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<h3>
Aaron M. Ucko pushed to branch master
at <a href="https://salsa.debian.org/med-team/ncbi-entrez-direct">Debian Med / ncbi-entrez-direct</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/94ca7b92be19c8755b506f70629f102b24998eb8">94ca7b92</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-06-28T21:00:44-04:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Start work on ncbi-entrez-direct 13.7.20200615+dfsg-2.
</pre>
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<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/146d078d88ded9dca04fbe38df7361a2d786fe2a">146d078d</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-06-28T21:08:52-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install ftp-cp, ftp-ls, nquire, and transmute as simple wrappers.
debian/rules: Install ftp-cp, ftp-ls, nquire, and transmute as simple
wrappers for edirect (with no .pl suffix) now that they're no longer
independent Perl scripts (as of 12.3.20191024[+ds]), fixing a
regression caught by autopkgtest.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/a124a1f422bcef042ca75dec15d23a9150c63e55">a124a1f4</a></strong>
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<span>by Aaron M. Ucko</span>
<i>at 2020-06-28T21:11:04-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/tests/run-unit-test: Correct invocation of filter-stop-words
filter-stop-words ignores its arguments and reads from standard input.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/36914b997fe7b6f71dbe208a0f2e29e2ca47f056">36914b99</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-06-28T21:11:51-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Finalize ncbi-entrez-direct 13.7.20200615+dfsg-2 for unstable.
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/14173f9c25d4b41220fb0566b89266390037131c...36914b997fe7b6f71dbe208a0f2e29e2ca47f056#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ncbi-entrez-direct (13.7.20200615+dfsg-2) unstable; urgency=medium</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"> * debian/rules: Install ftp-cp, ftp-ls, nquire, and transmute as simple</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> wrappers for edirect (with no .pl suffix) now that they're no longer</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> independent Perl scripts (as of 12.3.20191024[+ds]), fixing a</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> regression caught by autopkgtest.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * debian/tests/run-unit-test: Correct invocation of filter-stop-words</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> (which ignores its arguments and reads from standard input).</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Aaron M. Ucko <ucko@debian.org> Sun, 28 Jun 2020 21:11:51 -0400</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">ncbi-entrez-direct (13.7.20200615+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * New upstream release.</span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/14173f9c25d4b41220fb0566b89266390037131c...36914b997fe7b6f71dbe208a0f2e29e2ca47f056#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,8 @@ LIB_DIR = /usr/lib/$(PACKAGE)</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">MODES = address blast citmatch contact filter link notify post proxy search \</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> spell</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">STD_WRAPPERS = $(MODES:%=bin/e%)</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">WRAPPERS = $(STD_WRAPPERS) bin/esummary</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">OTHER_WRAPPERS = esummary ftp-cp ftp-ls nquire transmute</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">WRAPPERS = $(STD_WRAPPERS) $(OTHER_WRAPPERS:%=bin/%)</span>
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19
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">AS_IS_SCRIPTS = amino-acid-composition archive-pubmed between-two-genes \</span>
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20
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> enquire entrez-phrase-search esample exclude-uid-lists \</span>
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21
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> expand-current fetch-extras fetch-pubmed filter-stop-words \</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">@@ -26,8 +27,7 @@ BASH_SCRIPTS = index-extras index-themes</td>
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26
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">BIN_BASH_SCRIPTS = $(BASH_SCRIPTS:%=bin/%)</span>
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27
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">DL_SCRIPTS = download-ncbi-data download-pubmed download-sequence</span>
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28
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">BIN_DL_SCRIPTS = $(DL_SCRIPTS:%=bin/%)</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">PERL_SCRIPTS = edirutil ftp-cp ftp-ls gbf2xml nquire run-ncbi-converter \</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> transmute</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">PERL_SCRIPTS = edirutil gbf2xml run-ncbi-converter</span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">BIN_PERL_SCRIPTS = $(PERL_SCRIPTS:%=bin/%)</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"># Only bt-link and xplore need this treatment at present,</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"># but list all bt-* scripts to be safe.</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">@@ -82,6 +82,26 @@ bin/esummary: bin/edirect</td>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"> echo 'exec /usr/bin/edirect -fetch -format docsum "$$@"' >> $@</span>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"> chmod +x $@</span>
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">bin/ftp-cp: bin/edirect</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> echo '#!/bin/sh' > $@</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> echo 'exec /usr/bin/edirect -ftpcp "$$@"' >> $@</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> chmod +x $@</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">bin/ftp-ls: bin/edirect</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> echo '#!/bin/sh' > $@</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> echo 'exec /usr/bin/edirect -ftpls "$$@"' >> $@</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> chmod +x $@</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">bin/nquire: bin/edirect</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> echo '#!/bin/sh' > $@</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> echo 'exec /usr/bin/edirect -nquir "$$@"' >> $@</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> chmod +x $@</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">bin/transmute: bin/edirect</span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> echo '#!/bin/sh' > $@</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> echo 'exec /usr/bin/edirect -tmute "$$@"' >> $@</span>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> chmod +x $@</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"></span>
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85
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext">$(BIN_BASH_SCRIPTS): bin/%: %</span>
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86
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"> mkdir -p bin</span>
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87
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"> sed -e '$(FIX_BASH_SHEBANG)' $< > $@</span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/14173f9c25d4b41220fb0566b89266390037131c...36914b997fe7b6f71dbe208a0f2e29e2ca47f056#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" 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="38" 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">@@ -38,7 +38,7 @@ echo -e "\e[92m\e[1mPassed\e[0m"</td>
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38
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="diff-line-num old_line" data-linenumber="39" 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">
39
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<td class="diff-line-num new_line" data-linenumber="39" 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">
39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"></span>
</pre>
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40
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<td class="diff-line-num new_line" data-linenumber="40" 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">
40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 4: filter-stop-words</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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41
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<td class="diff-line-num new_line old" data-linenumber="41" 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="LC41" class="line" lang="shell">filter-stop-words stopwords</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell">filter-stop-words <span class="idiff left right">< </span>stopwords</span>
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42
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<td class="diff-line-num new_line" data-linenumber="42" 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">
42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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<td class="diff-line-num old_line" data-linenumber="43" 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">
43
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<td class="diff-line-num new_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span></span>
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44
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<td class="diff-line-num new_line" data-linenumber="44" 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">
44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 5: gbf2xml</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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