[med-svn] [Git][med-team/python-ncls][master] Fix for building and passing tests for 32-bit archs

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / python-ncls


Commits:
4d64cecc by Nilesh Patra at 2020-10-10T21:24:54+05:30
Fix for building and passing tests for 32-bit archs

Waiting for upstream's action with respect to https://github.com/biocore-ntnu/ncls/pull/39

- - - - -


2 changed files:

- + debian/patches/fix-for-32bit.patch
- + debian/patches/series


Changes:

=====================================
debian/patches/fix-for-32bit.patch
=====================================
@@ -0,0 +1,86 @@
+--- a/tests/test_ncls.py
++++ b/tests/test_ncls.py
+@@ -3,38 +3,32 @@
+ 
+ import numpy as np
+ 
+-starts = np.array([5, 9_223_372_036_854_775_805], dtype=np.long)
+-
+-ends = np.array([6, 9_223_372_036_854_775_807], dtype=np.long)
+-
+-ids = np.array([2147483647, 3], dtype=np.long)
+-
+ def test_ncls():
+-    # ids = starts
+ 
+-    print(starts, ends, ids)
++    starts = np.array([5, 9_223_100], dtype=np.int64)
++    ends = np.array([6, 1_223_370_036], dtype=np.int64)
++    ids = np.array([2147483, 1], dtype=np.int64)
+ 
+     ncls = NCLS(starts, ends, ids)
+     print(ncls)
+     print(ncls.intervals())
+ 
+     assert list(ncls.find_overlap(0, 2)) == []
+-    print("aaa", list(ncls.find_overlap(9_223_372_036_854_775_805, 9_223_372_036_854_775_806)))
+-    assert list(ncls.find_overlap(0, 9_223_372_036_854_775_806)) == [(5, 6, 2147483647), (9223372036854775805, 9223372036854775807, 3)]
++    print("aaa", list(ncls.find_overlap(9_223_100, 1_223_370_036)))
++    assert list(ncls.find_overlap(0, 1_223_370_036)) == [(5, 6, 2147483), (9223100, 1223370036, 1)]
+ 
+     r, l = ncls.all_overlaps_both(starts, ends, ids)
+-    assert list(r) == [2147483647, 3]
+-    assert list(l) == [2147483647, 3]
++    assert list(r) == [2147483, 1]
++    assert list(l) == [2147483, 1]
+ 
+ def test_all_containments_both():
+ 
+-    starts = np.array([1291845632, 3002335232], dtype=int)
+-    ends = np.array([1292894207, 3002597375], dtype=int)
+-    ids = np.array([0, 1], dtype=int)
++    starts = np.array([1291845632, 2002335232], dtype=np.int64)
++    ends = np.array([1292894207, 2002597375], dtype=np.int64)
++    ids = np.array([0, 1], dtype=np.int64)
+ 
+     ncls = NCLS(starts, ends, ids)
+     subs, covers = ncls.all_containments_both(starts, ends, ids)
+-
+     print(ncls.intervals())
+ 
+     assert list(subs) == [0, 1] == list(covers)
+--- a/ncls/src/ncls.pyx
++++ b/ncls/src/ncls.pyx
+@@ -159,8 +159,8 @@
+         cdef int nfound = 0
+         cdef int max_end = -1
+ 
+-        output_arr = np.zeros(length, dtype=long)
+-        output_arr_other = np.zeros(length, dtype=long)
++        output_arr = np.zeros(length, dtype=np.long)
++        output_arr_other = np.zeros(length, dtype=np.long)
+         cdef long [::1] output
+         cdef long [::1] output_other
+ 
+@@ -590,8 +590,8 @@
+ 
+         output_arr = np.zeros(length, dtype=np.long)
+         output_arr_other = np.zeros(length, dtype=np.long)
+-        cdef int64_t [::1] output
+-        cdef int64_t [::1] output_other
++        cdef long [::1] output
++        cdef long [::1] output_other
+ 
+         output = output_arr
+         output_other = output_arr_other
+@@ -632,8 +632,8 @@
+ 
+         output_arr = np.zeros(length, dtype=np.long)
+         output_arr_other = np.zeros(length, dtype=np.long)
+-        cdef int64_t [::1] output
+-        cdef int64_t [::1] output_other
++        cdef long [::1] output
++        cdef long [::1] output_other
+ 
+         output = output_arr
+         output_other = output_arr_other


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+fix-for-32bit.patch



View it on GitLab: https://salsa.debian.org/med-team/python-ncls/-/commit/4d64cecce52e7b5d3976b760074e7c10142cd001

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-ncls/-/commit/4d64cecce52e7b5d3976b760074e7c10142cd001
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