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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pbgenomicconsensus">Debian Med / pbgenomicconsensus</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/30192dfc107dc19d23f2b5eef036e13cbc7d47b3">30192dfc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-03-29T15:31:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Ignore one more H5pyDeprecationWarning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/10aa5212a1b2125ad980b4e38334455cf3799b97">10aa5212</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-04-02T08:01:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Simplify tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/15dbea8f5025dc244fe40be4e2245ffbca54bc44">15dbea8f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-04-02T08:01:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix for
DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
which despite its only a warning causes test suite errors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/8b365451f82a4882fad16c10f1ec5d44448811b6">8b365451</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-04-02T08:08:07Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Ignore warning output for unit tests - otherwise python-pbcore would need to be fixed
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#2293cf15b44229f39e25b7928b96dfeba8eda9f0">
debian/patches/ignore_warnings.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#d20a4ea3fff449a7c84c94baa3a54f278944a032">
<span class="new-file">
+
debian/patches/use_frombuffer.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="2293cf15b44229f39e25b7928b96dfeba8eda9f0">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/compare/b8f621cae0509b9f7108506fae51ac743913f0ab...8b365451f82a4882fad16c10f1ec5d44448811b6#2293cf15b44229f39e25b7928b96dfeba8eda9f0"><strong>debian/patches/ignore_warnings.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,3 +50,15 @@ Last-Update: Thu, 28 Mar 2019 13:40:21 +0100</td>
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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"> I like to show the head of the output files inline here so that glaringly obvious changes will</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> pop right out, but I verify that the files are exactly correct by looking at the md5 sums.</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/cram/extra/plurality-fluidigm.t</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/cram/extra/plurality-fluidigm.t</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -7,7 +7,8 @@ Some tests of a "fluidigm amplicons" dat</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> Set the QV threshold to 10.</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </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;">- $ variantCaller --algorithm=plurality -r $REFERENCE -q 10 -o variants.gff -o consensus.csv -o consensus.fastq $INPUT</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;">+ $ variantCaller --algorithm=plurality -r $REFERENCE -q 10 -o variants.gff -o consensus.csv -o consensus.fastq $INPUT 2>&1 | tee | grep -v H5pyDeprecationWarning</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;">+ [1]</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> There are two true SNVs (and one diploid SNV that we miss right now).</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/compare/b8f621cae0509b9f7108506fae51ac743913f0ab...8b365451f82a4882fad16c10f1ec5d44448811b6#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,3 +5,4 @@ no-poa-convenience-script.patch</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">ignore_test_requiring_pbtestdata.patch</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">ignore_test_using_local_data.patch</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">ignore_warnings.patch</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">use_frombuffer.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/compare/b8f621cae0509b9f7108506fae51ac743913f0ab...8b365451f82a4882fad16c10f1ec5d44448811b6#d20a4ea3fff449a7c84c94baa3a54f278944a032"><strong>debian/patches/use_frombuffer.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Fix for</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> which despite its only a warning causes test suite errors</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/925909</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">Last-Update: Thu, 28 Mar 2019 13:40:21 +0100</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></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;">--- a/tests/unit/AlignmentHitStubs.py</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;">+++ b/tests/unit/AlignmentHitStubs.py</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -38,8 +38,8 @@ class AlignmentHitStub(object):</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> self.forwardStrand = not reverseStrand</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> self.referenceStart = referenceStart</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> self.referenceEnd = referenceStart + sum(b != '-' for b in nativeReference)</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;">- self._reference = np.fromstring(nativeReference, dtype="S1")</span></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._read = np.fromstring(read, dtype="S1")</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._reference = np.frombuffer(nativeReference, dtype="S1")</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._read = np.frombuffer(read, dtype="S1")</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"> self._baseFeatures = {}</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> for featureName, feature in kwargs.iteritems():</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -62,7 +62,7 @@ class AlignmentHitStub(object):</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> return val.tostring()</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> def referencePositions(self, orientation="native"):</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- genomicReference = np.fromstring(self.reference(orientation="genomic"), dtype="S1")</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ genomicReference = np.frombuffer(self.reference(orientation="genomic"), dtype="S1")</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> genomicPositions = \</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> self.referenceStart + \</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> np.append(0, np.cumsum(genomicReference != "-")[:-1])</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;">--- a/GenomicConsensus/quiver/model.py</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;">+++ b/GenomicConsensus/quiver/model.py</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -78,7 +78,7 @@ class Model(object):</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> # For cmp.h5 input, we have to use the AlnArray to see where the</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> # gaps are (see bug 20752), in order to support old files.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> #</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;">- alnRead = np.fromstring(aln.read(), dtype=np.int8)</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;">+ alnRead = np.frombuffer(aln.read(), dtype=np.int8)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> gapMask = alnRead == ord("-")</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> _args = [ alnRead[~gapMask].tostring() ]</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> for feature in ALL_FEATURES:</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/GenomicConsensus/utils.py</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/GenomicConsensus/utils.py</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -53,7 +53,7 @@ def complement(s):</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> if type(s) == str:</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> return cStr</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return np.fromstring(cStr, "S1")</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return np.frombuffer(cStr, "S1")</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> def reverseComplement(s):</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> return complement(s)[::-1]</span></pre>
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<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/compare/b8f621cae0509b9f7108506fae51ac743913f0ab...8b365451f82a4882fad16c10f1ec5d44448811b6#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># test_tool_contract.py requires https://github.com/PacificBiosciences/PacBioTestData which is not packaged yet (see #832311)</span>
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2
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Test-Command:</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> cp -r Makefile tests $AUTOPKGTEST_TMP</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> && cd $AUTOPKGTEST_TMP</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> && find . -name test_tool_contract.py -delete</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> && make tests</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> make unit-tests || true</span>
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7
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Depends:</span>
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8
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> @,</span>
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9
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> python-nose,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,9 +9,17 @@ Depends:</td>
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13
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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14
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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15
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Test-Command:</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> cp -r Makefile tests $AUTOPKGTEST_TMP</span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> && cd $AUTOPKGTEST_TMP</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> && make extra-tests</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> make basic-tests</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Depends:</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> @,</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> python-nose,</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> python-cram,</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> make,</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> poa</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Test-Command:</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> make extra-tests</span>
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19
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Depends:</span>
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20
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> @,</span>
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21
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> python-cram,</span>
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