diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
index 334643c9697c47c91d758a194cfa66a353cb4889..40e30452acbbc1fde3cbb7440ff96e665dc6bbe1 100644
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diff --git a/docs/build/doctrees/examples.doctree b/docs/build/doctrees/examples.doctree
index 6d560e2684b3bd6717f3bf783e2d194e4f2aeac7..0d72b96b86b24199b553333048e925ba14e25432 100644
Binary files a/docs/build/doctrees/examples.doctree and b/docs/build/doctrees/examples.doctree differ
diff --git a/docs/build/html/_sources/examples.rst.txt b/docs/build/html/_sources/examples.rst.txt
index 54559fdd873af11f8d612743234a31aae0456122..619224b9c847e5cb18bc55eb22c43f60382e5398 100644
--- a/docs/build/html/_sources/examples.rst.txt
+++ b/docs/build/html/_sources/examples.rst.txt
@@ -6,9 +6,4 @@ This chapter serves to document several of the example usages
 .. automodule:: examples.examples
    :members:
    :undoc-members:
-   :show-inheritance:
-
-
-Checking if this works
-======================
-..autofunction:: run_example_binary
\ No newline at end of file
+   :show-inheritance:
\ No newline at end of file
diff --git a/docs/build/html/custom_logging_functions.html b/docs/build/html/custom_logging_functions.html
index 36244b50ca37452501852a183d6d7f26b6206a13..20e373ca93820b2fe587d79e7ee701ff6fa0f4ff 100644
--- a/docs/build/html/custom_logging_functions.html
+++ b/docs/build/html/custom_logging_functions.html
@@ -130,7 +130,6 @@
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">examples</a></li>
-<li class="toctree-l1"><a class="reference internal" href="examples.html#checking-if-this-works">Checking if this works</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="modules.html">binaryc_python_utils</a><ul class="current">
 <li class="toctree-l2 current"><a class="current reference internal" href="#">custom_logging_functions module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="functions.html">functions module</a></li>
diff --git a/docs/build/html/examples.html b/docs/build/html/examples.html
index 554cd653bfa8aa5dc52d58aaae3f425c6edd147f..ce43a726633bad33f693456cbce11d41c3216396 100644
--- a/docs/build/html/examples.html
+++ b/docs/build/html/examples.html
@@ -65,10 +65,6 @@ Note, if you dont use the custom_logging functionality binary_c should be config
 <dd><p>Same as above but when giving the log_filename argument the log filename will be written</p>
 </dd></dl>
 
-</div>
-<div class="section" id="checking-if-this-works">
-<h1>Checking if this works<a class="headerlink" href="#checking-if-this-works" title="Permalink to this headline">¶</a></h1>
-<p>..autofunction:: run_example_binary</p>
 </div>
 
 
@@ -92,7 +88,6 @@ Note, if you dont use the custom_logging functionality binary_c should be config
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">examples</a></li>
-<li class="toctree-l1"><a class="reference internal" href="#checking-if-this-works">Checking if this works</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules.html">binaryc_python_utils</a></li>
 </ul>
 
diff --git a/docs/build/html/functions.html b/docs/build/html/functions.html
index e43f929cce4a2bc9bd2349ba5dc04d231a50bf28..41d8727423ce3a541ec39e27011b2567d8e2dfcd 100644
--- a/docs/build/html/functions.html
+++ b/docs/build/html/functions.html
@@ -102,7 +102,6 @@ TODO: Think about exporting to numpy array or pandas</p>
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">examples</a></li>
-<li class="toctree-l1"><a class="reference internal" href="examples.html#checking-if-this-works">Checking if this works</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="modules.html">binaryc_python_utils</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="custom_logging_functions.html">custom_logging_functions module</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">functions module</a></li>
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
index 597aab8792c66d1231c3986681fb03907e2b7133..a1f032b8e9c2ababac8e5328fa11e9f05e150638 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -183,7 +183,6 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">examples</a></li>
-<li class="toctree-l1"><a class="reference internal" href="examples.html#checking-if-this-works">Checking if this works</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules.html">binaryc_python_utils</a></li>
 </ul>
 
diff --git a/docs/build/html/index.html b/docs/build/html/index.html
index 9d5a4e038ff8f7ea8dfc3cfc4773eb3929a70701..bf41e422cdb46a5704ec612e7841b2961302aaea 100644
--- a/docs/build/html/index.html
+++ b/docs/build/html/index.html
@@ -44,7 +44,6 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">examples</a></li>
-<li class="toctree-l1"><a class="reference internal" href="examples.html#checking-if-this-works">Checking if this works</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules.html">binaryc_python_utils</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="custom_logging_functions.html">custom_logging_functions module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="functions.html">functions module</a></li>
@@ -83,7 +82,6 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">examples</a></li>
-<li class="toctree-l1"><a class="reference internal" href="examples.html#checking-if-this-works">Checking if this works</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules.html">binaryc_python_utils</a></li>
 </ul>
 
diff --git a/docs/build/html/modules.html b/docs/build/html/modules.html
index 87a33f5184b4df354d89a06d15e2f4b456c24222..3d63a908964fe64e01beb5d6ffeeb53c5e8ccb03 100644
--- a/docs/build/html/modules.html
+++ b/docs/build/html/modules.html
@@ -63,7 +63,6 @@
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">examples</a></li>
-<li class="toctree-l1"><a class="reference internal" href="examples.html#checking-if-this-works">Checking if this works</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">binaryc_python_utils</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="custom_logging_functions.html">custom_logging_functions module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="functions.html">functions module</a></li>
diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html
index 62df493b931285de9e3102b80f244c00d602e9c9..b89f31983805c58b9b8f7a2b564177bcde0a881d 100644
--- a/docs/build/html/py-modindex.html
+++ b/docs/build/html/py-modindex.html
@@ -109,7 +109,6 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">examples</a></li>
-<li class="toctree-l1"><a class="reference internal" href="examples.html#checking-if-this-works">Checking if this works</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules.html">binaryc_python_utils</a></li>
 </ul>
 
