Merge pull request #91 from mvdbeek/fix_cython_3_compile

Fix compilation with cython 3

.github/workflows/deploy.yaml

@@ -34,8 +34,8 @@ jobs:
           CIBW_ARCHS: ${{matrix.arch}}
           # Skip building musllinux wheels for now, they take too long to build,
           # mainly because numpy doesn't have musllinux wheels on PyPI yet.
-          # Skip also building for PyPy 3.7, which is deprecated upstream.
-          CIBW_SKIP: '*-musllinux* pp37-*'
+          # Skip also building for PyPy 3.7-3.8, which are deprecated upstream.
+          CIBW_SKIP: '*-musllinux* pp37-* pp38-*'
       - name: Check packages
         run: twine check dist/*
       - uses: actions/upload-artifact@v3

.github/workflows/test.yaml

@@ -8,22 +8,22 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.10']
+        python-version: ['3.7', '3.11']
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install flake8
-        run: pip install flake8
+      - name: Install tox
+        run: pip install tox
       - name: Lint
-        run: flake8 .
+        run: tox -e lint
   test:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
@@ -34,4 +34,4 @@ jobs:
       - name: Install tox
         run: pip install tox
       - name: Test
-        run: tox
+        run: tox -e py

MANIFEST.in

@@ -4,3 +4,4 @@ recursive-include src *.c
 recursive-include lib *.h
 recursive-include lib *.c
 recursive-include lib *.pyx
+recursive-include lib *.pxd

lib/bx/_seqmapping.pyx

@@ -132,7 +132,7 @@ cdef class IntToIntMapping:
         cdef int *t_buf
         # Get direct access to string
         PyObject_AsReadBuffer( src, <const void **> &s_buf, &s_len )
-        s_len = s_len / sizeof( int )
+        s_len = s_len // sizeof( int )
         assert s_len == len( src ), "`src` argument must be a buffer of 32bit integers"
         # Initialize empty array
         rval = zeros( s_len, 'i' )

lib/bx/align/epo_tests.py

@@ -164,7 +164,7 @@ def ch(c, ci):
                     assert c[th : th + l] == "-" * l
                 th += l
 
-        for (a, b) in self.epo_records:
+        for a, b in self.epo_records:
             ca, cb = cigar_pairs[int(a.gabid)]
             ch(ca, a.cigar_iter(False))
             ch(cb, b.cigar_iter(False))

lib/bx/align/lav.py

@@ -349,7 +349,7 @@ def build_alignment(self, score, pieces):
         self.open_seqs()
         text1 = text2 = ""
         end1 = end2 = None
-        for (start1, start2, length, _pctId) in pieces:
+        for start1, start2, length, _pctId in pieces:
             if end1 is not None:
                 if start1 == end1:  # insertion in sequence 2
                     text1 += self.seq1_gap * (start2 - end2)
@@ -438,7 +438,6 @@ def build_alignment(self, score, pieces):
 
 
 class Writer:
-
     # blockHash is a hash from (src1,strand1,src2,strand2) to a list of blocks;
     # the blocks are collected on each call to write(), but the actual writing
     # does not occur until close().
@@ -568,7 +567,7 @@ def write_a_stanza(self, alignment):
         print("  s %s" % score, file=self.file)
         print("  b %d %d" % (start1 + 1, start2 + 1), file=self.file)
         print("  e %d %d" % (end1, end2), file=self.file)
-        for (start1, start2, size, pctId) in pieces:
+        for start1, start2, size, pctId in pieces:
             print("  l %d %d %d %d %d" % (start1 + 1, start2 + 1, start1 + size, start2 + size, pctId), file=self.file)
         print("}", file=self.file)
 
@@ -625,7 +624,7 @@ def rc_or_nothing(strand):
 
 
 def do_path_subs(path, path_subs):
-    for (prefix, replacement) in path_subs:
+    for prefix, replacement in path_subs:
         if path.startswith(prefix):
             return replacement + path[len(prefix) :]
     return path

lib/bx/align/lav_tests.py

@@ -11,7 +11,6 @@
 
 class lavTestCase(unittest.TestCase):
     def testReader(self):
-
         reader = lav.Reader(open(test_lav))
 
         a = next(reader)

lib/bx/align/maf_tests.py

@@ -77,7 +77,6 @@
 
 
 def test_reader():
-
     reader = maf.Reader(StringIO(test_maf))
     assert reader.attributes["version"] == "1"
     assert reader.attributes["scoring"] == "humor.v4"
@@ -103,7 +102,6 @@ def test_reader():
 
 
 def test_writer():
-
     val = StringIO()
     writer = maf.Writer(val, {"scoring": "foobar"})
 
@@ -134,7 +132,6 @@ def test_writer():
 
 
 def test_slice():
-
     b = complex_maf.slice_by_component(0, 101, 105)
 
     check_component(b.components[0], src="human_hoxa", start=101, size=4, strand="+", src_size=100257, text="CA-TT")
@@ -181,7 +178,6 @@ def test_slice():
 
 
 def test_reverse_complement():
-
     b = complex_maf.reverse_complement()
 
     check_component(

lib/bx/arrays/array_tree.pyx

@@ -7,8 +7,6 @@ from numpy import *
 
 cimport numpy
 
-cimport bx.arrays.wiggle
-
 from bx.misc.binary_file import (
     BinaryFileReader,
     BinaryFileWriter,

lib/bx/bbi/bbi_file.pxd

@@ -1,12 +1,16 @@
-from types cimport *
-
-from bpt_file cimport BPTFile
-from cirtree_file cimport CIRTreeFile
-
 import numpy
 
 cimport numpy
 
+from .bpt_file cimport BPTFile
+from .cirtree_file cimport CIRTreeFile
+from .types cimport (
+    bits16,
+    bits32,
+    bits64,
+    boolean,
+)
+
 
 cdef class SummaryBlock:
     """

lib/bx/bbi/bbi_file.pyx

@@ -9,27 +9,25 @@ mirrors Jim Kent's 'bbiRead.c' mostly.
 
