working out different languages

oesteban · oesteban · commit d2d7631b896f · 2018-07-30T00:44:23.000-07:00
diff --git a/fmriprep/cli/run.py b/fmriprep/cli/run.py
@@ -545,6 +545,7 @@ def build_workflow(opts, retval):
     logger.log(25, 'Works derived from this fMRIPrep execution should '
                'include the following boilerplate:\n\n%s', boilerplate)
 
+    # Generate HTML file resolving citations
     cmd = ['pandoc', '-s', '--bibliography',
            pkgrf('fmriprep', 'data/boilerplate.bib'),
            '--filter', 'pandoc-citeproc',
@@ -556,6 +557,16 @@ def build_workflow(opts, retval):
         logger.warning('Could not generate CITATION.html file:\n%s',
                        ' '.join(cmd))
 
+    # Generate LaTex file resolving citations
+    cmd = ['pandoc', '-s', '--bibliography',
+           pkgrf('fmriprep', 'data/boilerplate.bib'),
+           '--natbib', str(logs_path / 'CITATION.md'),
+           '-o', str(logs_path / 'CITATION.tex')]
+    try:
+        check_call(cmd, timeout=10)
+    except (FileNotFoundError, CalledProcessError, TimeoutExpired):
+        logger.warning('Could not generate CITATION.tex file:\n%s',
+                       ' '.join(cmd))
     return retval
 
 
diff --git a/fmriprep/viz/report.tpl b/fmriprep/viz/report.tpl
@@ -32,12 +32,19 @@ body {
     padding: 65px 10px 10px;
 }
 
-div.boiler-text {
+div#HTML {
     font-family: "Bitstream Charter", "Georgia", Times;
     border: 1px solid gray;
-    margin: 20px 70px;
-    padding: 10px;
+    /*margin: 20px 70px;*/
+    padding: 10px 20px;
 }
+
+div.pre {
+    font-family: "Lucida Console", Monaco, monospace;
+    border: 1px solid gray;
+    padding: 10px 20px;
+}
+
 </style>
 </head>
 <body>
@@ -126,13 +133,13 @@ div.boiler-text {
     <ul class="nav nav-tabs" id="myTab" role="tablist">
         {% for b in boilerplate %}
         <li class="nav-item">
-            <a class="nav-link {% if b[0] == 0 %}active{% endif %}" id="{{ b[1] }}-tab" data-toggle="tab" href="#{{ b[1] }}" role="tab" aria-controls="{{ b[1] }}" aria-selected="true">{{ b[1] }}</a>
+            <a class="nav-link {% if b[0] == 0 %}active{% endif %}" id="{{ b[1] }}-tab" data-toggle="tab" href="#{{ b[1] }}" role="tab" aria-controls="{{ b[1] }}" aria-selected="{% if b[0] == 0 %}true{%else%}false{% endif %}">{{ b[1] }}</a>
         </li>
         {% endfor %}
     </ul>
     <div class="tab-content" id="myTabContent">
       {% for b in boilerplate %}
-      <div class="tab-pane fade {% if b[0] == 0 %}show active{% endif %}" id="{{ b[1] }}" role="tabpanel" aria-labelledby="{{ b[1] }}-tab">{{ b[2] }}</div>
+      <div class="tab-pane fade {% if b[0] == 0 %}active show{% endif %}" id="{{ b[1] }}" role="tabpanel" aria-labelledby="{{ b[1] }}-tab">{{ b[2] }}</div>
       {% endfor %}
     </div>
     {% else %}
diff --git a/fmriprep/viz/reports.py b/fmriprep/viz/reports.py
@@ -174,19 +174,22 @@ def generate_report(self):
             text = re.compile(
                 '<body>(.*?)</body>',
                 re.DOTALL | re.IGNORECASE).findall(text)[0].strip()
-            text = '<div class="boiler-text">%s</div>' % text
             boilerplate.append((boiler_idx, 'HTML', text))
             boiler_idx += 1
 
         if (logs_path / 'CITATION.md').exists():
-            text = '<pre>%s</pre>' % (logs_path / 'CITATION.md').read_text()
+            text = '<div class="pre">%s</div>\n' % (logs_path / 'CITATION.md').read_text()
             boilerplate.append((boiler_idx, 'Markdown', text))
             boiler_idx += 1
 
         if (logs_path / 'CITATION.tex').exists():
-            text = '<pre>%s</pre>\n' % (logs_path / 'CITATION.tex').read_text()
+            text = (logs_path / 'CITATION.tex').read_text()
+            text = re.compile(
+                r'\\begin{document}(.*?)\\end{document}',
+                re.DOTALL | re.IGNORECASE).findall(text)[0].strip()
+            text = '<div class="pre">%s</div>\n' % text
             text += '<h3>Bibliography</h3>\n'
-            text += '<pre>%s</pre>' % Path(
+            text += '<div class="pre">%s</div>\n' % Path(
                 pkgrf('fmriprep', 'data/boilerplate.bib')).read_text()
             boilerplate.append((boiler_idx, 'LaTeX', text))
             boiler_idx += 1