diff --git a/docs/build/html/readme_link.html b/docs/build/html/readme_link.html
index 5a9eeb0660b047749ed50e8192d1baaa87319be7..6b967e0efe6cef5dd403bd31219bb628ec8b7ced 100644
--- a/docs/build/html/readme_link.html
+++ b/docs/build/html/readme_link.html
@@ -110,7 +110,6 @@ export PYTHONPATH=&lt;full path to directory containing libbinary_c_api.so&gt;:$
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">examples</a></li>
-<li class="toctree-l1"><a class="reference internal" href="examples.html#checking-if-this-works">Checking if this works</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules.html">binaryc_python_utils</a></li>
 </ul>
 
diff --git a/docs/build/html/search.html b/docs/build/html/search.html
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--- a/docs/build/html/search.html
+++ b/docs/build/html/search.html
@@ -79,7 +79,6 @@
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-<li class="toctree-l1"><a class="reference internal" href="examples.html#checking-if-this-works">Checking if this works</a></li>
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function"]},objtypes:{"0":"py:module","1":"py:function"},terms:{"10e4":5,"catch":2,"default":[0,1],"export":[2,5],"function":[0,1,3,4],"import":5,"int":0,"return":[0,2],AND:2,That:5,Then:[2,5],There:1,abl:5,about:2,abov:[1,5],adress:[0,1],all:[1,2],also:[1,5],andrew:5,ani:2,anywher:5,api:2,approach:1,arg:2,arg_dict:2,argument:[1,2],arrai:2,autofunct:[],autogen_c_logging_cod:0,autogener:0,automat:[0,1,5],background:1,base:[2,5],bashrc:5,basic:1,becaus:5,befor:5,behind:1,binari:[1,5],binary_c:1,binary_c_inline_config:0,binary_c_log_cod:0,binary_c_write_log_cod:0,binaryc:[0,2,5],binaryc_config:0,binaryc_python_util:3,blog:0,build:[0,3],built:5,call:2,can:[2,5],cannot:5,cast:2,chapter:1,check:[],child:5,clean:[0,5],code:[0,1,5],com:0,command:0,compil:[0,1,5],compile_shared_lib:0,config_fil:0,configur:1,construct:[0,2],contain:[0,5],content:3,copi:5,correctli:5,creat:2,create_and_load_logging_funct:0,create_arg_str:2,ctype:0,custom:0,custom_log:1,custom_logging_cod:[0,2],custom_logging_dict:2,custom_logging_funct:[3,4],david:5,david_single_analysi:2,defin:2,describ:5,design:2,determin:2,develop:0,dictionari:[0,2],didnt:5,dir:5,directli:1,directori:5,document:1,doe:5,done:1,dont:1,easier:1,easili:5,environ:3,etc:5,exampl:[0,3,5],execut:5,exist_ok:0,experienc:5,experiment:5,extend:5,figur:5,file:[0,2],filenam:[0,1],flag:0,follow:5,found:5,from:5,from_binary_c_config:0,full:5,gcc:[0,5],gener:[0,1],get:2,get_arg_kei:2,get_default:2,give:[1,2],given:[0,1],happen:5,has:0,have:[1,5],header:[0,1],hendrik:5,here:1,how:1,html:5,http:[0,5],includ:[2,5],index:3,inspir:0,instal:5,instead:5,instruct:3,intput:0,issu:5,item:0,its:5,izzard:5,jeff:5,jupyt:5,just:1,kei:[0,2],kwarg:2,ld_library_path:5,libbinary_c:5,libbinary_c_api:5,libgsl:5,libmemo:5,librari:[0,5],library_path:5,librinterpol:5,like:[2,5],line:[0,1,2],linker:0,list:[0,2,5],load:[0,1],locat:5,log:[0,1,2,5],log_filenam:[1,2],logging_dict:0,make:[0,1,5],makedir:0,manual:5,mass:[0,2],matter:5,memori:[0,1],method:1,might:5,model:0,modul:[3,4],more:1,most:5,mostli:1,my_stellar_data:0,name:5,necessari:1,note:[1,3],notebook:5,numpi:[1,2],object:0,old_solut:5,one:5,origin:5,out:5,outfile_nam:0,output:[1,2,5],page:3,panda:[1,2],paramet:[0,2,5],pars:2,parse_output:[1,2],pass:[1,2],path:[0,5],perl:0,person:5,piec:1,place:2,point:5,possibl:2,print:5,printf:0,probabl:0,put:[0,2,5],python3:5,python:[0,1,2],python_api_test:5,pythonpath:5,raw:1,read:5,recommend:5,redhat:0,requir:[0,1,3],resolv:5,return_compilation_dict:0,ri0005:5,robert:5,root:5,run:[0,1,2,5],run_binari:1,run_example_binari:1,run_example_binary_with_custom_log:1,run_example_binary_with_run_system:1,run_example_binary_with_writing_logfil:1,run_system:[1,2],run_system_with_log:2,same:[1,5],scene:1,script:0,search:3,see:[1,5],select:1,selected_head:2,serv:1,set:[2,5],sever:1,share:[0,5],shim:5,should:[1,5],some:[0,5],sourcefile_nam:0,src:5,star:0,start:[1,2],statement:0,still:0,string:[0,2],sure:5,surrei:5,system:[1,2,5],take:1,task:1,temp_custom_logging_dir:0,test:5,thi:[0,1,2,5],thing:1,think:2,those:1,time:0,todo:[0,2],txt:5,type:0,underli:[2,5],updat:5,upon:2,usag:[1,3],use:[0,1,5],useful:5,usual:5,valu:[0,2,5],variabl:3,veri:1,version:5,via:2,virtual:5,wai:5,want:5,warn:5,well:5,whatev:5,when:[1,2,5],where:0,which:[0,1,2,5],work:5,would:5,wrapper:[1,2],write:0,written:[0,1],wrt:0,you:[1,2,5],your:5,zshrc:5},titles:["custom_logging_functions module","examples","functions module","Welcome to binary_c-python\u2019s documentation!","binaryc_python_utils","Python module for binary_c","stellar_types module"],titleterms:{"function":2,binary_c:[3,5],binaryc_python_util:4,build:5,check:[],custom_logging_funct:0,document:3,environ:5,exampl:1,indic:3,instruct:5,modul:[0,2,5,6],note:5,python:[3,5],requir:5,stellar_typ:6,tabl:3,thi:[],usag:5,variabl:5,welcom:3,work:[]}})
\ No newline at end of file
diff --git a/docs/build/html/stellar_types.html b/docs/build/html/stellar_types.html
index 78fcaf69f4965cb0a6955dcf035ec4801c25a5aa..ca7c36ac5674e7d997b1f5c9cffb5cf7744a41e6 100644
--- a/docs/build/html/stellar_types.html
+++ b/docs/build/html/stellar_types.html
@@ -55,7 +55,6 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">examples</a></li>
-<li class="toctree-l1"><a class="reference internal" href="examples.html#checking-if-this-works">Checking if this works</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules.html">binaryc_python_utils</a></li>
 </ul>
 
