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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/cyvcf2">Debian Med / cyvcf2</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/df9ade504e530e167fdaf16ea4ced6a6a4eb9734">df9ade50</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-11-21T14:23:50+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Commit NMU from Stefano Rivera
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#f886b595f629ccb65b5eb50c747d58998f1dcca3">
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+
debian/patches/python-3.10.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/df9ade504e530e167fdaf16ea4ced6a6a4eb9734#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">cyvcf2 (0.30.11-1.1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Non-maintainer upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Patch: Python 3.10 support - avoid a regression in gzip file handles</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> (Closes: #1000317)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Stefano Rivera <stefanor@debian.org> Sun, 21 Nov 2021 08:38:57 -0400</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">cyvcf2 (0.30.11-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Fix watch URL</span>
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<li id="f886b595f629ccb65b5eb50c747d58998f1dcca3">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/df9ade504e530e167fdaf16ea4ced6a6a4eb9734#f886b595f629ccb65b5eb50c747d58998f1dcca3"><strong>debian/patches/python-3.10.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Stefano Rivera <stefano@rivera.za.net></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Date: Sun, 21 Nov 2021 08:29:40 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Subject: Avoid a Python 3.10 regression in iterating GzipFiles</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">Open the file with a context manager, so we're holding onto a reference to it, for the lifetime of the iteration.</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">This avoids hitting https://bugs.python.org/issue45475 which affects python3.10 3.10.0-4 in Debian.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/1000317</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">Forwarded: https://github.com/brentp/cyvcf2/pull/225</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> cyvcf2/tests/test_reader.py | 21 +++++++++++----------</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> 1 file changed, 11 insertions(+), 10 deletions(-)</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff">diff --git a/cyvcf2/tests/test_reader.py b/cyvcf2/tests/test_reader.py</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">index 76cb9f8..f81b920 100644</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/cyvcf2/tests/test_reader.py</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/cyvcf2/tests/test_reader.py</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -456,16 +456,17 @@</span> def test_var_type():</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> def _get_line_for(v):</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> import gzip</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i, line in enumerate(gzip.open(VCF_PATH), start=1):</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- line = line.decode()</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if line[0] == "#": continue</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- toks = line.strip().split("\t")</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;">- if not (toks[0] == v.CHROM and int(toks[1]) == v.POS): continue</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if toks[3] != v.REF: continue</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if toks[4] not in v.ALT: continue</span></span>
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30
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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 toks</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else:</span></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;">- raise Exception("not found")</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ with gzip.open(VCF_PATH) as f:</span></span>
</pre>
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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;">+ for i, line in enumerate(f, start=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;">+ line = line.decode()</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if line[0] == "#": continue</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ toks = line.strip().split("\t")</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if not (toks[0] == v.CHROM and int(toks[1]) == v.POS): continue</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if toks[3] != v.REF: continue</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if toks[4] not in v.ALT: continue</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return toks</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;">+ else:</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;">+ raise Exception("not found")</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </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"> def _get_samples(v):</span></pre>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/df9ade504e530e167fdaf16ea4ced6a6a4eb9734#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">add_htslib_link_dependency.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">i386.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">python-3.10.patch</span></pre>
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