Merge branch 'master' into move-parameters-to-mco

.gitignore

@@ -2,4 +2,4 @@ __pycache__
 *.egg-info
 doc/build/
 *.pyc
-
+force_bdss/version.py

braindump/datasource.py

-class DataSource():
-    """Base class that performs calculation or extraction of information
-    """
-    __metaclass__ = abc.ABCMeta
-
-    def __init__(self, name):
-        self.name = name
-
-    @abstractclassmethod
-    def provides(cls):
-        return [CUBA.key]
-
-    def execute(self, parameters):
-        """Performs the evaluation and returns a list of Result.
-        """
-
-
-class Simulator(DataSource):
-    pass
-
-
-class Database(DataSource):
-    pass
-
-
-# Represents the result of a simulator.
-# It contains the resulting cuba key, the associated uncertainty and the
-# originating simulator.
-# Difference between uncertainty and quality: uncertainty is a numerical value
-# of the value, as in the case of an experimental simulation.
-# quality is the level of accuracy of the (e.g.c omputational) method, as
-# the importance and reliability of that value. It should be an enumeration
-# value such as HIGH, MEDIUM, POOR
-Result = namedtuple("Result", "cuba_key value uncertainty originator quality")
-

braindump/kpi_calculator.py

-class KPICalculator():
-    """Base class that defines the equaation to compute the KPIs values from
-    the results of the simulators
-
-    input: a list of SimulatorResult
-    output: a list of KPIs.
-    """
-    __metaclass__ = abc.ABCMeta
-
-    def execute(self, datasource_results)
-        """Returns the KPIResult"""
-
-
-KPIResult = namedtuple("KPIResult", "name cuba_key value uncertainty quality")
-
-

braindump/main.py

-from force_bdss import *
-
-wf=Workflow()
-wf.set_mco(Dakota())
-wf.set_datasources([
-    ViscositySimulator(),
-    CostExtractor(),
-])
-wf.objectives([
-    Objective(),
-    Objective()
-    ])
-
-
-wf.set_parameters({
-    "material_1": {
-        CUBA.FORMULA: "H2O",
-        CUBA.CONCENTRATION: Range(0, 100)
-    },
-    "material_2": {
-        CUBA.FORMULA: "glycol",
-        CUBA.CONCENTRATION: Formula("material_1",
-            lambda material_1: 100 - material_1[CUBA.CONCENTRATION])
-    }
-})
-
-wf.set_result_callback(callback)
-
-# constraints vs computed value
-# e.g. constraint = value from 0 to 100
-# computed value = 100 - other value
-# TODO: Study dakota better to understand how it works and what kind of
-# interface it expects
-
-pareto_front = wf.execute()
-
-plot(pareto_front)
-

braindump/mco.py

-class MCO():
-    """Receives a list of KPIResult to decide the next step in the parameter
-    space"""
-    __metaclass__ = abc.ABCMeta
-    starting_point
-    variable_constraints
-    objectives
-
-    def get_next_parameters(kpi_results):
-        pass
-
-
-class Dakota(MCO):
-    def __init__(self, options):
-        pass
-
-
-class DakotaInput():
-    """Read the parameters from the dakota input file and returns
-    the parameters for further consumption"""
-    def parse(filename):
-        """Returns the parameters"""
-
-
-class DakotaOutput():
-    """Writes the KPIs to the file for consumption by Dakota"""

braindump/workflow.py

-# This is a prototype for the Workflow in FORCE
-import abc
-
-
-class Workflow():
-    # calculates the KPIs from the list of the cuba keys coming from the
-    # simulators
-    mco = None
-    data_sources = None
-
-
-
-
-class ViscosityCalculator(Simulator):
-    pass
-
-
-class CostExtractor(Database):
-    provides_kpi = []
-
-
-class Objective()
-    kpi = None
-    optimization_type = MAXIMIZE
-

doc/source/api/force_bdss.cli.rst

-force\_bdss\.cli package
-========================
+force_bdss.cli package
+======================
 
 Subpackages
 -----------
@@ -11,8 +11,8 @@ Subpackages
 Submodules
 ----------
 
-force\_bdss\.cli\.force\_bdss module
-------------------------------------
+force_bdss.cli.force_bdss module
+--------------------------------
 
 .. automodule:: force_bdss.cli.force_bdss
     :members:

doc/source/api/force_bdss.cli.tests.rst

-force\_bdss\.cli\.tests package
-===============================
+force_bdss.cli.tests package
+============================
 
 Submodules
 ----------
 
-force\_bdss\.cli\.tests\.test\_execution module
------------------------------------------------
+force_bdss.cli.tests.test_execution module
+------------------------------------------
 
 .. automodule:: force_bdss.cli.tests.test_execution
     :members:

doc/source/api/force_bdss.core_plugins.dummy.csv_extractor.rst

-force\_bdss\.core\_plugins\.dummy\.csv\_extractor package
-=========================================================
+force_bdss.core_plugins.dummy.csv_extractor package
+===================================================
 
