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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-ncls">Debian Med / python-ncls</a>
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Commits:
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<strong><a href="https://salsa.debian.org/med-team/python-ncls/-/commit/4d64cecce52e7b5d3976b760074e7c10142cd001">4d64cecc</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-10-10T21:24:54+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">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
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<h4>2 changed files:</h4>
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<a href="#4e73d5e6152183ae5c444c7573da96ad072fcb5f">
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+
debian/patches/fix-for-32bit.patch
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debian/patches/series
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<h4>Changes:</h4>
<li id="4e73d5e6152183ae5c444c7573da96ad072fcb5f">
<a href="https://salsa.debian.org/med-team/python-ncls/-/commit/4d64cecce52e7b5d3976b760074e7c10142cd001#4e73d5e6152183ae5c444c7573da96ad072fcb5f"><strong>debian/patches/fix-for-32bit.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_ncls.py</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_ncls.py</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -3,38 +3,32 @@</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-starts = np.array([5, 9_223_372_036_854_775_805], dtype=np.long)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ends = np.array([6, 9_223_372_036_854_775_807], dtype=np.long)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ids = np.array([2147483647, 3], dtype=np.long)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> def test_ncls():</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # ids = starts</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print(starts, ends, ids)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ starts = np.array([5, 9_223_100], dtype=np.int64)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ends = np.array([6, 1_223_370_036], dtype=np.int64)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ids = np.array([2147483, 1], dtype=np.int64)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> ncls = NCLS(starts, ends, ids)</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> print(ncls)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> print(ncls.intervals())</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> assert list(ncls.find_overlap(0, 2)) == []</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("aaa", list(ncls.find_overlap(9_223_372_036_854_775_805, 9_223_372_036_854_775_806)))</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert list(ncls.find_overlap(0, 9_223_372_036_854_775_806)) == [(5, 6, 2147483647), (9223372036854775805, 9223372036854775807, 3)]</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("aaa", list(ncls.find_overlap(9_223_100, 1_223_370_036)))</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert list(ncls.find_overlap(0, 1_223_370_036)) == [(5, 6, 2147483), (9223100, 1223370036, 1)]</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> r, l = ncls.all_overlaps_both(starts, ends, ids)</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert list(r) == [2147483647, 3]</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert list(l) == [2147483647, 3]</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert list(r) == [2147483, 1]</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert list(l) == [2147483, 1]</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> def test_all_containments_both():</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- starts = np.array([1291845632, 3002335232], dtype=int)</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ends = np.array([1292894207, 3002597375], dtype=int)</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ids = np.array([0, 1], dtype=int)</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ starts = np.array([1291845632, 2002335232], dtype=np.int64)</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ends = np.array([1292894207, 2002597375], dtype=np.int64)</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ids = np.array([0, 1], dtype=np.int64)</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> ncls = NCLS(starts, ends, ids)</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> subs, covers = ncls.all_containments_both(starts, ends, ids)</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> print(ncls.intervals())</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> assert list(subs) == [0, 1] == list(covers)</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ncls/src/ncls.pyx</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ncls/src/ncls.pyx</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="p">@@ -159,8 +159,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> cdef int nfound = 0</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> cdef int max_end = -1</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- output_arr = np.zeros(length, dtype=long)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- output_arr_other = np.zeros(length, dtype=long)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ output_arr = np.zeros(length, dtype=np.long)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ output_arr_other = np.zeros(length, dtype=np.long)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> cdef long [::1] output</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> cdef long [::1] output_other</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -590,8 +590,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> output_arr = np.zeros(length, dtype=np.long)</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> output_arr_other = np.zeros(length, dtype=np.long)</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cdef int64_t [::1] output</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cdef int64_t [::1] output_other</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cdef long [::1] output</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cdef long [::1] output_other</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> output = output_arr</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> output_other = output_arr_other</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="p">@@ -632,8 +632,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> output_arr = np.zeros(length, dtype=np.long)</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> output_arr_other = np.zeros(length, dtype=np.long)</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cdef int64_t [::1] output</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cdef int64_t [::1] output_other</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cdef long [::1] output</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cdef long [::1] output_other</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> output = output_arr</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> output_other = output_arr_other</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fix-for-32bit.patch</span></pre>
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