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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pdb2pqr">Debian Med / pdb2pqr</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pdb2pqr/commit/216ad6fe4c85117a8e6d730f9f69cd012bd4b1f6">216ad6fe</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-12T20:08:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix opening of text file; replace scons calls by calls to Debian packaged scons.
</pre>
</li>
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<h4>1 changed file:</h4>
<ul>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/pdb2pqr/commit/216ad6fe4c85117a8e6d730f9f69cd012bd4b1f6#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -333,6 +333,32 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100</td>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="diff"> numpy_error = True</span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="diff"> if not numpy_error:</span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="p">@@ -234,9 +234,9 @@</span> if env['BUILD_PDB2PKA']:</span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> compile_targets.append(algorithms_pyc)</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> if os.name == 'nt':</span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alg_msvs_env = env.Clone(MSVSBUILDCOM='cd .. && '+pythonBin+' scons/scons.py algorithms DEBUG=True',</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- MSVSCLEANCOM='cd .. && '+pythonBin+' scons/scons.py -c algorithms',</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- MSVSREBUILDCOM='cd .. && '+pythonBin+' scons/scons.py -c algorithms && '+pythonBin+' scons/scons.py algorithms DEBUG=True')</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ alg_msvs_env = env.Clone(MSVSBUILDCOM='cd .. && scons algorithms DEBUG=True',</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ MSVSCLEANCOM='cd .. && scons -c algorithms',</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ MSVSREBUILDCOM='cd .. && scons -c algorithms && scons algorithms DEBUG=True')</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> algorithms_project = alg_msvs_env.MSVSProject(target = 'msvs/Algorithms' + env['MSVSPROJECTSUFFIX'],</span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> auto_build_solution=0,</span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="p">@@ -259,9 +259,9 @@</span> if env['BUILD_PDB2PKA']:</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> compile_targets.append(pmc_pyc)</span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"> if os.name == 'nt':</span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pmc_msvs_env = env.Clone(MSVSBUILDCOM='cd .. && '+pythonBin+' scons/scons.py pmc_mult DEBUG=True'+build_swig,</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- MSVSCLEANCOM='cd .. && '+pythonBin+' scons/scons.py -c pmc_mult',</span></span>
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<td class="diff-line-num new new_line" data-linenumber="355" 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">
355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- MSVSREBUILDCOM='cd .. && '+pythonBin+' scons/scons.py -c pmc_mult && '+pythonBin+' scons/scons.py pmc_mult DEBUG=True'+build_swig)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="356" 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">
356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pmc_msvs_env = env.Clone(MSVSBUILDCOM='cd .. && scons pmc_mult DEBUG=True'+build_swig,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="357" 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">
357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ MSVSCLEANCOM='cd .. && scons -c pmc_mult',</span></span>
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<td class="diff-line-num new new_line" data-linenumber="358" 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">
358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ MSVSREBUILDCOM='cd .. && scons -c pmc_mult && scons pmc_mult DEBUG=True'+build_swig)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="359" 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">
359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> </span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> pmc_mult_project = pmc_msvs_env.MSVSProject(target = 'msvs/pMC_mult' + env['MSVSPROJECTSUFFIX'],</span>
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<td class="diff-line-num new new_line" data-linenumber="361" 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">
361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> auto_build_solution=0,</span>
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336
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<td class="diff-line-num new_line" data-linenumber="362" 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">
362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="diff"><span class="p">@@ -285,65 +285,65 @@</span> SConscript('SConscript-install.py', expo</span>
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337
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="diff"> SConscript('SConscript-error.py')</span>
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338
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="385" 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="411" 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">@@ -385,7 +411,7 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100</td>
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385
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411
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print</span></span>
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386
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412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'Run "python scons/scons.py" to build pdb2pqr.'</span></span>
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387
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
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<td class="diff-line-num old old_line" data-linenumber="388" 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">
388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run "<span class="idiff left right">python3 scons/scons.py</span>" to build pdb2pqr.')</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run "<span class="idiff left right">scons</span>" to build pdb2pqr.')</span></span>
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389
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415
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="diff"> </span>
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390
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416
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print</span></span>
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<td class="diff-line-num old_line" data-linenumber="391" 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">
391
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'The preferred way to configure the build is by editing the file', config_file</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="396" 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="422" 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">@@ -396,13 +422,13 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100</td>
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<td class="diff-line-num old_line" data-linenumber="396" 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">
396
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<td class="diff-line-num new_line" data-linenumber="422" 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">
422
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('The preferred way to configure the build is by editing the file', config_file)</span></span>
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397
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
