Merge branch 'master' into 234_fix_readme

.github/ISSUE_TEMPLATE/bug_report.md

@@ -2,7 +2,7 @@
 name: Bug report
 about: Report an error which requires fixing
 title: ''
-labels: bug
+labels: Bug
 
 ---
 

.github/ISSUE_TEMPLATE/documentation_request.md

@@ -0,0 +1,13 @@
+---
+name: Documentation
+about: Suggest a improvement to user, developer or other documentation
+title: ''
+labels: Documentation
+
+---
+
+**Description of the documentation**
+A description of what area can benefit from better documentation.
+
+**Additional details**
+Add any other context or screenshots about this request.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -2,7 +2,7 @@
 name: Feature request
 about: Suggest a new feature
 title: ''
-labels: enhancement
+labels: Enhancement
 
 ---
 

.github/ISSUE_TEMPLATE/testing.md

@@ -2,7 +2,7 @@
 name: Test
 about: Specify a test that needs to be implemented
 title: ''
-labels: testing
+labels: Testing
 
 ---
 

fitbenchmarking/fitbenchmark_one_problem.py

@@ -7,11 +7,11 @@
 import sys
 import numpy as np
 
-from fitting import prerequisites as prereq
-from fitting import misc
-from fitting.plotting import plots
+from fitbenchmarking.fitting import prerequisites as prereq
+from fitbenchmarking.fitting import misc
+from fitbenchmarking.fitting.plotting import plots
 
-from utils.logging_setup import logger
+from fitbenchmarking.utils.logging_setup import logger
 
 
 def fitbm_one_prob(user_input, problem):

fitbenchmarking/fitting/mantid/__init__.py

@@ -1 +0,0 @@
-

fitbenchmarking/fitting/mantid/externals.py

@@ -6,21 +6,22 @@
 from __future__ import (absolute_import, division, print_function)
 
 import mantid.simpleapi as msapi
-from utils.logging_setup import logger
+from fitbenchmarking.utils.logging_setup import logger
 
 
 def gen_func_obj(function_name, params_set):
     """
     Generates a mantid function object.
 
     @param function_name :: the name of the function to be generated
-    @params_set :: set of parameters per function extracted from the problem definition file
+    @params_set :: set of parameters per function extracted from the
+        problem definition file
 
     @returns :: mantid function object that can be called in python
     """
     params_set = (params_set.split(', ties'))[0]
 
-    exec "function_object = msapi." + function_name + "("+ params_set +")"
+    exec "function_object = msapi." + function_name + "(" + params_set + ")"
 
     return function_object
 
@@ -39,12 +40,12 @@ def set_ties(function_object, ties):
         for tie in ties_per_func:
             """
             param_str is a string of the parameter name in the mantid format
-            For a Mantid Composite Function, a formatted parameter name would 
+            For a Mantid Composite Function, a formatted parameter name would
             start with the function number and end with the parameter name.
-            For instance, f0.A would refer to a parameter A of the first 
+            For instance, f0.A would refer to a parameter A of the first
             function is a Composite Function.
             """
-            param_str = 'f'+str(idx)+'.'+(tie.split("'"))[0]
+            param_str = 'f' + str(idx) + '.' + (tie.split("'"))[0]
             function_object.fix(param_str)
 
     return function_object

fitbenchmarking/fitting/mantid/main.py

@@ -9,9 +9,9 @@
 import numpy as np
 import mantid.simpleapi as msapi
 
-from utils.logging_setup import logger
-from fitting import misc
-from fitting.plotting import plot_helper
+from fitbenchmarking.utils.logging_setup import logger
+from fitbenchmarking.fitting import misc
+from fitbenchmarking.fitting.plotting import plot_helper
 
 
 MAX_FLOAT = sys.float_info.max
@@ -41,13 +41,14 @@ def benchmark(problem, wks_created, function, minimizers, cost_function):
         chi_sq, min_chi_sq, best_fit = \
             chisq(status, fit_wks, min_chi_sq, best_fit, minimizer)
         individual_result = \
-            misc.create_result_entry(problem, status, chi_sq, runtime, minimizer,
-                                     function, fin_function_def)
+            misc.create_result_entry(problem, status, chi_sq, runtime,
+                                     minimizer, function, fin_function_def)
 
         results_problem.append(individual_result)
 
     return results_problem, best_fit
 
+
 def fit(problem, wks_created, function, minimizer,
         cost_function='Least squares'):
     """
@@ -65,8 +66,6 @@ def fit(problem, wks_created, function, minimizer,
                 the final function definition
                 and how much time it took for the fit to finish (float)
     """
-
-
     fit_result, t_start, t_end = None, None, None
     try:
         ignore_invalid = get_ignore_invalid(problem, cost_function)
@@ -127,7 +126,7 @@ def parse_result(fit_result, t_start, t_end):
 
     status = 'failed'
     fit_wks, fin_function_def, runtime = None, None, np.nan
-    if not fit_result is None:
+    if fit_result is not None:
         status = fit_result.OutputStatus
         fit_wks = fit_result.OutputWorkspace
         fin_function_def = str(fit_result.Function)

fitbenchmarking/fitting/mantid/prepare_data.py

@@ -4,12 +4,9 @@
 
 from __future__ import (absolute_import, division, print_function)
 
-import copy
 import numpy as np
 import mantid.simpleapi as msapi
 
-from utils.logging_setup import logger
-
 
 def wks_cost_function(problem, use_errors=True):
     """
@@ -38,6 +35,7 @@ def wks_cost_function(problem, use_errors=True):
 
     return wks_created, cost_function
 
+
 def setup_errors(problem):
     """
     Gets errors on the data points from the problem object if there are
@@ -57,6 +55,7 @@ def setup_errors(problem):
         # True errors
         return problem.data_e
 
+
 def convert_back(wks_used, problem, use_errors):
     """
     Convert back so data is of equal lengths.

fitbenchmarking/fitting/mantid/tests/__init__.py

@@ -1 +0,0 @@
-