 Subpackages
 -----------
@@ -11,24 +11,24 @@ Subpackages
 Submodules
 ----------
 
-force\_bdss\.core\_plugins\.dummy\.csv\_extractor\.csv\_extractor\_bundle module
---------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.csv_extractor.csv_extractor_bundle module
+-----------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.csv_extractor.csv_extractor_bundle
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.csv\_extractor\.csv\_extractor\_data\_source module
---------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.csv_extractor.csv_extractor_data_source module
+----------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.csv_extractor.csv_extractor_data_source
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.csv\_extractor\.csv\_extractor\_model module
--------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.csv_extractor.csv_extractor_model module
+----------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.csv_extractor.csv_extractor_model
     :members:

doc/source/api/force_bdss.core_plugins.dummy.csv_extractor.tests.rst

-force\_bdss\.core\_plugins\.dummy\.csv\_extractor\.tests package
-================================================================
+force_bdss.core_plugins.dummy.csv_extractor.tests package
+=========================================================
 
 Submodules
 ----------
 
-force\_bdss\.core\_plugins\.dummy\.csv\_extractor\.tests\.test\_csv\_extractor\_bundle module
----------------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.csv_extractor.tests.test_csv_extractor_bundle module
+----------------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.csv_extractor.tests.test_csv_extractor_bundle
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.csv\_extractor\.tests\.test\_csv\_extractor\_data\_source module
----------------------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.csv_extractor.tests.test_csv_extractor_data_source module
+---------------------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.csv_extractor.tests.test_csv_extractor_data_source
     :members:

doc/source/api/force_bdss.core_plugins.dummy.dummy_dakota.rst

-force\_bdss\.core\_plugins\.dummy\.dummy\_dakota package
-========================================================
+force_bdss.core_plugins.dummy.dummy_dakota package
+==================================================
 
 Subpackages
 -----------
@@ -11,32 +11,32 @@ Subpackages
 Submodules
 ----------
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_dakota\.dakota\_bundle module
------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_dakota.dakota_bundle module
+---------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_dakota.dakota_bundle
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_dakota\.dakota\_communicator module
------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_dakota.dakota_communicator module
+---------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_dakota.dakota_communicator
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_dakota\.dakota\_model module
-----------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_dakota.dakota_model module
+--------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_dakota.dakota_model
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_dakota\.dakota\_optimizer module
---------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_dakota.dakota_optimizer module
+------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_dakota.dakota_optimizer
     :members:

doc/source/api/force_bdss.core_plugins.dummy.dummy_dakota.tests.rst

-force\_bdss\.core\_plugins\.dummy\.dummy\_dakota\.tests package
-===============================================================
+force_bdss.core_plugins.dummy.dummy_dakota.tests package
+========================================================
 
 Submodules
 ----------
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_dakota\.tests\.test\_dakota\_bundle module
-------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_dakota.tests.test_dakota_bundle module
+--------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_dakota.tests.test_dakota_bundle
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_dakota\.tests\.test\_dakota\_communicator module
-------------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_dakota.tests.test_dakota_communicator module
+--------------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_dakota.tests.test_dakota_communicator
     :members:
     :undoc-members:
     :show-inheritance:
 
+force_bdss.core_plugins.dummy.dummy_dakota.tests.test_dakota_optimizer module
+-----------------------------------------------------------------------------
+
+.. automodule:: force_bdss.core_plugins.dummy.dummy_dakota.tests.test_dakota_optimizer
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------

doc/source/api/force_bdss.core_plugins.dummy.dummy_data_source.rst

-force\_bdss\.core\_plugins\.dummy\.dummy\_data\_source package
-==============================================================
+force_bdss.core_plugins.dummy.dummy_data_source package
+=======================================================
 
 Subpackages
 -----------
@@ -11,24 +11,24 @@ Subpackages
 Submodules
 ----------
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_data\_source\.dummy\_data\_source module
-----------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_data_source.dummy_data_source module
+------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_data_source.dummy_data_source
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_data\_source\.dummy\_data\_source\_bundle module
-------------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_data_source.dummy_data_source_bundle module
+-------------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_data_source.dummy_data_source_bundle
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_data\_source\.dummy\_data\_source\_model module
------------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_data_source.dummy_data_source_model module
+------------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_data_source.dummy_data_source_model
     :members:

doc/source/api/force_bdss.core_plugins.dummy.dummy_data_source.tests.rst

-force\_bdss\.core\_plugins\.dummy\.dummy\_data\_source\.tests package
-=====================================================================
+force_bdss.core_plugins.dummy.dummy_data_source.tests package
+=============================================================
 
