Making package compatible with language_level=3

phasedibd/compressed_haplotype_alignment.pxd

@@ -1,6 +1,6 @@
 from libc.stdint cimport uint8_t, uint16_t, uint32_t
 from libc.stdio cimport *
-from haplotype_alignment cimport HaplotypeAlignment
+from .haplotype_alignment cimport HaplotypeAlignment
 
 
 cdef class CompressedHaplotypeAlignment(HaplotypeAlignment):

phasedibd/templated_pbwt_analysis.pxd

@@ -1,8 +1,8 @@
 
 from libc.stdio cimport *
-from haplotype_alignment cimport HaplotypeAlignment
-from compressed_haplotype_alignment cimport CompressedHaplotypeAlignment
-from vcf_haplotype_alignment cimport VcfHaplotypeAlignment
+from .haplotype_alignment cimport HaplotypeAlignment
+from .compressed_haplotype_alignment cimport CompressedHaplotypeAlignment
+from .vcf_haplotype_alignment cimport VcfHaplotypeAlignment
 from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
 
 

phasedibd/templated_pbwt_analysis.pyx

@@ -90,7 +90,7 @@ cdef class TPBWT:
         free(self.segments_end_bp)
         cdef uint32_t num_cols
         if self.current_matches_start != NULL:
-            num_cols = sizeof(self.current_matches_start)/sizeof(self.current_matches_start[0])
+            num_cols = sizeof(self.current_matches_start)//sizeof(self.current_matches_start[0])
             for i in xrange(num_cols):
                 free(self.current_matches_start[i])
                 free(self.current_matches_end[i])
@@ -162,7 +162,7 @@ cdef class TPBWT:
 
         # first free any already allocated memory
         if self.current_matches_start != NULL:
-            num_rows = sizeof(self.current_matches_start)/sizeof(self.current_matches_start[0])
+            num_rows = sizeof(self.current_matches_start)//sizeof(self.current_matches_start[0])
             for i in xrange(num_rows):
                 free(self.current_matches_start[i])
                 free(self.current_matches_end[i])

phasedibd/vcf_haplotype_alignment.pxd

@@ -2,7 +2,7 @@ from libc.stdint cimport uint8_t, uint32_t
 from libc.stdio cimport *
 from libc.stdlib cimport *
 from libc.string cimport *
-from haplotype_alignment cimport HaplotypeAlignment
+from .haplotype_alignment cimport HaplotypeAlignment
 
 
 cdef class VcfHaplotypeAlignment(HaplotypeAlignment):

phasedibd/vcf_haplotype_alignment.pyx

@@ -1,7 +1,7 @@
 # cython: profile=True
 
 from libc.stdlib cimport malloc, free
-from haplotype_alignment cimport HaplotypeAlignment
+from .haplotype_alignment cimport HaplotypeAlignment
 import numpy as np
 cimport numpy as np
 import pandas as pd

requirements.txt

@@ -0,0 +1,3 @@
+pandas==1.2.3
+numpy==1.20.2
+cython==0.29.23

setup.py

@@ -26,6 +26,6 @@
     packages=[name],
     include_package_data=True,
     url='https://github.com/23andme/' + name,
-    ext_modules=cythonize([Extension('phasedibd.*', ['phasedibd/*.pyx'], include_dirs=[np.get_include()])]),
+    ext_modules=cythonize([Extension('phasedibd.*', ['phasedibd/*.pyx'], include_dirs=[np.get_include()])], language_level="3"),
     include_dirs=[np.get_include()]
 )