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<h3>
Étienne Mollier pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/q2cli">Debian Med / q2cli</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1">4248084e</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-02T13:45:51+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2020.11.0</pre>
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<h4>30 changed files:</h4>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">
LICENSE
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#22fbe0b68848772d4b1c45f0d62dcd71a06cde00">
ci/recipe/meta.yaml
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<li class="file-stats">
<a href="#bbbaebc3b23edbc86f41413722d48d29eeeb5f58">
q2cli/__init__.py
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<li class="file-stats">
<a href="#752859f8b4cfcbae3c81b47f46842da291d9d825">
q2cli/__main__.py
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<li class="file-stats">
<a href="#ba66450cf2f4739dc96974820c344fd32edb89f0">
q2cli/_version.py
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<a href="#79ab0b14dff3d9ba5099bcc9a20f5260bd07a8e5">
q2cli/builtin/__init__.py
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<a href="#4b9183b04ea8b786b7629167ed36b068044653d0">
q2cli/builtin/dev.py
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<a href="#71b88b101d6e0e9e60898a2fdbc162df0c2b301a">
q2cli/builtin/info.py
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<a href="#fd958db9213491909191b55c302d3c4274621ebb">
q2cli/builtin/tools.py
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<a href="#2670690bb5fc3e71b0d71bad6dea0577a5b0a717">
q2cli/click/__init__.py
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<a href="#00a3610cef01cb0a07b0017655f3d8587b7eb372">
q2cli/click/command.py
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<a href="#34c31663d5050120ebf76a215b52500c49fb233e">
q2cli/click/option.py
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<a href="#515b09fdcee7316575e8e96ae9e326544ba615bc">
q2cli/click/parser.py
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<a href="#eecee2226af62de28bd22bef07e8b1dae7cd739a">
q2cli/click/type.py
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<li class="file-stats">
<a href="#9089f11caa4b0f6ef10f937f509084406dc6e3d0">
q2cli/commands.py
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<a href="#e316d94fbce14eef139dc85098304edc0f0ff0d2">
q2cli/core/__init__.py
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<a href="#874e9f895446a24ce25c1483df0fb7d11dad5f50">
q2cli/core/cache.py
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<a href="#eada752a2adf82b343f70a4bedf2ece9781b60f2">
q2cli/core/completion.py
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<a href="#228bb7257239f997ab37f036d1b626a9f7ecafc1">
q2cli/core/config.py
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q2cli/core/usage.py
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<a href="#c4467f99066e6470736c8885ad6d10ff73140180">
q2cli/tests/__init__.py
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<a href="#dc5f5985a047865b81ba832edeea7666a8a308b7">
q2cli/tests/test_cli.py
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<a href="#69859555882ae5b802d6b617deeaece2a2130265">
q2cli/tests/test_core.py
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<a href="#504dff2fc7cc96f328a03bfeacd40d11cefbc485">
q2cli/tests/test_dev.py
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<a href="#a118f7a6f38ac6924500fb5556f843fdf73e82fb">
q2cli/tests/test_tools.py
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<a href="#e1798f96760f66fd8fed79cda543c13d23c62f8f">
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q2cli/tests/test_usage.py
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<a href="#67c0d02b0c1dcfe41eea76bbf17741e56aa00544">
q2cli/util.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,7 +14,6 @@ install:</td>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py36-linux-conda.yml</span></span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda env create -q -n test-env --file qiime2-latest-py36-linux-conda.yml</span></span>
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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">source activate test-env</span></span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda install -q nose</span></span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install -q flake8</span></span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install -q https://github.com/qiime2/q2lint/archive/master.zip</span></span>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make install</span></span>
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<br>
</li>
<li id="0398ccd0f49298b10a3d76a47800d2ebecd49859">
<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#0398ccd0f49298b10a3d76a47800d2ebecd49859"><strong>LICENSE</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">BSD 3-Clause License</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">All rights reserved.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Redistribution and use in source and binary forms, with or without</span>
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<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +10,7 @@ lint:</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"> flake8</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="nl">test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="make"> <span class="nv" style="color: #008080;">QIIMETEST</span><span class="o" style="font-weight: 600;">=</span> <span class="idiff left right">nosetests</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="make"> <span class="nv" style="color: #008080;">QIIMETEST</span><span class="o" style="font-weight: 600;">=</span> <span class="idiff left right">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"><span class="nl">install</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"> <span class="nv" style="color: #008080;">$(PYTHON)</span> setup.py <span class="nb" style="color: #0086b3;">install</span> <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#22fbe0b68848772d4b1c45f0d62dcd71a06cde00"><strong>ci/recipe/meta.yaml</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">@@ -18,6 +18,8 @@ requirements:</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">host</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python {{ python }}</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">setuptools</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># q2cli leverages pytest functionality</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python {{ python }}</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#bbbaebc3b23edbc86f41413722d48d29eeeb5f58"><strong>q2cli/__init__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#752859f8b4cfcbae3c81b47f46842da291d9d825"><strong>q2cli/__main__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#ba66450cf2f4739dc96974820c344fd32edb89f0"><strong>q2cli/_version.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">@@ -23,9 +23,9 @@ def get_keywords():</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># setup.py/versioneer.py will grep for the variable names, so they must</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># each be defined on a line of their own. _version.py will just call</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># get_keywords().</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (<span class="idiff left right">tag: 2019.10</span>.0)"</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">271df1dcf0c419046811dd20832f9c13446732f8</span>"</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"20<span class="idiff left right">19-11-01 01:04:25</span> +0000"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (<span class="idiff left right">HEAD -> master, tag: 2020.11</span>.0)"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">e09576b507ecee9df78ed142aacad6dd595654ca</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"20<span class="idiff left right">20-11-25 17:13:09</span> +0000"</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">keywords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"refnames"</span><span class="p">:</span> <span class="n" style="color: #333;">git_refnames</span><span class="p">,</span> <span class="s" style="color: #d14;">"full"</span><span class="p">:</span> <span class="n" style="color: #333;">git_full</span><span class="p">,</span> <span class="s" style="color: #d14;">"date"</span><span class="p">:</span> <span class="n" style="color: #333;">git_date</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">keywords</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#79ab0b14dff3d9ba5099bcc9a20f5260bd07a8e5"><strong>q2cli/builtin/__init__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#4b9183b04ea8b786b7629167ed36b068044653d0"><strong>q2cli/builtin/dev.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#71b88b101d6e0e9e60898a2fdbc162df0c2b301a"><strong>q2cli/builtin/info.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#fd958db9213491909191b55c302d3c4274621ebb"><strong>q2cli/builtin/tools.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#2670690bb5fc3e71b0d71bad6dea0577a5b0a717"><strong>q2cli/click/__init__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#00a3610cef01cb0a07b0017655f3d8587b7eb372"><strong>q2cli/click/command.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#34c31663d5050120ebf76a215b52500c49fb233e"><strong>q2cli/click/option.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#515b09fdcee7316575e8e96ae9e326544ba615bc"><strong>q2cli/click/parser.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#eecee2226af62de28bd22bef07e8b1dae7cd739a"><strong>q2cli/click/type.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="105" 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">@@ -105,6 +105,7 @@ class QIIME2Type(click.ParamType):</td>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tempfile</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk.util</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</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">@@ -124,8 +125,13 @@ class QIIME2Type(click.ParamType):</td>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="s" style="color: #d14;">f'</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">value</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">!</span><span class="n" style="color: #333;">r</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> is not a valid filepath'</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ControlFlowException</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ControlFlowException</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If we made it here, QIIME 2 was confident that the thing we</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># are trying to load is a QIIME 2 Result, however, we have run</span></span>
