pandoc-ext / section-bibliographies Goto Github PK

As mentioned in #6 (comment) the filter ignores the metadata field nocite. (And suppress-bibliography?)

I can see two valid uses of the metadata nocite:

• if there's a global biblio in addition to the section ones, place the nocite citations in this biblio only.
• if there are only the section-level bibliographies, insert the nocite in each of them. (Not sure why one would want that, but perhaps.)

A related issue is whether the filter should provide section-level nocites and how. One solution would be to use special Divs. (Tricky case: a nocite div is present at the top of a section level 1, but the filter is run asking for bibliographies at section level 2.)

I have an unnumbered chapter (a preface) that should have citations and references just like other chapters, but the filter doesn't appear to generate a reference section for it. (running quarto 1.3.433)

Minimal example:

---
format: pdf
bibliography: example.bib
reference-section-title: References
filters:
  - section-bibliographies
citeproc: false
---

# Preface {-}

text citing @frank2012

# Chapter 1

text citing @lewis1973

# Chapter 2

text citing @kraus2019

Contrast with running pandoc's default citation handling, which does include the unnumbered chapter:

---
format: pdf
bibliography: example.bib
reference-section-title: References
citeproc: true
---

# Preface {-}

text citing @frank2012

# Chapter 1

text citing @lewis1973

# Chapter 2

text citing @kraus2019

Seems like this could be due to the filter checking that a section has a number attribute in line 23?

local function is_section_div (div)
  return div.t == 'Div'
    and div.classes[1] == 'section'
    and div.attributes.number
end

Hi,

I am trying to have multiple references sections in my PhD thesis.
One at the end of the "Manuscrit" part and one at the end of each Article (so three)

Unfortunately when I render in pdf, I have the reference title that appears but no references inside.

Here is my _quarto.yml file

project:
  type: book

book:
  title: "Book_PhD"
  author: "Name"
  date: "15.06.2023"

  chapters:
    - index.qmd
    - part: "Manuscrit (français)"
      chapters: 
        - Manuscrit/Intro.qmd
        - Manuscrit/Part1_Revue.qmd
        - Manuscrit/Part2_Terminologie.qmd
        - Manuscrit/Part3_Methodo.qmd
        - Manuscrit/Part4_Conclusion.qmd
        - Manuscrit/references.qmd
    - part: "Articles (english)"
      chapters:
        - Articles/Article1.qmd
        - Articles/Article2.qmd
        - Articles/Article_Methodology.qmd

filters: 
  - section-bibliographies
bibliography: Biblio.bib
reference-section-title: References
citeproc: false

format:
  html:
    theme: cosmo
  pdf:
    documentclass: scrreprt
    include-in-header: 
      text: |
        \usepackage{multirow} 
        \usepackage{hyperref} 
        \usepackage[capitalise,noabbrev]{cleveref} 
  
editor: visual

Any idea of what I could try to make the references appear ?

So far, your lua is the only one I have gotten to work for my dissertation. However, my reference lists consistently start on a new page, after the references header, then there is no page break before the new chpater, even if the new chapter is a separate file.

I think the issue is that I call pagebreak or newpage just before the next chapter heading and your code thinks it's supposed to come before the reference list, then doesn't call newpage after the reference list. Is there a way to override this? I'm using pandoc in RStudio on Windows.

Thanks!

Environment: RStudio 2022.12.0+353 for Ubuntu Jammy

I am writing a scientific manuscript using Quarto/RStudio. I just installed the section-bibliographies filter as an extension using quarto install extension pandoc-ext/section-bibliographies which concluded with "Extension installation complete". I also now see the _extensions/pandoc-ext/section-bibliographies subdirectories in the project directory. I then updated my yaml as described in the section-bibliographies/README. However, when I render the .qmd file, it errors with "Error running filter section-bibliographies: Could not find executable section-bibliographies". I've looked for solutions to this issue, but have come up empty and am hoping you can help. Thanks.

Hello

thanks for a great filter. Is there a way to specify where the references go? For context I'm working in quarto books -- the references just appear at the end of each section, and disregard the

::: {#refs}
:::

that I had included to make the references appear earlier.

I haven't found any way to do this, is it possible? Thanks again

It seems that the lang argument in quarto chapter _metadata.yml or yaml header is not taken into account for pdf output. Only the lang argument in _quarto.yml is taken into account.

Here are the files used to reproduce this bug :

_quarto.yml

project:
  type: book
  
lang: fr

book:
  chapters:
    - index.qmd
    - fr.qmd
    - en.qmd

bibliography: references.bib

filters:
  - section-bibliographies

format:
  html:
    theme: cosmo
  pdf:
    documentclass: scrreprt
    citeproc: false

editor: visual

index.qmd

# Preface {.unnumbered}

en.qmd

---
lang: en
---

# English

[@ethier2020]

fr.qmd

---
lang: fr
---

# French

[@ethier2020]

references.bib

@article{ethier2020,
	title = {Using microphone arrays to investigate microhabitat selection by declining breeding birds},
	author = {Ethier, Jeffrey P. and Wilson, David R.},
	year = {2020},
	month = {07},
	date = {2020-07-01},
	journal = {Ibis},
	pages = {873--884},
	volume = {162},
	number = {3},
	doi = {10.1111/ibi.12785},
	note = {DOI: 10.1111/ibi.12785
MAG ID: 2977097847}
}

The outputs of these files running quarto render index.qmd are a html website with correct citation, i.e. "and" between authors names for english chapter and "et" between authors names for french chapter, and a pdf file with only french formated citations (as lang: fr is specified in _quarto.yml).

Hi. I managed to generate the per-chapter references but the header will not follow the proper numbering. In the example below, it should be numbered as 2.8

Here is the relevant part of the config file:

project:
  type: book

book:
  title: "my book title"
  author: "Felipe Almeida"
  date: "5/13/2023"
  chapters:
    - index.qmd

    - chapters/ch_01.qmd
    
    - part: parts/part_01.qmd
      chapters:
        - chapters/ch_02.qmd


filters:
  - section-bibliographies
bibliography: references.bib
reference-section-title: References

format:
  html:
    toc: true
    toc-expand: 1
    toc-depth: 4
  pdf:
    documentclass: scrreprt

crossref:
  chapters: true

This package is great. I'm using it to format my CV. I noticed the section-bibs-level parameter wasn't working for me, Regardless of what value I set for section-bibs-level, it all refs were assigned to the top level headers.

I fixed it for my use case (wanting citations to follow second level headers) making a small change

  if not header or section_refs_level < header.level then
    -- Don't do anything for lower level sections.
    return nil
  elseif section_refs_level == header.level then
    blocks = div.content
    subsections = pandoc.List:new{}

I edited changed the < in line 78 to > & the == in line 81 to <

 if not header or section_refs_level > header.level then
   -- Don't do anything for lower level sections.
   return nil
 elseif section_refs_level < header.level then
   blocks = div.content
   subsections = pandoc.List:new{}

This might break things in other use cases, so theres probably a better fix for this issue.

There some demand for recursive citations, i.e. handling \cite commands within the bibliographies themselves, usually in the BibTeX note field. See this exchange on pandoc-discuss. Would you be interested in a PR adding this?

I've written a recursive citeproc filter that we use in the journal dialectica. I'm considering updating it for Quarto, but I'd be glad to contribute to section-bibliographies and multibib and use one of these instead.

I'd try to make the addition as lightweight as possible when no recursion is needed by first scanning the first citeproc pass's output with a filter {{ Citation = function(elem) has_citations = true end }}.

I updated my Quarto today to version 1.3.361 (the current main version) and all my section bibliographies went blank (i.e., no bibliography was rendered at all). I reverted back to version 1.2.475 that I had been using and they reappeared. Is this something other people have experienced?