diff --git a/docs/build/latex/binary_c-python.aux b/docs/build/latex/binary_c-python.aux
index 71df2be95e58c75e5c8a0694ed3ae503fc0812eb..7cbe4ccab4dd42d823bcacaac90af4c406ed8fb5 100644
--- a/docs/build/latex/binary_c-python.aux
+++ b/docs/build/latex/binary_c-python.aux
@@ -41,40 +41,36 @@
 \newlabel{examples:examples.examples.run_example_binary_with_custom_logging}{{2}{3}{examples}{section*.5}{}}
 \newlabel{examples:examples.examples.run_example_binary_with_run_system}{{2}{3}{examples}{section*.6}{}}
 \newlabel{examples:examples.examples.run_example_binary_with_writing_logfile}{{2}{3}{examples}{section*.7}{}}
-\@writefile{toc}{\contentsline {chapter}{\numberline {3}Checking if this works}{5}{chapter.3}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {3}binaryc\_python\_utils}{5}{chapter.3}}
 \@writefile{lof}{\addvspace {10\p@ }}
 \@writefile{lot}{\addvspace {10\p@ }}
-\newlabel{examples:checking-if-this-works}{{3}{5}{Checking if this works}{chapter.3}{}}
-\@writefile{toc}{\contentsline {chapter}{\numberline {4}binaryc\_python\_utils}{7}{chapter.4}}
+\newlabel{modules:binaryc-python-utils}{{3}{5}{binaryc\_python\_utils}{chapter.3}{}}
+\newlabel{modules::doc}{{3}{5}{binaryc\_python\_utils}{chapter.3}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {3.1}custom\_logging\_functions module}{5}{section.3.1}}
+\newlabel{custom_logging_functions:module-custom_logging_functions}{{3.1}{5}{custom\_logging\_functions module}{section.3.1}{}}
+\newlabel{custom_logging_functions:custom-logging-functions-module}{{3.1}{5}{custom\_logging\_functions module}{section.3.1}{}}
+\newlabel{custom_logging_functions::doc}{{3.1}{5}{custom\_logging\_functions module}{section.3.1}{}}
+\newlabel{custom_logging_functions:custom_logging_functions.autogen_C_logging_code}{{3.1}{5}{custom\_logging\_functions module}{section*.8}{}}
+\newlabel{custom_logging_functions:custom_logging_functions.binary_c_log_code}{{3.1}{5}{custom\_logging\_functions module}{section*.9}{}}
+\newlabel{custom_logging_functions:custom_logging_functions.binary_c_write_log_code}{{3.1}{5}{custom\_logging\_functions module}{section*.10}{}}
+\newlabel{custom_logging_functions:custom_logging_functions.compile_shared_lib}{{3.1}{5}{custom\_logging\_functions module}{section*.11}{}}
+\newlabel{custom_logging_functions:custom_logging_functions.create_and_load_logging_function}{{3.1}{5}{custom\_logging\_functions module}{section*.12}{}}
+\newlabel{custom_logging_functions:custom_logging_functions.from_binary_c_config}{{3.1}{5}{custom\_logging\_functions module}{section*.13}{}}
+\newlabel{custom_logging_functions:custom_logging_functions.return_compilation_dict}{{3.1}{5}{custom\_logging\_functions module}{section*.14}{}}
+\newlabel{custom_logging_functions:custom_logging_functions.temp_custom_logging_dir}{{3.1}{5}{custom\_logging\_functions module}{section*.15}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {3.2}functions module}{6}{section.3.2}}
+\newlabel{functions:module-functions}{{3.2}{6}{functions module}{section.3.2}{}}
+\newlabel{functions:functions-module}{{3.2}{6}{functions module}{section.3.2}{}}
+\newlabel{functions::doc}{{3.2}{6}{functions module}{section.3.2}{}}
+\newlabel{functions:functions.create_arg_string}{{3.2}{6}{functions module}{section*.16}{}}
+\newlabel{functions:functions.get_arg_keys}{{3.2}{6}{functions module}{section*.17}{}}
+\newlabel{functions:functions.get_defaults}{{3.2}{6}{functions module}{section*.18}{}}
+\newlabel{functions:functions.parse_output}{{3.2}{6}{functions module}{section*.19}{}}
+\newlabel{functions:functions.run_system}{{3.2}{6}{functions module}{section*.20}{}}
+\newlabel{functions:functions.run_system_with_log}{{3.2}{6}{functions module}{section*.21}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {4}Indices and tables}{7}{chapter.4}}
 \@writefile{lof}{\addvspace {10\p@ }}
 \@writefile{lot}{\addvspace {10\p@ }}
-\newlabel{modules:binaryc-python-utils}{{4}{7}{binaryc\_python\_utils}{chapter.4}{}}
-\newlabel{modules::doc}{{4}{7}{binaryc\_python\_utils}{chapter.4}{}}
-\@writefile{toc}{\contentsline {section}{\numberline {4.1}custom\_logging\_functions module}{7}{section.4.1}}
-\newlabel{custom_logging_functions:module-custom_logging_functions}{{4.1}{7}{custom\_logging\_functions module}{section.4.1}{}}
-\newlabel{custom_logging_functions:custom-logging-functions-module}{{4.1}{7}{custom\_logging\_functions module}{section.4.1}{}}
-\newlabel{custom_logging_functions::doc}{{4.1}{7}{custom\_logging\_functions module}{section.4.1}{}}
-\newlabel{custom_logging_functions:custom_logging_functions.autogen_C_logging_code}{{4.1}{7}{custom\_logging\_functions module}{section*.8}{}}
-\newlabel{custom_logging_functions:custom_logging_functions.binary_c_log_code}{{4.1}{7}{custom\_logging\_functions module}{section*.9}{}}
-\newlabel{custom_logging_functions:custom_logging_functions.binary_c_write_log_code}{{4.1}{7}{custom\_logging\_functions module}{section*.10}{}}
-\newlabel{custom_logging_functions:custom_logging_functions.compile_shared_lib}{{4.1}{7}{custom\_logging\_functions module}{section*.11}{}}
-\newlabel{custom_logging_functions:custom_logging_functions.create_and_load_logging_function}{{4.1}{7}{custom\_logging\_functions module}{section*.12}{}}
-\newlabel{custom_logging_functions:custom_logging_functions.from_binary_c_config}{{4.1}{7}{custom\_logging\_functions module}{section*.13}{}}
-\newlabel{custom_logging_functions:custom_logging_functions.return_compilation_dict}{{4.1}{7}{custom\_logging\_functions module}{section*.14}{}}
-\newlabel{custom_logging_functions:custom_logging_functions.temp_custom_logging_dir}{{4.1}{7}{custom\_logging\_functions module}{section*.15}{}}
-\@writefile{toc}{\contentsline {section}{\numberline {4.2}functions module}{8}{section.4.2}}
-\newlabel{functions:module-functions}{{4.2}{8}{functions module}{section.4.2}{}}
-\newlabel{functions:functions-module}{{4.2}{8}{functions module}{section.4.2}{}}
