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Merge pull request #493 from SysBioChalmers/fix/printOrange
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fix: checkInstallation printOrange function
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@edkerk
edkerk committed Jun 26, 2023
2 parents 59b27f0 + 9bbe2e3 commit 85491c4
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58 changes: 35 additions & 23 deletions doc/installation/checkInstallation.html
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Expand Up @@ -57,7 +57,7 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^

<h2><a name="_subfunctions"></a>SUBFUNCTIONS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
<ul style="list-style-image:url(../matlabicon.gif)">
<li><a href="#_sub1" class="code">function res = interpretResults(results)</a></li><li><a href="#_sub2" class="code">function str = myStr(InputStr,len)</a></li><li><a href="#_sub3" class="code">function status = makeBinaryExecutable()</a></li></ul>
<li><a href="#_sub1" class="code">function res = interpretResults(results)</a></li><li><a href="#_sub2" class="code">function str = myStr(InputStr,len)</a></li><li><a href="#_sub3" class="code">function status = makeBinaryExecutable()</a></li><li><a href="#_sub4" class="code">function printOrange(stringToPrint)</a></li></ul>

<h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function currVer = checkInstallation(developMode)</a>
Expand Down Expand Up @@ -112,13 +112,13 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0050 <span class="keyword">for</span> i=1:3
0051 <span class="keyword">if</span> currVerNum(i)&lt;newVerNum(i)
0052 fprintf([<a href="#_sub2" class="code" title="subfunction str = myStr(InputStr,len)">myStr</a>(<span class="string">' &gt; Latest RAVEN release available'</span>,40) <span class="string">'%f'</span>])
0053 printOrange([newVer,<span class="string">'\n'</span>])
0053 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>([newVer,<span class="string">'\n'</span>])
0054 hasGit=isfolder(fullfile(ravenDir,<span class="string">'.git'</span>));
0055 <span class="keyword">if</span> hasGit
0056 printOrange(<span class="string">' Run git pull in your favourite git client\n'</span>)
0057 printOrange(<span class="string">' to get the latest RAVEN release\n'</span>);
0056 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">' Run git pull in your favourite git client\n'</span>)
0057 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">' to get the latest RAVEN release\n'</span>);
0058 <span class="keyword">else</span>
0059 printOrange([<a href="#_sub2" class="code" title="subfunction str = myStr(InputStr,len)">myStr</a>(<span class="string">' Instructions on how to upgrade'</span>,40) <span class="string">'%f'</span>])
0059 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>([<a href="#_sub2" class="code" title="subfunction str = myStr(InputStr,len)">myStr</a>(<span class="string">' Instructions on how to upgrade'</span>,40) <span class="string">'%f'</span>])
0060 fprintf(<span class="string">'&lt;a href=&quot;https://github.com/SysBioChalmers/RAVEN/wiki/Installation#upgrade-to-latest-raven-release&quot;&gt;here&lt;/a&gt;\n'</span>);
0061 <span class="keyword">end</span>
0062 <span class="keyword">break</span>
Expand All @@ -128,8 +128,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0066 <span class="keyword">end</span>
0067 <span class="keyword">catch</span>
0068 fprintf([<a href="#_sub2" class="code" title="subfunction str = myStr(InputStr,len)">myStr</a>(<span class="string">' &gt; Checking for latest RAVEN release'</span>,40) <span class="string">'%f'</span>])
0069 printOrange(<span class="string">'Fail\n'</span>);
0070 printOrange(<span class="string">' Cannot reach GitHub for release info\n'</span>);
0069 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>);
0070 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">' Cannot reach GitHub for release info\n'</span>);
0071 <span class="keyword">end</span>
0072 <span class="keyword">end</span>
0073 <span class="keyword">else</span>
Expand All @@ -156,12 +156,12 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0094 savepath
0095 fprintf(<span class="string">'Pass\n'</span>)
0096 <span class="keyword">catch</span>
0097 printOrange(<span class="string">'Fail\n'</span>)
0097 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0098 fprintf([<span class="string">' You might have to rerun checkInstallation again\n'</span><span class="keyword">...</span>
