Issues with using include-before/include-after when output is pdf

Issues with using include-before/include-after when output is pdf

[Tahir B]

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I wanted to format the body of my article text such that paragraphs (all 
but first in a section) were indented and that lines were spaced out. But I 
wanted the bibliography to not be indented and have normal spacing.

Following the instructions I got from some Google searches I thought the 
following would do the trick:

---

title: This is a test
linestretch: 1.5
header-includes:
    - \usepackage{fullpage}
include-before:
    - \setlength{\parindent}{15pt}
include-after:
    - \setlength{\parindent}{0pt}
    - \setstretch{1}

---


Unfortunately this did not work as I had hoped. I tried three approaches for generating a pdf: just pandoc, pandoc+csl+latex, pandoc+biblatex+latex. In all three cases what I found was that the include-after lines were added actually after the bibliography command had been called.


Here is my attempt to reproduce the issue: 


https://gist.github.com/majorgreys/af344eb9824b947f393b


In the pandoc+csl+latex outputted tex file I got this:


\section*{References}\label{references}
\addcontentsline{toc}{section}{References}

Last, First. 1981. \emph{Book Title}. Publisher.

---------. 2001. \emph{Book Title 2}. Publisher.

\setlength{\parindent}{0pt}

\setstretch{1}


And, in the pandoc+biblatex+latex outputted tex file I got this:


\printbibliography[title=References]

\setlength{\parindent}{0pt}

\setstretch{1}


This then led me to look at the default latex template, where the relevant lines are:


$body$

$if(natbib)$
$if(bibliography)$
$if(biblio-title)$
$if(book-class)$
\renewcommand\bibname{$biblio-title$}
$else$
\renewcommand\refname{$biblio-title$}
$endif$
$endif$
\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}

$endif$
$endif$
$if(biblatex)$
\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$

$endif$
$for(include-after)$
$include-after$

$endfor$


Now it makes sense why in all three approaches the include-after clauses do not end up affecting the bibliography.


I can certainly modify the latex template so that the include-after block is before the natbib block. But that only resolves the issue when I'm not using citeproc.


I wonder if include-after behavior for straight pdf output should actually be like the modified latex template I just described. Should $body have the citeproc-generated bibliography appended to it or should the include-after applied before the bibliography is inserted into the document? I expected that the latter would be how things worked, but maybe there are many good reasons for the former to be the typical behavior.


Hope my issue and questions made sense.


Thanks!

Tahir

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Re: Issues with using include-before/include-after when output is pdf

[John MacFarlane]

Currently pandoc-citeproc adds the bibliography to the body.

You can use a pandoc filter to intercept this section (which
has the identifier "references") and put it inside a special
latex environment.  That would probably be the easiest
solution.

See http://pandoc.org/scripting for basic instructions; if
you need help, ask here.


+++ Tahir B [Jul 23 15 09:12 ]:
>   I wanted to format the body of my article text such that paragraphs
>   (all but first in a section) were indented and that lines were spaced
>   out. But I wanted the bibliography to not be indented and have normal
>   spacing.
>   Following the instructions I got from some Google searches I thought
>   the following would do the trick:
>   ---
>title: This is a test
>linestretch: 1.5
>header-includes:
>    - \usepackage{fullpage}
>include-before:
>    - \setlength{\parindent}{15pt}
>include-after:
>    - \setlength{\parindent}{0pt}
>    - \setstretch{1}
>---
>
>Unfortunately this did not work as I had hoped. I tried three approaches for gen
>erating a pdf: just pandoc, pandoc+csl+latex, pandoc+biblatex+latex. In all thre
>e cases what I found was that the include-after lines were added actually after
>the bibliography command had been called.
>
>Here is my attempt to reproduce the issue:
>
>[1]https://gist.github.com/majorgreys/af344eb9824b947f393b
>
>In the pandoc+csl+latex outputted tex file I got this:
>
>\section*{References}\label{references}
>\addcontentsline{toc}{section}{References}
>
>Last, First. 1981. \emph{Book Title}. Publisher.
>
>---------. 2001. \emph{Book Title 2}. Publisher.
>
>\setlength{\parindent}{0pt}
>
>\setstretch{1}
>
>
>And, in the pandoc+biblatex+latex outputted tex file I got this:
>
>\printbibliography[title=References]
>
>\setlength{\parindent}{0pt}
>
>\setstretch{1}
>
>
>This then led me to look at the default latex template, where the relevant lines
> are:
>
>$body$
>
>$if(natbib)$
>$if(bibliography)$
>$if(biblio-title)$
>$if(book-class)$
>\renewcommand\bibname{$biblio-title$}
>$else$
>\renewcommand\refname{$biblio-title$}
>$endif$
>$endif$
>\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
>
>$endif$
>$endif$
>$if(biblatex)$
>\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$
>
>$endif$
>$for(include-after)$
>$include-after$
>
>$endfor$
>
>
>Now it makes sense why in all three approaches the include-after clauses do not
>end up affecting the bibliography.
>
>I can certainly modify the latex template so that the include-after block is bef
>ore the natbib block. But that only resolves the issue when I'm not using citepr
>oc.
>
>I wonder if include-after behavior for straight pdf output should actually be li
>ke the modified latex template I just described. Should $body have the citeproc-
>generated bibliography appended to it or should the include-after applied before
> the bibliography is inserted into the document? I expected that the latter woul
>d be how things worked, but maybe there are many good reasons for the former to
>be the typical behavior.
>
>Hope my issue and questions made sense.
>
>Thanks!
>Tahir
>
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>
>References
>
>   1. https://gist.github.com/majorgreys/af344eb9824b947f393b
>   2. mailto:pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
>   3. mailto:pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
>   4. https://groups.google.com/d/msgid/pandoc-discuss/12a3b4c1-e64e-4f0d-ba1b-545311045f86-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org?utm_medium=email&utm_source=footer
>   5. https://groups.google.com/d/optout