In the installation instruction for Quarto, the command is given as,

quarto install extension tarleb/section-bibliographies

when I run this from Rstudio Cloud, I got this error,

Extension not found in local or remote sources

Now after going through the documentation of Quarto extension,

I tried the following command,

quarto install extension pandoc-ext/section-bibliographies

It worked smoothly.

Hello,

The filter works great when the chapters are normally numbered but when there is an unnumbered chapter (e.g., the Introduction of my thesis has the number 0 so that the following chapters ~ papers are numbered from 1). I use RMarkwdown, the chapters are added as child documents. Knitting to PDF using pdflatex.
Also, I believe it worked for the first time but ignored \newpage for new chapters. When I played with it a bit, the reference list for chapter 0 disappeared and the \newpage started to work.

Is there a way to suppress the final full list of references which gets rendered automatically?

I'm working in RMarkdown. SessionInfo:

R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=cs_CZ.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=cs_CZ.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=cs_CZ.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=cs_CZ.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] lmerTest_3.1-3 lme4_1.1-31 Matrix_1.5-3

loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 mvtnorm_1.1-3 lattice_0.20-45 zoo_1.8-11
[5] assertthat_0.2.1 digest_0.6.30 utf8_1.2.2 R6_2.5.1
[9] cellranger_1.1.0 coda_0.19-4 evaluate_0.18 ggplot2_3.4.0
[13] pillar_1.8.1 gdtools_0.2.4 rlang_1.0.6 multcomp_1.4-20
[17] uuid_1.1-0 readxl_1.4.1 rstudioapi_0.14 minqa_1.2.5
[21] data.table_1.14.6 nloptr_2.0.3 flextable_0.8.3 rmarkdown_2.18
[25] splines_4.2.2 TMB_1.9.1 munsell_0.5.0 compiler_4.2.2
[29] numDeriv_2016.8-1.1 xfun_0.35 pkgconfig_2.0.3 systemfonts_1.0.4
[33] base64enc_0.1-3 htmltools_0.5.3 tidyselect_1.2.0 tibble_3.1.8
[37] glmmTMB_1.1.5 codetools_0.2-18 fansi_1.0.3 dplyr_1.0.10
[41] MASS_7.3-58.1 grid_4.2.2 nlme_3.1-160 xtable_1.8-4
[45] gtable_0.3.1 lifecycle_1.0.3 DBI_1.1.3 magrittr_2.0.3
[49] scales_1.2.1 zip_2.2.2 estimability_1.4.1 cli_3.4.1
[53] xml2_1.3.3 generics_0.1.3 vctrs_0.5.1 boot_1.3-28.1
[57] sandwich_3.0-2 TH.data_1.1-1 tools_4.2.2 forcats_0.5.2
[61] glue_1.6.2 officer_0.4.4 emmeans_1.8.2 fastmap_1.1.0
[65] survival_3.4-0 yaml_2.3.6 colorspace_2.0-3 knitr_1.41

The YAML header of my main document:

title: ''
output: 
  pdf_document:
        latex_engine: pdflatex
        number_sections: TRUE
        pandoc_args: ['--lua-filter=section-bibliographies.lua']
always_allow_html: true
geometry: "left = 4cm, right = 2cm, top = 2cm, bottom = 2cm"
fontsize: 11pt
header-includes:
  - \usepackage{float}
  - \usepackage{sectsty}
  - \usepackage{paralist}
  - \usepackage{setspace}\spacing{1.5}
  - \usepackage{fancyhdr}
  - \usepackage{lastpage}
  - \usepackage{dcolumn}
  - \usepackage{natbib}
  - \usepackage[nottoc, numbib]{tocbibind}
  - \usepackage{ragged2e}
  - \usepackage{pdflscape} 
  - \usepackage{textgreek}
  - \usepackage{graphicx} 
  - \usepackage{titlesec}
classoption: twoside
bibliography: library.bib
reference-section-title: References
section-bibs-level: 2
citation_package: biblatex
csl: journal-of-ecology.csl