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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/ctdopts">Debian Med / ctdopts</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ctdopts/-/commit/c2c11f894ce0514441c682efdc25dfe3bc08d7d1">c2c11f89</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-10-01T13:44:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.4</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#61c5ccb699d3bd1d778dd867ea98e770ede7bc28">
CTDopts/CTDopts.py
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</li>
<li class="file-stats">
<a href="#c365ba83c537f05de69d64d658c846b72276ce7c">
dist/conda/meta.yaml
</a>
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<li class="file-stats">
<a href="#05e0372f8165776bed0a53b989eaffd9e3139848">
example.py
</a>
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="61c5ccb699d3bd1d778dd867ea98e770ede7bc28">
<a href="https://salsa.debian.org/med-team/ctdopts/-/commit/c2c11f894ce0514441c682efdc25dfe3bc08d7d1#61c5ccb699d3bd1d778dd867ea98e770ede7bc28"><strong>CTDopts/CTDopts.py</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">,</span> <span class="n" style="color: #333;">Mapping</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">chain</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections</span></span>
</pre>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections.abc</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">xml.etree.ElementTree</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Element</span><span class="p">,</span> <span class="n" style="color: #333;">SubElement</span><span class="p">,</span> <span class="n" style="color: #333;">tostring</span><span class="p">,</span> <span class="n" style="color: #333;">parse</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">xml.dom.minidom</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">parseString</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">warnings</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" 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="47" 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">@@ -46,12 +47,27 @@ class _OutFile(str):</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_OutPrefix</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">"""Same thing, a dummy class for output-prefix CTD type."""</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_InPrefix</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">"""Same thing, a dummy class for output-prefix CTD type."""</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># module globals for some common operations (python types to CTD-types back and forth)</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"><span class="n" style="color: #333;">TYPE_TO_CTDTYPE</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">int</span><span class="p">:</span> <span class="s" style="color: #d14;">'int'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">:</span> <span class="s" style="color: #d14;">'double'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span> <span class="s" style="color: #d14;">'string'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">:</span> <span class="s" style="color: #d14;">'bool'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">_InFile</span><span class="p">:</span> <span class="s" style="color: #d14;">'input-file'</span><span class="p">,</span> <span class="n" style="color: #333;">_OutFile</span><span class="p">:</span> <span class="s" style="color: #d14;">'output-file'</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"><span class="n" style="color: #333;">CTDTYPE_TO_TYPE</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'int'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="s" style="color: #d14;">'float'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="s" style="color: #d14;">'double'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="s" style="color: #d14;">'string'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="s" style="color: #d14;">'boolean'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span> <span class="s" style="color: #d14;">'bool'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">'input-file'</span><span class="p">:</span> <span class="n" style="color: #333;">_InFile</span><span class="p">,</span> <span class="s" style="color: #d14;">'output-file'</span><span class="p">:</span> <span class="n" style="color: #333;">_OutFile</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="nb" style="color: #0086b3;">bool</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span> <span class="n" style="color: #333;">_InFile</span><span class="p">:</span> <span class="n" style="color: #333;">_InFile</span><span class="p">,</span> <span class="n" style="color: #333;">_OutFile</span><span class="p">:</span> <span class="n" style="color: #333;">_OutFile</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">_InFile</span><span class="p">:</span> <span class="s" style="color: #d14;">'input-file'</span><span class="p">,</span> <span class="n" style="color: #333;">_OutFile</span><span class="p">:</span> <span class="s" style="color: #d14;">'output-file'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">_OutPrefix</span><span class="p">:</span> <span class="s" style="color: #d14;">'output-prefix'</span><span class="p">,</span> <span class="n" style="color: #333;">_InPrefix</span><span class="p">:</span> <span class="s" style="color: #d14;">'input-prefix'</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"><span class="n" style="color: #333;">CTDTYPE_TO_TYPE</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'int'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="s" style="color: #d14;">'float'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="s" style="color: #d14;">'double'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="s" style="color: #d14;">'string'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="s" style="color: #d14;">'boolean'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span> <span class="s" style="color: #d14;">'bool'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="s" style="color: #d14;">'input-file'</span><span class="p">:</span> <span class="n" style="color: #333;">_InFile</span><span class="p">,</span> <span class="s" style="color: #d14;">'output-file'</span><span class="p">:</span> <span class="n" style="color: #333;">_OutFile</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="s" style="color: #d14;">'output-prefix'</span><span class="p">:</span> <span class="n" style="color: #333;">_OutPrefix</span><span class="p">,</span> <span class="s" style="color: #d14;">'input-prefix'</span><span class="p">:</span> <span class="n" style="color: #333;">_InPrefix</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="nb" style="color: #0086b3;">int</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="nb" style="color: #0086b3;">bool</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span> <span