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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/falcon">Debian Med / falcon</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/falcon/-/commit/0f51ee7a0acd794e00e4f51f5feb79864f80a875">0f51ee7a</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-08-29T03:35:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Down to 17 failed tests, 79 passed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/falcon/-/commit/5509c29f3d0729d6fef6a6de1423d78a5ec98658">5509c29f</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-08-29T03:36:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cosmetics.
</pre>
</li>
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<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#06477578e35a911b5aae2acd8e113067ac2bfcb4">
<span class="new-file">
+
debian/patches/fixUnicodeReadHelpers.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#fef9c82c781e746de67b59c9dd5a6f29dbb7ddad">
<span class="new-file">
+
debian/patches/introduceRawStrings.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#73edb67a952087ac62e6a7ae5e7ba31e11dfe4c7">
<span class="new-file">
+
debian/patches/networkx_addPath.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#c95b49fcdcf94cb632aec008933196e57cb26c3c">
debian/patches/python2to3.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/falcon/-/compare/3492618ac8be3cb1cae995da7c7582e574494305...5509c29f3d0729d6fef6a6de1423d78a5ec98658#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" 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>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" 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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,9 +5,11 @@ Section: science</td>
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5
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<td class="diff-line-num new_line" data-linenumber="5" 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">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<td class="diff-line-num old_line" data-linenumber="6" 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">
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<td class="diff-line-num new_line" data-linenumber="6" 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">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<td class="diff-line-num old_line" data-linenumber="7" 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">
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<td class="diff-line-num new_line" data-linenumber="7" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<td class="diff-line-num new old_line" data-linenumber="8" 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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<td class="diff-line-num new new_line" data-linenumber="8" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python3-all-dev,</span>
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<td class="diff-line-num new old_line" data-linenumber="8" 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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<td class="diff-line-num new new_line" data-linenumber="9" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<td class="diff-line-num old_line" data-linenumber="8" 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">
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<td class="diff-line-num new_line" data-linenumber="10" 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">
10
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> cython3,</span>
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<td class="diff-line-num old_line" data-linenumber="9" 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">
9
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<td class="diff-line-num new_line" data-linenumber="11" 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">
11
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> nim,</span>
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<td class="diff-line-num old old_line" data-linenumber="10" 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">
10
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<td class="diff-line-num new_line old" data-linenumber="12" 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">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> <span class="idiff left right">python3-all-dev</span>,</span>
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<td class="diff-line-num new old_line" data-linenumber="11" 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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<td class="diff-line-num new new_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> <span class="idiff left right">rsync</span>,</span>
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<td class="diff-line-num old_line" data-linenumber="11" 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">
11
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<td class="diff-line-num new_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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-future (>= 0.16.0),</span>
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<td class="diff-line-num old_line" data-linenumber="12" 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">
12
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<td class="diff-line-num new_line" data-linenumber="14" 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">
14
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> python3-msgpack,</span>
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<td class="diff-line-num 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">
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<td class="diff-line-num new_line" data-linenumber="15" 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">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> python3-networkx (>= 2.5),</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" 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>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" 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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,8 +17,6 @@ Build-Depends: debhelper-compat (= 13),</td>
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<td class="diff-line-num old_line" data-linenumber="15" 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">
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<td class="diff-line-num new_line" data-linenumber="17" 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">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> python3-numpy,</span>
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<td class="diff-line-num old_line" data-linenumber="16" 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">
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<td class="diff-line-num new_line" data-linenumber="18" 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">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> python3-h5py,</span>
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<td class="diff-line-num old_line" data-linenumber="17" 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">
17
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<td class="diff-line-num new_line" data-linenumber="19" 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">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> python3-pytest,</span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