 Submodules
 ----------
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_data\_source\.tests\.test\_dummy\_data\_source module
------------------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_data_source.tests.test_dummy_data_source module
+-----------------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_data_source.tests.test_dummy_data_source
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_data\_source\.tests\.test\_dummy\_data\_source\_bundle module
--------------------------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_data_source.tests.test_dummy_data_source_bundle module
+------------------------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_data_source.tests.test_dummy_data_source_bundle
     :members:

doc/source/api/force_bdss.core_plugins.dummy.dummy_kpi_calculator.rst

-force\_bdss\.core\_plugins\.dummy\.dummy\_kpi\_calculator package
-=================================================================
+force_bdss.core_plugins.dummy.dummy_kpi_calculator package
+==========================================================
 
 Subpackages
 -----------
@@ -11,24 +11,24 @@ Subpackages
 Submodules
 ----------
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_kpi\_calculator\.dummy\_kpi\_calculator module
-----------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_kpi_calculator.dummy_kpi_calculator module
+------------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_kpi_calculator.dummy_kpi_calculator
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_kpi\_calculator\.dummy\_kpi\_calculator\_bundle module
-------------------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_kpi_calculator.dummy_kpi_calculator_bundle module
+-------------------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_kpi_calculator.dummy_kpi_calculator_bundle
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_kpi\_calculator\.dummy\_kpi\_calculator\_model module
------------------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_kpi_calculator.dummy_kpi_calculator_model module
+------------------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_kpi_calculator.dummy_kpi_calculator_model
     :members:

doc/source/api/force_bdss.core_plugins.dummy.dummy_kpi_calculator.tests.rst

-force\_bdss\.core\_plugins\.dummy\.dummy\_kpi\_calculator\.tests package
-========================================================================
+force_bdss.core_plugins.dummy.dummy_kpi_calculator.tests package
+================================================================
 
 Submodules
 ----------
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_kpi\_calculator\.tests\.test\_dummy\_kpi\_calculator\_bundle module
--------------------------------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_kpi_calculator.tests.test_dummy_kpi_calculator_bundle module
+------------------------------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_kpi_calculator.tests.test_dummy_kpi_calculator_bundle
     :members:

doc/source/api/force_bdss.core_plugins.dummy.kpi_adder.rst

-force\_bdss\.core\_plugins\.dummy\.kpi\_adder package
-=====================================================
+force_bdss.core_plugins.dummy.kpi_adder package
+===============================================
 
 Subpackages
 -----------
@@ -11,24 +11,24 @@ Subpackages
 Submodules
 ----------
 
-force\_bdss\.core\_plugins\.dummy\.kpi\_adder\.kpi\_adder\_bundle module
-------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.kpi_adder.kpi_adder_bundle module
+---------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.kpi_adder.kpi_adder_bundle
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.kpi\_adder\.kpi\_adder\_calculator module
-----------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.kpi_adder.kpi_adder_calculator module
+-------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.kpi_adder.kpi_adder_calculator
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.kpi\_adder\.kpi\_adder\_model module
------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.kpi_adder.kpi_adder_model module
+--------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.kpi_adder.kpi_adder_model
     :members:

doc/source/api/force_bdss.core_plugins.dummy.kpi_adder.tests.rst

-force\_bdss\.core\_plugins\.dummy\.kpi\_adder\.tests package
-============================================================
+force_bdss.core_plugins.dummy.kpi_adder.tests package
+=====================================================
 
 Submodules
 ----------
 
-force\_bdss\.core\_plugins\.dummy\.kpi\_adder\.tests\.test\_kpi\_adder\_bundle module
--------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.kpi_adder.tests.test_kpi_adder_bundle module
+--------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.kpi_adder.tests.test_kpi_adder_bundle
     :members:

doc/source/api/force_bdss.core_plugins.dummy.rst

-force\_bdss\.core\_plugins\.dummy package
-=========================================
+force_bdss.core_plugins.dummy package
+=====================================
 
 Subpackages
 -----------
@@ -16,8 +16,8 @@ Subpackages
 Submodules
 ----------
 
-force\_bdss\.core\_plugins\.dummy\.dummy\_plugin module
--------------------------------------------------------
+force_bdss.core_plugins.dummy.dummy_plugin module
+-------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.dummy_plugin
     :members:

doc/source/api/force_bdss.core_plugins.dummy.tests.rst

-force\_bdss\.core\_plugins\.dummy\.tests package
-================================================
+force_bdss.core_plugins.dummy.tests package
+===========================================
 
 Submodules
 ----------
 
-force\_bdss\.core\_plugins\.dummy\.tests\.data\_source\_bundle\_test\_mixin module
-----------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.tests.data_source_bundle_test_mixin module
+------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.tests.data_source_bundle_test_mixin
     :members:
     :undoc-members:
     :show-inheritance:
 
-force\_bdss\.core\_plugins\.dummy\.tests\.kpi\_calculator\_bundle\_test\_mixin module
--------------------------------------------------------------------------------------
+force_bdss.core_plugins.dummy.tests.kpi_calculator_bundle_test_mixin module
+---------------------------------------------------------------------------
 
 .. automodule:: force_bdss.core_plugins.dummy.tests.kpi_calculator_bundle_test_mixin
     :members: