Merge branch 'development' of https://github.com/numbbo/coco into fix…

…-logger-filenames

code-experiments/build/python/example/example_experiment2.py

@@ -39,19 +39,14 @@
 from __future__ import division, print_function, unicode_literals
 __author__ = "Nikolaus Hansen and ..."
 import sys
-import time  # output some timings per evaluation
-from collections import defaultdict
-import os, webbrowser  # to show post-processed results in the browser
-import numpy as np  # for median, zeros, random, asarray
-import cocoex  # experimentation module
-try: import cocopp  # post-processing module
-except: pass
 
 ### MKL bug fix
 def set_num_threads(nt=1, disp=1):
     """see https://github.com/numbbo/coco/issues/1919
+    and https://github.com/CMA-ES/pycma/issues/238
     and https://twitter.com/jeremyphoward/status/1185044752753815552
     """
+    import os
     try: import mkl
     except ImportError: disp and print("mkl is not installed")
     else:
@@ -65,7 +60,14 @@ def set_num_threads(nt=1, disp=1):
     disp and print("setting mkl threads num to", nt)
 
 if sys.platform.lower() not in ('darwin', 'windows'):
-    set_num_threads(1)
+    set_num_threads(1)  # execute before numpy is imported
+
+import time  # output some timings per evaluation
+from collections import defaultdict
+import numpy as np  # for median, zeros, random, asarray
+import cocoex  # experimentation module
+try: import cocopp  # post-processing module
+except: pass
 
 ### solver imports (add other imports if necessary)
 import scipy.optimize  # to define the solver to be benchmarked
@@ -193,7 +195,6 @@ def random_search(f, lbounds, ubounds, evals):
     print("    %3d       %.1e" % (dimension, np.median(timings[dimension])))
 print("  -------------------------------------")
 
-### post-process data
+### post-process data and open browser
 if batches == 1 and 'cocopp' in globals() and cocopp not in (None, 'None'):
     cocopp.main(observer.result_folder)  # re-run folders look like "...-001" etc
-    webbrowser.open("file://" + os.getcwd() + "/ppdata/index.html")

code-experiments/build/python/example/example_experiment_for_beginners.py

@@ -9,9 +9,10 @@
 re-defined accordingly. For example, using `cma.fmin` instead of
 `scipy.optimize.fmin` can be done like::
 
->>> import cma  # doctest:+SKIP
->>> def fmin(fun, x0):
-...     return cma.fmin(fun, x0, 2, {'verbose':-9})
+    import cma
+    def fmin(fun, x0, **kwargs):
+        return cma.fmin2(fun, x0, 2, {'verbose': -9} if not kwargs.get('disp')
+                                     else None)[0]
 
 """
 from __future__ import division, print_function

code-experiments/build/python/src/cocoex/interface.pyx

@@ -762,10 +762,10 @@ cdef class Problem:
         return coco_problem_get_evaluations_constraints(self.problem)
     @property
     def final_target_hit(self):
-        """return 1 if the final target is known and has been hit, 0 otherwise
+        """return `True` if the final target has been hit, `False` otherwise
         """
         assert(self.problem)
-        return coco_problem_final_target_hit(self.problem)
+        return bool(coco_problem_final_target_hit(self.problem))
     #@property
     #def final_target_fvalue1(self):
     #    assert(self.problem)

code-experiments/build/python/src/cocoex/utilities.py

@@ -143,6 +143,8 @@ def write_setting(dict_, filename, ignore_list=None):
 
     See also `dict_to_eval` and `read_setting`.
     """
+    if isinstance(filename, (tuple, list)):
+        filename = _os.path.join(*filename)
     if not _os.path.exists(filename):
         with open(filename, 'wt') as f:
             if ignore_list is None:
@@ -172,6 +174,36 @@ def read_setting(filename, warn=True):
     warn and _warnings.warn("Parameter file '{}' (to check setting consistency)"
                             " does not exist".format(filename))
 
+def forgiving_import(module, warn_level=0):
+    """Do nothing if import fails, return the imported module otherwise.
+
+    Usage::
+
+        cma = forgiving_import('cma')
+
+    in place of::
+
+        import cma
+
+    This is helpful to keep some code smoothly working when `cma` is not
+    installed and not used in the current use case.
+    """
+    try:
+        import importlib
+    except ImportError:
+        print('Please replace \n\n   {}\n\n with \n\n    {}\n\n'
+              'or incomment the respective line.'.format(
+            "module = forgiving_import('module')", 
+            "import module"))
+        raise
+    try:
+        return importlib.import_module(module)
+    except ImportError:
+        if warn_level:
+            print("importing module `{}` with `importlib` failed".format(module))
+        if warn_level > 1:
+            raise
+
 class ObserverOptions(dict):
     """a `dict` with observer options which can be passed to
     the (C-based) `Observer` via the `as_string` property.
@@ -397,8 +429,10 @@ class MiniPrint:
     """
     def __init__(self):
         self.dimension = None
+        self.id_function = None
         self.last_index = -1
-        self._calls = 0
+        self._calls = 0  # formatting aid
+        self._functions = 0  # not in use
         self._sweeps = 0
         self._day0 = _time.localtime()[2]
     @property
@@ -410,17 +444,29 @@ def stime(self):
             s = s + "+%dd" % (ltime[0] - self._day0)
         return s
     def __call__(self, problem, final=False, restarted=False, final_message=False):
-        if self.dimension != problem.dimension or self.last_index > problem.index:
+        new_dimension = self.dimension != problem.dimension or (
+            self.last_index > problem.index)
+        if new_dimension:
+            _sys.stdout.flush()
             if self.dimension is not None:
                 print('')
             print("%dD %s" % (problem.dimension, self.stime))
             self.dimension = problem.dimension
             self._calls = 0
-        elif not self._calls % 10:
-            if self._calls % 50:
-                print(' ', end='')
-            else:
+            self._functions = 0
+        # elif not self._calls % 10:
+        #     if self._calls % 50:
+        #         print(' ', end='')
+        #     else:
+        #         print()
+        if self.id_function != problem.id_function or new_dimension:
+            self.id_function = problem.id_function
+            if not new_dimension and self._calls >= 50:
+                self._calls = 0
                 print()
+            print('{}f{}'.format(' ' if self.id_function < 10 else '',
+                                 self.id_function), end='', flush=True)
+            self._functions += 1
         self.last_index = problem.index
         self._calls += 1
         print('|' if problem.final_target_hit else ':' if restarted else '.', end='')

code-postprocessing/cocopp/compall/pptables.py

@@ -54,20 +54,19 @@ def get_table_caption():
         (preceded by the target !!DF!!-value in \textit{italics}) in the first row. 
         \#succ is the number of trials that reached the target value of the last column.
         """
-
     table_caption_rest = (r"""%
         The median number of conducted function evaluations is additionally given in 
         \textit{italics}, if the target in the last column was never reached.
-        Entries, succeeded by a star, are statistically significantly better (according to
-        the rank-sum test) when compared to all other algorithms of the table, with
-        $p = 0.05$ or $p = 10^{-k}$ when the number $k$ following the star is larger
-        than 1, with Bonferroni correction by the number of functions (!!TOTAL-NUM-OF-FUNCTIONS!!). """ +
+        The best entry is marked by a star when the largest $p$-value of pairwise
+        rank-sum tests with the other algorithms either obeys $0.01 < p \le 0.05$
+        or $10^{-k-1} < p \le 10^{-k}$ when the star is followed by the number $k$,
+        with Bonferroni correction by the number of functions (!!TOTAL-NUM-OF-FUNCTIONS!!). """ +
                 (r"""A ${}$ signifies the number of trials that were worse than the ERT of !!THE-REF-ALG!! """
                  r"""shown only when less than 10 percent were worse and the ERT was better."""
                  .format(significance_vs_ref_symbol)
                     if not (testbedsettings.current_testbed.reference_algorithm_filename == '' or
                             testbedsettings.current_testbed.reference_algorithm_filename is None)
-                 else "") + r"""Best results are printed in bold.
+                 else "") + r""" Best results are printed in bold.
         """)
 
     table_caption = None