 from cpython.version cimport PY_MAJOR_VERSION
 
+import math
 import sys
-
-cimport cython
-
+import zlib
 from collections import deque
-
-from types cimport *
-
-from bpt_file cimport BPTFile
-from cirtree_file cimport CIRTreeFile
-from libc cimport limits
+from io import BytesIO
 
 import numpy
 
-cimport numpy
+from bx.misc.binary_file import BinaryFileReader
 
-import math
-import zlib
-from io import BytesIO
+cimport cython
+from libc cimport limits
 
-from bx.misc.binary_file import BinaryFileReader
+from .bpt_file cimport BPTFile
+from .cirtree_file cimport CIRTreeFile
+from .types cimport (
+    bits32,
+    bits64,
+)
 
 
 cdef extern from "Python.h":
@@ -95,7 +93,7 @@ cdef class SummarizedData:
             e = self.end
         if s >= e: 
             return
-        base_step = ( self.end - self.start ) / self.size
+        base_step = ( self.end - self.start ) // self.size
         for j from 0 <= j < self.size:
             base_start = self.start + ( base_step * j )
             base_end = base_start + base_step
@@ -206,8 +204,8 @@ cdef class BBIFile:
 
         # Find appropriate zoom level
         cdef bits32 base_size = end - start
-        cdef int full_reduction = base_size / summary_size
-        cdef int zoom = full_reduction / 2
+        cdef int full_reduction = base_size // summary_size
+        cdef int zoom = full_reduction // 2
         if zoom < 0:
             zoom = 0
         cdef ZoomLevel zoom_level = self._best_zoom_level( zoom )
@@ -418,7 +416,7 @@ cdef class ZoomLevel:
         reader.seek( self.index_offset )
         summaries = self._summary_blocks_in_region(chrom_id, start, end)
 
-        base_step = (end - start) / summary_size
+        base_step = (end - start) // summary_size
         base_start = start
         base_end = start
 

lib/bx/bbi/bigbed_file.pyx

@@ -2,20 +2,23 @@
 BigBed file.
 """
 
-from bbi_file cimport *
-from cirtree_file cimport CIRTreeFile
+import zlib
+from io import BytesIO
 
 import numpy
 
-from types cimport *
+from bx.intervals.io import GenomicInterval
+from bx.misc.binary_file import BinaryFileReader
 
 cimport numpy
 
-import zlib
-from io import BytesIO
-
-from bx.intervals.io import GenomicInterval
-from bx.misc.binary_file import BinaryFileReader
+from .bbi_file cimport (
+    BBIFile,
+    BlockHandler,
+    SummarizedData,
+)
+from .cirtree_file cimport CIRTreeFile
+from .types cimport bits32
 
 DEF big_bed_sig = 0x8789F2EB
 

lib/bx/bbi/bigwig_file.pyx

@@ -2,21 +2,28 @@
 BigWig file.
 """
 
+import zlib
 from collections import deque
-
-from bbi_file cimport *
-from cirtree_file cimport CIRTreeFile
+from io import BytesIO
 
 import numpy
 
-from types cimport *
+from bx.misc.binary_file import BinaryFileReader
 
 cimport numpy
 
-import zlib
-from io import BytesIO
-
-from bx.misc.binary_file import BinaryFileReader
+from .bbi_file cimport (
+    BBIFile,
+    BlockHandler,
+    SummarizedData,
+)
+from .cirtree_file cimport CIRTreeFile
+from .types cimport (
+    bits8,
+    bits16,
+    bits32,
+    UBYTE,
+)
 
 DEF big_wig_sig = 0x888FFC26
 DEF bwg_bed_graph = 1

lib/bx/bbi/bpt_file.pxd

@@ -1,6 +1,6 @@
 from bx.misc.binary_file import BinaryFileReader
 
-from types cimport *
+from .types cimport *
 
 
 cdef class BPTFile:

lib/bx/bbi/cirtree_file.pxd

@@ -1,4 +1,4 @@
-from types cimport *
+from .types cimport *
 
 
 cdef class CIRTreeFile:

lib/bx/bbi/types.pxd

@@ -1,9 +1,9 @@
-ctypedef unsigned char UBYTE 
-ctypedef signed char BYTE 
-ctypedef unsigned short UWORD 
-ctypedef short WORD         
-ctypedef unsigned long long bits64 
-ctypedef unsigned bits32    
+ctypedef unsigned char UBYTE
+ctypedef signed char BYTE
+ctypedef unsigned short UWORD
+ctypedef short WORD
+ctypedef unsigned long long bits64
+ctypedef unsigned bits32
 ctypedef unsigned short bits16
 ctypedef unsigned char bits8
 ctypedef int signed32