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<td class="diff-line-num old_line" data-linenumber="398" 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">
398
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<td class="diff-line-num new_line" data-linenumber="424" 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">
424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run scons with the python3 that you intend to use with pdb2pqr.')</span></span>
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<td class="diff-line-num old old_line" data-linenumber="399" 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">
399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('For example: "<span class="idiff left right">/usr/bin/python3 scons/scons.py" will setup pdb2pqr to be run with /usr/bin/python3</span>')</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('For example: "<span class="idiff left right">scons" will setup pdb2pqr to be run with Debian default Python3 interpreter</span>')</span></span>
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400
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426
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="diff"> </span>
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401
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427
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="diff"> if 'install' not in target_list:</span>
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402
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428
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print</span></span>
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403
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429
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'Run "python scons/scons.py install" to install pdb2pqr in', env['PREFIX']</span></span>
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404
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
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405
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run "<span class="idiff left right">python3 scons/scons.py</span> install" to install pdb2pqr in', env['PREFIX'])</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run "<span class="idiff left right">scons</span> install" to install pdb2pqr in', env['PREFIX'])</span></span>
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406
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432
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="diff"> </span>
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407
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433
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print</span></span>
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408
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434
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'Run "python scons/scons.py basic-test" for a basic functionality test'</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">@@ -418,16 +444,16 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100</td>
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418
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444
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging.'</span></span>
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419
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445
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'The resulting projects will need to modified to use VS natively to compile the code or debug.'</span></span>
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420
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446
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
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421
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run "<span class="idiff left right">python3 scons/scons.py</span> basic-test" for a basic functionality test')</span></span>
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422
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<td class="diff-line-num new_line old" data-linenumber="447" 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="LC422" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run "<span class="idiff left right">python3 scons/scons.py</span> advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled.')</span></span>
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423
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<td class="diff-line-num new_line old" data-linenumber="447" 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="LC423" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run "<span class="idiff left right">python3 scons/scons.py</span> complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled.')</span></span>
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424
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run "<span class="idiff left right">python3 scons/scons.py</span> pdb2pka-test" for a test of PDB2PKA functionality.')</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run "<span class="idiff left right">scons</span> basic-test" for a basic functionality test')</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run "<span class="idiff left right">scons</span> advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled.')</span></span>
</pre>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run "<span class="idiff left right">scons</span> complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled.')</span></span>
</pre>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run "<span class="idiff left right">scons</span> pdb2pka-test" for a test of PDB2PKA functionality.')</span></span>
</pre>
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425
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451
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(' Requires numpy, PDB2PKA support compiled AND the APBS python3 libraries compiled and installed in the pdb2pka directory.')</span></span>
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426
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452
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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427
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453
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
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428
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('To setup a web service create a symbolic link to', env['PREFIX'], 'that enables you to view', env['URL'],'after running "scons<span class="idiff left right">/scons.py</span> install"')</span></span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('To setup a web service create a symbolic link to', env['PREFIX'], 'that enables you to view', env['URL'],'after running "scons install"')</span></span>
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429
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455
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
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430
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run "<span class="idiff left right">python3 scons/scons.py</span> msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules.')</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Run "<span class="idiff left right">scons</span> msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules.')</span></span>
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431
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457
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging.')</span></span>
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432
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458
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('The resulting projects will need to modified to use VS natively to compile the code or debug.')</span></span>
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433
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459