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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;"># into some kind of catastrophic error.</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'There was a problem loading %s as a '</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="s" style="color: #d14;">'QIIME 2 Result:'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="p">.</span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">exit_with_error</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">header</span><span class="p">)</span></span>
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129
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">ControlFlowException</span><span class="p">:</span></span>
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130
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="s" style="color: #d14;">'%r is not a QIIME 2 Artifact (.qza)'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span></span>
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131
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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;">ctx</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="185" 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="191" 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">@@ -185,7 +191,7 @@ class QIIME2Type(click.ParamType):</td>
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185
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">metadata_column</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">get_column</span><span class="p">(</span><span class="n" style="color: #333;">column</span><span class="p">)</span></span>
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186
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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187
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<td class="diff-line-num new_line" data-linenumber="193" 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">
193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="s" style="color: #d14;">"There was an issue with retrieving column %r from "</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="s" style="color: #d14;">"the metadata<span class="idiff left right">:</span>"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">column</span><span class="p">)</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="s" style="color: #d14;">"the metadata<span class="idiff left right">.</span>"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">column</span><span class="p">)</span></span>
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189
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"></span>
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190
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metadata_column</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">type_expr</span><span class="p">:</span></span>
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191
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="s" style="color: #d14;">"Metadata column is of type %r, but expected %r."</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#9089f11caa4b0f6ef10f937f509084406dc6e3d0"><strong>q2cli/commands.py</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</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="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></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="python"><span class="c1" style="color: #998; font-style: italic;">#</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">@@ -219,6 +219,7 @@ class ActionCommand(BaseCommandMixin, click.Command):</td>
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"> <span class="s" style="color: #d14;">'during execution of this action. Or silence '</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"> <span class="s" style="color: #d14;">'output if execution is successful (silence is '</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"> <span class="s" style="color: #d14;">'golden).'</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="p">.</span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">usage_example_option</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_action</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="p">.</span><span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">citations_option</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_citation_records</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#e316d94fbce14eef139dc85098304edc0f0ff0d2"><strong>q2cli/core/__init__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#874e9f895446a24ce25c1483df0fb7d11dad5f50"><strong>q2cli/core/cache.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</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">@@ -265,6 +265,7 @@ class DeploymentCache:</td>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_action_state</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span></span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.core.usage</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">cache_examples</span></span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"></span>
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"> <span class="s" style="color: #d14;">'id'</span><span class="p">:</span> <span class="n" style="color: #333;">action</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</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">@@ -272,6 +273,7 @@ class DeploymentCache:</td>
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"> <span class="s" style="color: #d14;">'description'</span><span class="p">:</span> <span class="n" style="color: #333;">action</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">,</span></span>
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273
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"> <span class="s" style="color: #d14;">'signature'</span><span class="p">:</span> <span class="p">[],</span></span>
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"> <span class="s" style="color: #d14;">'deprecated'</span><span class="p">:</span> <span class="n" style="color: #333;">action</span><span class="p">.</span><span class="n" style="color: #333;">deprecated</span><span class="p">,</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="s" style="color: #d14;">'examples'</span><span class="p">:</span> <span class="n" style="color: #333;">cache_examples</span><span class="p">(</span><span class="n" style="color: #333;">action</span><span class="p">)</span></span>
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275
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"> <span class="p">}</span></span>
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">sig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">action</span><span class="p">.</span><span class="n" style="color: #333;">signature</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#eada752a2adf82b343f70a4bedf2ece9781b60f2"><strong>q2cli/core/completion.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#228bb7257239f997ab37f036d1b626a9f7ecafc1"><strong>q2cli/core/config.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#c5294f6a9406f7ac7065f91ded809adc5b79b15c"><strong>q2cli/core/usage.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-2020, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">textwrap</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.sdk</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">usage</span><span class="p">,</span> <span class="n" style="color: #333;">util</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">to_cli_name</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_collection</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">)</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CLIUsage</span><span class="p">(</span><span class="n" style="color: #333;">usage</span><span class="p">.</span><span class="n" style="color: #333;">Usage</span><span class="p">):</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" 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>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_cache_recorder</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cache</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_cache_recorder</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_add_cache_record</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">source</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_cache_recorder</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_init_data_</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">factory</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ref</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_init_metadata_</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">factory</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ref</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_init_data_collection_</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">collection_type</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># All collection types are saved as a list, for ordering,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># and for JSON serialization.