MCMC is now running again after all the changes to move CADETMatch to…

… PyPi
cadet · Oct 10, 2019 · 81ad0ef · 81ad0ef
1 parent f0f9913
commit 81ad0ef
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Showing 4 changed files with 14 additions and 14 deletions.
diff --git a/CADETMatch/CADETMatch.pyproj b/CADETMatch/CADETMatch.pyproj
@@ -14,7 +14,7 @@
     <IsWindowsApplication>False</IsWindowsApplication>
     <InterpreterId>CondaEnv|CondaEnv|CADETMatch</InterpreterId>
     <LaunchProvider>Standard Python launcher</LaunchProvider>
-    <CommandLineArguments>"C:\Users\kosh_000\CADET\lessons\lesson_0\example.json"  2</CommandLineArguments>
+    <CommandLineArguments>"F:\temp\cadet_tutorial\lesson_7\bypass\example_bypass.json"  2</CommandLineArguments>
     <EnableNativeCodeDebugging>False</EnableNativeCodeDebugging>
     <InterpreterArguments>-m scoop -n 6</InterpreterArguments>
   </PropertyGroup>

diff --git a/CADETMatch/match.py b/CADETMatch/match.py
@@ -199,6 +199,15 @@ def setupTemplates(cache):
 
         util.setupSimulation(template, cache.target[name]['time'], cache.target[name]['smallest_peak'], cache)
 
+        start = time.time()
+        util.runExperiment(None, experiment, cache.settings, cache.target, template, float(experiment['timeout'])*10, cache)
+        elapsed = time.time() - start
+
+        scoop.logger.info("simulation took %s", elapsed)
+
+        #timeout needs to be stored in the template so all processes have it without calculating it
+        template.root.timeout = elapsed * 10
+
         if cache.settings['searchMethod'] != 'MCMC' and "kde_synthetic" in cache.settings:
             #the base case needs to be saved since the normal template file is what the rest of the code will look for
             template_base_path = Path(cache.settings['resultsDirMisc'], "template_%s_base.h5" % name)
@@ -212,18 +221,9 @@ def setupTemplates(cache):
             template_bias.save()
             template = template_bias
 
-        start = time.time()
-        util.runExperiment(None, experiment, cache.settings, cache.target, template, float(experiment['timeout'])*10, cache)
-        elapsed = time.time() - start
-
-        scoop.logger.info("simulation took %s", elapsed)
-
         #change to where we want the template created
         template.filename = template_path.as_posix()
-
-        #timeout needs to be stored in the template so all processes have it without calculating it
-        template.root.timeout = elapsed * 10
-
+
         template.save()
 
         experiment['simulation'] = template

diff --git a/CADETMatch/pareto.py b/CADETMatch/pareto.py
@@ -52,6 +52,6 @@ def __init__(self, similar=None):
             similar = eq
         super().__init__(similar)
 
-    def update(self, population, cache):
+    def update(self, population):
         "do not put anything in this front, it is just needed to maintain compatibility"
         pass
diff --git a/CADETMatch/search/mcmc.py b/CADETMatch/search/mcmc.py
@@ -371,9 +371,9 @@ def run(cache, tools, creator):
 
         result_data = {'input':[], 'output':[], 'output_meta':[], 'results':{}, 'times':{}, 'input_transform':[], 'input_transform_extended':[], 'strategy':[], 
                    'mean':[], 'confidence':[], 'mcmc_score':[]}
-        halloffame = pareto.DummyFront(similar=util.similar, similar_fit=util.similar_fit)
+        halloffame = pareto.DummyFront(similar=util.similar)
         meta_hof = pareto.ParetoFront(similar=util.similar, similar_fit=util.similar_fit_meta)
-        grad_hof = pareto.DummyFront(similar=util.similar, similar_fit=util.similar_fit)
+        grad_hof = pareto.DummyFront(similar=util.similar)
 
         def local(results):
             return process(cache, halloffame, meta_hof, grad_hof, result_data, results, writer, csvfile, sampler)