Re: Issues with using include-before/include-after when output is pdf

[Tahir B]

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Hi John --

I am finally getting back to try writing such a filter. I am opting to use 
the python pandocfilters package to intercept this with toJSONFilter. But I 
don't seem to be getting it.

I think I have it close but don't know how to handle the lines in the 
metadata include-after before the start of the reference header.

But when I run pandoc with the filter, I get pandoc: The key "MetaList" was 
not found

How should I be handling the metadata lines in the jsonfilter? How do I 
prepend this before the reference Header object?

Thanks!

from pandocfilters import toJSONFilter, RawBlock, Header
import sys


def latex(x):
    return RawBlock('latex', x)


def references_includeafter(key, value, format, meta):
    if key == 'Header':
        [level, [ident, _, _], content] = value
        if ident == "references":
            if format == "latex":
                # insert include-after lines before start of reference 
header
                includeafter = meta.get('include-after', {})
                print >> sys.stderr, str(includeafter)
                return includeafter

if __name__ == "__main__":
    toJSONFilter(references_includeafter)



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Re: Issues with using include-before/include-after when output is pdf

[John MACFARLANE]

First, are you using a recent pandoc version?

Second, let's start simple.  Use

                   includeafter = meta.get('include-after', {})
                   print >> sys.stderr, str(includeafter)
                   return None

'return None' will cause the header object to be returned
unchanged.  This way you can verify that it is finding
the includeafter list.  Once you verify that, we can move
forward to actually modifying the document.

+++ Tahir B [Aug 24 15 09:27 ]:
>   Hi John --
>   I am finally getting back to try writing such a filter. I am opting to
>   use the python pandocfilters package to intercept this with
>   toJSONFilter. But I don't seem to be getting it.
>   I think I have it close but don't know how to handle the lines in the
>   metadata include-after before the start of the reference header.
>   But when I run pandoc with the filter, I get pandoc: The key "MetaList"
>   was not found
>   How should I be handling the metadata lines in the jsonfilter? How do I
>   prepend this before the reference Header object?
>   Thanks!
>   from pandocfilters import toJSONFilter, RawBlock, Header
>   import sys
>   def latex(x):
>       return RawBlock('latex', x)
>   def references_includeafter(key, value, format, meta):
>       if key == 'Header':
>           [level, [ident, _, _], content] = value
>           if ident == "references":
>               if format == "latex":
>                   # insert include-after lines before start of reference
>   header
>                   includeafter = meta.get('include-after', {})
>                   print >> sys.stderr, str(includeafter)
>                   return includeafter
>   if __name__ == "__main__":
>       toJSONFilter(references_includeafter)
>
>   --
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>   b258-036540acba31%40googlegroups.com.
>   For more options, visit [4]https://groups.google.com/d/optout.
>
>References
>
>   1. mailto:pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
>   2. mailto:pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
>   3. https://groups.google.com/d/msgid/pandoc-discuss/7cc8e08e-14fd-4d56-b258-036540acba31-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org?utm_medium=email&utm_source=footer
>   4. https://groups.google.com/d/optout

Re: Issues with using include-before/include-after when output is pdf

[Tahir B]

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It seems like the script I have found the "reference" Header object 
perfectly fine.

I can replace the Header object in the output latex.

But I don't know how to take the include-after metadata, convert it into 
the raw commands, and then prepend it before the \section{References} would 
be written.

I'm using the most recent pandoc version, 1.15.0.6.

On Monday, August 24, 2015 at 1:15:01 PM UTC-4, John MacFarlane wrote:
>
> First, are you using a recent pandoc version? 
>
> Second, let's start simple.  Use 
>
>                    includeafter = meta.get('include-after', {}) 
>                    print >> sys.stderr, str(includeafter) 
>                    return None 
>
> 'return None' will cause the header object to be returned 
> unchanged.  This way you can verify that it is finding 
> the includeafter list.  Once you verify that, we can move 
> forward to actually modifying the document. 
>

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Re: Issues with using include-before/include-after when output is pdf

[Tahir B]

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Ok, I think I got it now... but not sure if there isn't a better way to 
translate the include-after lines into a latex raw block.

John and others, is there a better way to do this?

def references_includeafter(key, value, format, meta):
    if key == 'Header':
        [level, [ident, i1, i2], content] = value
        if ident == "references":
            if format == "latex":
                # insert include-after lines before start of reference 
header
                includeafter = meta.get('include-after', {})
                rawinserts = []
                if includeafter:
                    for metainline in includeafter.get('c', []):
                        for rawinline in metainline.get('c', []):
                            rawinserts.append(rawinline['c'][1])
                return [latex('\n'.join(rawinserts)), Header(level, [ident, 
i1, i2], content)]

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