</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">([</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ref</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">records</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_merge_metadata_</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">([</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ref</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">records</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_metadata_column_</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">column_name</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Returns a list for JSON serialization.</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">column_name</span><span class="p">]</span></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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_comment_</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">text</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_cache_record</span><span class="p">(</span><span class="n" style="color: #333;">source</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'comment'</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">text</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_action_</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="p">,</span> <span class="n" style="color: #333;">input_opts</span><span class="p">,</span> <span class="n" style="color: #333;">output_opts</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">action_f</span><span class="p">,</span> <span class="n" style="color: #333;">action_sig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">action</span><span class="p">.</span><span class="n" style="color: #333;">get_action</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">signature</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;">_destructure_signature</span><span class="p">(</span><span class="n" style="color: #333;">action_sig</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">inputs</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">mds</span><span class="p">,</span> <span class="n" style="color: #333;">outputs</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;">_destructure_opts</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">signature</span><span class="p">,</span> <span class="n" style="color: #333;">input_opts</span><span class="p">,</span> <span class="n" style="color: #333;">output_opts</span><span class="p">)</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 class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">plugin_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">action_f</span><span class="p">.</span><span class="n" style="color: #333;">plugin_id</span><span class="p">,</span> <span class="n" style="color: #333;">action_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">action_f</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">inputs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">inputs</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">mds</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mds</span><span class="p">,</span> <span class="n" style="color: #333;">outputs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outputs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_cache_record</span><span class="p">(</span><span class="n" style="color: #333;">source</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'action'</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">output_opts</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_assert_has_line_matching_</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">expression</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: implement this method - we can model the</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># `assert_has_line_matching` behavior that @thermokarst added</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># to galaxy.</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_destructure_signature</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">action_sig</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># In the future this could return a more robust spec subset,</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if necessary.</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">distill_spec</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">.</span><span class="n" style="color: #333;">qiime_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">inputs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="n" style="color: #333;">distill_spec</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">action_sig</span><span class="p">.</span><span class="n" style="color: #333;">inputs</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()}</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">outputs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="n" style="color: #333;">distill_spec</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">action_sig</span><span class="p">.</span><span class="n" style="color: #333;">outputs</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()}</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">mds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{},</span> <span class="p">{}</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">param_name</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">action_sig</span><span class="p">.</span><span class="n" style="color: #333;">inputs</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">inputs</span><span class="p">[</span><span class="n" style="color: #333;">param_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">distill_spec</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">)</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">param_name</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">action_sig</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">is_metadata_type</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">.</span><span class="n" style="color: #333;">qiime_type</span><span class="p">):</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">mds</span><span class="p">[</span><span class="n" style="color: #333;">param_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">distill_spec</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">)</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">params</span><span class="p">[</span><span class="n" style="color: #333;">param_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">distill_spec</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">{</span><span class="s" style="color: #d14;">'inputs'</span><span class="p">:</span> <span class="n" style="color: #333;">inputs</span><span class="p">,</span> <span class="s" style="color: #d14;">'params'</span><span class="p">:</span> <span class="n" style="color: #333;">params</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="s" style="color: #d14;">'mds'</span><span class="p">:</span> <span class="n" style="color: #333;">mds</span><span class="p">,</span> <span class="s" style="color: #d14;">'outputs'</span><span class="p">:</span> <span class="n" style="color: #333;">outputs</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_destructure_opts</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">signature</span><span class="p">,</span> <span class="n" style="color: #333;">input_opts</span><span class="p">,</span> <span class="n" style="color: #333;">output_opts</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">inputs</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">mds</span><span class="p">,</span> <span class="n" style="color: #333;">outputs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{},</span> <span class="p">{},</span> <span class="p">{},</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">opt_name</span><span class="p">,</span> <span class="n" style="color: #333;">val</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">input_opts</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opt_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">signature</span><span class="p">[</span><span class="s" style="color: #d14;">'inputs'</span><span class="p">].</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">inputs</span><span class="p">[</span><span class="n" style="color: #333;">opt_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">signature</span><span class="p">[</span><span class="s" style="color: #d14;">'inputs'</span><span class="p">][</span><span class="n" style="color: #333;">opt_name</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">opt_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">signature</span><span class="p">[</span><span class="s" style="color: #d14;">'params'</span><span class="p">].</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Coerce all collection types into lists, to</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># allow for JSON serialization.</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_collection</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">):</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">params</span><span class="p">[</span><span class="n" style="color: #333;">opt_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">signature</span><span class="p">[</span><span class="s" style="color: #d14;">'params'</span><span class="p">][</span><span class="n" style="color: #333;">opt_name</span><span class="p">])</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">opt_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">signature</span><span class="p">[</span><span class="s" style="color: #d14;">'mds'</span><span class="p">].