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<td class="diff-line-num new_line old" data-linenumber="20" 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">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> python3-setuptools,</span>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
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<td class="diff-line-num new_line old" data-linenumber="20" 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">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> rsync</span>
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<td class="diff-line-num old_line" data-linenumber="20" 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">
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<td class="diff-line-num new_line" data-linenumber="20" 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">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<td class="diff-line-num old_line" data-linenumber="21" 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">
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<td class="diff-line-num new_line" data-linenumber="21" 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">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/falcon</span>
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<td class="diff-line-num old_line" data-linenumber="22" 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">
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<td class="diff-line-num new_line" data-linenumber="22" 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">
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/falcon.git</span>
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</li>
<li id="06477578e35a911b5aae2acd8e113067ac2bfcb4">
<a href="https://salsa.debian.org/med-team/falcon/-/compare/3492618ac8be3cb1cae995da7c7582e574494305...5509c29f3d0729d6fef6a6de1423d78a5ec98658#06477578e35a911b5aae2acd8e113067ac2bfcb4"><strong>debian/patches/fixUnicodeReadHelpers.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: falcon/FALCON/test/helpers.py</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- falcon.orig/FALCON/test/helpers.py</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ falcon/FALCON/test/helpers.py</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -30,9 +30,10 @@</span> def get_test_data_dir():</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"> def assert_filecmp(got, expected_path):</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #result = [line.strip() for line in StringIO(got)] # fails on unicode</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;">+ result = [line.strip() for line in StringIO(got)] # fails on unicode</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> #result = [line.strip() for line in io.TextIOWrapper(io.StringIO(got))] # for unicode</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;">- result = [line.strip() for line in StringIO(bytes(got, 'utf-8'))]</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;">+ #result = [line.strip() for line in StringIO(bytes(got, 'utf-8'))]</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;">+ #result = [line.strip() for line in StringIO(got.encode('utf-8'))]</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> expected = [line.strip() for line in open(expected_path)]</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> diffs = list(difflib.context_diff(result, expected, fromfile='got', tofile='expected'))</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> if diffs:</span></pre>
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<li id="fef9c82c781e746de67b59c9dd5a6f29dbb7ddad">
<a href="https://salsa.debian.org/med-team/falcon/-/compare/3492618ac8be3cb1cae995da7c7582e574494305...5509c29f3d0729d6fef6a6de1423d78a5ec98658#fef9c82c781e746de67b59c9dd5a6f29dbb7ddad"><strong>debian/patches/introduceRawStrings.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Steffen Moeller</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Reacting to deprecation warnings like</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> /home/moeller/git/med-team/falcon/FALCON/falcon_kit/run_support.py:311: DeprecationWarning: The SafeConfigParser class has been renamed to ConfigParser in Python 3.2. This alias will be removed in future versions. Use ConfigParser directly instead.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> And to the use of backstrings in non-raw Python strings.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">Index: falcon/FALCON/falcon_kit/functional.py</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></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;">--- falcon.orig/FALCON/falcon_kit/functional.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ falcon/FALCON/falcon_kit/functional.py</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -312,7 +312,7 @@</span> def parsed_readlengths_from_dbdump_outpu</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> """Given output text from the DBump command,</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> yield all read-lengths.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> """</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;">- re_length = re.compile('^L\s+\d+\s+(\d+)\s+(\d+)$')</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ re_length = re.compile(r'^L\s+\d+\s+(\d+)\s+(\d+)$')</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> for line in output.splitlines():</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> mo = re_length.search(line)</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> if mo:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -331,8 +331,8 @@</span> def mapped_readlengths_from_dbdump_outpu</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> https://dazzlerblog.wordpress.com/command-guides/dazz_db-command-guide/</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> lengths = dict()</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- re_rid = re.compile('^R\s+(\d+)$')</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- re_length = re.compile('^L\s+(\d+)\s+(\d+)\s+(\d+)$')</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ re_rid = re.compile(r'^R\s+(\d+)$')</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ re_length = re.compile(r'^L\s+(\d+)\s+(\d+)\s+(\d+)$')</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> for line in output.splitlines():</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> mo = re_rid.search(line)</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> if mo:</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gh" style="color: #999;">Index: falcon/FALCON/falcon_kit/mains/ovlp_to_graph.py</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- falcon.orig/FALCON/falcon_kit/mains/ovlp_to_graph.py</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ falcon/FALCON/falcon_kit/mains/ovlp_to_graph.py</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="p">@@ -1443,7 +1443,7 @@</span> def ovlp_to_graph(args):</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> compound_path_file.close()</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"> # remove short utg using local flow consistent rule</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ r"""</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> short UTG like this can be removed, this kind of utg are likely artifects of repeats</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> >____ _____></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> \__UTG_>__/</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gh" style="color: #999;">Index: falcon/FALCON/falcon_kit/stats_preassembly.py</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></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;">--- falcon.orig/FALCON/falcon_kit/stats_preassembly.py</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ falcon/FALCON/falcon_kit/stats_preassembly.py</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="p">@@ -141,7 +141,7 @@</span> def metric_fragmentation(preads_fofn):</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> # sed -nr 's;>prolog/([0-9]*)[0-9]/.