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8468" 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="8494" 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">@@ -8468,7 +8494,18 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100</td>
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8468
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8494
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<pre style="margin: 0;"> <span id="LC8494" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="8469" 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">
8469
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<td class="diff-line-num new_line" data-linenumber="8495" 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">
8495
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<pre style="margin: 0;"> <span id="LC8495" class="line" lang="diff"> put('pdb2pqr.tgz', '~/')</span>
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8470
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<td class="diff-line-num new_line" data-linenumber="8496" 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">
8496
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<pre style="margin: 0;"> <span id="LC8496" class="line" lang="diff"> with settings(warn_only=True):</span>
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8471
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<td class="diff-line-num new_line old" data-linenumber="8497" 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="LC8471" class="line" lang="diff"><span class="p">@@ -114,7 +114,7 @@</span> def deploy():</span>
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8497
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<pre style="margin: 0;">+<span id="LC8497" class="line" lang="diff"><span class="p">@@ -106,15 +106,15 @@</span> def deploy():</span>
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8498
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<pre style="margin: 0;">+<span id="LC8498" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="8499" 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">
8499
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<pre style="margin: 0;">+<span id="LC8499" class="line" lang="diff"> with cd('~/tmp/'):</span>
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<td class="diff-line-num new new_line" data-linenumber="8500" 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">
8500
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<pre style="margin: 0;">+<span id="LC8500" class="line" lang="diff"> run('tar -zxvf ~/pdb2pqr.tgz')</span>
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<td class="diff-line-num new new_line" data-linenumber="8501" 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">
8501
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<pre style="margin: 0;">+<span id="LC8501" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run(python+' scons/scons.py')</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8502" 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">
8502
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<pre style="margin: 0;">+<span id="LC8502" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run('scons')</span></span>
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8503
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<pre style="margin: 0;">+<span id="LC8503" class="line" lang="diff"> </span>
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8504
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<pre style="margin: 0;">+<span id="LC8504" class="line" lang="diff"> if run_tests:</span>
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8505
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<pre style="margin: 0;">+<span id="LC8505" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run(python+' scons/scons.py -j 4 pdb2pka-test')</span></span>
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8506
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<pre style="margin: 0;">+<span id="LC8506" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run(python+' scons/scons.py -j 4 complete-test')</span></span>
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8507
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<pre style="margin: 0;">+<span id="LC8507" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run('scons -j 4 pdb2pka-test')</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8508" 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">
8508
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<pre style="margin: 0;">+<span id="LC8508" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run('scons -j 4 complete-test')</span></span>
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8472
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8509
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<pre style="margin: 0;"> <span id="LC8509" class="line" lang="diff"> </span>
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8473
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8510
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<pre style="margin: 0;"> <span id="LC8510" class="line" lang="diff"> </span>
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8474
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8511
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<pre style="margin: 0;"> <span id="LC8511" class="line" lang="diff"> def install_on_deployed():</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8477" 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="8514" 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">@@ -8477,6 +8514,17 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100</td>
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8477
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8514
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<pre style="margin: 0;"> <span id="LC8514" class="line" lang="diff"> </span>
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8478
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<td class="diff-line-num new_line" data-linenumber="8515" 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">
8515
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<pre style="margin: 0;"> <span id="LC8515" class="line" lang="diff"> with settings(warn_only=True):</span>
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8479
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8516
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<pre style="margin: 0;"> <span id="LC8516" class="line" lang="diff"> with cd('~/www/pdb2pqr'):</span>
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8517
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<pre style="margin: 0;">+<span id="LC8517" class="line" lang="diff"><span class="p">@@ -147,8 +147,8 @@</span> def install_on_deployed():</span>
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8518
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<pre style="margin: 0;">+<span id="LC8518" class="line" lang="diff"> # configopts += ' PREFIX=/Users/d3k084/www/pdb2pqr/'</span>
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8519
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<pre style="margin: 0;">+<span id="LC8519" class="line" lang="diff"> # configopts += ' URL=http://PT24098/d3k084/pdb2pqr'</span>
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8520
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<pre style="margin: 0;">+<span id="LC8520" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="8521" 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">
8521
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<pre style="margin: 0;">+<span id="LC8521" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run(python+' scons/scons.py ' + configopts)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8522" 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">
8522