</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">mds</span><span class="p">[</span><span class="n" style="color: #333;">opt_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">signature</span><span class="p">[</span><span class="s" style="color: #d14;">'mds'</span><span class="p">][</span><span class="n" style="color: #333;">opt_name</span><span class="p">])</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">opt_name</span><span class="p">,</span> <span class="n" style="color: #333;">val</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">output_opts</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">opt_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">signature</span><span class="p">[</span><span class="s" style="color: #d14;">'outputs'</span><span class="p">][</span><span class="n" style="color: #333;">opt_name</span><span class="p">])</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">inputs</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">mds</span><span class="p">,</span> <span class="n" style="color: #333;">outputs</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CLIRenderer</span><span class="p">:</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" 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;">records</span><span class="p">):</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cache_records</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">records</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">render</span><span class="p">(</span><span class="bp" style="color: #999;">self</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;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cache_records</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="s" style="color: #d14;">'No examples have been registered for this action yet.'</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" 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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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cache_records</span><span class="p">:</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">dispatch</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">dispatch</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">):</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="s" style="color: #d14;">'source'</span><span class="p">]</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'comment'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">template_comment</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">[</span><span class="s" style="color: #d14;">'value'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'action'</span><span class="p">:</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">template_action</span><span class="p">(</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="s" style="color: #d14;">'value'</span><span class="p">][</span><span class="s" style="color: #d14;">'plugin_id'</span><span class="p">],</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="s" style="color: #d14;">'value'</span><span class="p">][</span><span class="s" style="color: #d14;">'action_id'</span><span class="p">],</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="s" style="color: #d14;">'value'</span><span class="p">][</span><span class="s" style="color: #d14;">'inputs'</span><span class="p">],</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="s" style="color: #d14;">'value'</span><span class="p">][</span><span class="s" style="color: #d14;">'params'</span><span class="p">],</span></span>
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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;">record</span><span class="p">[</span><span class="s" style="color: #d14;">'value'</span><span class="p">][</span><span class="s" style="color: #d14;">'mds'</span><span class="p">],</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="s" style="color: #d14;">'value'</span><span class="p">][</span><span class="s" style="color: #d14;">'outputs'</span><span class="p">],</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="p">)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">template_comment</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">comment</span><span class="p">):</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">f'# </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">comment</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">template_action</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">plugin_id</span><span class="p">,</span> <span class="n" style="color: #333;">action_id</span><span class="p">,</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">inputs</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">mds</span><span class="p">,</span> <span class="n" style="color: #333;">outputs</span><span class="p">):</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">templates</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_template_inputs</span><span class="p">(</span><span class="n" style="color: #333;">inputs</span><span class="p">)),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_template_parameters</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">)),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_template_metadata</span><span class="p">(</span><span class="n" style="color: #333;">mds</span><span class="p">)),</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_template_outputs</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="p">]</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">base_cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="s" style="color: #d14;">f'qiime </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">plugin_id</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">action_id</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">action_t</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;">_format_templates</span><span class="p">(</span><span class="n" style="color: #333;">base_cmd</span><span class="p">,</span> <span class="n" style="color: #333;">templates</span><span class="p">)</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">action_t</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_format_templates</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">command</span><span class="p">,</span> <span class="n" style="color: #333;">templates</span><span class="p">):</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">wrapper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">textwrap</span><span class="p">.</span><span class="n" style="color: #333;">TextWrapper</span><span class="p">(</span><span class="n" style="color: #333;">initial_indent</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">templates</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">command</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">wrapper</span><span class="p">.</span><span class="n" style="color: #333;">fill</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">templates</span><span class="p">]</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">' </span><span class="se" style="color: #d14;">\\\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">)</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_template_inputs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">input_opts</span><span class="p">):</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">opt_name</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">input_opts</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ref</span> <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;">ref</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">[</span><span class="n" style="color: #333;">ref</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ref</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">refs</span><span class="p">:</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">opt_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="n" style="color: #333;">opt_name</span><span class="p">)</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="s" style="color: #d14;">f'--i-</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">opt_name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">ref</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">.qza'</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_template_parameters</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">param_opts</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">opt_name</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">param_opts</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_collection</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">[</span><span class="n" style="color: #333;">val</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">val</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">vals</span><span class="p">):</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">opt_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="n" style="color: #333;">opt_name</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="s" style="color: #d14;">f'--p-</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">opt_name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">val</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_template_metadata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">md_opts</span><span class="p">):</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">opt_name</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">qiime_type</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">md_opts</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">qiime_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">parse_type</span><span class="p">(</span><span class="n" style="color: #333;">qiime_type</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">is_mdc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">is_metadata_column_type</span><span class="p">(</span><span class="n" style="color: #333;">qiime_type</span><span class="p">)</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Make this into a tuple to differentiate in the following loop</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_mdc</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">ref</span></span>