*;\1;p' %s/*.fasta | sort | uniq -c | awk '{print $1}' | sort | uniq -c</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> fastas = abs_filenames(preads_fofn)</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> assert fastas, 'No fasta found in {!r}'.format(preads_fofn)</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- call = """perl -e 'while (<>) { if ( m{>[^/]+/(\d+)\d/} ) { $id{$1}++; } }; while (my ($k, $v) = each %%id) { $counts{$v}++; }; while (my ($k, $v) = each %%counts) { print "$v $k\n"; };' %s""" % (' '.join(fastas))</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ call = r"""perl -e 'while (<>) { if ( m{>[^/]+/(\d+)\d/} ) { $id{$1}++; } }; while (my ($k, $v) = each %%id) { $counts{$v}++; }; while (my ($k, $v) = each %%counts) { print "$v $k\n"; };' %s""" % (' '.join(fastas))</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> counts = syscall(call)</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> return functional.calc_metric_fragmentation(counts)</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -150,7 +150,7 @@</span> def metric_truncation(db, preads_fofn):</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> # https://jira.pacificbiosciences.com/browse/SAT-105</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> fastas = abs_filenames(preads_fofn)</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> assert fastas, 'No fasta found in {!r}'.format(preads_fofn)</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;">- call = """perl -e 'while (<>) { if ( m{>[^/]+/0*(\d+)\d/(\d+)_(\d+)} ) { $lengths{(1 + $1)} += ($3 - $2); } }; while (my ($k, $v) = each %%lengths) { print "$k $v\n"; };' %s""" % (' '.join(fastas))</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;">+ call = r"""perl -e 'while (<>) { if ( m{>[^/]+/0*(\d+)\d/(\d+)_(\d+)} ) { $lengths{(1 + $1)} += ($3 - $2); } }; while (my ($k, $v) = each %%lengths) { print "$k $v\n"; };' %s""" % (' '.join(fastas))</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> # The +1 is because of the DBdump readids start at 1, but these start at 0.</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> length_pairs_output = syscall(call)</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> call = 'DBdump -rh {}'.format(db)</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gh" style="color: #999;">Index: falcon/FALCON/falcon_kit/run_support.py</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- falcon.orig/FALCON/falcon_kit/run_support.py</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ falcon/FALCON/falcon_kit/run_support.py</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span> import uuid</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> logger = logging.getLogger(__name__)</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from configparser import SafeConfigParser as ConfigParser</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from configparser import ConfigParser</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> def _prepend_env_paths(content, names):</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="p">@@ -310,7 +310,7 @@</span> def parse_cfg_with_sections(stream):</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> config = ConfigParser() #strict=False?</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> config.optionxform = str</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- config.readfp(NativeIO(content))</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ config.read_file(NativeIO(content))</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> sections = config.sections()</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> for sec in sections:</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> result[sec] = dict(config.items(sec))</span></pre>
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<li id="73edb67a952087ac62e6a7ae5e7ba31e11dfe4c7">
<a href="https://salsa.debian.org/med-team/falcon/-/compare/3492618ac8be3cb1cae995da7c7582e574494305...5509c29f3d0729d6fef6a6de1423d78a5ec98658#73edb67a952087ac62e6a7ae5e7ba31e11dfe4c7"><strong>debian/patches/networkx_addPath.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="gh" style="color: #999;">Index: falcon/FALCON/falcon_kit/fc_asm_graph.py</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- falcon.orig/FALCON/falcon_kit/fc_asm_graph.py</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ falcon/FALCON/falcon_kit/fc_asm_graph.py</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -133,10 +133,10 @@</span> class AsmGraph(object):</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> s, v, t = svt.split("~")</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> type_, length, score, one_path = self.utg_data[(s, t, v)]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> one_path = one_path.split("~")</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sg.add_path(one_path)</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nx.add_path(sg,one_path)</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> else:</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> one_path = path_or_edges.split("~")</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sg.add_path(one_path)</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nx.add_path(sg,one_path)</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> return sg</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> def get_sg_for_ctg(self, ctg_id):</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -150,13 +150,13 @@</span> class AsmGraph(object):</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> for t, utg in utgs:</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> if t == "simple":</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> one_path = utg.split("~")</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sg.add_path(one_path)</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nx.add_path(sg,one_path)</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> elif t == "compound":</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> for svt in utg.split("|"):</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> s, v, t = svt.split("~")</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> type_, length, score, one_path = self.utg_data[(s, t, v)]</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> one_path = one_path.split("~")</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;">- sg.add_path(one_path)</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nx.add_path(sg,one_path)</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> return sg</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gh" style="color: #999;">Index: falcon/FALCON/src/utils/fetch_preads.py</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- falcon.orig/FALCON/src/utils/fetch_preads.py</span></span>
</pre>
