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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/pyqi">Debian Med / pyqi</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pyqi/-/commit/dc11ad21408d1eb4b0d7ec935f2d4dda3448a1af">dc11ad21</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-03-30T17:59:38+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove redundant cgi import line
</pre>
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
</a>
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<h4>Changes:</h4>
<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/pyqi/-/commit/dc11ad21408d1eb4b0d7ec935f2d4dda3448a1af#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.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">@@ -5,7 +5,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/doc/conf.py</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/conf.py</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -40,8 +40,8 @@</span><span class="idiff left right"> source_suffix = '.rst'</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -40,8 +40,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> master_doc = 'index'</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> # General information about the project.</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">@@ -16,7 +16,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> # The version info for the project you're documenting, acts as replacement for</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> # |version| and |release|, also used in various other places throughout the</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="p">@@ -181,8 +181,8 @@</span><span class="idiff left right"> latex_elements = {</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -181,8 +181,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> # Grouping the document tree into LaTeX files. List of tuples</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> # (source start file, target name, title, author, documentclass [howto/manual]).</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> latex_documents = [</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">@@ -27,7 +27,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> ]</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> # The name of an image file (relative to this directory) to place at the top of</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="p">@@ -211,8 +211,8 @@</span><span class="idiff left right"> latex_documents = [</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -211,8 +211,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> # One entry per manual page. List of tuples</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> # (source start file, name, description, authors, manual section).</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> man_pages = [</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">@@ -38,7 +38,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> ]</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> # If true, show URL addresses after external links.</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="p">@@ -225,8 +225,8 @@</span><span class="idiff left right"> man_pages = [</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="p">@@ -225,8 +225,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> # (source start file, target name, title, author,</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> # dir menu entry, description, category)</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> texinfo_documents = [</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">@@ -51,7 +51,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/tutorials/defining_new_commands.rst</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/tutorials/defining_new_commands.rst</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span><span class="idiff left right"> To create our sequence collection summar</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> If you run this command locally, substituting your own name where applicable, you'll have a new file called ``sequence_collection_summarizer.py``, which will look roughly like the following::</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> </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">@@ -60,7 +60,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> from __future__ import division</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> __credits__ = ["Greg Caporaso"]</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="p">@@ -117,7 +117,7 @@</span><span class="idiff left right"> A complete example Command</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="p">@@ -117,7 +117,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"> The following illustrates a complete python file defining a new pyqi ``Command``::</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> </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">@@ -69,7 +69,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"> from __future__ import division</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> __credits__ = ["Greg Caporaso"]</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="p">@@ -180,11 +180,11 @@</span><span class="idiff left right"> At this stage you have defined a new com</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="p">@@ -180,11 +180,11 @@</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"> >>> r</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> {'max_length': 12, 'min_length': 6, 'num_seqs': 2}</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> # Alternatively, you can access each value independently, as with any dictionary.</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">@@ -86,7 +86,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"> # For example, we can call the command again passing the</span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/tutorials/defining_new_interfaces.rst</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/tutorials/defining_new_interfaces.rst</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="p">@@ -24,7 +24,7 @@</span><span class="idiff left right"> To create your interface, you'll need to</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="p">@@ -24,7 +24,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="diff"> The resulting file will look something like this::</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="diff"> </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">@@ -95,7 +95,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="diff"> from __future__ import division</span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="diff"> __credits__ = ["Greg Caporaso"]</span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="p">@@ -281,7 +281,7 @@</span><span class="idiff left right"> Complete OptparseInterface configuration</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="p">@@ -281,7 +281,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="diff"> At this stage we've fully configured our interface. The final interface configuration file should look like this::</span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="diff"> </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">@@ -130,7 +130,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="diff"> #-----------------------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="diff"> # Copyright (c) 2013, The BiPy Development Team.</span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"><span class="p">@@ -61,12 +61,12 @@</span><span class="idiff left right"> class CodeHeaderGenerator(Command):</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="p">@@ -61,12 +61,12 @@</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="diff"> credits = [head['author']]</span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="diff"> if kwargs['credits'] is not None:</span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="diff"> credits.extend(kwargs['credits'])</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">@@ -187,7 +187,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="diff"> from operator import attrgetter</span>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="diff"> from pyqi.core.command import (Command, CommandIn, CommandOut,</span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="diff"> ParameterCollection)</span>
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="diff"><span class="p">@@ -137,7 +137,7 @@</span><span class="idiff left right"> class MakeOptparse(CodeHeaderGenerator):</span></span>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="p">@@ -137,7 +137,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="diff"> # construct inputs based off of CommandIns</span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="diff"> cmdin_formatted = []</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">@@ -196,7 +196,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="diff"> key=attrgetter('Name')):</span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="diff"> if cmdin.Required:</span>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="diff"> default_block = ''</span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="diff"><span class="p">@@ -162,7 +162,7 @@</span><span class="idiff left right"> class MakeOptparse(CodeHeaderGenerator):</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="p">@@ -162,7 +162,7 @@</span></span>