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<td class="diff-line-num new new_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ref</span> <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;">ref</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">[</span><span class="n" style="color: #333;">ref</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ref</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">refs</span><span class="p">:</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">opt_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="n" style="color: #333;">opt_name</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ref</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_mdc</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="186" 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">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="s" style="color: #d14;">f'--m-</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">opt_name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">-file </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">ref</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">.tsv'</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="s" style="color: #d14;">f'--m-</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">opt_name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">-column </span><span class="se" style="color: #d14;">\'</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">col</span><span class="si" style="color: #d14;">}</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">'</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_template_outputs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">output_opts</span><span class="p">):</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">opt_name</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">qiime_type</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">output_opts</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">opt_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="n" style="color: #333;">opt_name</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">qiime_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">parse_type</span><span class="p">(</span><span class="n" style="color: #333;">qiime_type</span><span class="p">)</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'qzv'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">util</span><span class="p">.</span><span class="n" style="color: #333;">is_visualization_type</span><span class="p">(</span><span class="n" style="color: #333;">qiime_type</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'qza'</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="s" style="color: #d14;">f'--o-</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">opt_name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">ref</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">.</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">ext</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cache_examples</span><span class="p">(</span><span class="n" style="color: #333;">action</span><span class="p">):</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">all_examples</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">example</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">action</span><span class="p">.</span><span class="n" style="color: #333;">examples</span><span class="p">:</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">use</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CLIUsage</span><span class="p">()</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">example</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'_'</span><span class="p">,</span> <span class="s" style="color: #d14;">' '</span><span class="p">)</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">use</span><span class="p">.</span><span class="n" style="color: #333;">_comment_</span><span class="p">(</span><span class="s" style="color: #d14;">f'### example: </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">header</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> ###'</span><span class="p">)</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="p">.</span><span class="n" style="color: #333;">examples</span><span class="p">[</span><span class="n" style="color: #333;">example</span><span class="p">](</span><span class="n" style="color: #333;">use</span><span class="p">)</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">cache</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">use</span><span class="p">.</span><span class="n" style="color: #333;">cache</span><span class="p">()</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">all_examples</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">cache</span><span class="p">)</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">all_examples</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">examples</span><span class="p">(</span><span class="n" style="color: #333;">action</span><span class="p">):</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.core.cache</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">plugin_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="n" style="color: #333;">action</span><span class="p">.</span><span class="n" style="color: #333;">plugin_id</span><span class="p">)</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">cached_plugin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">cache</span><span class="p">.</span><span class="n" style="color: #333;">CACHE</span><span class="p">.</span><span class="n" style="color: #333;">plugins</span><span class="p">[</span><span class="n" style="color: #333;">plugin_id</span><span class="p">]</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">cached_action</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cached_plugin</span><span class="p">[</span><span class="s" style="color: #d14;">'actions'</span><span class="p">][</span><span class="n" style="color: #333;">action</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">cached_examples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cached_action</span><span class="p">[</span><span class="s" style="color: #d14;">'examples'</span><span class="p">]</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">cache_render</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CLIRenderer</span><span class="p">(</span><span class="n" style="color: #333;">cached_examples</span><span class="p">)</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rendered</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cache_render</span><span class="p">.</span><span class="n" style="color: #333;">render</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">rendered</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#c4467f99066e6470736c8885ad6d10ff73140180"><strong>q2cli/tests/__init__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#dc5f5985a047865b81ba832edeea7666a8a308b7"><strong>q2cli/tests/test_cli.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</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">@@ -311,6 +311,22 @@ class CliTests(unittest.TestCase):</td>
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311
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python"> <span class="s" style="color: #d14;">f'</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">temp</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">!</span><span class="n" style="color: #333;">r</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</span><span class="p">):</span></span>
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312
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"> <span class="n" style="color: #333;">obj</span><span class="p">.</span><span class="n" style="color: #333;">_convert_input</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">artifact1_path</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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313
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_syntax_error_in_env</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">qiime_cli</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RootCommand</span><span class="p">()</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime_cli</span><span class="p">.</span><span class="n" style="color: #333;">get_command</span><span class="p">(</span><span class="n" style="color: #333;">ctx</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;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'dummy-plugin'</span><span class="p">)</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">viz_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tempdir</span><span class="p">,</span> <span class="s" style="color: #d14;">'viz'</span><span class="p">)</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">mock</span><span class="p">.</span><span class="n" style="color: #333;">patch</span><span class="p">(</span><span class="s" style="color: #d14;">'qiime2.sdk.Result.load'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">side_effect</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">SyntaxError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">result</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;">runner</span><span class="p">.</span><span class="n" style="color: #333;">invoke</span><span class="p">(</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">command</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'most-common-viz'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-ints'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">artifact1_path</span><span class="p">,</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"> <span class="s" style="color: #d14;">'--o-visualization'</span><span class="p">,</span> <span class="n" style="color: #333;">viz_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'--verbose'</span><span class="p">])</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="s" style="color: #d14;">'problem loading'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">artifact1_path</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"></span>
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314
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_deprecated_help_text</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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315
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"> <span class="n" style="color: #333;">qiime_cli</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RootCommand</span><span class="p">()</span></span>
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316
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime_cli</span><span class="p">.</span><span class="n" style="color: #333;">get_command</span><span class="p">(</span><span class="n" style="color: #333;">ctx</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;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'dummy-plugin'</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">@@ -340,6 +356,26 @@ class CliTests(unittest.TestCase):</td>