0099 <span class="string">' next time you start up MATLAB\n'</span>])
0100 <span class="keyword">end</span>
0101 <span class="keyword">catch</span>
0102 printOrange(<span class="string">'Fail\n'</span>)
0102 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0103 <span class="keyword">end</span>
0104
0105 <span class="keyword">if</span> isunix
Expand All @@ -170,7 +170,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0108 <span class="keyword">if</span> status == 0
0109 fprintf(<span class="string">'Pass\n'</span>)
0110 <span class="keyword">else</span>
0111 printOrange(<span class="string">'Fail\n'</span>)
0111 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0112 <span class="keyword">end</span>
0113 <span class="keyword">end</span>
0114
Expand All @@ -182,7 +182,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0120 addJavaPaths();
0121 fprintf(<span class="string">'Pass\n'</span>)
0122 <span class="keyword">catch</span>
0123 printOrange(<span class="string">'Fail\n'</span>)
0123 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0124 <span class="keyword">end</span>
0125 fprintf([<a href="#_sub2" class="code" title="subfunction str = myStr(InputStr,len)">myStr</a>(<span class="string">' &gt; Checking libSBML version'</span>,40) <span class="string">'%f'</span>])
0126 <span class="keyword">try</span>
Expand All @@ -191,11 +191,11 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0129 libSBMLver=OutputSBML; <span class="comment">% Only works in libSBML 5.17.0+</span>
0130 fprintf([libSBMLver.libSBML_version_string <span class="string">'\n'</span>]);
0131 <span class="keyword">catch</span>
0132 printOrange(<span class="string">'Fail\n'</span>)
0132 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0133 fprintf(<span class="string">' An older libSBML version was found, update to version 5.17.0 or higher for a significant improvement of model import\n'</span>);
0134 <span class="keyword">end</span>
0135 <span class="keyword">catch</span>
0136 printOrange(<span class="string">'Fail\n'</span>)
0136 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0137 fprintf(<span class="string">' Download libSBML from http://sbml.org/Software/libSBML/Downloading_libSBML and add to MATLAB path\n'</span>);
0138 <span class="keyword">end</span>
0139 fprintf(<span class="string">' &gt; Checking model import and export\n'</span>)
Expand All @@ -205,7 +205,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0143 <span class="keyword">if</span> res(1).Passed == 1
0144 fprintf(<span class="string">'Pass\n'</span>)
0145 <span class="keyword">else</span>
0146 printOrange(<span class="string">'Fail\n'</span>)
0146 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0147 addList = matlab.addons.installedAddons;
0148 <span class="keyword">if</span> any(strcmpi(addList.Name,<span class="string">'Text Analytics Toolbox'</span>))
0149 fprintf([<span class="string">' Excel import/export is incompatible with MATLAB Text Analytics Toolbox.\n'</span> <span class="keyword">...</span>
Expand All @@ -217,21 +217,21 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0155 <span class="keyword">if</span> res(3).Passed == 1
0156 fprintf(<span class="string">'Pass\n'</span>)
0157 <span class="keyword">else</span>
0158 printOrange(<span class="string">'Fail\n'</span>)
0158 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0159 <span class="keyword">end</span>
0160
0161 fprintf([<a href="#_sub2" class="code" title="subfunction str = myStr(InputStr,len)">myStr</a>(<span class="string">' &gt; Import SBML format'</span>,40) <span class="string">'%f'</span>])
0162 <span class="keyword">if</span> res(2).Passed == 1
0163 fprintf(<span class="string">'Pass\n'</span>)
0164 <span class="keyword">else</span>
0165 printOrange(<span class="string">'Fail\n'</span>)
0165 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0166 <span class="keyword">end</span>
0167
0168 fprintf([<a href="#_sub2" class="code" title="subfunction str = myStr(InputStr,len)">myStr</a>(<span class="string">' &gt; Export SBML format'</span>,40) <span class="string">'%f'</span>])
0169 <span class="keyword">if</span> res(4).Passed == 1
0170 fprintf(<span class="string">'Pass\n'</span>)
0171 <span class="keyword">else</span>
0172 printOrange(<span class="string">'Fail\n'</span>)
0172 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0173 <span class="keyword">end</span>
0174
0175 <span class="keyword">if</span> res(1).Passed~=1 &amp;&amp; res(3).Passed~=1 &amp;&amp; exist(<span class="string">'vaderSentimentScores.m'</span>,<span class="string">'file'</span>)==2