-\newlabel{functions::doc}{{4.2}{8}{functions module}{section.4.2}{}}
-\newlabel{functions:functions.create_arg_string}{{4.2}{8}{functions module}{section*.16}{}}
-\newlabel{functions:functions.get_arg_keys}{{4.2}{8}{functions module}{section*.17}{}}
-\newlabel{functions:functions.get_defaults}{{4.2}{8}{functions module}{section*.18}{}}
-\newlabel{functions:functions.parse_output}{{4.2}{8}{functions module}{section*.19}{}}
-\newlabel{functions:functions.run_system}{{4.2}{8}{functions module}{section*.20}{}}
-\newlabel{functions:functions.run_system_with_log}{{4.2}{8}{functions module}{section*.21}{}}
-\@writefile{toc}{\contentsline {chapter}{\numberline {5}Indices and tables}{9}{chapter.5}}
-\@writefile{lof}{\addvspace {10\p@ }}
-\@writefile{lot}{\addvspace {10\p@ }}
-\newlabel{index:indices-and-tables}{{5}{9}{Indices and tables}{chapter.5}{}}
-\@writefile{toc}{\contentsline {chapter}{Python Module Index}{11}{section*.22}}
-\@writefile{toc}{\contentsline {chapter}{Index}{13}{section*.23}}
+\newlabel{index:indices-and-tables}{{4}{7}{Indices and tables}{chapter.4}{}}
+\@writefile{toc}{\contentsline {chapter}{Python Module Index}{9}{section*.22}}
+\@writefile{toc}{\contentsline {chapter}{Index}{11}{section*.23}}
diff --git a/docs/build/latex/binary_c-python.fdb_latexmk b/docs/build/latex/binary_c-python.fdb_latexmk
index f7dc740b5eda27feada5bdbf952a925cb16d95b7..af4fe43f289e98ddde2581f3ddb3932d7f022cda 100644
--- a/docs/build/latex/binary_c-python.fdb_latexmk
+++ b/docs/build/latex/binary_c-python.fdb_latexmk
@@ -1,10 +1,10 @@
 # Fdb version 3
-["makeindex binary_c-python.idx"] 1574000003 "binary_c-python.idx" "binary_c-python.ind" "binary_c-python" 1574000003
-  "binary_c-python.idx" 1574000003 3376 429123684710a89bffe33367e6e16d03 ""
+["makeindex binary_c-python.idx"] 1574288781 "binary_c-python.idx" "binary_c-python.ind" "binary_c-python" 1574288781
+  "binary_c-python.idx" 1574288781 3225 aa74b1d7bb65ae135e08b22704750cba ""
   (generated)
   "binary_c-python.ilg"
   "binary_c-python.ind"
-["pdflatex"] 1574000003 "binary_c-python.tex" "binary_c-python.pdf" "binary_c-python" 1574000003
+["pdflatex"] 1574288781 "binary_c-python.tex" "binary_c-python.pdf" "binary_c-python" 1574288781
   "/etc/texmf/web2c/texmf.cnf" 1571601231 475 c0e671620eb5563b2130f56340a5fde8 ""
   "/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc" 1480098666 4850 80dc9bab7f31fb78a000ccfed0e27cab ""
   "/usr/share/texlive/texmf-dist/fonts/map/fontname/texfonts.map" 1511824771 3332 103109f5612ad95229751940c61aada0 ""
@@ -152,21 +152,21 @@
   "/usr/share/texmf/web2c/texmf.cnf" 1520210507 32485 c64754543d8ac501bea6e75e209ea521 ""
   "/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map" 1571933265 2700761 ac0584cc9514ab21918550a6948c4ee2 ""
   "/var/lib/texmf/web2c/pdftex/pdflatex.fmt" 1571933283 4127049 2405b3f44d10220df7960de22302550a ""
-  "binary_c-python.aux" 1574000003 5993 b0cc9e4c2325fc4713f52a6ca616f272 ""
-  "binary_c-python.ind" 1574000003 2531 e52e1ddc3c6796db1c8c892ae2b752b2 "makeindex binary_c-python.idx"
-  "binary_c-python.out" 1574000003 1828 f08408ab177be40b4b48028405a6e27b ""
-  "binary_c-python.tex" 1574000002 19962 2157654cc1a3b4dfea4d46e57993fa76 ""
-  "binary_c-python.toc" 1574000003 970 1e5a69fb133339380865d44efa91bb3c ""
-  "footnotehyper-sphinx.sty" 1573642027 8888 1bbd7bdeae8c8bed1d10d551bddb1cc9 ""
-  "sphinx.sty" 1573642027 77684 8fb97306ac83d50d8517c97072345a1d ""
-  "sphinxhighlight.sty" 1574000002 8137 38a433148fcb7611515a989ff1750dd5 ""
-  "sphinxmanual.cls" 1573642027 3764 e7c0a8da02dc45450256dd4cfdafb426 ""
-  "sphinxmessages.sty" 1574000002 731 4c7a75a0ce6092b44bece19aa46febe9 ""
-  "sphinxmulticell.sty" 1573642027 14618 0defbdc8536ad2e67f1eac6a1431bc55 ""
+  "binary_c-python.aux" 1574288781 5733 43f4adf309cd1a6d00a228ecc76acb2d ""
+  "binary_c-python.ind" 1574288781 2513 cdcfff08a36b5731307fc073b0760af0 "makeindex binary_c-python.idx"
+  "binary_c-python.out" 1574288781 1665 e1564592c69d66ddf198a9ea56a34d1b ""
+  "binary_c-python.tex" 1574288780 19447 d83282ed156ea83811fa3028b611a6a4 ""
+  "binary_c-python.toc" 1574288781 892 cc5e2f0ca84f121d18d123b2c783f968 ""
+  "footnotehyper-sphinx.sty" 1574288720 8888 1bbd7bdeae8c8bed1d10d551bddb1cc9 ""
+  "sphinx.sty" 1574288720 77684 8fb97306ac83d50d8517c97072345a1d ""
+  "sphinxhighlight.sty" 1574288780 8137 38a433148fcb7611515a989ff1750dd5 ""
+  "sphinxmanual.cls" 1574288720 3764 e7c0a8da02dc45450256dd4cfdafb426 ""
+  "sphinxmessages.sty" 1574288780 731 4c7a75a0ce6092b44bece19aa46febe9 ""
+  "sphinxmulticell.sty" 1574288720 14618 0defbdc8536ad2e67f1eac6a1431bc55 ""
   (generated)
-  "binary_c-python.aux"
-  "binary_c-python.toc"
-  "binary_c-python.log"
-  "binary_c-python.idx"
   "binary_c-python.pdf"
+  "binary_c-python.log"
   "binary_c-python.out"
+  "binary_c-python.idx"
+  "binary_c-python.toc"
+  "binary_c-python.aux"
diff --git a/docs/build/latex/binary_c-python.idx b/docs/build/latex/binary_c-python.idx
index b5d0e12ffb840e26237fd62a2276f05ae36a64bc..829d398d27e4931dccda179293f02b037be8931e 100644
--- a/docs/build/latex/binary_c-python.idx
+++ b/docs/build/latex/binary_c-python.idx
@@ -3,20 +3,19 @@
 \indexentry{run\_example\_binary\_with\_custom\_logging() (in module examples.examples)@\spxentry{run\_example\_binary\_with\_custom\_logging()}\spxextra{in module examples.examples}|hyperpage}{3}
 \indexentry{run\_example\_binary\_with\_run\_system() (in module examples.examples)@\spxentry{run\_example\_binary\_with\_run\_system()}\spxextra{in module examples.examples}|hyperpage}{3}
 \indexentry{run\_example\_binary\_with\_writing\_logfile() (in module examples.examples)@\spxentry{run\_example\_binary\_with\_writing\_logfile()}\spxextra{in module examples.examples}|hyperpage}{3}
-\indexentry{run\_example\_binary() (in module examples.examples)@\spxentry{run\_example\_binary()}\spxextra{in module examples.examples}|hyperpage}{5}
-\indexentry{custom\_logging\_functions (module)@\spxentry{custom\_logging\_functions}\spxextra{module}|hyperpage}{7}
