\babel@toc {english}{}
\contentsline {chapter}{\numberline {1}Contents}{3}{chapter.1}%
\contentsline {section}{\numberline {1.1}Getting started with hpc\sphinxhyphen {}tools}{3}{section.1.1}%
\contentsline {subsection}{\numberline {1.1.1}Installation instructions}{3}{subsection.1.1.1}%
\contentsline {subsubsection}{Installation not using any conda dependencies}{3}{subsubsection*.3}%
\contentsline {subsubsection}{Installation using conda}{4}{subsubsection*.4}%
\contentsline {subsubsection}{Post Python install}{4}{subsubsection*.5}%
\contentsline {paragraph}{Setup a mapping file}{4}{paragraph*.6}%
\contentsline {paragraph}{Add the \sphinxstyleliteralintitle {\sphinxupquote {bin}} directory to your \sphinxstyleliteralintitle {\sphinxupquote {PATH}}}{5}{paragraph*.7}%
\contentsline {section}{\numberline {1.2}General Workflow}{5}{section.1.2}%
\contentsline {subsection}{\numberline {1.2.1}Array Jobs}{5}{subsection.1.2.1}%
\contentsline {section}{\numberline {1.3}Example job array}{7}{section.1.3}%
\contentsline {subsection}{\numberline {1.3.1}Creating example files}{7}{subsection.1.3.1}%
\contentsline {subsection}{\numberline {1.3.2}Creating a job array file}{7}{subsection.1.3.2}%
\contentsline {subsection}{\numberline {1.3.3}Testing the task script}{9}{subsection.1.3.3}%
\contentsline {subsection}{\numberline {1.3.4}Job array arguments}{10}{subsection.1.3.4}%
\contentsline {subsection}{\numberline {1.3.5}Running the jobs}{11}{subsection.1.3.5}%
\contentsline {section}{\numberline {1.4}Command\sphinxhyphen {}line endpoints}{15}{section.1.4}%
\contentsline {subsection}{\numberline {1.4.1}\sphinxstyleliteralintitle {\sphinxupquote {pyjasub}}}{15}{subsection.1.4.1}%
\contentsline {subsubsection}{Setup}{15}{subsubsection*.8}%
\contentsline {subsubsection}{Usage}{16}{subsubsection*.9}%
\contentsline {paragraph}{Positional Arguments}{16}{paragraph*.10}%
\contentsline {paragraph}{Named Arguments}{16}{paragraph*.11}%
\contentsline {subsubsection}{Job submission workflow}{17}{subsubsection*.12}%
\contentsline {subsubsection}{Checks on the job array file}{20}{subsubsection*.13}%
\contentsline {subsubsection}{Defining a completed job}{20}{subsubsection*.14}%
\contentsline {subsection}{\numberline {1.4.2}\sphinxstyleliteralintitle {\sphinxupquote {make\sphinxhyphen {}jaf}}}{20}{subsection.1.4.2}%
\contentsline {subsubsection}{Usage}{20}{subsubsection*.15}%
\contentsline {paragraph}{Positional Arguments}{20}{paragraph*.16}%
\contentsline {paragraph}{Named Arguments}{21}{paragraph*.17}%
\contentsline {subsubsection}{Output file}{21}{subsubsection*.18}%
\contentsline {subsubsection}{Basic API usage}{22}{subsubsection*.19}%
\contentsline {section}{\numberline {1.5}Contributing to the project}{22}{section.1.5}%
\contentsline {section}{\numberline {1.6}Package management}{23}{section.1.6}%
\contentsline {subsection}{\numberline {1.6.1}Versioning}{23}{subsection.1.6.1}%
\contentsline {subsection}{\numberline {1.6.2}Building the documentation}{25}{subsection.1.6.2}%
\contentsline {subsubsection}{Initialisation}{26}{subsubsection*.20}%
\contentsline {subsubsection}{Configuration}{27}{subsubsection*.21}%
\contentsline {subsubsection}{Building HTML}{27}{subsubsection*.22}%
\contentsline {subsubsection}{Building PDF}{27}{subsubsection*.23}%
\contentsline {subsubsection}{Helper script}{27}{subsubsection*.24}%
\contentsline {chapter}{\numberline {2}Indices and tables}{29}{chapter.2}%