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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;">+++ falcon/FALCON/src/utils/fetch_preads.py</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="p">@@ -46,7 +46,7 @@</span> for id_ in a_tig_path:</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> if id_[:4] == p_tig_id:</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> a_path = a_tig_path[id_]</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> if a_path[0] in main_path_nodes and a_path[-1] in main_path_nodes:</span>
</pre>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- p_ugraph.add_path(a_path)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nx.add_path(p_ugraph,a_path)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> for pp in a_path:</span>
</pre>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> all_nodes.add(pp)</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="p">@@ -54,7 +54,7 @@</span> for v, w in u_edges:</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> if v in all_nodes and w in all_nodes:</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> for p, s in u_edges[(v, w)]:</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> p = p.split("-")</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- p_sgraph.add_path(p)</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nx.add_path(p_sgraph,p)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> # print p</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> for pp in p:</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> all_nodes.add(pp)</span></pre>
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<li id="c95b49fcdcf94cb632aec008933196e57cb26c3c">
<a href="https://salsa.debian.org/med-team/falcon/-/compare/3492618ac8be3cb1cae995da7c7582e574494305...5509c29f3d0729d6fef6a6de1423d78a5ec98658#c95b49fcdcf94cb632aec008933196e57cb26c3c"><strong>debian/patches/python2to3.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">@@ -66,6 +66,15 @@ Index: falcon/FALCON/falcon_kit/bash.py</td>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- falcon.orig/FALCON/falcon_kit/bash.py</span></span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ falcon/FALCON/falcon_kit/bash.py</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="p">@@ -8,7 +8,7 @@</span> from . import functional</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> import functools</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> import getpass</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> import logging</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import md5</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from hashlib import md5</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> import tempfile</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> import traceback</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"><span class="p">@@ -176,7 +176,7 @@</span> def script_build_rdb(config, input_fofn_</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="diff"> params = dict(config)</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff"> length_cutoff = params.get('length_cutoff')</span>
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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">@@ -585,8 +594,8 @@ Index: falcon/FALCON/makefile</td>
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585
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594
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- which py.test || pip install --user pytest</span></span>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- py.test ${MY_TEST_FLAGS} --junit-xml=test.xml --doctest-modules ${DOCTEST_MODULES} test/</span></span>
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587
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596
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PYTHONPATH=${FALCON_WORKSPACE}/pypeFLOW:${FALCON_WORKSPACE}/FALCON:${FALCON_WORKSPACE}/FALCON/build/lib.linux-x86_64-3.8/:$$PYTHONPATH python3 -c 'import falcon_kit; print(falcon_kit.falcon)'</span></span>
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588
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ which py.test<span class="idiff left right"> || pip3 install --user pytest</span></span></span>
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589
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PYTHONPATH=${FALCON_WORKSPACE}/pypeFLOW:${FALCON_WORKSPACE}/FALCON:${FALCON_WORKSPACE}/FALCON/build/lib.linux-x86_64-3.8/:$$PYTHONPATH py.test ${MY_TEST_FLAGS} --junit-xml=test.xml --doctest-modules ${DOCTEST_MODULES} test/</span></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ which py.test<span class="idiff left right">-3</span></span></span>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PYTHONPATH=${FALCON_WORKSPACE}/pypeFLOW:${FALCON_WORKSPACE}/FALCON:${FALCON_WORKSPACE}/FALCON/build/lib.linux-x86_64-3.8/:$$PYTHONPATH py.test<span class="idiff left right">-3</span> ${MY_TEST_FLAGS} --junit-xml=test.xml --doctest-modules ${DOCTEST_MODULES} test/</span></span>
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590
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="diff"> autopep8:</span>
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="diff"> autopep8 --max-line-length=120 -ir -j0 falcon_kit/ examples/ test/ setup.py</span>
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592
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="769" 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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -760,3 +769,151 @@ Index: falcon/pypeFLOW/pwatcher/blocking.py</td>
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760
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="diff"> </span>
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761
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="diff"> class JobThread(threading.Thread):</span>
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762
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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="diff"> def run(self):</span>
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"><span class="gh" style="color: #999;">Index: falcon/FALCON/src/c/ext_falcon.c</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- falcon.orig/FALCON/src/c/ext_falcon.c</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ falcon/FALCON/src/c/ext_falcon.c</span></span>
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"><span class="p">@@ -1,13 +1,57 @@</span></span>
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="diff"> #include "Python.h"</span>
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-static PyMethodDef SpamMethods[] = {</span></span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+static PyMethodDef FalconMethods[] = {</span></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="diff"> {NULL, NULL, 0, NULL} /* Sentinel */</span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="diff"> };</span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if 0</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// Python 2</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="diff"> PyMODINIT_FUNC</span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="diff"> initext_falcon(void)</span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="diff"> {</span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="diff"> PyObject *m;</span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="diff"> </span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- m = Py_InitModule("ext_falcon", SpamMethods);</span></span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ m = Py_InitModule("ext_falcon", FalconMethods);</span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="diff"> if (m == NULL)</span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="diff"> return;</span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return m;</span></span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#else</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// Python 3</span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+static PyObject *FalconError;</span></span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="807" 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">