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200
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="diff"> cmdin_formatted.append(input_format % fmt)</span>
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201
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="diff"> </span>
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202
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="diff"> cmdout_formatted = []</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">@@ -215,7 +215,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="diff"> </span>
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="diff"> #-----------------------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="diff"> # Copyright (c) 2013, The BiPy Development Team.</span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="diff"><span class="p">@@ -74,7 +74,7 @@</span><span class="idiff left right"> class MakeRelease(Command):</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="p">@@ -74,7 +74,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="diff"> def _bump_version(self, version):</span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="diff"> try:</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">@@ -266,7 +266,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="diff"> __credits__ = ["Greg Caporaso", "Daniel McDonald", "Doug Wendel",</span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="diff"> "Jai Ram Rideout"]</span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="diff"><span class="p">@@ -162,7 +162,7 @@</span><span class="idiff left right"> class Command(object):</span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="p">@@ -162,7 +162,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="diff"> self_str = str(self.__class__)</span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="diff"> # check required parameters</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">@@ -275,7 +275,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="diff"> if p.Required and p.Name not in kwargs:</span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="diff"> err_msg = 'Missing required CommandIn %s in %s' % (p.Name,</span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="diff"> self_str)</span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="diff"><span class="p">@@ -187,7 +187,7 @@</span><span class="idiff left right"> class Command(object):</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="p">@@ -187,7 +187,7 @@</span></span>
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="diff"> """Validate the result from a ``Command.run``"""</span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="diff"> self_str = str(self.__class__)</span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="284" 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">@@ -284,7 +284,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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284
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="diff"> if p.Name not in result:</span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="diff"> err_msg = "CommandOut %s not in %s" % (p.Name, self_str)</span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="diff"> self._logger.fatal(err_msg)</span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="diff"><span class="p">@@ -200,7 +200,7 @@</span><span class="idiff left right"> class Command(object):</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="p">@@ -200,7 +200,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="diff"> def _set_defaults(self, kwargs):</span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="diff"> """Set defaults for optional parameters"""</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">@@ -341,7 +341,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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341
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="diff"> </span>
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="diff"> #-----------------------------------------------------------------------------</span>
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343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="diff"> # Copyright (c) 2013, The BiPy Development Team.</span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="diff"><span class="p">@@ -18,<span class="idiff left">7 +18,7 @@</span></span><span class="idiff right"> import sys</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="p">@@ -18,<span class="idiff left right">11 +18,10 @@</span></span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="diff"> </span>
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346
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="diff"> from pyqi.util import is_py2</span>
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347
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="diff"> if is_py2():</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">@@ -350,7 +350,11 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="diff"> else:</span>
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351
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="diff"> from http.server import BaseHTTPRequestHandler, HTTPServer</span>
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352
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352
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="diff"> </span>
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353
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="diff"><span class="p">@@ -125,7 +125,7 @@</span> class HTMLInputOption(InterfaceInputOpti</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from cgi import parse_header, parse_multipart, parse_qs, FieldStorage</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> from copy import copy</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> from glob import glob</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> from os.path import abspath, exists, isdir, isfile, split</span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="p">@@ -125,7 +124,7 @@</span></span>
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354
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="diff"> if self.Choices is None:</span>
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355
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="diff"> raise IncompetentDeveloperError(</span>
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356
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="diff"> "must supply a list of Choices for type '%s'" % self.type, self)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -359,7 +363,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="diff"> raise IncompetentDeveloperError(</span>
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="diff"> "choices must be a list of strings ('%s' supplied)"</span>
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361
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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="diff"> % str(type(self.Choices)).split("'")[1], self)</span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="diff"><span class="p">@@ -513,7 +51<span class="idiff left">3,7 @@</span></span><span class="idiff right"> def get_http_handler(module):</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="p">@@ -513,7 +51<span class="idiff left right">2,7 @@</span></span></span>
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367
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="diff"> def start_server(port, module):</span>
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364
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="diff"> """Start a server for the HTMLInterface on the specified port"""</span>
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="diff"> interface_server = HTTPServer(("", port), get_http_handler(module))</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -433,7 +437,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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433
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437
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="diff"> </span>
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434
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438
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="diff"> """Manage IPython.parallel clusters in the notebook.</span>
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435
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439
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="diff"> </span>
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436
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="diff"><span class="p">@@ -73,7 +73,7 @@</span><span class="idiff left right"> class ClusterManager(LoggingConfigurable</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"><span class="p">@@ -73,7 +73,7 @@</span></span>
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441
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="diff"> def update_profiles(self):</span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="diff"> """List all profiles in the ipython_dir and cwd.</span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="diff"> """</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">@@ -442,7 +446,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="diff"> for profile in list_profiles_in(path):</span>
