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<h3>
Aaron M. Ucko pushed to branch master
at <a href="https://salsa.debian.org/med-team/iitii">Debian Med / iitii</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/iitii/-/commit/52474065ae2bb050b8b78ee60831143eac395980">52474065</a></strong>
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<span>by Aaron M. Ucko</span>
<i>at 2020-06-09T11:48:41-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use_namespace_iitii_in_test.patch: Address formal part of API break.
Prefix tests' references to iit<...> and iitii<...> with the iitii::
namespace qualifier, with the ekg fork in use here introduced.
NB: This fork also gives builders a mandatory backing-file-path
argument, which this patch does not attempt to supply.
</pre>
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<h4>2 changed files:</h4>
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#29f5a346ce0e989845436e9c187a214837e7439a">
<span class="new-file">
+
debian/patches/use_namespace_iitii_in_test.patch
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</a>
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<h4>Changes:</h4>
<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/iitii/-/commit/52474065ae2bb050b8b78ee60831143eac395980#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use_debian_packaged_libs.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">dynamic_linking.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">use_debian_packages_libs_in_test.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">use_namespace_iitii_in_test.patch</span></pre>
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<li id="29f5a346ce0e989845436e9c187a214837e7439a">
<a href="https://salsa.debian.org/med-team/iitii/-/commit/52474065ae2bb050b8b78ee60831143eac395980#29f5a346ce0e989845436e9c187a214837e7439a"><strong>debian/patches/use_namespace_iitii_in_test.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/test/util.h</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/test/util.h</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -204,5 +204,5 @@</span> vector<variant> load_variants_parallel(c</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> return ans;</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> </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;">-using variant_iit = iit<int, variant, variant_beg, variant_end>;</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-using variant_iitii = iitii<int, variant, variant_beg, variant_end>;</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+using variant_iit = iitii::iit<int, variant, variant_beg, variant_end>;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+using variant_iitii = iitii::iitii<int, variant, variant_beg, variant_end>;</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;">--- a/test/dumb_benchmark.cc</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/dumb_benchmark.cc</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -10,8 +10,8 @@</span> struct dumb_item {</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> uint32_t dumb_beg(const dumb_item& it) { return it.beg; }</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> uint32_t dumb_end(const dumb_item& it) { return it.end; }</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-using dumb_iit = iit<uint32_t, dumb_item, dumb_beg, dumb_end>;</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-using dumb_iitii = iitii<uint32_t, dumb_item, dumb_beg, dumb_end>;</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;">+using dumb_iit = iitii::iit<uint32_t, dumb_item, dumb_beg, dumb_end>;</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+using dumb_iitii = iitii::iitii<uint32_t, dumb_item, dumb_beg, dumb_end>;</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> vector<dumb_item> generate(size_t N) {</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> // each item ranked i has begin position 10*i, with geometrically distributed length mean 20.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/test_iitii.cc</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/test_iitii.cc</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -18,11 +18,11 @@</span> pos get_end(const pospair& p) {</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> auto build_iit(const vector<pospair>& examples) {</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return iit<pos, pospair, &get_beg, &get_end>::builder(examples.begin(), examples.end()).build();</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return iitii::iit<pos, pospair, &get_beg, &get_end>::builder(examples.begin(), examples.end()).build();</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> auto build_iitii(const vector<pospair>& examples, size_t domains) {</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return iitii<pos, pospair, &get_beg, &get_end>::builder(examples.begin(), examples.end()).build(domains);</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return iitii::iitii<pos, pospair, &get_beg, &get_end>::builder(examples.begin(), examples.end()).build(domains);</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> }</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"> TEST_CASE("cgranges example") {</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="p">@@ -182,8 +182,8 @@</span> TEST_CASE("gnomAD chr2") {</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> uniform_int_distribution<uint32_t> begD(0, max_end);</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> const size_t trials = 1000000;</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- auto tree = iit<int, variant, variant_beg, variant_end>::builder(variants.begin(), variants.end()).build();</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- auto treeii = iitii<int, variant, variant_beg, variant_end>::builder(variants.begin(), variants.end()).build(megabases*10);</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ auto tree = iitii::iit<int, variant, variant_beg, variant_end>::builder(variants.begin(), variants.end()).build();</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ auto treeii = iitii::iitii<int, variant, variant_beg, variant_end>::builder(variants.begin(), variants.end()).build(megabases*10);</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> size_t cost = 0, costii=0, count=0;</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> vector<variant> results, resultsii;</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span></pre>
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