807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+static struct PyModuleDef falconmodule = {</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PyModuleDef_HEAD_INIT,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="809" 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">
809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "ext_falcon",</span></span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ NULL,</span></span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -1,</span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ FalconMethods</span></span>
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<td class="diff-line-num new new_line" data-linenumber="813" 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">
813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+};</span></span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="815" 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">
815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+PyMODINIT_FUNC</span></span>
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<td class="diff-line-num new new_line" data-linenumber="816" 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">
816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+PyInit_ext_falcon(void)</span></span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+{</span></span>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PyObject *m;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="819" 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">
819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="820" 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">
820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ m = PyModule_Create(&falconmodule);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="821" 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">
821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (m == NULL)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="822" 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">
822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return NULL;</span></span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="824" 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">
824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ FalconError = PyErr_NewException("falcon.error", NULL, NULL);</span></span>
</pre>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Py_XINCREF(FalconError);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="826" 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">
826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (PyModule_AddObject(m, "error", FalconError) < 0) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="827" 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">
827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Py_XDECREF(FalconError);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="828" 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">
828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Py_CLEAR(FalconError);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="829" 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">
829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Py_DECREF(m);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="830" 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">
830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return NULL;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="831" 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">
831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="832" 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">
832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="833" 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">
833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return m;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="834" 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">
834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="835" 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">
835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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<td class="diff-line-num new new_line" data-linenumber="836" 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">
836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="diff"><span class="gh" style="color: #999;">Index: falcon/FALCON/falcon_kit/FastaReader.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="837" 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">
837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="838" 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">
838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- falcon.orig/FALCON/falcon_kit/FastaReader.py</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="763" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="839" 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">
839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ falcon/FALCON/falcon_kit/FastaReader.py</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="840" 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">
840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="diff"><span class="p">@@ -8,7 +8,7 @@</span> from os.path import abspath, expanduser</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="841" 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">
841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="diff"> from .io import NativeIO as StringIO</span>
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<td class="diff-line-num new new_line" data-linenumber="842" 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">
842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="diff"> import contextlib</span>
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<td class="diff-line-num new new_line" data-linenumber="843" 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">
843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="diff"> import gzip</span>
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<td class="diff-line-num new new_line" data-linenumber="844" 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">
844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import md5</span></span>
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<td class="diff-line-num new new_line" data-linenumber="845" 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">
845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from hashlib import md5</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="diff"> import re</span>
</pre>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="diff"> import subprocess</span>
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<td class="diff-line-num new new_line" data-linenumber="848" 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">
848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="849" 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">
