Merge pull request #284 from fitbenchmarking/215_ralfit

215 Adding RALfit

.travis.yml

@@ -13,18 +13,29 @@ stages:
     if: type = cron
 
 before_install:
+  # Adding RALfit packages
+  - sudo apt-get update
+  - sudo apt-get install gfortran
+  - sudo apt-get install lcov
+  - sudo apt-get install libblas-dev
+  - sudo apt-get install liblapack-dev
   - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O
     miniconda.sh
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
   - conda update --yes conda
   - conda install --yes python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib
     h5py yaml ipython
+
 install:
+  # Builds RALfit
+  - ./build_ralfit.sh
   - pip install -r requirements.txt
   - python setup.py install
   - python setup.py externals
   - python -m easy_install --upgrade pyOpenSSL
+  - export LD_LIBRARY_PATH=$HOME/build/fitbenchmarking/fitbenchmarking/RALFit/libRALFit/build/src:$LD_LIBRARY_PATH
+
 
 jobs:
   include:

build_ralfit.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+SCRIPTPATH=$PWD
+
+git clone https://github.com/ralna/RALFit
+
+cd $SCRIPTPATH/RALFit/libRALFit/
+mkdir build
+cd build
+cmake ..
+make
+python setup.py build_ext
+python setup.py install
+
+cd $SCRIPTPATH

docs/source/users/getting_started.rst

@@ -24,7 +24,7 @@ on setting up python see :ref:`setting-up-python`.
    :target: https://www.python.org/downloads/release/python-2715/
 
 .. _setting-up-python:
-      
+
 ******************
 Setting up Python
 ******************
@@ -193,3 +193,14 @@ manually, first install gdebi: ``sudo apt-get install gdebi`` then
 install mantid using: ``sudo gdebi pkgname.deb`` while you are in the
 folder from where you downloaded mantid and replace pckgname with the
 name of the downloaded file.
+
+
+.. _setting-up-ralfit:
+
+*****************
+Installing RAlfit
+*****************
+
+The fitbenchmarking setup does not currently support installing RALfit
+through it. RALfit can be downloaded and installed from
+`here https://github.com/ralna/RALFit>`__.

docs/source/users/options.rst

@@ -118,7 +118,7 @@ Scipy:
   - ``"dogbox"``
   - ``"lm"``
   - and ``"trf"``
- 
+
 
   Information about these can be found on the
   `Scipy documentation
@@ -128,9 +128,16 @@ DFO-GN:
   - ``"dfogn"``
   Information about this can be found on the
   `DFO-GN documentation
-  <http://people.maths.ox.ac.uk/robertsl/dfogn/>`__  
-
-
+  <http://people.maths.ox.ac.uk/robertsl/dfogn/>`__
+
+
+RALfit:
+  - ``"ralfit"``
+  Information about this can be found on the
+  `RALfit documentation
+  <https://github.com/ralna/RALFit>`__
+
+
 ``comparison_mode``
 -------------------
 The comparison mode is used when displaying results to select the value

fitbenchmarking/fitbenchmark_one_problem.py

@@ -18,6 +18,10 @@
     from fitbenchmarking.fitting.controllers.mantid_controller import MantidController
 except ImportError:
     MantidController = None
+try:
+    from fitbenchmarking.fitting.controllers.ralfit_controller import RALFitController
+except ImportError:
+    RALFitController = None
 try:
     from fitbenchmarking.fitting.controllers.sasview_controller import SasviewController
 except ImportError:
@@ -47,6 +51,7 @@ def fitbm_one_prob(user_input, problem):
 
     controllers = {'dfogn': DFOGNController,
                    'mantid': MantidController,
+                   'ralfit': RALFitController,
                    'sasview': SasviewController,
                    'scipy': ScipyController}
 

fitbenchmarking/fitbenchmarking_default_options.json

@@ -8,8 +8,9 @@
                     "Trust Region"],
         "scipy" : ["lm", "trf", "dogbox"],
         "sasview" : ["amoeba", "lm", "newton", "de", "pt", "mp"],
-        "dfogn" : ["dfogn"]
+        "dfogn" : ["dfogn"],
+        "ralfit" : ["ralfit"]
         },
 
-    "comparison_mode" : "both" 
+    "comparison_mode" : "both"
 }

fitbenchmarking/fitting/controllers/ralfit_controller.py

@@ -0,0 +1,69 @@
+"""
+Implements a controller for RALFit
+https://github.com/ralna/RALFit
+"""
+
+import ral_nlls
+from scipy.optimize._numdiff import approx_derivative
+
+from fitbenchmarking.fitting.controllers.base_controller import Controller
+
+
+class RALFitController(Controller):
+    """
+    Controller for the RALFit fitting software.
+    """
+
+    def __init__(self, problem, use_errors):
+        """
+        Initialises variable used for temporary storage.
+        """
+        super(RALFitController, self).__init__(problem, use_errors)
+
+        self._x = None
+        self._inform = None
+
+    def setup(self):
+        """
+        Setup for RALFit
+        """
+        pass
+
+    def _eval_f_arg_swap(self, params, x):
+        return self.problem.eval_f(x=x,
+                                   params=params,
+                                   function_id=self.function_id)
+
+    def _prediction_error(self, params, x, y):
+        return self._eval_f_arg_swap(params, x) - y
+
+    def _jac(self, params, x, y):
+        return approx_derivative(self._eval_f_arg_swap,
+                                 params,
+                                 args=tuple([x]))
+
+    def fit(self):
+        """
+        Run problem with RALFit.
+        """
+        self.success = False
+        try:
+            (self._x, self._inform) = ral_nlls.solve(self.initial_params,
+                                                     self._prediction_error,
+                                                     self._jac,
+                                                     params=(self.data_x,
+                                                             self.data_y))
+            self.success = True
+        except:
+            self.success = False
+
+    def cleanup(self):
+        """
+        Convert the result to a numpy array and populate the variables results
+        will be read from.
+        """
+        if self.success:
+            self.results = self.problem.eval_f(x=self.data_x,
+                                               params=self._x,
+                                               function_id=self.function_id)
+            self.final_params = self._x

fitbenchmarking/fitting/tests/test_controllers.py

@@ -7,6 +7,8 @@
     DFOGNController
 from fitbenchmarking.fitting.controllers.mantid_controller import \
     MantidController
+from fitbenchmarking.fitting.controllers.ralfit_controller import \
+    RALFitController
 from fitbenchmarking.fitting.controllers.sasview_controller import \
     SasviewController
 from fitbenchmarking.fitting.controllers.scipy_controller import \
@@ -35,6 +37,7 @@ class DummyController(Controller):
     """
     Minimal instantiatable subclass of Controller class for testing
     """
+
     def setup(self):
         self.setup_result = 53
 
@@ -49,6 +52,7 @@ class BaseControllerTests(unittest.TestCase):
     """
     Tests for base software controller class methods.
     """
+
     def setUp(self):
         self.problem = FittingProblem(misra1a_file())
 
@@ -99,6 +103,7 @@ class ControllerTests(unittest.TestCase):
     """
     Tests for each controller class
     """
+
     def setUp(self):
         self.problem = FittingProblem(misra1a_file())
 
@@ -134,6 +139,14 @@ def test_dfogn(self):
         controller.minimizer = 'dfogn'
         self.shared_testing(controller)
 
+    def test_ralfit(self):
+        """
+        RALFitController: Tests for output shape
+        """
+        controller = RALFitController(self.problem, True)
+        controller.minimizer = 'ralfit'
+        self.shared_testing(controller)
+
     def shared_testing(self, controller):
         """
         Utility function to run controller and check output is in generic form