Merge remote branch 'pub/master'

diff --git a/pysawsim/histogram.py b/pysawsim/histogram.py
index 5b4480b856fa1abd17623e022c08ef8e8c8a49ae..bb66c05f2bb0c3eebd74cb40b67ae1bafa21ebfb 100644 (file)
--- a/pysawsim/histogram.py
+++ b/pysawsim/histogram.py
@@ -69,7 +69,7 @@ class Histogram (object):
         bin_is = numpy.floor((data - self.bin_edges[0])/bin_width)
         self.counts = []
         for i in range(len(self.bin_edges)-1):
-            self.counts.append(sum(bin_is == i))
+            self.counts.append(sum(bin_is == i).sum())
         self.total = float(len(data)) # some data might be outside the bins
         self.mean = data.mean()
         self.std_dev = data.std()

diff --git a/pysawsim/parameter_error.py b/pysawsim/parameter_error.py
index b75b31043a4392700c1d114c545cb65b28d09afa..f56ba26da72511d93cd49590fa39177c22dd80f9 100644 (file)
--- a/pysawsim/parameter_error.py
+++ b/pysawsim/parameter_error.py
@@ -124,6 +124,7 @@ def main(argv=None):
             'one ends).',
             ])
     parser = OptionParser(usage, epilog=epilog)
+    parser.format_epilog = lambda formatter: epilog+'\n'
     for option in sr.optparse_options:
         if option.dest == 'param_string':
             continue

diff --git a/testing/README b/testing/README
deleted file mode 100644 (file)
index 5e63141..0000000
--- a/testing/README
+++ /dev/null
@@ -1,22 +0,0 @@
-A bunch of validation checks.  Run automatically before allowing
-merges/commits to the main branch.  The smaller, faster subset is run
-before allowing commits/merges to any branch.
-
-Since this software is being developed on a cluster, many of the tests
-take advantage of the more powerful environment.  You should still be
-able to run the tests if you're on a standard machine though, it will
-just take more time :p.  To allow for the differences in invocation,
-the most tests are broken out into two scripts, a X.cl to be run on a
-cluster and an X.sh to be run on a standard machine.
-
-Each test directory contains the script run_test.sh, which gives
-automated testing scripts a common file name to look for.  Exporting
-the global variable ISACLUSTER allows more efficient execution on a
-cluster.  This can be accomplised (in Bash) with the command
-
-  $ export ISACLUSTER=1
-
-Note that it is also necessary to `touch' the testing directory after
-you add or remove a test to update bin/run-test.sh.
-
-The common directory stores code shared among the tests.

diff --git a/testing/common/fitHist.pyc b/testing/common/fitHist.pyc
deleted file mode 100644 (file)
index 91c4938..0000000
Binary files a/testing/common/fitHist.pyc and /dev/null differ

diff --git a/testing/test_cluster.sh b/testing/test_cluster.sh
deleted file mode 100755 (executable)
index d76d77f..0000000
--- a/testing/test_cluster.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/bash
-#
-# Check to make sure the PBS queue is working before going
-# whole hog on the simulations.
-
-if [ "$ISACLUSTER" -eq 1 ]
-then
-    qcmd printenv
-fi
-
-exit 0