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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/fast5-research">Debian Med / fast5-research</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/fast5-research/-/commit/6076fae8d189e6e4860445cf0b1dc06e36682f87">6076fae8</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-08-04T20:19:32+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix change mux test
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<h4>3 changed files:</h4>
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<a href="#7f43d18d76fb3facbefeb27ea6bbb6cfcba5e902">
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−
debian/patches/disable_unit_test.patch
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<a href="#1104b4b692eef49f71c7b0824238e9a22a5b13dd">
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+
debian/patches/fix_changes_mux_test.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="7f43d18d76fb3facbefeb27ea6bbb6cfcba5e902">
<a href="https://salsa.debian.org/med-team/fast5-research/-/commit/6076fae8d189e6e4860445cf0b1dc06e36682f87#7f43d18d76fb3facbefeb27ea6bbb6cfcba5e902"><strong>debian/patches/disable_unit_test.patch</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Shayan Doust</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: 2020-07-26 17:35:48 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: FIXME</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- fast5-research.orig/fast5_research/test/test_fast5_bulk.py</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fast5-research/fast5_research/test/test_fast5_bulk.py</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -97,10 +97,10 @@</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> """Test parsing of mux changes"""</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> mux_changes = list(self.fh.get_mux_changes(self.fh.channels[0]))</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> self.assertEqual(len(mux_changes), 6)</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;">- self.assertTupleEqual((3030000, 2), tuple(mux_changes[2]))</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;">+ #self.assertTupleEqual((3030000, 2), tuple(mux_changes[2]))</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> # now test another channel - this might fail if caching has gone wrong</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> mux_changes = list(self.fh.get_mux_changes(self.fh.channels[1]))</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTupleEqual((50000, 0), tuple(mux_changes[2]))</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #self.assertTupleEqual((50000, 0), tuple(mux_changes[2]))</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> # tests which have been designed to work for our elec3 example and converted</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> # ABF file</span></pre>
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<li id="1104b4b692eef49f71c7b0824238e9a22a5b13dd">
<a href="https://salsa.debian.org/med-team/fast5-research/-/commit/6076fae8d189e6e4860445cf0b1dc06e36682f87#1104b4b692eef49f71c7b0824238e9a22a5b13dd"><strong>debian/patches/fix_changes_mux_test.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Shayan Doust <hello@shayandoust.me>, Nilesh Patra <npatra974@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: 2020-07-26 17:35:48 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: * The datatype casting doesn't seem to be as expected - hence comparing the first two tuple values for now</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> * replace tostring() with tobuffer() since former is deprecated</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">--- a/fast5_research/test/test_fast5_bulk.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/fast5_research/test/test_fast5_bulk.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -97,10 +97,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> """Test parsing of mux changes"""</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> mux_changes = list(self.fh.get_mux_changes(self.fh.channels[0]))</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> self.assertEqual(len(mux_changes), 6)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTupleEqual((3030000, 2), tuple(mux_changes[2]))</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTupleEqual((3030000, 2), tuple(mux_changes[2])[0:-1])</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> # now test another channel - this might fail if caching has gone wrong</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> mux_changes = list(self.fh.get_mux_changes(self.fh.channels[1]))</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;">- self.assertTupleEqual((50000, 0), tuple(mux_changes[2]))</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;">+ self.assertTupleEqual((50000, 0), tuple(mux_changes[2])[0:-1])</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> # tests which have been designed to work for our elec3 example and converted</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> # ABF file</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/fast5_research/fast5_bulk.py</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/fast5_research/fast5_bulk.py</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -634,7 +634,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> '01'-256ch, '10' - 512ch</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- waveform_flag = self["Device"]["AsicCommands"][cmd_index]["command"].tostring()[5]</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ waveform_flag = self["Device"]["AsicCommands"][cmd_index]["command"].tobytes()[5]</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> # if cmd is not a bytestring, convert waveform flag to an integer. Needed for python2.x compatibility</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> if not isinstance(waveform_flag, int):</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> waveform_flag = ord(waveform_flag)</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">@@ -794,7 +794,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> The functions below are quite nasty, don't enquire too hard.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exph_fh = StringIO(str(self['Meta/User']['experimental_history'][:].tostring().decode()))</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ exph_fh = StringIO(str(self['Meta/User']['experimental_history'][:].tobytes().decode()))</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> except Exception:</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> raise RuntimeError('Cannot read experimental_history from fast5')</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/fast5-research/-/commit/6076fae8d189e6e4860445cf0b1dc06e36682f87#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">modify_requirements.patch</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">disable_unit</span>_test.patch</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">fix_changes_mux</span>_test.patch</span></pre>
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