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Changeset 11176 – NEMO

Changeset 11176


Ignore:
Timestamp:
2019-06-24T21:55:11+02:00 (5 years ago)
Author:
nicolasmartin
Message:

Implementation of multi-indexes instead of an indiscrimate aggregate index
Creation of 5 sections under Indexes chapter for the most relevant lists of index entries:
namelist blocks and parameters, CPP keys, modules and subroutines.

  • indexes.tex & index.ist: new file in global directory for index management
  • Add symbolic links under main to non-existing *.idx before LaTeX compilation to reduce trivial error messages with makeindex
  • Create latexmkrc init file loaded latexmk with '-r' option in order to apply the style rules to the indexes with the sequence of several compilations

Other changes:

  • Define a preamble.tex with the list of files to load from global folder
  • Integrate 'Citation' subsubsection in new info_page.tex for the 2nd page along with 'frontpage.tex' for the cover, in order to have a clear distinction with \maketitle in the main LaTeX document
  • Move 'Foreword' chapter from subfiles to main as more appropriate

Bugfixes with few attempts of HTML export

  • One single location for defining the paths to search for images with \graphicspath in packages.tex
  • Renaming of authors variables (\1stauthor -> \firstauthor and so one)
  • Update of LaTeX dependencies in terms of new pkgs (DEPS)
Location:
NEMO/trunk/doc
Files:
8 added
1 deleted
12 edited
3 moved

Legend:

Unmodified
Added
Removed

  • NEMO/trunk/doc/latex/NEMO/build

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        99*.ind 
        1010*.log 
         11*.lot 
        1112*.maf 
        1213*.mtc* 

  • NEMO/trunk/doc/latex/NEMO/main

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  • NEMO/trunk/doc/latex/NEMO/main/definitions.tex

    r11171 r11176  
    66 
    77%% Authors (thanks will apply to the second author) 
    8 \def \1stauthor{Gurvan Madec~} 
    9 \def \2ndauthor{NEMO System Team} 
     8\def \firstauthor{Gurvan Madec~} 
     9\def \secondauthor{NEMO System Team} 
    1010 
    1111%% IPSL publication number 

  • NEMO/trunk/doc/latex/NEMO/main/foreword.tex

    r11172 r11176  
    1 \documentclass[../main/NEMO_manual]{subfiles} 
    2  
    3 \begin{document} 
    4  
    51% ================================================================ 
    6 % Chapter Foreword 
     2% Foreword 
    73% ================================================================ 
    84\chapter*{Foreword} 
    … …  
    2521via the \href{https://portal.enes.org/oasis}{OASIS} coupler, with several atmospheric general circulation models. 
    2622It also support two-way grid embedding via the \href{http://agrif.imag.fr}{AGRIF} software. 
    27  
    28 \biblio 
    29  
    30 \pindex 
    31  
    32 \end{document} 

  • NEMO/trunk/doc/latex/NEMO/subfiles

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      *.aux
      *.bbl
      *.blg
      *.dvi
      *.fdb*
      *.fls
      *.idx
      *.ilg
      *.ind
      *.log
      *.maf
      *.mtc*
      *.out
      *.pdf
      *.toc
      _minted-*

  • NEMO/trunk/doc/latex/global

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  • NEMO/trunk/doc/latex/global/document.tex

