Fix sphinx formatting issues

cal_tools/cal_tools/tools.py

@@ -108,22 +108,24 @@ def make_report(run_path, tmp_path, out_path, project, author, version, report_t
         if isfile("{}/{}".format(run_path, entry)):
             name, ext = splitext("{}".format(entry))            
             if ext == ".rst" and "index" not in name:
-                files_to_handle.append(name)
+                files_to_handle.append(name.strip())
 
     with open("{}/index.rst.tmp".format(run_path), "w") as mf:
         with open("{}/index.rst".format(run_path), "r") as mfr:
             indexTmp = Template('''
                 .. toctree::
-                    :maxdepth: 2
-                     {% for k in keys %}
-                     {{ k }}
-                     {%- endfor %}
+                   :maxdepth: 2
+                   {% for k in keys %}
+                   {{ k }}
+                   {%- endfor %}
                 ''')
             for line in mfr:
                 line = line.replace(".. toctree::", textwrap.dedent(
                         indexTmp.render(keys=files_to_handle)))
                 line = line.replace(":maxdepth: 2", "")
                 line = line.replace("Documentation", "Calibration")
+                if ":caption." in line:
+                    continue
                 mf.write(line)
                 cdir = os.getcwd()
                 
@@ -147,7 +149,7 @@ def make_report(run_path, tmp_path, out_path, project, author, version, report_t
         print(f)
         shutil.copy(f, out_path)
     print("Removing temporary files at: {}".format(tmp_path))
-#    shutil.rmtree(tmp_path)
+    shutil.rmtree(tmp_path)
     
         
 def finalize(joblist, run_path, out_path, project, calibration, author, version, report_to):