-\indexentry{autogen\_C\_logging\_code() (in module custom\_logging\_functions)@\spxentry{autogen\_C\_logging\_code()}\spxextra{in module custom\_logging\_functions}|hyperpage}{7}
-\indexentry{binary\_c\_log\_code() (in module custom\_logging\_functions)@\spxentry{binary\_c\_log\_code()}\spxextra{in module custom\_logging\_functions}|hyperpage}{7}
-\indexentry{binary\_c\_write\_log\_code() (in module custom\_logging\_functions)@\spxentry{binary\_c\_write\_log\_code()}\spxextra{in module custom\_logging\_functions}|hyperpage}{7}
-\indexentry{compile\_shared\_lib() (in module custom\_logging\_functions)@\spxentry{compile\_shared\_lib()}\spxextra{in module custom\_logging\_functions}|hyperpage}{7}
-\indexentry{create\_and\_load\_logging\_function() (in module custom\_logging\_functions)@\spxentry{create\_and\_load\_logging\_function()}\spxextra{in module custom\_logging\_functions}|hyperpage}{7}
-\indexentry{from\_binary\_c\_config() (in module custom\_logging\_functions)@\spxentry{from\_binary\_c\_config()}\spxextra{in module custom\_logging\_functions}|hyperpage}{7}
-\indexentry{return\_compilation\_dict() (in module custom\_logging\_functions)@\spxentry{return\_compilation\_dict()}\spxextra{in module custom\_logging\_functions}|hyperpage}{7}
-\indexentry{temp\_custom\_logging\_dir() (in module custom\_logging\_functions)@\spxentry{temp\_custom\_logging\_dir()}\spxextra{in module custom\_logging\_functions}|hyperpage}{7}
-\indexentry{functions (module)@\spxentry{functions}\spxextra{module}|hyperpage}{8}
-\indexentry{create\_arg\_string() (in module functions)@\spxentry{create\_arg\_string()}\spxextra{in module functions}|hyperpage}{8}
-\indexentry{get\_arg\_keys() (in module functions)@\spxentry{get\_arg\_keys()}\spxextra{in module functions}|hyperpage}{8}
-\indexentry{get\_defaults() (in module functions)@\spxentry{get\_defaults()}\spxextra{in module functions}|hyperpage}{8}
-\indexentry{parse\_output() (in module functions)@\spxentry{parse\_output()}\spxextra{in module functions}|hyperpage}{8}
-\indexentry{run\_system() (in module functions)@\spxentry{run\_system()}\spxextra{in module functions}|hyperpage}{8}
-\indexentry{run\_system\_with\_log() (in module functions)@\spxentry{run\_system\_with\_log()}\spxextra{in module functions}|hyperpage}{8}
+\indexentry{custom\_logging\_functions (module)@\spxentry{custom\_logging\_functions}\spxextra{module}|hyperpage}{5}
+\indexentry{autogen\_C\_logging\_code() (in module custom\_logging\_functions)@\spxentry{autogen\_C\_logging\_code()}\spxextra{in module custom\_logging\_functions}|hyperpage}{5}
+\indexentry{binary\_c\_log\_code() (in module custom\_logging\_functions)@\spxentry{binary\_c\_log\_code()}\spxextra{in module custom\_logging\_functions}|hyperpage}{5}
+\indexentry{binary\_c\_write\_log\_code() (in module custom\_logging\_functions)@\spxentry{binary\_c\_write\_log\_code()}\spxextra{in module custom\_logging\_functions}|hyperpage}{5}
+\indexentry{compile\_shared\_lib() (in module custom\_logging\_functions)@\spxentry{compile\_shared\_lib()}\spxextra{in module custom\_logging\_functions}|hyperpage}{5}
+\indexentry{create\_and\_load\_logging\_function() (in module custom\_logging\_functions)@\spxentry{create\_and\_load\_logging\_function()}\spxextra{in module custom\_logging\_functions}|hyperpage}{5}
+\indexentry{from\_binary\_c\_config() (in module custom\_logging\_functions)@\spxentry{from\_binary\_c\_config()}\spxextra{in module custom\_logging\_functions}|hyperpage}{5}
+\indexentry{return\_compilation\_dict() (in module custom\_logging\_functions)@\spxentry{return\_compilation\_dict()}\spxextra{in module custom\_logging\_functions}|hyperpage}{5}
+\indexentry{temp\_custom\_logging\_dir() (in module custom\_logging\_functions)@\spxentry{temp\_custom\_logging\_dir()}\spxextra{in module custom\_logging\_functions}|hyperpage}{5}
+\indexentry{functions (module)@\spxentry{functions}\spxextra{module}|hyperpage}{6}
+\indexentry{create\_arg\_string() (in module functions)@\spxentry{create\_arg\_string()}\spxextra{in module functions}|hyperpage}{6}
+\indexentry{get\_arg\_keys() (in module functions)@\spxentry{get\_arg\_keys()}\spxextra{in module functions}|hyperpage}{6}
+\indexentry{get\_defaults() (in module functions)@\spxentry{get\_defaults()}\spxextra{in module functions}|hyperpage}{6}
+\indexentry{parse\_output() (in module functions)@\spxentry{parse\_output()}\spxextra{in module functions}|hyperpage}{6}
+\indexentry{run\_system() (in module functions)@\spxentry{run\_system()}\spxextra{in module functions}|hyperpage}{6}
+\indexentry{run\_system\_with\_log() (in module functions)@\spxentry{run\_system\_with\_log()}\spxextra{in module functions}|hyperpage}{6}
diff --git a/docs/build/latex/binary_c-python.ilg b/docs/build/latex/binary_c-python.ilg
index 03547bcb90c3ddce60eb4ceb29a2b21b46a87966..862f7b48e60433df7cdd54667532fcf3b736c96b 100644
--- a/docs/build/latex/binary_c-python.ilg
+++ b/docs/build/latex/binary_c-python.ilg
@@ -1,7 +1,7 @@
 This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support).
 Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored).
-Scanning input file binary_c-python.idx....done (22 entries accepted, 0 rejected).
-Sorting entries....done (97 comparisons).
-Generating output file binary_c-python.ind....done (66 lines written, 0 warnings).
+Scanning input file binary_c-python.idx....done (21 entries accepted, 0 rejected).
+Sorting entries....done (96 comparisons).
+Generating output file binary_c-python.ind....done (65 lines written, 0 warnings).
 Output written in binary_c-python.ind.
 Transcript written in binary_c-python.ilg.
diff --git a/docs/build/latex/binary_c-python.ind b/docs/build/latex/binary_c-python.ind
index c02468f7ef65e1c24e81887d792ce2907066153c..bb8332b10b0c14e2ab220b55ab162d54a3e725eb 100644
--- a/docs/build/latex/binary_c-python.ind
+++ b/docs/build/latex/binary_c-python.ind
@@ -6,23 +6,23 @@
 
