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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/spades">Debian Med / spades</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/3b3309c093ad1de1635b10e06f7b54e71e7fe88a">3b3309c0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-13T13:24:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix pyyaml patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/639914be81dc5d563998c58ee9c98d64640d6369">639914be</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-13T13:25:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix Python3 patch
</pre>
</li>
</ul>
<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
debian/patches/python3.patch
</a>
</li>
<li class="file-stats">
<a href="#6b4e31cdf8f9338db47a4fa236a08014b3851935">
debian/patches/yaml_load.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
<a href="https://salsa.debian.org/med-team/spades/compare/9207cab94da2e59b88cc9a282b48efa7b0233e84...639914be81dc5d563998c58ee9c98d64640d6369#e246f69e945a7c2e9a8e25cfacfcac7714c92b69"><strong>debian/patches/python3.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="120" 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="120" 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">@@ -120,7 +120,7 @@ Description: Make sure Python3 interpreter is used in scripts</td>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="diff"> with open(cfg_file) as infile:</span>
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<td class="diff-line-num old_line" data-linenumber="121" 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="121" 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="LC121" class="line" lang="diff"> for line in infile:</span>
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<td class="diff-line-num new_line" data-linenumber="122" 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="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for src, target in replacements.iteritems():</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for src, target in <span class="idiff left right">list(replacements.iteritems()</span>):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for src, target in <span class="idiff left right">replacements.items(</span>):</span></span>
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<td class="diff-line-num old_line" data-linenumber="124" 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="LC124" class="line" lang="diff"> line = line.replace(src, target)</span>
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<td class="diff-line-num old_line" data-linenumber="125" 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="125" 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="LC125" class="line" lang="diff"> lines.append(line)</span>
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<td class="diff-line-num old_line" data-linenumber="126" 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="126" 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="LC126" class="line" lang="diff"> with open(cfg_file, 'w') as outfile:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="129" 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="129" 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">@@ -129,7 +129,7 @@ Description: Make sure Python3 interpreter is used in scripts</td>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="diff"> with open(cfg_file) as infile:</span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="diff"> for line in infile:</span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for src, target in replacements.iteritems():</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for src, target in <span class="idiff left right">list(replacements.iteritems()</span>):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for src, target in <span class="idiff left right">replacements.items(</span>):</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="diff"> line = line.replace(src, target)</span>
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<td class="diff-line-num old_line" data-linenumber="134" 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="LC134" class="line" lang="diff"> lines.append(line)</span>
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<td class="diff-line-num old_line" data-linenumber="135" 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="135" 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="LC135" class="line" lang="diff"> with open(cfg_file, 'w') as outfile:</span>
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</li>
<li id="6b4e31cdf8f9338db47a4fa236a08014b3851935">
<a href="https://salsa.debian.org/med-team/spades/compare/9207cab94da2e59b88cc9a282b48efa7b0233e84...639914be81dc5d563998c58ee9c98d64640d6369#6b4e31cdf8f9338db47a4fa236a08014b3851935"><strong>debian/patches/yaml_load.patch</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 @@ Description: Specify yaml loader</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> log.info(" Reads:")</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename, 'r'))</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename, 'r'), Loader=yaml.FullLoader)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename, 'r'), Loader=<span class="idiff left right">py</span>yaml.FullLoader)</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(cfg["dataset"].yaml_filename))</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> support.pretty_print_reads(dataset_data, log)</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> </span></pre>
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