class="n" style="color: #333;">_InFile</span><span class="p">:</span> <span class="n" style="color: #333;">_InFile</span><span class="p">,</span> <span class="n" style="color: #333;">_OutFile</span><span class="p">:</span> <span class="n" style="color: #333;">_OutFile</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">_OutPrefix</span><span class="p">:</span> <span class="n" style="color: #333;">_OutPrefix</span><span class="p">,</span> <span class="n" style="color: #333;">_InPrefix</span><span class="p">:</span> <span class="n" style="color: #333;">_InPrefix</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"><span class="n" style="color: #333;">PARAM_DEFAULTS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'advanced'</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="s" style="color: #d14;">'required'</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="s" style="color: #d14;">'restrictions'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'description'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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56
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="s" style="color: #d14;">'supported_formats'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'tags'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'position'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;"># unused. TODO.</span></span>
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="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">@@ -115,7 +131,7 @@ def flatten_dict(arg_dict, as_string=False):</td>
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115
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># recursive closure that accesses and modifies result dict and registers nested elements</span></span>
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116
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># as it encounters them</span></span>
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117
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">subgroup</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">Mapping</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># collections.Mapping instead of dict for generality</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">collections</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">abc</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">Mapping</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># collections.Mapping instead of dict for generality</span></span>
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119
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">flattener</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">])</span></span>
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120
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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121
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="566" 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">@@ -550,7 +566,7 @@ class Parameter(object):</td>
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550
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566
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># XML attributes to be created (depending on whether they are needed or not):</span></span>
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551
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567
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># name, value, type, description, tags, restrictions, supported_formats</span></span>
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552
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="python"></span>
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553
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="python"> <span class="n" style="color: #333;">attribs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># LXML keeps the order, ElemenTree doesn't. We use ElementTree though.</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="python"> <span class="n" style="color: #333;">attribs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">collections</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">OrderedDict</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># LXML keeps the order, ElemenTree doesn't. We use ElementTree though.</span></span>
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554
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="python"> <span class="n" style="color: #333;">attribs</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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555
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">is_list</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># we'll deal with list parameters later, now only normal:</span></span>
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556
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: once Param_1_6_3.xsd gets fixed, we won't have to set an empty value='' attrib.</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="613" 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">@@ -597,7 +613,7 @@ class Parameter(object):</td>
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597
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python"></span>
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598
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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ParameterGroup</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">collections</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">OrderedDict</span><span class="p">()</span></span>
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601
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">parent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parent</span></span>
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">description</span></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">@@ -1091,7 +1107,7 @@ class CTDModel(object):</td>
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1107
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<pre style="margin: 0;"> <span id="LC1107" class="line" lang="python"><span class="s" style="color: #d14;"> 'error': standard error or whatever error log the user wants to store</span></span>
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1092
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1108
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<pre style="margin: 0;"> <span id="LC1108" class="line" lang="python"><span class="s" style="color: #d14;"> `cli`: boolean whether or not cli elements should be generated (needed for GenericKNIMENode for example)</span></span>
