fixes to latex report generation.

cal_tools/cal_tools/tools.py

@@ -39,11 +39,18 @@ def combine_report(run_path, calibration):
                         gfile.write( "=" *len (title) + "\n")
                         gfile.write("\n")
                     with open("{}/{}".format(run_path, entry), "r") as ifile:
+                        skip_next = False
                         for line in ifile.readlines():
+                            if skip_next:
+                                skip_next = False
+                                continue
                             if conc_param == "None":
                                 gfile.write(line)
                             elif " ".join(calibration.split()) != " ".join(line.split()):
                                 gfile.write(line)
+                            else:
+                                skip_next = True
+
                     gfile.write("\n\n")
         if isdir("{}/{}".format(run_path, entry)):
             shutil.copytree("{}/{}".format(run_path, entry), "{}/{}".format(sphinx_path, entry))
@@ -71,15 +78,22 @@ def make_report(run_path, tmp_path, out_path, project, author, version, report_t
         # now conf.py exists in temp folder, so add latex options to remove empty pages 
         patch_path = "{}".format(os.path.abspath(os.path.dirname(__file__)))
         patch_file = ("{}/conf_latex.patch".format(patch_path))
-        subprocess.check_call(["patch", 
-                               "{}/sphinx_rep/conf.py".format(tmp_path),
-                               patch_file])
+        try:
+            subprocess.check_call(["patch",
+                                   "{}/sphinx_rep/conf.py".format(tmp_path),
+                                   patch_file])
+        except:
+            print("Patching latex conf failed")
+
+        try:
 
-        subprocess.check_call(["sed",
-                               "-i",
-                               "-e",
-                               "s/{}.tex/{}.tex/g".format(project.replace(" ",""), report_name),
-                               "{}/sphinx_rep/conf.py".format(tmp_path)], shell=False)
+            subprocess.check_call(["sed",
+                                   "-i",
+                                   "-e",
+                                   "s/{}.tex/{}.tex/g".format(project.replace(" ", ""), report_name),
+                                   "{}/sphinx_rep/conf.py".format(tmp_path)], shell=False)
+        except:
+            print("SEDing tex failed")
 
     except subprocess.CalledProcessError:
         raise Exception("Failed to run sphinx-quickbuild. Is sphinx installed?"
@@ -94,22 +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()
                 
@@ -133,7 +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):