   \bigletter A
   \item \spxentry{autogen\_C\_logging\_code()}\spxextra{in module custom\_logging\_functions}, 
-		\hyperpage{7}
+		\hyperpage{5}
 
   \indexspace
   \bigletter B
   \item \spxentry{binary\_c\_log\_code()}\spxextra{in module custom\_logging\_functions}, 
-		\hyperpage{7}
+		\hyperpage{5}
   \item \spxentry{binary\_c\_write\_log\_code()}\spxextra{in module custom\_logging\_functions}, 
-		\hyperpage{7}
+		\hyperpage{5}
 
   \indexspace
   \bigletter C
   \item \spxentry{compile\_shared\_lib()}\spxextra{in module custom\_logging\_functions}, 
-		\hyperpage{7}
+		\hyperpage{5}
   \item \spxentry{create\_and\_load\_logging\_function()}\spxextra{in module custom\_logging\_functions}, 
-		\hyperpage{7}
-  \item \spxentry{create\_arg\_string()}\spxextra{in module functions}, \hyperpage{8}
-  \item \spxentry{custom\_logging\_functions}\spxextra{module}, \hyperpage{7}
+		\hyperpage{5}
+  \item \spxentry{create\_arg\_string()}\spxextra{in module functions}, \hyperpage{6}
+  \item \spxentry{custom\_logging\_functions}\spxextra{module}, \hyperpage{5}
 