849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="diff"><span class="p">@@ -68,7 +68,7 @@</span> class FastaRecord(object):</span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="diff"> assert self.DELIMITER not in sequence</span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="diff"> self._name = name</span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="diff"> self._sequence = sequence</span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._md5 = md5.md5(self.sequence).hexdigest()</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self._md5 = md5(self.sequence.encode('utf-8')).hexdigest()</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="diff"> self._id, self._metadata = splitFastaHeader(name)</span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="diff"> except AssertionError:</span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="diff"> raise ValueError("Invalid FASTA record data")</span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="diff"><span class="gh" style="color: #999;">Index: falcon/FALCON/test/test_run_support.py</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- falcon.orig/FALCON/test/test_run_support.py</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ falcon/FALCON/test/test_run_support.py</span></span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="diff"><span class="p">@@ -1,5 +1,5 @@</span></span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="diff"> import pytest</span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import StringIO</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from io import StringIO</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="diff"> import falcon_kit.run_support as mod</span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="diff"> </span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="diff"> </span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="diff"><span class="p">@@ -8,7 +8,7 @@</span> def parse_config(content):</span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="diff"> (Clean this code up later.)</span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="diff"> """</span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="diff"> config = dict()</span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- stream = StringIO.StringIO</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ stream = StringIO</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="diff"> cfg2 = mod.parse_cfg_with_sections(stream(content))</span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="diff"> mod.update_config_from_sections(config, cfg2)</span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="diff"> mod.update_job_sections(config)</span>
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="diff"><span class="p">@@ -102,7 +102,7 @@</span> def test_update_config_from_sections():</span>
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="diff"> def test_update_config_from_sections_foo():</span>
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="diff"> config = dict()</span>
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cfg2 = mod.parse_cfg_with_sections(StringIO.StringIO(FC_RUN_CFG))</span></span>
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cfg2 = mod.parse_cfg_with_sections(StringIO(FC_RUN_CFG))</span></span>
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="diff"> import collections</span>
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="diff"> cfg2['foo'] = collections.defaultdict(list)</span>
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="diff"><span class="gh" style="color: #999;">Index: falcon/FALCON/falcon_kit/run_support.py</span></span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- falcon.orig/FALCON/falcon_kit/run_support.py</span></span>
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ falcon/FALCON/falcon_kit/run_support.py</span></span>
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span> import uuid</span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="diff"> logger = logging.getLogger(__name__)</span>
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from ConfigParser import SafeConfigParser as ConfigParser</span></span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from configparser import SafeConfigParser as ConfigParser</span></span>
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="diff"> </span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="diff"> def _prepend_env_paths(content, names):</span>
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="diff"><span class="gh" style="color: #999;">Index: falcon/FALCON/test/test_util_io.py</span></span>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- falcon.orig/FALCON/test/test_util_io.py</span></span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ falcon/FALCON/test/test_util_io.py</span></span>
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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="diff"><span class="p">@@ -10,12 +10,13 @@</span> def test_io_se1331():</span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="diff"> """</span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="diff"> x = ''</span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="diff"> cmd = 'seq 20000'</span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- beg = time.clock()</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # processor time in seconds</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ beg = time.time()</span></span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="diff"> reader = M.CapturedProcessReaderContext(cmd)</span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="diff"> with reader:</span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="diff"> for line in reader.readlines():</span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="diff"> x += line</span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- end = time.clock()</span></span>
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916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ end = time.time()</span></span>
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="diff"> assert end-beg < 1</span>
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918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="diff"> </span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/falcon/-/compare/3492618ac8be3cb1cae995da7c7582e574494305...5509c29f3d0729d6fef6a6de1423d78a5ec98658#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">@@ -11,3 +11,6 @@ nimUndeclearedIdentifier.patch</td>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">nimundeclaredWordWrap.patch</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">nimTypeMismatch.patch</span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">python2to3.patch</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">networkx_addPath.patch</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">introduceRawStrings.patch</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">fixUnicodeReadHelpers.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/falcon/-/compare/3492618ac8be3cb1cae995da7c7582e574494305...5509c29f3d0729d6fef6a6de1423d78a5ec98658#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -53,3 +53,5 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> $(RM) -r pypeFLOW/build/lib</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> $(RM) -r pypeFLOW/pypeflow.egg-info</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"> $(RM) -r FALCON/falcon_kit.egg-info</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> $(RM) -r FALCON/.pytest_cache</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> find . -name "*.exe" -delete</span></pre>
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