updated tests

mdrasmus · Jul 18, 2013 · 7b741d6 · 7b741d6
1 parent 6f408b0
commit 7b741d6
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Showing 26 changed files with 13 additions and 2 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,2 @@
+*.pyc
+*.o
diff --git a/arghmm/__init__.py b/arghmm/__init__.py
@@ -15,6 +15,7 @@
 # if they are not available already
 try:
     import rasmus, compbio
+    rasmus, compbio  # suppress unused pyflakes warning
 except ImportError:
     from . import dep
     dep.load_deps()

diff --git a/arghmm/arghmmc.py b/arghmm/arghmmc.py
@@ -1413,6 +1413,7 @@ def get_treeset(arg, times, start=None, end=None):
     sprs = []
     blocks = []
     all_nodes = []
+    last_tree2 = None
 
     for block, tree, last_tree, spr in iter_arg_sprs(arg, start, end):
 
@@ -1457,6 +1458,7 @@ def get_treeset(arg, times, start=None, end=None):
 
         # setup last tree
         last_tree = tree
+        last_tree2 = tree2
         last_ptree, last_nodes, last_nodelookup = ptree, nodes, nodelookup
 
     return (ptrees, ages, sprs, blocks), all_nodes

diff --git a/arghmm/ctypes_export.py b/arghmm/ctypes_export.py
@@ -7,6 +7,7 @@
 
 import sys
 import os
+from ctypes import c_void_p
 from ctypes import c_bool
 from ctypes import c_char
 from ctypes import c_char_p
@@ -16,6 +17,7 @@
 from ctypes import cast
 from ctypes import cdll
 from ctypes import POINTER
+c_void_p  # pyflaskes ignore
 
 
 def c_list(c_type, lst):

diff --git a/arghmm/deps/compbio/__init__.pyc b/arghmm/deps/compbio/__init__.pyc
diff --git a/arghmm/deps/compbio/alignlib.pyc b/arghmm/deps/compbio/alignlib.pyc
diff --git a/arghmm/deps/compbio/arglib.pyc b/arghmm/deps/compbio/arglib.pyc
diff --git a/arghmm/deps/compbio/birthdeath.pyc b/arghmm/deps/compbio/birthdeath.pyc
diff --git a/arghmm/deps/compbio/coal.pyc b/arghmm/deps/compbio/coal.pyc
diff --git a/arghmm/deps/compbio/fasta.pyc b/arghmm/deps/compbio/fasta.pyc
diff --git a/arghmm/deps/compbio/phylo.pyc b/arghmm/deps/compbio/phylo.pyc
diff --git a/arghmm/deps/compbio/seqlib.pyc b/arghmm/deps/compbio/seqlib.pyc
diff --git a/arghmm/deps/rasmus/__init__.pyc b/arghmm/deps/rasmus/__init__.pyc
diff --git a/arghmm/deps/rasmus/hmm.pyc b/arghmm/deps/rasmus/hmm.pyc
diff --git a/arghmm/deps/rasmus/intervals.pyc b/arghmm/deps/rasmus/intervals.pyc
diff --git a/arghmm/deps/rasmus/linked_list.pyc b/arghmm/deps/rasmus/linked_list.pyc
diff --git a/arghmm/deps/rasmus/plotting.pyc b/arghmm/deps/rasmus/plotting.pyc
diff --git a/arghmm/deps/rasmus/stats.pyc b/arghmm/deps/rasmus/stats.pyc
diff --git a/arghmm/deps/rasmus/svg.pyc b/arghmm/deps/rasmus/svg.pyc
diff --git a/arghmm/deps/rasmus/tablelib.pyc b/arghmm/deps/rasmus/tablelib.pyc
diff --git a/arghmm/deps/rasmus/textdraw.pyc b/arghmm/deps/rasmus/textdraw.pyc
diff --git a/arghmm/deps/rasmus/timer.pyc b/arghmm/deps/rasmus/timer.pyc
diff --git a/arghmm/deps/rasmus/treelib.pyc b/arghmm/deps/rasmus/treelib.pyc
diff --git a/arghmm/deps/rasmus/util.pyc b/arghmm/deps/rasmus/util.pyc
diff --git a/arghmm/popsize.py b/arghmm/popsize.py
@@ -4,7 +4,10 @@
 from math import exp, log, sqrt
 import random
 
-import scipy.optimize
+try:
+    import scipy.optimize
+except ImportError:
+    pass
 
 from rasmus import stats, util
 from compbio import arglib

diff --git a/test/test_codequality.py b/test/test_codequality.py
@@ -94,7 +94,8 @@ def get_python_scripts(*paths):
 
         # Return filenames containing 'python' in the first line
         with open(filename) as infile:
-            if "python" in infile.readline():
+            line = infile.readline()
+            if "python" in line and "python-i" not in line:
                 yield filename