   \indexspace
   \bigletter E
@@ -31,36 +31,35 @@
   \indexspace
   \bigletter F
   \item \spxentry{from\_binary\_c\_config()}\spxextra{in module custom\_logging\_functions}, 
-		\hyperpage{7}
-  \item \spxentry{functions}\spxextra{module}, \hyperpage{8}
+		\hyperpage{5}
+  \item \spxentry{functions}\spxextra{module}, \hyperpage{6}
 
   \indexspace
   \bigletter G
-  \item \spxentry{get\_arg\_keys()}\spxextra{in module functions}, \hyperpage{8}
-  \item \spxentry{get\_defaults()}\spxextra{in module functions}, \hyperpage{8}
+  \item \spxentry{get\_arg\_keys()}\spxextra{in module functions}, \hyperpage{6}
+  \item \spxentry{get\_defaults()}\spxextra{in module functions}, \hyperpage{6}
 
   \indexspace
   \bigletter P
-  \item \spxentry{parse\_output()}\spxextra{in module functions}, \hyperpage{8}
+  \item \spxentry{parse\_output()}\spxextra{in module functions}, \hyperpage{6}
 
   \indexspace
   \bigletter R
   \item \spxentry{return\_compilation\_dict()}\spxextra{in module custom\_logging\_functions}, 
-		\hyperpage{7}
-  \item \spxentry{run\_example\_binary()}\spxextra{in module examples.examples}, \hyperpage{3}, 
 		\hyperpage{5}
+  \item \spxentry{run\_example\_binary()}\spxextra{in module examples.examples}, \hyperpage{3}
   \item \spxentry{run\_example\_binary\_with\_custom\_logging()}\spxextra{in module examples.examples}, 
 		\hyperpage{3}
   \item \spxentry{run\_example\_binary\_with\_run\_system()}\spxextra{in module examples.examples}, 
 		\hyperpage{3}
   \item \spxentry{run\_example\_binary\_with\_writing\_logfile()}\spxextra{in module examples.examples}, 
 		\hyperpage{3}
-  \item \spxentry{run\_system()}\spxextra{in module functions}, \hyperpage{8}
-  \item \spxentry{run\_system\_with\_log()}\spxextra{in module functions}, \hyperpage{8}
+  \item \spxentry{run\_system()}\spxextra{in module functions}, \hyperpage{6}
+  \item \spxentry{run\_system\_with\_log()}\spxextra{in module functions}, \hyperpage{6}
 
   \indexspace
   \bigletter T
   \item \spxentry{temp\_custom\_logging\_dir()}\spxextra{in module custom\_logging\_functions}, 
-		\hyperpage{7}
+		\hyperpage{5}
 
 \end{sphinxtheindex}
diff --git a/docs/build/latex/binary_c-python.log b/docs/build/latex/binary_c-python.log
index 495a68e8a7e3f13c74b33d957d2a0ecc4d081bf4..448c04d4d3bafe5b9234c6db8a56790ee9c6ef97 100644
--- a/docs/build/latex/binary_c-python.log
+++ b/docs/build/latex/binary_c-python.log
@@ -1,4 +1,4 @@
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-) [7] [8]
-Chapter 5.
-[9
+) [5] [6]
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+] [8
 
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-] (./binary_c-python.ind [12
+] (./binary_c-python.ind [10
 
 
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@@ -1226,38 +1222,38 @@ ule cus-
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+Underfull \hbox (badness 10000) in paragraph at lines 50--51
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+Overfull \hbox (10.1225pt too wide) in paragraph at lines 51--53
 []\T1/pcr/m/n/10 run_example_binary_with_custom_logging()
  []
 
 
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+Overfull \hbox (16.1225pt too wide) in paragraph at lines 55--57
 []\T1/pcr/m/n/10 run_example_binary_with_writing_logfile()
  []
 
