debian/changelog

+python-bx (0.8.5-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Steffen Moeller <moeller@debian.org>  Fri, 08 Nov 2019 19:12:56 +0100
+
 python-bx (0.8.4-2) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -15,7 +15,7 @@ Build-Depends: debhelper-compat (= 12),
                python3-numpy,
                python3-six,
                cython3
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-bx
 Vcs-Git: https://salsa.debian.org/med-team/python-bx.git
 Homepage: https://github.com/bxlab/bx-python

debian/patches/no-download.patch

@@ -6,7 +6,7 @@ Index: python-bx/setup.py
 ===================================================================
 --- python-bx.orig/setup.py
 +++ python-bx/setup.py
-@@ -9,8 +9,8 @@ elif sys.version_info > (3, ) and sys.ve
+@@ -11,8 +11,8 @@ elif sys.version_info > (3, ) and sys.ve
  try:
      from setuptools import setup, find_packages
  except ImportError:
@@ -15,5 +15,5 @@ Index: python-bx/setup.py
 +    print >> sys.stderr, "ERROR: setuptools not installed. Please report this bug as instructed on https://bugs.debian.org/cgi-bin/pkgreport.cgi?package=python-bx"
 +    sys.exit()
  
- from setuptools import *
- from glob import glob
+ from setuptools import Extension  # noqa: E402
+ 

lib/bx/bbi/bigwig_file.pyx

@@ -123,6 +123,36 @@ cdef class ArrayAccumulatingBlockHandler( BigWigBlockHandler ):
         for i from s - self.start <= i < e - self.start:
             array[ i ] = val
 
+cdef class BigWigHeaderBlockHandler( BigWigBlockHandler ):
+    "Reads and returns headers"
+    cdef list headers
+
+    def __init__( self, bits32 start, bits32 end ):
+        BigWigBlockHandler.__init__( self, start, end )
+        self.headers = []
+
+    cdef handle_block( self, bytes block_data, BBIFile bbi_file ):
+        cdef bits32 b_chrom_id, b_start, b_end, b_valid_count
+        cdef bits32 b_item_step, b_item_span
+        cdef bits16 b_item_count
+        cdef UBYTE b_type
+        cdef int s, e
+        cdef float val
+        # parse the block header
+        block_reader = BinaryFileReader( BytesIO( block_data ), is_little_endian=bbi_file.reader.is_little_endian )
+        b_chrom_id = block_reader.read_uint32()
+        b_start = block_reader.read_uint32()
+        b_end = block_reader.read_uint32()
+        b_item_step = block_reader.read_uint32()
+        b_item_span = block_reader.read_uint32()
+        b_type = block_reader.read_uint8()
+        block_reader.skip(1)
+        b_item_count = block_reader.read_uint16()
+        self.handle_header( b_start, b_end,  b_item_step, b_item_span, b_type, b_item_count )
+
+    cdef handle_header( self, bits32 start, bits32 end, bits32 step, bits32 span, bits8 type, bits16 itemCount ):
+        self.headers.append( ( start, end, step, span, type, itemCount ) )
+
 cdef class BigWigFile( BBIFile ):
     """
     A "big binary indexed" file whose raw data is in wiggle format.
@@ -167,6 +197,15 @@ cdef class BigWigFile( BBIFile ):
         self.visit_blocks_in_region( chrom_id, start, end, v )
         return v.array
 
+    cpdef get_headers( self, char * chrom, bits32 start, bits32 end ):
+        if start >= end:
+            return None
+        chrom_id, chrom_size = self._get_chrom_id_and_size( chrom )
+        if chrom_id is None:
+            return None
+        v = BigWigHeaderBlockHandler( start, end )
+        self.visit_blocks_in_region( chrom_id, start, end, v )
+        return v.headers
 
 
 

lib/bx/bbi/bpt_file.pyx

@@ -71,6 +71,6 @@ cdef class BPTFile:
             return None
         # Key is less than key_size, right pad with 0 bytes
         if len(key) < self.key_size:
-            key += ( '\0' * ( self.key_size - len(key) ) )
+            key += b'\0' * (self.key_size - len(key))
         # Call the recursive finder
         return self.r_find(self.root_offset, key)

setup.py

 import platform
 import sys
+from distutils.core import Command
+from glob import glob
 
 if sys.version_info < (2, 6):
     sys.exit("ERROR: bx-python requires Python 2.6 or greater")
@@ -12,14 +14,14 @@ except ImportError:
     from ez_setup import use_setuptools
     use_setuptools()
 
-from setuptools import *
-from glob import glob
+from setuptools import Extension  # noqa: E402
+
 
 def main():
 
