HTSeq 2.0.7__tar.gz → 2.0.8__tar.gz

htseq-2.0.8/HTSeq/_version.py

@@ -0,0 +1 @@
+__version__ = "2.0.8"

{htseq-2.0.7 → htseq-2.0.8}/HTSeq.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: HTSeq
-Version: 2.0.7
+Version: 2.0.8
 Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays
 Home-page: https://github.com/htseq
 Author: Simon Anders, Fabio Zanini

{htseq-2.0.7 → htseq-2.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: HTSeq
-Version: 2.0.7
+Version: 2.0.8
 Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays
 Home-page: https://github.com/htseq
 Author: Simon Anders, Fabio Zanini

htseq-2.0.8/VERSION

@@ -0,0 +1 @@
+2.0.8

htseq-2.0.8/scripts/htseq-count

@@ -0,0 +1,6 @@
+#!/usr/bin/env python
+
+import HTSeq.scripts.count
+
+if __name__ == "__main__":
+    HTSeq.scripts.count.main()

{htseq-2.0.7 → htseq-2.0.8}/setup.py

@@ -3,6 +3,7 @@ import os
 import sys
 from setuptools import setup, Command, Extension
 from setuptools.command.build_py import build_py
+import numpy
 
 
 this_directory = os.path.abspath(os.path.dirname(__file__))
@@ -193,7 +194,8 @@ setup(name='HTSeq',
          Extension(
              'HTSeq._HTSeq',
              ['src/_HTSeq.c'],
-             include_dirs=[lazy_numpy_include_dir()],#+get_include_dirs(),
+             #include_dirs=[lazy_numpy_include_dir()],#+get_include_dirs(),
+             include_dirs=[numpy.get_include()],
              extra_compile_args=['-w']),
          Extension(
              'HTSeq._StepVector',

{htseq-2.0.7 → htseq-2.0.8}/src/HTSeq/_HTSeq.pyx

@@ -1168,7 +1168,7 @@ cdef class Sequence(object):
 
     cpdef object add_bases_to_count_array(Sequence self, numpy.ndarray count_array_):
 
-        cdef numpy.ndarray[numpy.int_t, ndim = 2] count_array = count_array_
+        cdef numpy.ndarray[numpy.int64_t, ndim = 2] count_array = count_array_
         cdef int seq_length = len(self.seq)
 
         if numpy.PyArray_DIMS(count_array)[0] < seq_length:
@@ -1383,7 +1383,7 @@ cdef class SequenceWithQualities(Sequence):
     cpdef object add_qual_to_count_array(SequenceWithQualities self,
                                          numpy.ndarray count_array_):
 
-        cdef numpy.ndarray[numpy.int_t, ndim = 2] count_array = count_array_
+        cdef numpy.ndarray[numpy.int64_t, ndim = 2] count_array = count_array_
         if self._qualarr is None:
             self._fill_qual_arr()
         cdef numpy.ndarray[numpy.uint8_t, ndim = 1] qual_array = self._qualarr