diff --git a/.gitignore b/.gitignore new file mode 100644 index 00000000..c10fb766 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +*.pyc +*.o diff --git a/arghmm/__init__.py b/arghmm/__init__.py index 4125609e..ea9b4270 100644 --- 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 index 62170754..5f7c6824 100644 --- 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 index 56b3e569..efa8bac3 100644 --- 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 deleted file mode 100644 index 1ef39a5c..00000000 Binary files a/arghmm/deps/compbio/__init__.pyc and /dev/null differ diff --git a/arghmm/deps/compbio/alignlib.pyc b/arghmm/deps/compbio/alignlib.pyc deleted file mode 100644 index 84e8ae64..00000000 Binary files a/arghmm/deps/compbio/alignlib.pyc and /dev/null differ diff --git a/arghmm/deps/compbio/arglib.pyc b/arghmm/deps/compbio/arglib.pyc deleted file mode 100644 index 5b4400d7..00000000 Binary files a/arghmm/deps/compbio/arglib.pyc and /dev/null differ diff --git a/arghmm/deps/compbio/birthdeath.pyc b/arghmm/deps/compbio/birthdeath.pyc deleted file mode 100644 index fe7eb227..00000000 Binary files a/arghmm/deps/compbio/birthdeath.pyc and /dev/null differ diff --git a/arghmm/deps/compbio/coal.pyc b/arghmm/deps/compbio/coal.pyc deleted file mode 100644 index 18c6d766..00000000 Binary files a/arghmm/deps/compbio/coal.pyc and /dev/null differ diff --git a/arghmm/deps/compbio/fasta.pyc b/arghmm/deps/compbio/fasta.pyc deleted file mode 100644 index d8ec7c92..00000000 Binary files a/arghmm/deps/compbio/fasta.pyc and /dev/null differ diff --git a/arghmm/deps/compbio/phylo.pyc b/arghmm/deps/compbio/phylo.pyc deleted file mode 100644 index 962fd17b..00000000 Binary files a/arghmm/deps/compbio/phylo.pyc and /dev/null differ diff --git a/arghmm/deps/compbio/seqlib.pyc b/arghmm/deps/compbio/seqlib.pyc deleted file mode 100644 index 82f5001a..00000000 Binary files a/arghmm/deps/compbio/seqlib.pyc and /dev/null differ diff --git a/arghmm/deps/rasmus/__init__.pyc b/arghmm/deps/rasmus/__init__.pyc deleted file mode 100644 index b88e6330..00000000 Binary files a/arghmm/deps/rasmus/__init__.pyc and /dev/null differ diff --git a/arghmm/deps/rasmus/hmm.pyc b/arghmm/deps/rasmus/hmm.pyc deleted file mode 100644 index 8b620e2d..00000000 Binary files a/arghmm/deps/rasmus/hmm.pyc and /dev/null differ diff --git a/arghmm/deps/rasmus/intervals.pyc b/arghmm/deps/rasmus/intervals.pyc deleted file mode 100644 index c3d0a466..00000000 Binary files a/arghmm/deps/rasmus/intervals.pyc and /dev/null differ diff --git a/arghmm/deps/rasmus/linked_list.pyc b/arghmm/deps/rasmus/linked_list.pyc deleted file mode 100644 index 5ab268df..00000000 Binary files a/arghmm/deps/rasmus/linked_list.pyc and /dev/null differ diff --git a/arghmm/deps/rasmus/plotting.pyc b/arghmm/deps/rasmus/plotting.pyc deleted file mode 100644 index ee410f48..00000000 Binary files a/arghmm/deps/rasmus/plotting.pyc and /dev/null differ diff --git a/arghmm/deps/rasmus/stats.pyc b/arghmm/deps/rasmus/stats.pyc deleted file mode 100644 index b61489a3..00000000 Binary files a/arghmm/deps/rasmus/stats.pyc and /dev/null differ diff --git a/arghmm/deps/rasmus/svg.pyc b/arghmm/deps/rasmus/svg.pyc deleted file mode 100644 index 42ddda7e..00000000 Binary files a/arghmm/deps/rasmus/svg.pyc and /dev/null differ diff --git a/arghmm/deps/rasmus/tablelib.pyc b/arghmm/deps/rasmus/tablelib.pyc deleted file mode 100644 index 49a689cd..00000000 Binary files a/arghmm/deps/rasmus/tablelib.pyc and /dev/null differ diff --git a/arghmm/deps/rasmus/textdraw.pyc b/arghmm/deps/rasmus/textdraw.pyc deleted file mode 100644 index a0e8ea6f..00000000 Binary files a/arghmm/deps/rasmus/textdraw.pyc and /dev/null differ diff --git a/arghmm/deps/rasmus/timer.pyc b/arghmm/deps/rasmus/timer.pyc deleted file mode 100644 index 00f15a0d..00000000 Binary files a/arghmm/deps/rasmus/timer.pyc and /dev/null differ diff --git a/arghmm/deps/rasmus/treelib.pyc b/arghmm/deps/rasmus/treelib.pyc deleted file mode 100644 index 61ed9dce..00000000 Binary files a/arghmm/deps/rasmus/treelib.pyc and /dev/null differ diff --git a/arghmm/deps/rasmus/util.pyc b/arghmm/deps/rasmus/util.pyc deleted file mode 100644 index 6db66314..00000000 Binary files a/arghmm/deps/rasmus/util.pyc and /dev/null differ diff --git a/arghmm/popsize.py b/arghmm/popsize.py index 6221ba24..27bd95b7 100644 --- 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 index c424e397..4eddb964 100644 --- 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