-    metadata = \
-      dict( name = "bx-python",
-            version = "0.8.4",
+    metadata = dict(
+        name="bx-python",
+        version="0.8.5",
         setup_requires=['numpy', 'cython'],
         install_requires=['numpy', 'six'],
         py_modules=['psyco_full'],
@@ -40,15 +42,14 @@ def main():
             "License :: OSI Approved :: MIT License",
             "Operating System :: POSIX",
             "Programming Language :: Python :: 2",
-                "Programming Language :: Python :: 2.6",
             "Programming Language :: Python :: 2.7",
             "Programming Language :: Python :: 3",
-                "Programming Language :: Python :: 3.3",
-                "Programming Language :: Python :: 3.4",
             "Programming Language :: Python :: 3.5",
+            "Programming Language :: Python :: 3.6",
+            "Programming Language :: Python :: 3.7",
+            "Programming Language :: Python :: 3.8",
             "Topic :: Scientific/Engineering :: Bio-Informatics",
-                "Topic :: Software Development :: Libraries :: Python Modules"
-            ],
+            "Topic :: Software Development :: Libraries :: Python Modules"],
         zip_safe=False,
         dependency_links=[],
         cmdclass=command_classes)
@@ -58,11 +59,11 @@ def main():
         import numpy
         # Suppress numpy tests
         numpy.test = None
-    except:
+    except Exception:
         pass
 
-    if len(sys.argv) >= 2 and ('--help' in sys.argv[1:] or
-            sys.argv[1] in ('--help-commands', 'egg_info', '--version', 'clean')):
+    if len(sys.argv) >= 2 and \
+            ('--help' in sys.argv[1:] or sys.argv[1] in ('--help-commands', 'egg_info', '--version', 'clean')):
         # For these actions, NumPy is not required.
         #
         # They are required to succeed without Numpy for example when
@@ -80,14 +81,12 @@ def main():
 
 # ---- Commands -------------------------------------------------------------
 
-from distutils.core import Command
-
 # Use build_ext from Cython if found
 command_classes = {}
 try:
     import Cython.Distutils
     command_classes['build_ext'] = Cython.Distutils.build_ext
-except:
+except Exception:
     pass
 
 # Run 2to3 builder if we're on Python 3.x, from
@@ -103,14 +102,20 @@ command_classes['build_py'] = build_py
 try:
     import pkg_resources
     pkg_resources.require("epydoc")
-    import epydoc.cli, sys, os, os.path
+    import epydoc.cli
+    import os
+    import os.path
+
     # Create command class to build API documentation
     class BuildAPIDocs(Command):
         user_options = []
+
         def initialize_options(self):
             pass
+
         def finalize_options(self):
             pass
+
         def run(self):
             # Save working directory and args
             old_argv = sys.argv
@@ -133,7 +138,7 @@ try:
             os.chdir(old_cwd)
     # Add to extra_commands
     command_classes['build_apidocs'] = BuildAPIDocs
-except:
+except Exception:
     pass
 
 # ---- Extension Modules ----------------------------------------------------
@@ -143,6 +148,7 @@ except:
 # _Extension = Extension
 # Extension = partial(_Extension, extra_compile_args=["-Wno-cpp"])
 
+
 def get_extension_modules(numpy_include=None):
     extensions = []
     # Bitsets
@@ -168,10 +174,8 @@ def get_extension_modules( numpy_include=None ):
                                 include_dirs=["src/samtools"],
                                 libraries=['z']))
 
-    
     # The following extensions won't (currently) compile on windows
     if platform.system() not in ('Microsoft', 'Windows'):
-        
         # Interval clustering
         extensions.append(Extension("bx.intervals.cluster",
                                     ["lib/bx/intervals/cluster.pyx",
@@ -202,9 +206,8 @@ def get_extension_modules( numpy_include=None ):
         extensions.append(Extension("bx.arrays.bed", ["lib/bx/arrays/bed.pyx"]))
         extensions.append(Extension("bx.arrays.wiggle", ["lib/bx/arrays/wiggle.pyx"]))
 
-
         # CpG masking
-        extensions.append( Extension( "bx.align.sitemask._cpg", \
+        extensions.append(Extension("bx.align.sitemask._cpg",
                                     ["lib/bx/align/sitemask/_cpg.pyx",
                                      "lib/bx/align/sitemask/find_cpg.c"]))
 
@@ -219,5 +222,6 @@ def get_extension_modules( numpy_include=None ):
                                     include_dirs=["src/bunzip"]))
     return extensions
 
+
 if __name__ == "__main__":
     main()