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340
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"></span>
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341
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="s" style="color: #d14;">'deprecated'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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342
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python"></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_examples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">qiime_cli</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RootCommand</span><span class="p">()</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime_cli</span><span class="p">.</span><span class="n" style="color: #333;">get_command</span><span class="p">(</span><span class="n" style="color: #333;">ctx</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;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'dummy-plugin'</span><span class="p">)</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">result</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;">runner</span><span class="p">.</span><span class="n" style="color: #333;">invoke</span><span class="p">(</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">command</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'typical-pipeline'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--examples'</span><span class="p">]</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"> <span class="p">)</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_no_examples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"> <span class="n" style="color: #333;">qiime_cli</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RootCommand</span><span class="p">()</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime_cli</span><span class="p">.</span><span class="n" style="color: #333;">get_command</span><span class="p">(</span><span class="n" style="color: #333;">ctx</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;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'dummy-plugin'</span><span class="p">)</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;">result</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;">runner</span><span class="p">.</span><span class="n" style="color: #333;">invoke</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">command</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'unioned-primitives'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--examples'</span><span class="p">]</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"> <span class="p">)</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="376" 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">
376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"> <span class="s" style="color: #d14;">"No examples have been registered for this action yet.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"> <span class="p">)</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python"></span>
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343
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"></span>
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344
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestOptionalArtifactSupport</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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345
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="473" 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="509" 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">@@ -473,7 +509,7 @@ class TestMetadataSupport(MetadataTestsBase):</td>
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473
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509
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python"></span>
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474
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510
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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475
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<td class="diff-line-num new_line" data-linenumber="511" 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">
511
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'Usage:'</span><span class="p">))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
476
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<td class="diff-line-num new_line old" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option </span><span class="se" style="color: #d14;"><span class="idiff left">\"</span></span><span class="s" style="color: #d14;"><span class="idiff">--m-metadata-file</span></span><span class="se" style="color: #d14;"><span class="idiff right">\"</span></span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="477" 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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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option <span class="idiff left right">'--m-metadata-file'</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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477
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="python"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="478" 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">
478
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514
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_optional_metadata_missing</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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479
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515
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">result</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;">_run_command</span><span class="p">(</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="557" 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="593" 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">@@ -557,7 +593,7 @@ class TestMetadataColumnSupport(MetadataTestsBase):</td>
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557
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<td class="diff-line-num new_line" data-linenumber="593" 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">
593
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="python"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="558" 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">
558
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<td class="diff-line-num new_line" data-linenumber="594" 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">
594
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
</pre>
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559
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595
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'Usage:'</span><span class="p">))</span></span>
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560
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<td class="diff-line-num new_line old" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option </span><span class="se" style="color: #d14;"><span class="idiff left">\"</span></span><span class="s" style="color: #d14;"><span class="idiff">--m-metadata-file</span></span><span class="se" style="color: #d14;"><span class="idiff right">\"</span></span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option <span class="idiff left right">'--m-metadata-file'</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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561
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597
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="python"></span>
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562
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_optional_metadata_missing</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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563
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599
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="python"> <span class="n" style="color: #333;">result</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;">_run_command</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="575" 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="611" 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">@@ -575,7 +611,7 @@ class TestMetadataColumnSupport(MetadataTestsBase):</td>
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575
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="python"></span>
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576
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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577
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<td class="diff-line-num 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">
613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'Usage:'</span><span class="p">))</span></span>
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578
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<td class="diff-line-num new_line old" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option </span><span class="se" style="color: #d14;"><span class="idiff left">\"</span></span><span class="s" style="color: #d14;"><span class="idiff">--m-metadata-column</span></span><span class="se" style="color: #d14;"><span class="idiff right">\"</span></span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option <span class="idiff left right">'--m-metadata-column'</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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579
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615
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="python"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="580" 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">
580
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616
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_optional_column_without_metadata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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581