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447
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="diff"> pd = self.get_profile_dir(profile, path)</span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="diff"> if profile not in self.profiles:</span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="diff"><span class="p">@@ -94,7 +94,7 @@</span><span class="idiff left right"> class ClusterManager(LoggingConfigurable</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="p">@@ -94,7 +94,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="diff"> def check_profile(self, profile):</span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="diff"> if profile not in self.profiles:</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">@@ -451,7 +455,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="diff"> def profile_info(self, profile):</span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="diff"> self.check_profile(profile)</span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="diff"><span class="p">@@ -112,7 +112,7 @@</span><span class="idiff left right"> class ClusterManager(LoggingConfigurable</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="p">@@ -112,7 +112,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="diff"> self.check_profile(profile)</span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="diff"> data = self.profiles[profile]</span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="diff"> if data['status'] == 'running':</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">@@ -460,7 +464,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="diff"> cl, esl, default_n = self.build_launchers(data['profile_dir'])</span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="diff"> n = n if n is not None else default_n</span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="diff"><span class="p">@@ -154,7 +154,7 @@</span><span class="idiff left right"> class ClusterManager(LoggingConfigurable</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"><span class="p">@@ -154,7 +154,7 @@</span></span>
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468
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="diff"> self.check_profile(profile)</span>
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469
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="diff"> data = self.profiles[profile]</span>
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470
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="diff"> if data['status'] == 'stopped':</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">@@ -469,7 +473,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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473
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="diff"> data = self.profiles[profile]</span>
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474
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="diff"> cl = data['controller_launcher']</span>
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475
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="diff"> esl = data['engine_set_launcher']</span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="diff"><span class="p">@@ -172,7 +172,7 @@</span><span class="idiff left right"> class ClusterManager(LoggingConfigurable</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"><span class="p">@@ -172,7 +172,7 @@</span></span>
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477
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="diff"> return result</span>
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478
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="diff"> def stop_all_clusters(self):</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">@@ -486,7 +490,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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490
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="diff"> </span>
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491
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="diff"> from pyqi.core.interface import Interface, InterfaceOption</span>
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="diff"> from testing import FilterSamples, FilterObservations</span>
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489
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="diff"><span class="p">@@ -7,6 +7,7 @@</span><span class="idiff left right"> from types import NoneType</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"><span class="p">@@ -7,6 +7,7 @@</span></span>
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494
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="diff"> from pyqi.core.factory import general_factory</span>
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495
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="diff"> from biom.table import Table as BIOMTable</span>
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496
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="diff"> from biom.parse import parse_biom_table</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">@@ -494,7 +498,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="diff"> </span>
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499
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="diff"> </span>
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500
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="diff"> class Functional(Interface):</span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="diff"><span class="p">@@ -67,11 +68,11 @@</span><span class="idiff left right"> t3 = parse_biom_table(</span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="p">@@ -67,11 +68,11 @@</span></span>
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="diff"> open('/Users/mcdonadt/ResearchWork/software/biom-format/examples/rich_sparse_otu_table.biom'))</span>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="diff"> </span>
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504
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="diff"> res = g(f("asdasdasd", seqs_per_sample=3), seqs_per_observation=1)</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">@@ -661,7 +665,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="diff"> #-----------------------------------------------------------------------------</span>
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667
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="diff"> # Copyright (c) 2013, The BiPy Development Team.</span>
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="diff"><span class="p">@@ -88,7 +88,7 @@</span><span class="idiff left right"> def old_to_new_command(driver_name, proj</span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"><span class="p">@@ -88,7 +88,7 @@</span></span>
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669
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="diff"> </span>
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670
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="diff"> Use like this (put in the script you want to deprecate):</span>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="diff"> </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">@@ -742,7 +746,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="diff"> #-----------------------------------------------------------------------------</span>
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748
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="diff"> # Copyright (c) 2013, The BiPy Development Team.</span>
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="diff"><span class="p">@@ -32,8 +32,8 @@</span><span class="idiff left right"> classes = """</span></span>
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff"><span class="p">@@ -32,8 +32,8 @@</span></span>
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750
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="diff"> Topic :: Software Development :: Libraries :: Application Frameworks</span>
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="diff"> Topic :: Software Development :: User Interfaces </span>
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752
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="diff"> Programming Language :: Python</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">@@ -753,7 +757,7 @@ Last-Update: Wed, 11 Sep 2019 11:43:51 +0200</td>
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="diff"> Programming Language :: Python :: Implementation :: CPython</span>
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="diff"> Operating System :: OS Independent</span>
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755
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759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="diff"> Operating System :: POSIX</span>
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="diff"><span class="p">@@ -43,8 +43,8 @@</span><span class="idiff left right"> classifiers = [s.strip() for s in classe</span></span>
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="diff"><span class="p">@@ -43,8 +43,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="diff"> # Verify Python version</span>
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="diff"> ver = '.'.join(map(str, [sys.version_info.major, sys.version_info.minor]))</span>
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