Expand Down Expand Up @@ -259,28 +259,28 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0197 <span class="keyword">if</span> res(1).Passed == 1
0198 fprintf(<span class="string">'Pass\n'</span>)
0199 <span class="keyword">else</span>
0200 printOrange(<span class="string">'Fail\n'</span>)
0200 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0201 <span class="keyword">end</span>
0202
0203 fprintf([<a href="#_sub2" class="code" title="subfunction str = myStr(InputStr,len)">myStr</a>(<span class="string">' &gt; gurobi'</span>,40) <span class="string">'%f'</span>])
0204 <span class="keyword">if</span> res(2).Passed == 1
0205 fprintf(<span class="string">'Pass\n'</span>)
0206 <span class="keyword">else</span>
0207 printOrange(<span class="string">'Fail\n'</span>)
0207 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0208 <span class="keyword">end</span>
0209
0210 fprintf([<a href="#_sub2" class="code" title="subfunction str = myStr(InputStr,len)">myStr</a>(<span class="string">' &gt; soplex'</span>,40) <span class="string">'%f'</span>])
0211 <span class="keyword">if</span> res(3).Passed == 1
0212 fprintf(<span class="string">'Pass\n'</span>)
0213 <span class="keyword">else</span>
0214 printOrange(<span class="string">'Fail\n'</span>)
0214 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0215 <span class="keyword">end</span>
0216
0217 fprintf([<a href="#_sub2" class="code" title="subfunction str = myStr(InputStr,len)">myStr</a>(<span class="string">' &gt; cobra'</span>,40) <span class="string">'%f'</span>])
0218 <span class="keyword">if</span> res(4).Passed == 1
0219 fprintf(<span class="string">'Pass\n'</span>)
0220 <span class="keyword">else</span>
0221 printOrange(<span class="string">'Fail\n'</span>)
0221 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0222 <span class="keyword">end</span>
0223 fprintf([<a href="#_sub2" class="code" title="subfunction str = myStr(InputStr,len)">myStr</a>(<span class="string">' &gt; Set RAVEN solver'</span>,40) <span class="string">'%f'</span>])
0224 <span class="keyword">try</span>
Expand Down Expand Up @@ -358,7 +358,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0296 fprintf(<span class="string">'Pass\n'</span>);
0297 res=true;
0298 <span class="keyword">else</span>
0299 printOrange(<span class="string">'Fail\n'</span>)
0299 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
0300 fprintf(<span class="string">' Download/compile the binary and rerun checkInstallation\n'</span>);
0301 res=false;
0302 <span class="keyword">end</span>
Expand Down Expand Up @@ -400,7 +400,19 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0338 warning(<span class="string">'Failed to make %s executable: %s '</span>,binList{i},strip(cmdout))
0339 <span class="keyword">end</span>
0340 <span class="keyword">end</span>
0341 <span class="keyword">end</span></pre></div>
0341 <span class="keyword">end</span>
0342
0343 <a name="_sub4" href="#_subfunctions" class="code">function printOrange(stringToPrint)</a>
0344 <span class="comment">% printOrange</span>
0345 <span class="comment">% Duplicate of RAVEN/core/printOrange is also kept here, as this function</span>
0346 <span class="comment">% should be able to run before adding RAVEN to the MATLAB path.</span>
0347 <span class="keyword">try</span> useDesktop = usejava(<span class="string">'desktop'</span>); <span class="keyword">catch</span>, useDesktop = false; <span class="keyword">end</span>
0348 <span class="keyword">if</span> useDesktop
0349 fprintf([<span class="string">'[\b'</span> stringToPrint,<span class="string">']\b'</span>])
0350 <span class="keyword">else</span>
0351 fprintf(stringToPrint)
0352 <span class="keyword">end</span>
0353 <span class="keyword">end</span></pre></div>
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</body>
</html>
12 changes: 12 additions & 0 deletions installation/checkInstallation.m
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Original file line number Diff line number Diff line change
Expand Up @@ -339,3 +339,15 @@
end
end
end

function printOrange(stringToPrint)
% printOrange
% Duplicate of RAVEN/core/printOrange is also kept here, as this function
% should be able to run before adding RAVEN to the MATLAB path.
try useDesktop = usejava('desktop'); catch, useDesktop = false; end
if useDesktop
fprintf(['[\b' stringToPrint,']\b'])
else
fprintf(stringToPrint)
end
end

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