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<pre style="margin: 0;">+<span id="LC8522" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run(python+' scons/scons.py install ' + configopts)</span></span>
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8523
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<pre style="margin: 0;">+<span id="LC8523" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run('scons ' + configopts)</span></span>
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8524
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<pre style="margin: 0;">+<span id="LC8524" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run('scons install ' + configopts)</span></span>
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8525
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<pre style="margin: 0;">+<span id="LC8525" class="line" lang="diff"> </span>
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8526
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<pre style="margin: 0;">+<span id="LC8526" class="line" lang="diff"> def build_binary_from_deploy():</span>
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<td class="diff-line-num new new_line" data-linenumber="8527" 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">
8527
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<pre style="margin: 0;">+<span id="LC8527" class="line" lang="diff"> create_dist_folder()</span>
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8480
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<td class="diff-line-num new_line" data-linenumber="8528" 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">
8528
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<pre style="margin: 0;"> <span id="LC8528" class="line" lang="diff"><span class="p">@@ -190,11 +190,11 @@</span> def linux_bin_cross_platform_test():</span>
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8481
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8529
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<pre style="margin: 0;"> <span id="LC8529" class="line" lang="diff"> @runs_once</span>
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8482
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8530
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<pre style="margin: 0;"> <span id="LC8530" class="line" lang="diff"> def build_windows():</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13658" 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="13706" 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">@@ -13658,7 +13706,12 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100</td>
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13658
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<td class="diff-line-num new_line" data-linenumber="13706" 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">
13706
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<pre style="margin: 0;"> <span id="LC13706" class="line" lang="diff"> if callable(v):</span>
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<td class="diff-line-num old_line" data-linenumber="13659" 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">
13659
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<td class="diff-line-num new_line" data-linenumber="13707" 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">
13707
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<pre style="margin: 0;"> <span id="LC13707" class="line" lang="diff"> d[k] = env.subst(v())</span>
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<td class="diff-line-num old_line" data-linenumber="13660" 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">
13660
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<td class="diff-line-num new_line" data-linenumber="13708" 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">
13708
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<pre style="margin: 0;"> <span id="LC13708" class="line" lang="diff"> elif SCons.Util.is_String(v):</span>
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<td class="diff-line-num old old_line" data-linenumber="13661" 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">
13661
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<td class="diff-line-num new_line old" data-linenumber="13709" 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="LC13661" class="line" lang="diff"><span class="p">@@ -112,21 +112,21 @@</span> def CopySubAction(targetfile, sourcefile</span>
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<td class="diff-line-num new old_line" data-linenumber="13662" 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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<td class="diff-line-num new new_line" data-linenumber="13709" 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">
13709
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<pre style="margin: 0;">+<span id="LC13709" class="line" lang="diff"><span class="p">@@ -108,25 +108,25 @@</span> def CopySubAction(targetfile, sourcefile</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="13662" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="13710" 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">
13710
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<pre style="margin: 0;">+<span id="LC13710" class="line" lang="diff"> 1.2345 etc.</span>
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<td class="diff-line-num new old_line" data-linenumber="13662" 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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<td class="diff-line-num new new_line" data-linenumber="13711" 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">
13711
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<pre style="margin: 0;">+<span id="LC13711" class="line" lang="diff"> """</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="13662" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="13712" 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">
13712
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<pre style="margin: 0;">+<span id="LC13712" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="13662" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="13713" 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">
13713
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<pre style="margin: 0;">+<span id="LC13713" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f = open(sourcefile, 'rb')</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="13662" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="13714" 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">
13714
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<pre style="margin: 0;">+<span id="LC13714" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f = open(sourcefile, 'r')</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="13662" 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">
13662
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<td class="diff-line-num new_line" data-linenumber="13715" 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">
13715
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<pre style="margin: 0;"> <span id="LC13715" class="line" lang="diff"> contents = f.read()</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="13663" 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">
13663
</td>
<td class="diff-line-num new_line" data-linenumber="13716" 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">
13716
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<pre style="margin: 0;"> <span id="LC13716" class="line" lang="diff"> f.close()</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="13664" 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">
13664
</td>
<td class="diff-line-num new_line" data-linenumber="13717" 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">
13717
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<pre style="margin: 0;"> <span id="LC13717" class="line" lang="diff"> except:</span>
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