMintensity.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/__init__.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/chunks.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/countGampSet.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/dataSimulatorFarm.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/devTestFarm.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/fnGenerator.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/gampSlist.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/generatePureWave.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/likelihood.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/minuitLikelihood.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/phaseMotion.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/plotGampEvents.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/plotNTrue.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/plotter.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/pwa_controls
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/randM.py
#	bugfixed-isobar/pythonPWA/pythonPWA/utilities/rotation.py
#	setup.py

PyPWA/__init__.py

@@ -31,7 +31,7 @@
 __email__ = "maj@jlab.org"
 __status__ = "development"
 __maintainer__ = ["Mark Jones"]
-__version__ = "2.0.0-rc4"
+__version__ = "2.0.0-rc5"
 
 VERSION = __version__
 STATUS = __status__

PyPWA/builtin_plugins/data/__init__.py

@@ -86,7 +86,7 @@ def _option_types(self):
             "user plugin": str
         }
 
-    def _main_comment(self):
+    def _module_comment(self):
         return "This is the builtin data parser, you can replace " \
                "this with your own data parser if you wish."
 
@@ -146,7 +146,7 @@ def _option_types(self):
             "user plugin": str
         }
 
-    def _main_comment(self):
+    def _module_comment(self):
         return "This is the builtin data parser, you can replace " \
                "this with your own data parser if you wish."
 

PyPWA/builtin_plugins/minuit/__init__.py

@@ -64,7 +64,7 @@ def _option_types(self):
             "number of calls": int
         }
 
-    def _main_comment(self):
+    def _module_comment(self):
         return "Minuit is the tried and tested minimizer, developed " \
                "by ROOT"
 

PyPWA/builtin_plugins/nestle/__init__.py

@@ -0,0 +1,140 @@
+#    PyPWA, a scientific analysis toolkit.
+#    Copyright (C) 2016  JLab
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+from PyPWA import VERSION, LICENSE, STATUS
+from PyPWA.builtin_plugins.nestle import nested
+from PyPWA.core.templates import option_templates
+
+__author__ = ["Mark Jones"]
+__credits__ = ["Mark Jones"]
+__maintainer__ = ["Mark Jones"]
+__email__ = "maj@jlab.org"
+__status__ = STATUS
+__license__ = LICENSE
+__version__ = VERSION
+
+
+class NestleOptions(option_templates.PluginsOptionsTemplate):
+    def _plugin_name(self):
+        return "Nestle"
+
+    def _plugin_interface(self):
+        return nested.NestledSampling
+
+    def _plugin_type(self):
+        return self._minimization
+
+    def _user_defined_function(self):
+        return None
+
+    def _default_options(self):
+        return {
+            "prior location": "/location/to/prior.py",
+            "prior name": "prior_function",
+            "ndim": 1,
+            "npoints": 100,
+            "method": "single",
+            "update interval": None,
+            "npdim": None,
+            "maxiter": None,
+            "maxcall": None,
+            "dlogz": None,
+            "decline_factor": None
+        }
+
+    def _option_levels(self):
+        return {
+            "prior location": self._required,
+            "prior name": self._required,
+            "ndim": self._required,
+            "npoints": self._optional,
+            "method": self._optional,
+            "update interval": self._advanced,
+            "npdim": self._advanced,
+            "maxiter": self._advanced,
+            "maxcall": self._advanced,
+            "dlogz": self._advanced,
+            "decline_factor": self._advanced
+        }
+
+    def _option_types(self):
+        return {
+            "prior location": str,
+            "prior name": str,
+            "ndim": int,
+            "npoints": int,
+            "method": ["classic", "single", "multi"],
+            "update interval": int,
+            "npdim": int,
+            "maxiter": int,
+            "maxcall": int,
+            "dlogz": float,
+            "decline_factor": float
+        }
+
+    def _module_comment(self):
+        return "Nestle, a python based multinest implementation."
+
+    def _option_comments(self):
+        return {
+            "prior location":
+                "The path of the file containing the prior.",
+            "prior name":
+                "The name of the prior function.",
+            "ndim":
+                "Number of parameters returned by prior and accepted by "
+                "loglikelihood.",
+            "npoints":
+                "Number of active points. Larger numbers result in a more "
+                "finely sampled posterior (more accurate evidence), "
+                "but also a larger number of iterations required to "
+                "converge.",
+            "method":
+                "Method to select new points. Options are classic, "
+                "single-ellipsoidal (single), and multi-ellipsoidal (multi)",
+            "update interval":
+                "Only update the new point selector every "
+                "``update_interval``-th likelihood call. Update intervals "
+                "larger than 1 can be more efficient when the likelihood "
+                "function is very fast, particularly when using the "
+                "multi-ellipsoid method.",
+            "npdim":
+                "Number of parameters accepted by prior. This might differ "
+                "from *ndim* in the case where a parameter of loglikelihood "
+                "is dependent upon multiple independently distributed "
+                "parameters, some of which may be nuisance parameters.",
+            "maxiter":
+                "Maximum number of iterations. Iteration may stop earlier "
+                "if termination condition is reached.",
+            "maxcall":
+                "Maximum number of likelihood evaluations. Iteration may "
+                "stop earlier if termination condition is reached.",
+            "dlogz" :
+                "If supplied, iteration will stop when the estimated "
+                "contribution of the remaining prior volume to the total "
+                "evidence falls below this threshold. Explicitly, "
+                "the stopping criterion is "
+                "``log(z + z_est) - log(z) < dlogz`` where *z* is the "
+                "current evidence from all saved samples, and *z_est* is "
+                "the estimated contribution from the remaining volume. This "
+                "option and decline_factor are mutually exclusive.",
+            "decline_factor":
+                "If supplied, iteration will stop when the weight ("
+                "likelihood times prior volume) of newly saved samples has "
+                "been declining for ``decline_factor * nsamples`` "
+                "consecutive samples. A value of 1.0 seems to work pretty "
+                "well. This option and dlogz are mutually exclusive."
+        }