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                    <h3>Code</h3>
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                    <h3>code2html</h3>
<p>The following Python code allows to generate HTML (and CSS) code from source files in C++ and Python languages. It is based on <a href="http://pygments.org/" target="blank">Pygment</a>, a Python syntax highlighter. All code in our Wiki is formatted using this script.
<div height="20%" class="highlight"><pre><span class="kn">from</span> <span class="nn">pygments</span> <span class="kn">import</span> <span class="n">highlight</span>
<span class="kn">from</span> <span class="nn">pygments.lexers</span> <span class="kn">import</span> <span class="n">PythonLexer</span>
<span class="kn">from</span> <span class="nn">pygments.lexers</span> <span class="kn">import</span> <span class="n">CppLexer</span>
<span class="kn">from</span> <span class="nn">pygments.formatters</span> <span class="kn">import</span> <span class="n">HtmlFormatter</span>

<span class="c"># C++ extensions</span>
<span class="n">cpp</span> <span class="o">=</span> <span class="p">[</span><span class="s">&quot;cpp&quot;</span><span class="p">,</span><span class="s">&quot;cxx&quot;</span><span class="p">,</span><span class="s">&quot;cc&quot;</span><span class="p">,</span><span class="s">&quot;h&quot;</span><span class="p">]</span>

<span class="c"># Python extensions</span>
<span class="n">py</span> <span class="o">=</span> <span class="p">[</span><span class="s">&quot;py&quot;</span><span class="p">]</span>

<span class="k">def</span> <span class="nf">load_file_as_sting</span><span class="p">(</span><span class="n">fname</span><span class="p">):</span>
    <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">    Open the file FNAME and save all its content in an unformatted string</span>
<span class="sd">    &quot;&quot;&quot;</span>
    
    <span class="n">content</span> <span class="o">=</span> <span class="s">&quot;&quot;</span>
    
    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span><span class="s">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span> <span class="c"># Open the file (read only)</span>
        <span class="n">content</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">()</span> <span class="c"># Read file and store it in an unformatted string</span>
        <span class="c"># The file is automatically closed</span>
    
    <span class="k">return</span> <span class="n">content</span>
    
<span class="k">def</span> <span class="nf">save_string_as_file</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span><span class="n">string</span><span class="p">):</span>
    <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">    Save the unformatted string STRING into the file FNAME</span>
<span class="sd">    &quot;&quot;&quot;</span>
    
    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span><span class="s">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span> <span class="c"># Open the file (write only)</span>
        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">string</span><span class="p">)</span>
        <span class="c"># The file is automatically closed</span>
        
<span class="k">def</span> <span class="nf">lexer_formatter</span><span class="p">(</span><span class="n">language</span><span class="p">,</span><span class="n">css</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
    <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">    Return the lexer for the appropriate language and the HTML formatter</span>
<span class="sd">    &quot;&quot;&quot;</span>
    
    <span class="n">L</span> <span class="o">=</span> <span class="bp">None</span>
    
    <span class="k">if</span> <span class="n">language</span> <span class="ow">in</span> <span class="n">py</span><span class="p">:</span>
        <span class="c"># Python Lexer</span>
        <span class="n">L</span> <span class="o">=</span> <span class="n">PythonLexer</span><span class="p">()</span>
        
    <span class="k">elif</span> <span class="n">language</span> <span class="ow">in</span> <span class="n">cpp</span><span class="p">:</span>
        <span class="c"># C++ Lexer</span>
        <span class="n">L</span> <span class="o">=</span> <span class="n">CppLexer</span><span class="p">()</span> 
    <span class="k">else</span><span class="p">:</span>
        <span class="k">raise</span> <span class="ne">NameError</span><span class="p">(</span><span class="s">&quot;Invalid language.&quot;</span><span class="p">)</span>
        
    <span class="n">HF</span> <span class="o">=</span> <span class="n">HtmlFormatter</span><span class="p">(</span><span class="n">full</span><span class="o">=</span><span class="n">css</span><span class="p">,</span><span class="n">style</span><span class="o">=</span><span class="s">&quot;monokai&quot;</span><span class="p">)</span>
        
    <span class="k">return</span> <span class="n">L</span><span class="p">,</span> <span class="n">HF</span>


<span class="k">def</span> <span class="nf">code_to_htmlcss</span><span class="p">(</span><span class="n">code</span><span class="p">,</span><span class="n">language</span><span class="p">):</span>
    <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">    Transform CODE into html and css (separate files)</span>
<span class="sd">    &quot;&quot;&quot;</span>
    
    <span class="c"># Obtain lexer and HtmlFormatter</span>
    <span class="n">L</span><span class="p">,</span> <span class="n">HF</span> <span class="o">=</span> <span class="n">lexer_formatter</span><span class="p">(</span><span class="n">language</span><span class="p">,</span><span class="n">css</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
    
    <span class="c"># Create html code</span>
    <span class="n">html</span> <span class="o">=</span> <span class="n">highlight</span><span class="p">(</span><span class="n">code</span><span class="p">,</span><span class="n">L</span><span class="p">,</span><span class="n">HF</span><span class="p">)</span>
    
    <span class="c"># Create css code</span>
    <span class="n">css</span> <span class="o">=</span> <span class="n">HF</span><span class="o">.</span><span class="n">get_style_defs</span><span class="p">(</span><span class="s">&#39;.highlight&#39;</span><span class="p">)</span>
    
    <span class="k">return</span> <span class="n">html</span><span class="p">,</span><span class="n">css</span>
    
<span class="k">def</span> <span class="nf">code_to_html</span><span class="p">(</span><span class="n">code</span><span class="p">,</span><span class="n">language</span><span class="p">):</span>
    <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">    Transform CODE into html and css (all in the same file)</span>
<span class="sd">    &quot;&quot;&quot;</span>
    
    <span class="c"># Obtain lexer and HtmlFormatter</span>
    <span class="n">L</span><span class="p">,</span> <span class="n">HF</span> <span class="o">=</span> <span class="n">lexer_formatter</span><span class="p">(</span><span class="n">language</span><span class="p">)</span>
    
    <span class="c"># Create fill html code</span>
    <span class="n">html</span> <span class="o">=</span> <span class="n">highlight</span><span class="p">(</span><span class="n">code</span><span class="p">,</span><span class="n">L</span><span class="p">,</span><span class="n">HF</span><span class="p">)</span>
    
    <span class="k">return</span> <span class="n">html</span>

<span class="kn">import</span> <span class="nn">sys</span>

<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">&quot;__main__&quot;</span><span class="p">:</span>
    <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">    Command:</span>
<span class="sd">    </span>
<span class="sd">    ######################################</span>
<span class="sd">    </span>
<span class="sd">        python code2html INPUTFILE [CSS]</span>
<span class="sd">        </span>
<span class="sd">    ######################################</span>
<span class="sd">        </span>
<span class="sd">    INPUTFILE: name (with path) of the file to convert to html</span>
<span class="sd">    CSS: write &quot;true&quot; in order to obtain separate .html and .css files (&quot;false&quot; by default)</span>
<span class="sd">    &quot;&quot;&quot;</span>
    
    <span class="c"># Command line arguments</span>
    <span class="n">args</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span>
    
    <span class="c"># Check command line arguments</span>
    <span class="n">ncla</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="c"># number of command line arguments</span>
    
    <span class="k">if</span> <span class="n">ncla</span> <span class="o">!=</span> <span class="mi">2</span> <span class="ow">and</span> <span class="n">ncla</span> <span class="o">!=</span> <span class="mi">3</span> <span class="p">:</span>
        <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">&quot;Invalid number of command line arguments.&quot;</span><span class="p">)</span>
        
    <span class="n">css_bool</span> <span class="o">=</span> <span class="bp">False</span>
    
    <span class="k">if</span> <span class="n">ncla</span> <span class="o">==</span> <span class="mi">3</span> <span class="ow">and</span> <span class="n">args</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">&quot;true&quot;</span><span class="p">:</span>
        <span class="n">css_bool</span> <span class="o">=</span> <span class="bp">True</span> <span class="c"># Export css separately</span>
    
    <span class="c"># Input file</span>
    <span class="n">fname_code</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="c"># Name of the file containing the code to convert in html</span>
    
    <span class="c"># Input file extension</span>
    <span class="n">language</span> <span class="o">=</span> <span class="n">fname_code</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;.&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
    
    <span class="c"># Output files</span>
    <span class="n">fname_html</span> <span class="o">=</span> <span class="n">fname_code</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s">&quot;.html&quot;</span> <span class="c"># Name of the file where the html code will be stored</span>
    <span class="n">fname_css</span> <span class="o">=</span> <span class="n">fname_code</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s">&quot;.css&quot;</span> <span class="c"># Name of the file where the css code will be stored</span>
    
    <span class="c"># Save code into a unformatted string</span>
    <span class="n">code</span> <span class="o">=</span> <span class="n">load_file_as_sting</span><span class="p">(</span><span class="n">fname_code</span><span class="p">)</span>
    
    <span class="k">if</span> <span class="n">css_bool</span> <span class="o">==</span> <span class="bp">False</span><span class="p">:</span> <span class="c"># Convert to standalone html</span>
        <span class="n">html</span> <span class="o">=</span> <span class="n">code_to_html</span><span class="p">(</span><span class="n">code</span><span class="p">,</span><span class="n">language</span><span class="p">)</span>
    <span class="k">else</span><span class="p">:</span> <span class="c"># Convert to html and css separately</span>
        <span class="n">html</span><span class="p">,</span><span class="n">css</span> <span class="o">=</span> <span class="n">code_to_htmlcss</span><span class="p">(</span><span class="n">code</span><span class="p">,</span><span class="n">language</span><span class="p">)</span>
    
    <span class="c"># Save html</span>
    <span class="n">save_string_as_file</span><span class="p">(</span><span class="n">fname_html</span><span class="p">,</span><span class="n">html</span><span class="p">)</span>
    
    <span class="k">if</span> <span class="n">css_bool</span> <span class="o">==</span> <span class="bp">True</span><span class="p">:</span>
        <span class="c"># Save css</span>
        <span class="n">save_string_as_file</span><span class="p">(</span><span class="n">fname_css</span><span class="p">,</span><span class="n">css</span><span class="p">)</span>
</pre></div>

</div></div></div></div>

    <div class="second-section">
        <div class="container">
            <div class="row">
                <div class="col-md-12 col-centered">
                    <h3>ODE Generator</h3>
                
                <div class="highlight"><pre><span class="k">class</span> <span class="nc">Reaction</span><span class="p">:</span>
	<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">reaction_</span><span class="p">,</span> <span class="n">cst_name_</span><span class="p">,</span> <span class="n">cst_value_</span><span class="p">,</span> <span class="n">description_</span><span class="p">):</span>
		<span class="bp">self</span><span class="o">.</span><span class="n">reaction</span> <span class="o">=</span> <span class="n">reaction_</span>
		<span class="bp">self</span><span class="o">.</span><span class="n">cst_name</span> <span class="o">=</span> <span class="n">cst_name_</span>
		<span class="bp">self</span><span class="o">.</span><span class="n">cst_value</span> <span class="o">=</span> <span class="n">cst_value_</span>
		<span class="bp">self</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span> <span class="n">description_</span>
		
	<span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
		    <span class="k">return</span> <span class="s">&quot;{}</span><span class="se">\n</span><span class="s">{} = {}</span><span class="se">\n</span><span class="s">{}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">reaction</span><span class="p">,</span>
		    <span class="bp">self</span><span class="o">.</span><span class="n">cst_name</span><span class="p">,</span>
		    <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">cst_value</span><span class="p">),</span>
		    <span class="bp">self</span><span class="o">.</span><span class="n">description</span><span class="p">)</span>
		
<span class="k">class</span> <span class="nc">ReactionParser</span><span class="p">:</span>
	
	<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_</span><span class="p">,</span> <span class="n">sep_</span><span class="o">=</span><span class="s">&quot;:&quot;</span><span class="p">,</span> <span class="n">comment_</span><span class="o">=</span><span class="s">&quot;#&quot;</span><span class="p">):</span>
		<span class="bp">self</span><span class="o">.</span><span class="n">sep</span> <span class="o">=</span> <span class="n">sep_</span>
		<span class="bp">self</span><span class="o">.</span><span class="n">comment</span> <span class="o">=</span> <span class="n">comment_</span>
		
		<span class="bp">self</span><span class="o">.</span><span class="n">file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_</span><span class="p">,</span> <span class="s">&#39;r&#39;</span><span class="p">)</span> <span class="c"># TODO: OPEN SAFELY</span>
		
		<span class="bp">self</span><span class="o">.</span><span class="n">reactions</span> <span class="o">=</span> <span class="p">[]</span>
		
		<span class="bp">self</span><span class="o">.</span><span class="n">_load</span><span class="p">()</span>
	
	<span class="k">def</span> <span class="nf">__del__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
		<span class="bp">self</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
		
	<span class="k">def</span> <span class="nf">_load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
		<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">file</span><span class="p">:</span>
			<span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">==</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span> <span class="ow">or</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">==</span> <span class="s">&quot;&quot;</span><span class="p">:</span> <span class="c"># Check for empty lines</span>
				<span class="k">continue</span>
				
			<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> <span class="o">!=</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">comment</span><span class="p">:</span> <span class="c"># Check for comments</span>
				<span class="k">continue</span>
		
			<span class="n">splitted</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&quot;:&quot;</span><span class="p">)</span>
			
			<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">splitted</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">4</span><span class="p">:</span>
				<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">&#39;ReactionParser: problem with the input file (not enough arguments)&#39;</span><span class="p">)</span>
			
			<span class="n">reaction</span> <span class="o">=</span> <span class="n">Reaction</span><span class="p">(</span><span class="n">splitted</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
								<span class="n">splitted</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
								<span class="nb">float</span><span class="p">(</span><span class="n">splitted</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()),</span>
								<span class="n">splitted</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
								
			<span class="bp">self</span><span class="o">.</span><span class="n">reactions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">reaction</span><span class="p">)</span>
			
	<span class="k">def</span> <span class="nf">print_reactions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
		<span class="k">for</span> <span class="n">reaction</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">reactions</span><span class="p">:</span>
			<span class="k">print</span><span class="p">(</span><span class="n">reaction</span><span class="p">)</span>
			<span class="k">print</span><span class="p">()</span>
			
	<span class="k">def</span> <span class="nf">reaction_table</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
		<span class="n">kin</span> <span class="o">=</span> <span class="p">[]</span>
		
		<span class="k">for</span> <span class="n">reaction</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">reactions</span><span class="p">:</span>
			<span class="n">splitted</span> <span class="o">=</span> <span class="n">reaction</span><span class="o">.</span><span class="n">reaction</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&quot;-&gt;&quot;</span><span class="p">)</span>
		
			<span class="n">left</span> <span class="o">=</span> <span class="n">splitted</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
			<span class="n">right</span> <span class="o">=</span> <span class="n">splitted</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
			
			<span class="n">kin</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">([</span><span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">],</span> <span class="p">(</span><span class="n">reaction</span><span class="o">.</span><span class="n">cst_name</span><span class="p">,</span> <span class="n">reaction</span><span class="o">.</span><span class="n">description</span><span class="p">,</span> <span class="n">reaction</span><span class="o">.</span><span class="n">cst_value</span><span class="p">)</span> <span class="p">)</span> <span class="p">)</span>
		
		<span class="k">return</span> <span class="n">kin</span>
		
			
		
<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">&quot;__main__&quot;</span><span class="p">:</span>
	<span class="n">myParser</span> <span class="o">=</span> <span class="n">ReactionParser</span><span class="p">(</span><span class="s">&quot;reactions.dat&quot;</span><span class="p">)</span>
	
	<span class="c">#myParser.load()</span>
	<span class="n">myParser</span><span class="o">.</span><span class="n">print_reactions</span><span class="p">()</span>
	
	<span class="n">kin</span> <span class="o">=</span> <span class="n">myParser</span><span class="o">.</span><span class="n">reaction_table</span><span class="p">()</span>
	
	<span class="k">print</span><span class="p">(</span><span class="n">kin</span><span class="p">)</span>
</pre></div>

                    
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