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<pre style="margin: 0;"> <span id="LC1109" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC1094" class="line" lang="python"> <span class="n" style="color: #333;">tool_attribs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="python"> <span class="n" style="color: #333;">tool_attribs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">collections</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">OrderedDict</span><span class="p">()</span></span>
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1095
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<pre style="margin: 0;"> <span id="LC1111" class="line" lang="python"> <span class="n" style="color: #333;">tool_attribs</span><span class="p">[</span><span class="s" style="color: #d14;">'version'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">version</span></span>
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1112
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<pre style="margin: 0;"> <span id="LC1112" class="line" lang="python"> <span class="n" style="color: #333;">tool_attribs</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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1113
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<pre style="margin: 0;"> <span id="LC1113" class="line" lang="python"> <span class="n" style="color: #333;">tool_attribs</span><span class="p">[</span><span class="s" style="color: #d14;">'xmlns:xsi'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"http://www.w3.org/2001/XMLSchema-instance"</span></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">package</span><span class="pi">:</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">ctdopts</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">1.<span class="idiff left right">2</span>"</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">1.<span class="idiff left right">4</span>"</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">source</span><span class="pi">:</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">git_rev</span><span class="pi">:</span> <span class="s" style="color: #d14;">v1.<span class="idiff left right">2</span></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">git_rev</span><span class="pi">:</span> <span class="s" style="color: #d14;">v1.<span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">git_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://github.com/WorkflowConversion/CTDopts.git</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">noarch<span class="idiff left">_python</span></span><span class="pi"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">True</span></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">noarch</span><span class="pi"><span class="idiff left">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">python</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">requirements</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>
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<li id="05e0372f8165776bed0a53b989eaffd9e3139848">
<a href="https://salsa.debian.org/med-team/ctdopts/-/commit/c2c11f894ce0514441c682efdc25dfe3bc08d7d1#05e0372f8165776bed0a53b989eaffd9e3139848"><strong>example.py</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">@@ -45,6 +45,15 @@ model.add(</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'A list of filenames to feed this dummy tool with'</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">'output'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'output-prefix'</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># or 'input-prefix'</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">is_list</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">file_formats</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'fastq.gz'</span><span class="p">],</span> <span class="c1" style="color: #998; font-style: italic;"># filename restrictions</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Output directory'</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"><span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span></span>
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="s" style="color: #d14;">'this_that'</span><span class="p">,</span></span>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></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">@@ -194,7 +203,7 @@ print("So how to deal with command line arguments? If we have a model, we can lo</td>
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194
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="s" style="color: #d14;">"Call CTDModel.parse_cl_args() with either a string of the command line call or a list with the split words. "</span></span>
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="s" style="color: #d14;">"By default, it will assume a '--' prefix before parameter names, but it can be overridden with prefix='-'."</span></span>
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196
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="s" style="color: #d14;">"Grouped parameters are expected in --group:subgroup:param_x format."</span><span class="p">)</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"><span class="n" style="color: #333;">cl_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">parse_cl_args</span><span class="p">(</span><span class="s" style="color: #d14;">'--positive_int 44 --subparams:param_2 5.0 5.5 6.0 --input_files a.fastq b.fastq'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"><span class="n" style="color: #333;">cl_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">parse_cl_args</span><span class="p">(</span><span class="s" style="color: #d14;">'--positive_int 44 --subparams:param_2 5.0 5.5 6.0 --input_files a.fastq b.fastq<span class="idiff left right"> --output out_dir/</span>'</span><span class="p">)</span></span>
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198
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"><span class="n" style="color: #333;">pretty_print</span><span class="p">(</span><span class="n" style="color: #333;">cl_args</span><span class="p">)</span></span>
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199
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># # you can get unmatchable command line arguments with get_remaining=True like:</span></span>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/ctdopts/-/commit/c2c11f894ce0514441c682efdc25dfe3bc08d7d1#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ from distutils.core import setup</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'CTDopts'</span><span class="p">,</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'1.<span class="idiff left right">3</span>'</span><span class="p">,</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'1.<span class="idiff left right">4</span>'</span><span class="p">,</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'CTDopts'</span><span class="p">],</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'https://github.com/genericworkflownodes/CTDopts'</span><span class="p">,</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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