Merge pull request #11 from joezuntz/fix-sampler-chain

Fix bug in sampler chaining and add test

cosmosis/main.py

@@ -148,7 +148,7 @@ def setup_output(sampler_class, sampler_number, ini, pool, number_samplers, samp
     if ("filename" in output_options) and (sampler_number<number_samplers-1):
         filename = output_options['filename']
         filename, ext = os.path.splitext(filename)
-        filename += '.' + sampler_name
+        filename += '.' + sampler_class.name
         filename += ext
         output_options['filename'] = filename
 
@@ -349,20 +349,24 @@ def make_graph(inifile, dotfile, params=None, variables=None):
     data = pipeline.run_parameters(pipeline.start_vector())
     pipeline.make_graph(data, dotfile)
 
+
+# Make this global because it is useful for testing
+parser = argparse.ArgumentParser(description="Run a pipeline with a single set of parameters", add_help=True)
+parser.add_argument("inifile", help="Input ini file of parameters")
+parser.add_argument("--mpi",action='store_true',help="Run in MPI mode.")
+parser.add_argument("--smp",type=int,default=0,help="Run with the given number of processes in shared memory multiprocessing (this is experimental and does not work for multinest).")
+parser.add_argument("--pdb",action='store_true',help="Start the python debugger on an uncaught error. Only in serial mode.")
+parser.add_argument("--segfaults", "--experimental-fault-handling", action='store_true',help="Activate a mode that gives more info on segfault")
+parser.add_argument("--mem", type=int, default=0, help="Print out memory usage every this many seconds from root process")
+parser.add_argument("-p", "--params", nargs="*", action=ParseExtraParameters, help="Override parameters in inifile, with format section.name1=value1 section.name2=value2...")
+parser.add_argument("-v", "--variables", nargs="*", action=ParseExtraParameters, help="Override variables in values file, with format section.name1=value1 section.name2=value2...")
+parser.add_argument("--only", nargs="*", help="Fix all parameters except the ones listed")
+parser.add_argument("--graph", type=str, default='', help="Do not run a sampler; instead make a graphviz dot file of the pipeline")
+parser.add_argument('--version', action='version', version=__version__, help="Print out a version number")
+
+
 def main():
     try:
-        parser = argparse.ArgumentParser(description="Run a pipeline with a single set of parameters", add_help=True)
-        parser.add_argument("inifile", help="Input ini file of parameters")
-        parser.add_argument("--mpi",action='store_true',help="Run in MPI mode.")
-        parser.add_argument("--smp",type=int,default=0,help="Run with the given number of processes in shared memory multiprocessing (this is experimental and does not work for multinest).")
-        parser.add_argument("--pdb",action='store_true',help="Start the python debugger on an uncaught error. Only in serial mode.")
-        parser.add_argument("--segfaults", "--experimental-fault-handling", action='store_true',help="Activate a mode that gives more info on segfault")
-        parser.add_argument("--mem", type=int, default=0, help="Print out memory usage every this many seconds from root process")
-        parser.add_argument("-p", "--params", nargs="*", action=ParseExtraParameters, help="Override parameters in inifile, with format section.name1=value1 section.name2=value2...")
-        parser.add_argument("-v", "--variables", nargs="*", action=ParseExtraParameters, help="Override variables in values file, with format section.name1=value1 section.name2=value2...")
-        parser.add_argument("--only", nargs="*", help="Fix all parameters except the ones listed")
-        parser.add_argument("--graph", type=str, default='', help="Do not run a sampler; instead make a graphviz dot file of the pipeline")
-        parser.add_argument('--version', action='version', version=__version__, help="Print out a version number")
         args = parser.parse_args(sys.argv[1:])
 
         if args.graph:

cosmosis/samplers/sampler.py

@@ -24,6 +24,7 @@ def __new__(meta, name, bases, class_dict):
             meta.registry = {name : cls for name, cls in meta.registry.items() if cls not in bases}
             config_name = name[:-len("Sampler")].lower()
             cls = type.__new__(meta, name, bases, class_dict)
+            cls.name = config_name
             meta.registry[config_name] = cls
             return cls
         else:
@@ -51,7 +52,6 @@ def __init__(self, ini, pipeline, output=None):
         self.output = output
         self.attribution = PipelineAttribution(self.pipeline.modules)
         self.distribution_hints = Hints()
-        self.name = self.__class__.__name__[:-len("Sampler")].lower()
         self.write_header()
 
     def write_header(self):

cosmosis/test/test_chaining.py

@@ -0,0 +1,58 @@
+from cosmosis.runtime.config import Inifile
+from cosmosis.main import run_cosmosis, parser
+import tempfile
+import os
+import sys
+import pytest
+import numpy as np
+
+
+def test_sampler_chain():
+
+
+    with tempfile.TemporaryDirectory() as dirname:
+        values_file = f"{dirname}/values.txt"
+        maxlike_file = f"{dirname}/chain.maxlike.txt"
+        fisher_file = f"{dirname}/chain.fisher.txt"
+        emcee_file = f"{dirname}/chain.txt"
+        with open(values_file, "w") as values:
+            values.write(
+                "[parameters]\n"
+                "p1=-3.0  0.0  3.0\n"
+                "p2=-3.0  0.0  3.0\n")
+
+        params = {
+            ('runtime', 'root'): os.path.split(os.path.abspath(__file__))[0],
+            ('runtime', 'sampler'):  "maxlike fisher emcee",
+            ("pipeline", "debug"): "T",
+            ("pipeline", "quiet"): "F",
+            ("pipeline", "modules"): "test1",
+            ("pipeline", "extra_output"): "parameters/p3",
+            ("pipeline", "values"): values_file,
+            ("test1", "file"): "test_module.py",
+            ("output", "filename"): emcee_file,
+            ("emcee", "walkers"): "8",
+            ("emcee", "samples"): "100",
+            ("maxlike", "tolerance"): "0.05",
+            ("fisher", "step_size"): "0.01"
+        }
+
+
+        args = parser.parse_args(["not_a_real_file"])
+        ini = Inifile(None, override=params)
+
+        status = run_cosmosis(args, ini=ini)
+
+        data = np.loadtxt(fisher_file)
+        print(data.shape)
+
+        data = np.loadtxt(maxlike_file)
+        print(data.shape)
+
+        data = np.loadtxt(emcee_file)
+        print(data.shape)
+
+
+
+    assert status == 0
+

cosmosis/version.py

@@ -1 +1 @@
-__version__ = '2.0.1'
+__version__ = '2.0.2'