    r11174 r11176  
     1 
    12%% ============================================================================== 
    2 %% Reference Manual 
     3%% Template structure for reference manual 
    34%% ============================================================================== 
    45 
    56%% NEMO release version 
    6 \def\version{4.0rc~} 
     7\def \version{4.0rc~} 
    78 
    89%% Preamble 
    … …  
    1213\documentclass[draft]{scrreport} 
    1314 
    14 %% Load manual definitions 
    15 \input{definitions} 
     15%% Load the configuration of the manual 
     16\input{../main/definitions} 
    1617 
    17 %% Load all *.tex files from './latex/global' directory 
    18 \input{../../global/packages} 
    19 \input{../../global/highlighting} 
    20 \input{../../global/new_cmds} 
    21 \input{../../global/styles} 
    22 \input{../../global/todonotes} 
     18%% Load global *.tex files 
     19\input{../../global/preamble} 
    2320 
    24 %% Include references and index for single subfile compilation 
    25 \newcommand{\biblio}{\bibliography{../main/bibliography}} 
    26 \newcommand{\pindex}{\printindex} 
     21\dominitoc 
    2722 
    28 \makeindex 
     23%% Launch the creation of the indexes 
     24\input{../../global/indexes} 
     25 
    2926 
    3027%% End of common preamble between main and sub-files 
     28%% Override custom cmds for full manual compilation 
     29\newcommand{\onlyinsubfile}[1]{#1} 
     30\newcommand{\notinsubfile}[1]{} 
     31 
    3132\begin{document} 
    32 \pagenumbering{gobble} 
    3333 
    34 %% Override custom cmds for full manual compilation 
     34\renewcommand{\onlyinsubfile}[1]{} 
     35\renewcommand{\notinsubfile}[1]{#1} 
     36 
    3537\renewcommand{\biblio}{} 
    3638\renewcommand{\pindex}{} 
    … …  
    4042%% ============================================================================== 
    4143 
    42 %% Title and information pages 
    43 \input{../../global/frontpages} 
     44\pagenumbering{gobble} 
    4445 
    45 %% Engine citation 
    46 \input{../../global/citation} 
     46%% Title page 
     47\input{../../global/frontpage} 
     48 
     49\maketitle 
     50\emptythanks 
     51 
     52%% Information page (2nd page) 
     53\input{../../global/info_page} 
    4754 
    4855%% Foreword 
    49 \newpage 
    5056%\frontmatter   %% Chapter numbering off and Roman numerals for page numbers 
    5157\pagenumbering{roman} 
    52 \subfile{../subfiles/foreword} 
     58\input{foreword} 
    5359 
    54 %% ToC i.e. Table of Contents 
    55 \newpage 
    56 \dominitoc 
     60%% Table of Contents 
    5761\tableofcontents 
     62%\listoffigures 
     63\listoftables 
    5864 
    5965\clearpage 
    … …  
    6773\pagenumbering{arabic} 
    6874 
    69 \graphicspath{{../../figures/\engine/}} 
    7075\input{chapters} 
    7176 
    … …  
    9398\clearpage 
    9499\phantomsection 
    95 \addcontentsline{toc}{chapter}{Index} 
    96 \printindex 
     100\addcontentsline{toc}{chapter}{Indexes} 
     101\printindex[keys] 
     102\printindex[modules] 
     103\printindex[blocks] 
     104\printindex[parameters] 
     105\printindex[subroutines] 
    97106 
    98107\end{document} 
     108 

  • NEMO/trunk/doc/latex/global/frontpage.tex

    r11170 r11176  
     1 
    12\title{\heading} 
    2 \author{\1stauthor \and \2ndauthor\thanks{\protect\input{thanks}}} 
     3\author{\firstauthor \and \secondauthor\thanks{\protect\input{thanks}}} 
    34\date{\today} 
    4  
    5 \graphicspath{{../../figures/}} 
    65 
    76\pretitle{ 
    … …  
    4645  \end{center} 
    4746} 
     47 
    4848\thanksmarkseries{fnsymbol} 
    49 \maketitle 
    50 \emptythanks 
    5149 
    52 \thispagestyle{plain} 
    53  
    54 % ================================================================ 
    55 % Disclaimer 
    56 % ================================================================ 
    57 \subsubsection*{Disclaimer} 
    58  
    59 Like all components of the modelling framework, 
    60 the \engine~core engine is developed under the \href{http://www.cecill.info}{CECILL license}, 
    61 which is a French adaptation of the GNU GPL (General Public License). 
    62 Anyone may use it freely for research purposes, and is encouraged to 
    63 communicate back to the NEMO team its own developments and improvements. 
    64  
    65 The model and the present document have been made available as a service to the community. 
    66 We cannot certify that the code and its manual are free of errors. 
    67 Bugs are inevitable and some have undoubtedly survived the testing phase. 
    68 Users are encouraged to bring them to our attention. 
    69  
    70 The authors assume no responsibility for problems, errors, or incorrect usage of NEMO. 
    71  
    72 % ================================================================ 
    73 % External resources 
    74 % ================================================================ 
    75 \subsubsection*{Other resources} 
    76  
    77 Additional information can be found on: 
    78 \begin{itemize} 
    79 \item the \href{http://www.nemo-ocean.eu}{website} of the project detailing several 
    80   associated applications and an exhaustive users bibliography 
    81 \item the \href{http://forge.ipsl.jussieu.fr/nemo}{development platform} of the model with 
    82   the code repository and some main resources (wiki, ticket system, forums, \ldots) 
    83 \item the \href{http://zenodo.org/communities/nemo-ocean}{online archive} 
    84   delivering the publications issued by the consortium 
    85 \item two mailing lists: 
    86   the \href{http://listes.ipsl.fr/sympa/info/nemo-newsletter}{newsletter} for 
    87   top-down communications from the project 
    88   (announcements, calls, job opportunities, \ldots) 
    89   and the \href{http://listes.ipsl.fr/sympa/info/nemo-forge}{forge updates} 
    90   (commits, tickets and forums) 
    91 \end{itemize} 
    92  
    93 % ================================================================ 
    94 % Citation 
    95 % ================================================================ 
    96 \subsubsection*{Citation} 
    97  
    98 Reference for papers and other publications is as follows: 
    99 \vspace{0.5cm} 
    100  
    101 \begin{figure}[b] 
    102   \begin{minipage}[c]{0.72\textwidth} 
    103     \small\ttfamily{Scientific Notes of Climate Modelling Center \\ 
    104       ISSN 1288-1619                                             \\ 
    105       Institut Pierre-Simon Laplace (IPSL) 
    106     } 
    107   \end{minipage} 
    108   \hfill 
    109   \begin{minipage}[c]{0.25\textwidth} 
    110     \href{http://www.cmc.ipsl.fr}{\includegraphics[width=\textwidth]{logos/IPSL_upright}} 
    111   \end{minipage} 
    112 \end{figure} 

  • NEMO/trunk/doc/latex/global/highlighting.tex

    r11174 r11176  
    1 %% Minted package: syntax highlighting configuration 
     1%% Syntax highlighting configuration 
    22%% ============================================================================== 
     3 
     4\usepackage[outputdir=../build]{minted} 
    35 
    46%% Global highlighting style 

  • NEMO/trunk/doc/latex/global/index.ist

    r11175 r11176  
    1 delim_0 "\\dotfill" 
    2 delim_1 "\\dotfill" 
    3 delim_2 "\\dotfill" 
     1headings_flag 1 
     2heading_prefix "{\\medskip\\hfill\\large\\textsf{\\textbf{" 
     3heading_suffix "}}\\hfill}\\medskip\\nopagebreak\n" 
     4 
     5delim_0 "\\dotfill~" 
     6delim_1 "\\dotfill~" 
     7delim_2 "\\dotfill~" 
     8 

  • NEMO/trunk/doc/latex/global/new_cmds.tex

    r11174 r11176  
    22%% ============================================================================== 
    33 
     4%% Include references and index for compilation of single subfile  
     5\newcommand{\mtoc}{\minitoc} 
     6\newcommand{\biblio}{\bibliography{../main/bibliography}} 
     7\newcommand{\pindex}{\printindex} 
     8 
    49%% NEMO and Fortran in small capitals 
    5 \newcommand{\NEMO}{\textsc{nemo}} 
    6 \newcommand{\fortran}{\textsc{Fortran}} 
    7 \newcommand{\fninety}{\textsc{Fortran 90}} 
     10\newcommand{\NEMO}{\textsc{nemo}~} 
     11\newcommand{\fortran}{\textsc{Fortran}~} 
     12\newcommand{\fninety}{\textsc{Fortran 90}~} 
    813 
    914%% Common aliases 
    … …  
    1318\newcommand{\ztilde}{\ensuremath{\tilde z}} 
    1419\newcommand{\stilde}{\ensuremath{\tilde s}} 
    15 \newcommand{\ie}{\ensuremath{i.e.}} 
    16 \newcommand{\eg}{\ensuremath{e.g.}} 
     20\newcommand{\ie}{\ensuremath{i.e.}~} 
     21\newcommand{\eg}{\ensuremath{e.g.}~} 
    1722 
    1823%% Inline maths 
    … …  
    2227%% Text env. for Gurvan 
    2328\newcommand{\gmcomment}[1]{} 
    24  
    25 %% Index entries (italic font for files, preformat for code) 
    26 \newcommand{\hf}[1]{\textit{#1.h90}            \index{h90 files!#1}} 
    27 \newcommand{\ifile}[1]{\textit{#1.nc}          \index{Input NetCDF files!#1.nc}} 
    28 \newcommand{\jp}[1]{\texttt{#1}                \index{Model parameters!#1}} 
    29 \newcommand{\key}[1]{\texttt{\textbf{key\_#1}} \index{CPP keys!key\_#1}} 
    30 \newcommand{\mdl}[1]{\textit{#1.F90}           \index{Modules!#1}} 
    31 \newcommand{\ngn}[1]{\texttt{#1}               \index{Namelist Group Names!#1}} 
    32 \newcommand{\np}[1]{\texttt{#1}                \index{Namelist parameters!#1}} 
    33 \newcommand{\rou}[1]{\texttt{#1}               \index{Routines!#1}} 
    3429 
    3530%% Maths 

  • NEMO/trunk/doc/latex/global/packages.tex

    r11174 r11176  
    77\usepackage{times}                       %% font 
    88\usepackage{hyperref}                    %% hyper 
    9 %\usepackage{idxlayout}                   %% index 
    109\usepackage{enumitem}                    %% list 
    11 \usepackage[outputdir=../build]{minted}  %% listing 
    1210\usepackage{amsmath}                     %% maths 
    1311%\usepackage{fancyhdr}                    %% page 
    … …  
    1816 
    1917%% Extensions in bundle package 
    20 \usepackage{amssymb, graphicx, makeidx, tabularx, textcomp} 
     18\usepackage{amssymb, graphicx, tabularx, textcomp} 
    2119\usepackage[utf8]{inputenc}              %% input encoding 
    2220 
    2321%% Configuration 
    24 \captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}} 
    25 %\idxlayout{font=footnotesize, columns=3} 
    26 %\renewcommand{\bibfont}{\footnotesize} 
     22\graphicspath{ {../../figures/} {../../figures/\engine/} } 
     23%\captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}} 
     24\renewcommand{\bibfont}{\small} 
    2725%\renewcommand{\bibsep}{3pt} 
     26 

  • NEMO/trunk/doc/latex/global/styles.tex

    r11174 r11176  
    1111\hypersetup{ 
    1212%  pdftitle={\heading}, 
    13 %  pdfauthor={\1stauthor and \2ndauthor}, 
     13%  pdfauthor={\firstauthor and \secondauthor}, 
    1414  colorlinks 
    1515} 

  • NEMO/trunk/doc/manual_build.sh

    r11120 r11176  
    44##--------------- 
    55 
    6 ## latekmk options 
    7 opts='-shell-escape -pdf -quiet' 
     6## Env. variable for using relative paths with latexmk 
    87export openout_any='a' 
    98 
    … …  
    4544    build $model 
    4645    printf "\t¤ End of building run\n" 
    47     printf "\t  The export should be available at root\n" 
    48     printf "\t  If not check LaTeX log in ./latex/$model/build/${model}_manual.log\n" 
    4946    echo 
    5047done 
    5148 
    5249exit 0 
     50 

  • NEMO/trunk/doc/tools/shr_func.sh

    r11120 r11176  
    1515build() { 
    1616    printf "\t¤ Generation of the PDF format\n" 
    17     latexmk $opts -outdir=../build -cd ./latex/$1/main/$1_manual 1> /dev/null 
     17    latexmk -r  ./latex/$1/main/latexmkrc \ 
     18       -cd ./latex/$1/main/$1_manual \ 
     19       -outdir=../build              \ 
     20       1> /dev/null 
    1821    [ -f ./latex/$1/build/$1_manual.pdf ] && mv ./latex/$1/build/$1_manual.pdf . 
    19 #    cd - > /dev/null 
    2022    echo 
    2123} 
     24 
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