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617
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="python"> <span class="n" style="color: #333;">result</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;">_run_command</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="585" 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="621" 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">@@ -585,7 +621,7 @@ class TestMetadataColumnSupport(MetadataTestsBase):</td>
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585
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621
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python"></span>
</pre>
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586
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622
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
</pre>
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587
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623
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'Usage:'</span><span class="p">))</span></span>
</pre>
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588
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option </span><span class="se" style="color: #d14;"><span class="idiff left">\"</span></span><span class="s" style="color: #d14;"><span class="idiff">--m-metadata-file</span></span><span class="se" style="color: #d14;"><span class="idiff right">\"</span></span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option <span class="idiff left right">'--m-metadata-file'</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_metadata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">command</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'identity-with-metadata-column'</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#69859555882ae5b802d6b617deeaece2a2130265"><strong>q2cli/tests/test_core.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-2020, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.core.usage</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">examples</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.core.testing.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_dummy_plugin</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">dummy_plugin</span><span class="p">(</span><span class="n" style="color: #333;">monkeypatch</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">monkeypatch</span><span class="p">.</span><span class="n" style="color: #333;">setenv</span><span class="p">(</span><span class="s" style="color: #d14;">'QIIMETEST'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">)</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">get_dummy_plugin</span><span class="p">()</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'concatenate_ints'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;"># ### example: concatenate ints simple ###</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="s" style="color: #d14;"># This example demonstrates basic usage.</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;">qiime dummy-plugin concatenate-ints </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints1 ints_a.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints2 ints_b.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints3 ints_c.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;"> --p-int1 4 </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;"> --p-int2 2 </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;"> --o-concatenated-ints ints_d.qza</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;"># ### example: concatenate ints complex ###</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;"># This example demonstrates chained usage (pt 1).</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;">qiime dummy-plugin concatenate-ints </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints1 ints_a.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints2 ints_b.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints3 ints_c.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;"> --p-int1 4 </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;"> --p-int2 2 </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;"> --o-concatenated-ints ints_d.qza</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;"># This example demonstrates chained usage (pt 2).</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;">qiime dummy-plugin concatenate-ints </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints1 ints_d.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints2 ints_b.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints3 ints_c.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;"> --p-int1 41 </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;"> --p-int2 0 </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;"> --o-concatenated-ints concatenated_ints.qza</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;"># ### example: comments only ###</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;"># comment 1</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;"># comment 2"""</span><span class="p">,</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 class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="s" style="color: #d14;">'identity_with_metadata'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="s" style="color: #d14;"># ### example: identity with metadata simple ###</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;">qiime dummy-plugin identity-with-metadata </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints ints.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"><span class="s" style="color: #d14;"> --m-metadata-file md.tsv </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;"> --o-out out.qza</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"><span class="s" style="color: #d14;"># ### example: identity with metadata merging ###</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"><span class="s" style="color: #d14;">qiime dummy-plugin identity-with-metadata </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints ints.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;"> --m-metadata-file md1.tsv </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"><span class="s" style="color: #d14;"> --m-metadata-file md2.tsv </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"><span class="s" style="color: #d14;"> --o-out out.qza"""</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="s" style="color: #d14;">'identity_with_metadata_column'</span><span class="p">,</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"><span class="s" style="color: #d14;"># ### example: identity with metadata column get mdc ###</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"><span class="s" style="color: #d14;">qiime dummy-plugin identity-with-metadata-column </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints ints.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"><span class="s" style="color: #d14;"> --m-metadata-file md.tsv </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"><span class="s" style="color: #d14;"> --m-metadata-column 'a' </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"><span class="s" style="color: #d14;"> --o-out out.qza"""</span><span class="p">,</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="s" style="color: #d14;">'typical_pipeline'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;"># ### example: typical pipeline simple ###</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"><span class="s" style="color: #d14;">qiime dummy-plugin typical-pipeline </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"><span class="s" style="color: #d14;"> --i-int-sequence ints.qza </span><span class="se" style="color: #d14;">\\</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"><span class="s" style="color: #d14;"> --i-mapping mapper.qza </span><span class="se" style="color: #d14;">\\</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"><span class="s" style="color: #d14;"> --p-do-extra-thing True </span><span class="se" style="color: #d14;">\\</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"><span class="s" style="color: #d14;"> --o-out-map out_map.qza </span><span class="se" style="color: #d14;">\\</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;"> --o-left left.qza </span><span class="se" style="color: #d14;">\\</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"><span class="s" style="color: #d14;"> --o-right right.qza </span><span class="se" style="color: #d14;">\\</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;"> --o-left-viz left_viz.qzv </span><span class="se" style="color: #d14;">\\</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;"> --o-right-viz right_viz.qzv</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;"># ### example: typical pipeline complex ###</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"><span class="s" style="color: #d14;">qiime dummy-plugin typical-pipeline </span><span class="se" style="color: #d14;">\\</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;"> --i-int-sequence ints1.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"><span class="s" style="color: #d14;"> --i-mapping mapper1.