-[13
+[11
 
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  (./binary_c-python.aux)
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-Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 424.
+Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 413.
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-Output written on binary_c-python.pdf (17 pages, 121684 bytes).
+Output written on binary_c-python.pdf (15 pages, 119138 bytes).
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diff --git a/docs/build/latex/binary_c-python.out b/docs/build/latex/binary_c-python.out
index 9099ff972723a4842ee110c289f61cbdb2b54cdc..3122f0715810a785b4cc2809ce2a4c09d4fe7ab8 100644
--- a/docs/build/latex/binary_c-python.out
+++ b/docs/build/latex/binary_c-python.out
@@ -4,10 +4,9 @@
 \BOOKMARK [1][-]{section.1.3}{\376\377\000B\000u\000i\000l\000d\000\040\000i\000n\000s\000t\000r\000u\000c\000t\000i\000o\000n\000s}{chapter.1}% 4
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-\BOOKMARK [0][-]{chapter.3}{\376\377\000C\000h\000e\000c\000k\000i\000n\000g\000\040\000i\000f\000\040\000t\000h\000i\000s\000\040\000w\000o\000r\000k\000s}{}% 7
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-\BOOKMARK [0][-]{chapter.5}{\376\377\000I\000n\000d\000i\000c\000e\000s\000\040\000a\000n\000d\000\040\000t\000a\000b\000l\000e\000s}{}% 11
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-\BOOKMARK [0][-]{section*.23}{\376\377\000I\000n\000d\000e\000x}{}% 13
+\BOOKMARK [0][-]{chapter.3}{\376\377\000b\000i\000n\000a\000r\000y\000c\000\137\000p\000y\000t\000h\000o\000n\000\137\000u\000t\000i\000l\000s}{}% 7
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+\BOOKMARK [1][-]{section.3.2}{\376\377\000f\000u\000n\000c\000t\000i\000o\000n\000s\000\040\000m\000o\000d\000u\000l\000e}{chapter.3}% 9
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diff --git a/docs/build/latex/binary_c-python.pdf b/docs/build/latex/binary_c-python.pdf
index ec0ba9b0c3358043acbda219083a78cfe798e875..d3d03b9a2f80c6f171b413e78fb1c9e363c2279e 100644
Binary files a/docs/build/latex/binary_c-python.pdf and b/docs/build/latex/binary_c-python.pdf differ
diff --git a/docs/build/latex/binary_c-python.tex b/docs/build/latex/binary_c-python.tex
index 2c39acba25eb272b4518d5393558036077860020..fb342a0667e43c8a8672bf1de4dde3f7b7838036 100644
--- a/docs/build/latex/binary_c-python.tex
+++ b/docs/build/latex/binary_c-python.tex
@@ -72,7 +72,7 @@
 
 
 \title{binary\_c-python}
-\date{Nov 17, 2019}
+\date{Nov 20, 2019}
 \release{}
 \author{Jeff Andrews, Robert Izzard, David Hendriks}
 \newcommand{\sphinxlogo}{\vbox{}}
@@ -211,17 +211,6 @@ Same as above but when giving the log\_filename argument the log filename will b
 
 
 
-\chapter{Checking if this works}
-\label{\detokenize{examples:checking-if-this-works}}\index{run\_example\_binary() (in module examples.examples)@\spxentry{run\_example\_binary()}\spxextra{in module examples.examples}}
-
-\begin{fulllineitems}
-\pysiglinewithargsret{\sphinxcode{\sphinxupquote{examples.examples.}}\sphinxbfcode{\sphinxupquote{run\_example\_binary}}}{}{}
-Function to run a binary system. Very basic approach which directly adresses the run\_binary(..) python-c wrapper function.
-
-\end{fulllineitems}
-
-
-
 \chapter{binaryc\_python\_utils}
 \label{\detokenize{modules:binaryc-python-utils}}\label{\detokenize{modules::doc}}
 
diff --git a/docs/build/latex/binary_c-python.toc b/docs/build/latex/binary_c-python.toc
index e0c6d62de862d7a22a628b1caa8318bd501ca71e..87813efeca54c76d2a798869f44fc267dacf593d 100644
--- a/docs/build/latex/binary_c-python.toc
+++ b/docs/build/latex/binary_c-python.toc
@@ -5,10 +5,9 @@
 \contentsline {section}{\numberline {1.3}Build instructions}{1}{section.1.3}
 \contentsline {section}{\numberline {1.4}Usage notes}{2}{section.1.4}
 \contentsline {chapter}{\numberline {2}examples}{3}{chapter.2}
-\contentsline {chapter}{\numberline {3}Checking if this works}{5}{chapter.3}
-\contentsline {chapter}{\numberline {4}binaryc\_python\_utils}{7}{chapter.4}
-\contentsline {section}{\numberline {4.1}custom\_logging\_functions module}{7}{section.4.1}
-\contentsline {section}{\numberline {4.2}functions module}{8}{section.4.2}
-\contentsline {chapter}{\numberline {5}Indices and tables}{9}{chapter.5}
-\contentsline {chapter}{Python Module Index}{11}{section*.22}
-\contentsline {chapter}{Index}{13}{section*.23}
+\contentsline {chapter}{\numberline {3}binaryc\_python\_utils}{5}{chapter.3}
+\contentsline {section}{\numberline {3.1}custom\_logging\_functions module}{5}{section.3.1}
+\contentsline {section}{\numberline {3.2}functions module}{6}{section.3.2}
+\contentsline {chapter}{\numberline {4}Indices and tables}{7}{chapter.4}
+\contentsline {chapter}{Python Module Index}{9}{section*.22}
+\contentsline {chapter}{Index}{11}{section*.23}
diff --git a/docs/output/.doctrees/custom_logging_functions.doctree b/docs/output/.doctrees/custom_logging_functions.doctree
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diff --git a/docs/output/.doctrees/modules.doctree b/docs/output/.doctrees/modules.doctree
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diff --git a/docs/output/output.txt b/docs/output/output.txt
deleted file mode 100644
index 7abddff22d8a1a43f259aa97c14ffa0e841bfbc2..0000000000000000000000000000000000000000
--- a/docs/output/output.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-Results of doctest builder run on 2019-11-17 14:16:36
-=====================================================
-
-Doctest summary
-===============
-    0 tests
-    0 failures in tests
-    0 failures in setup code
-    0 failures in cleanup code