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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-biopython">Debian Med / python-biopython</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/commit/bb94263daca0cd51968305805e444d0254c01c48">bb94263d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-19T16:46:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Ignore some failing test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/commit/e22d86592d4c29c723297d3d5eb9cc63aa6f8fb8">e22d8659</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-19T18:12:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">exclude docstring tests - thanks to Peter Cock
</pre>
</li>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#22dad11c4258d7172f59c0983ae1670bf75c20b8">
<span class="new-file">
+
debian/patches/5af680b5043c9f160a19e4bb0deab0ccc271280d.patch
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</a>
</li>
<li class="file-stats">
<a href="#7c682a827c589a6a3102862176bda55435525544">
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+
debian/patches/exclude_docstring_tests.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
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<h4>Changes:</h4>
<li id="22dad11c4258d7172f59c0983ae1670bf75c20b8">
<a href="https://salsa.debian.org/med-team/python-biopython/compare/3dbc41144094f7a25205d0a4445f68e95609ccce...e22d86592d4c29c723297d3d5eb9cc63aa6f8fb8#22dad11c4258d7172f59c0983ae1670bf75c20b8"><strong>debian/patches/5af680b5043c9f160a19e4bb0deab0ccc271280d.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From 5af680b5043c9f160a19e4bb0deab0ccc271280d Mon Sep 17 00:00:00 2001</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Peter Cock <p.j.a.cock@googlemail.com></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Date: Tue, 19 Nov 2019 09:59:16 +0000</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Subject: [PATCH] Ignore C modules with no docstrings</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> Does not work as expected</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>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> Tests/run_tests.py | 9 +++++++++</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> 1 file changed, 9 insertions(+)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff">diff --git a/Tests/run_tests.py b/Tests/run_tests.py</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gh" style="color: #999;">index 15503f65d5..084df08afc 100644</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Tests/run_tests.py</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Tests/run_tests.py</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -358,6 +358,15 @@</span> def runTest(self, name):</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> except MissingPythonDependencyError:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> sys.stderr.write("skipped, missing Python dependency\n")</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> return True</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;">+ except ValueError as e:</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;">+ if str(e).startswith("module ") and str(e).endswith("has no docstrings"):</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Seen with some C modules via Debian build testing</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;">+ sys.stderr.write("skipped, has no docstrings\n")</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return True</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sys.stderr.write("FAIL, ValueError\n")</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ result.stream.write("ERROR while importing %s: %s\n" % (name, e))</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ result.printErrors()</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return False</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> except ImportError as e:</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> sys.stderr.write("FAIL, ImportError\n")</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> result.stream.write("ERROR while importing %s: %s\n" % (name, e))</span></pre>
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<li id="7c682a827c589a6a3102862176bda55435525544">
<a href="https://salsa.debian.org/med-team/python-biopython/compare/3dbc41144094f7a25205d0a4445f68e95609ccce...e22d86592d4c29c723297d3d5eb9cc63aa6f8fb8#7c682a827c589a6a3102862176bda55435525544"><strong>debian/patches/exclude_docstring_tests.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Peter Cock <p.j.a.cock@googlemail.com></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 19 Nov 2019 10:03:25 +0000</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/944242</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Description: Test issues with BioPython 1.75</span></span>
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5
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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/Tests/run_tests.py</span>
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7
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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/Tests/run_tests.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -148,9 +148,9 @@</span> except ImportError:</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> # Skip Bio.Seq doctest under Python 2, see http://bugs.python.org/issue7490</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> # Can't easily write exceptions with consistent class name in python 2 and 3</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;">-if sys.version_info[0] == 2:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXCLUDE_DOCTEST_MODULES.append("Bio.Seq")</span></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;">- EXCLUDE_DOCTEST_MODULES.append("Bio.Phylo")</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if sys.version_info[0] == 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;">+# EXCLUDE_DOCTEST_MODULES.append("Bio.Seq")</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;">+# EXCLUDE_DOCTEST_MODULES.append("Bio.Phylo")</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"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> def find_modules(path):</span></pre>
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<a href="https://salsa.debian.org/med-team/python-biopython/compare/3dbc41144094f7a25205d0a4445f68e95609ccce...e22d86592d4c29c723297d3d5eb9cc63aa6f8fb8#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">@@ -2,3 +2,5 @@ remove_mathml-qname.patch</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">privacy_breach.patch</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">reportlab3.5.patch</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">python_3.8_iteration_fix.patch</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"># 5af680b5043c9f160a19e4bb0deab0ccc271280d.patch</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">exclude_docstring_tests.patch</span></pre>
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