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;"> --p-do-extra-thing True </span><span class="se" style="color: #d14;">\\</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"><span class="s" style="color: #d14;"> --o-out-map out_map1.qza </span><span class="se" style="color: #d14;">\\</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;"> --o-left left1.qza </span><span class="se" style="color: #d14;">\\</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"><span class="s" style="color: #d14;"> --o-right right1.qza </span><span class="se" style="color: #d14;">\\</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;"> --o-left-viz left_viz1.qzv </span><span class="se" style="color: #d14;">\\</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"><span class="s" style="color: #d14;"> --o-right-viz right_viz1.qzv</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"><span class="s" style="color: #d14;">qiime dummy-plugin typical-pipeline </span><span class="se" style="color: #d14;">\\</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;"> --i-int-sequence left1.qza </span><span class="se" style="color: #d14;">\\</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;"> --i-mapping out_map1.qza </span><span class="se" style="color: #d14;">\\</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"><span class="s" style="color: #d14;"> --p-do-extra-thing False </span><span class="se" style="color: #d14;">\\</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"><span class="s" style="color: #d14;"> --o-out-map out_map2.qza </span><span class="se" style="color: #d14;">\\</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"><span class="s" style="color: #d14;"> --o-left left2.qza </span><span class="se" style="color: #d14;">\\</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"><span class="s" style="color: #d14;"> --o-right right2.qza </span><span class="se" style="color: #d14;">\\</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"><span class="s" style="color: #d14;"> --o-left-viz left_viz2.qzv </span><span class="se" style="color: #d14;">\\</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"><span class="s" style="color: #d14;"> --o-right-viz right_viz2.qzv"""</span><span class="p">,</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="p">),</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="p">(</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">'optional_artifacts_method'</span><span class="p">,</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span><span class="se" style="color: #d14;">\</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"><span class="s" style="color: #d14;"># ### example: optional inputs ###</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"><span class="s" style="color: #d14;">qiime dummy-plugin optional-artifacts-method </span><span class="se" style="color: #d14;">\\</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints ints.qza </span><span class="se" style="color: #d14;">\\</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"><span class="s" style="color: #d14;"> --p-num1 1 </span><span class="se" style="color: #d14;">\\</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"><span class="s" style="color: #d14;"> --o-output output.qza</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"><span class="s" style="color: #d14;">qiime dummy-plugin optional-artifacts-method </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints ints.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"><span class="s" style="color: #d14;"> --p-num1 1 </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"><span class="s" style="color: #d14;"> --p-num2 2 </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"><span class="s" style="color: #d14;"> --o-output output.qza</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"><span class="s" style="color: #d14;">qiime dummy-plugin optional-artifacts-method </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints ints.qza </span><span class="se" style="color: #d14;">\\</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"><span class="s" style="color: #d14;"> --p-num1 1 </span><span class="se" style="color: #d14;">\\</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"><span class="s" style="color: #d14;"> --p-num2 None </span><span class="se" style="color: #d14;">\\</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"><span class="s" style="color: #d14;"> --o-output ints_b.qza</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"><span class="s" style="color: #d14;">qiime dummy-plugin optional-artifacts-method </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints ints.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"><span class="s" style="color: #d14;"> --i-optional1 ints_b.qza </span><span class="se" style="color: #d14;">\\</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"><span class="s" style="color: #d14;"> --p-num1 3 </span><span class="se" style="color: #d14;">\\</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"><span class="s" style="color: #d14;"> --p-num2 4 </span><span class="se" style="color: #d14;">\\</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"><span class="s" style="color: #d14;"> --o-output output.qza"""</span><span class="p">,</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="p">),</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="p">(</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="s" style="color: #d14;">'variadic_input_method'</span><span class="p">,</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span><span class="se" style="color: #d14;">\</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"><span class="s" style="color: #d14;"># ### example: variadic input simple ###</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"><span class="s" style="color: #d14;">qiime dummy-plugin variadic-input-method </span><span class="se" style="color: #d14;">\\</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints ints_a.qza </span><span class="se" style="color: #d14;">\\</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"><span class="s" style="color: #d14;"> --i-ints ints_b.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"><span class="s" style="color: #d14;"> --i-int-set single_int1.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"><span class="s" style="color: #d14;"> --i-int-set single_int2.qza </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"><span class="s" style="color: #d14;"> --p-nums 7 </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;"> --p-nums 8 </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"><span class="s" style="color: #d14;"> --p-nums 9 </span><span class="se" style="color: #d14;">\\</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"><span class="s" style="color: #d14;"> --o-output out.qza"""</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">'action, exp'</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_examples</span><span class="p">(</span><span class="n" style="color: #333;">dummy_plugin</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dummy_plugin</span><span class="p">.</span><span class="n" style="color: #333;">actions</span><span class="p">[</span><span class="n" style="color: #333;">action</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">examples</span><span class="p">(</span><span class="n" style="color: #333;">action</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span></span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</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">@@ -36,6 +36,10 @@ def to_cli_name(name):</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'_'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">to_snake_case</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">,</span> <span class="s" style="color: #d14;">'_'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">exit_with_error</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'An error has been encountered:'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">traceback</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'stderr'</span><span class="p">,</span> <span class="n" style="color: #333;">status</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="182" 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">@@ -178,3 +182,23 @@ def citations_option(get_citation_records):</td>
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">click</span><span class="p">.</span><span class="n" style="color: #333;">Option</span><span class="p">([</span><span class="s" style="color: #d14;">'--citations'</span><span class="p">],</span> <span class="n" style="color: #333;">is_flag</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">expose_value</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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179
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">is_eager</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">callback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">callback</span><span class="p">,</span></span>
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180
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Show citations and exit.'</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">usage_example_option</span><span class="p">(</span><span class="n" style="color: #333;">action</span><span class="p">):</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.core.usage</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">examples</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">callback</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">resilient_parsing</span><span class="p">:</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">command</span><span class="p">.</span><span class="n" style="color: #333;">_get_action</span><span class="p">()</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="197" 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">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">examples</span><span class="p">(</span><span class="n" style="color: #333;">action</span><span class="p">):</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="p">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">click</span><span class="p">.</span><span class="n" style="color: #333;">Option</span><span class="p">([</span><span class="s" style="color: #d14;">'--examples'</span><span class="p">],</span> <span class="n" style="color: #333;">is_flag</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">expose_value</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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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">is_eager</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">callback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">callback</span><span class="p">,</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Show usage examples and exit.'</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2cli/-/commit/4248084e94472cf7195715369d515502741dfcd1#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></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="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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