pandoc

Summary

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pandoc

Summary

[[pandoc]] converts text files into different formats. I'm hoping to use it to convert Markdown files to:

PDF
Word doc
HTML


Installation (WSL2)



Install Ubuntu packages.

sudo apt install texlive-full pandoc



Create a conda environment.

mamba create -n pandoc -y python=3.7 pandoc nodejs click
conda activate pandoc




Links

The ObsidianObsidian
Obsidian

Tasks

Pending

table tags
from ""
where project=[[Obsidian]] and status!="done"


Completed

table tags
from ""
where project=[[Obsidian]] and status="done"


Summary

Obsidian is software that performs…

HTML

For future reference, the following HTML tags work:

<iframe>
<figure>
<figcaption>
<table>
<div>
<progress>


[[div]]

<div style="page-break-after: always;"></div>


[[iframe]]

<iframe id="igraph" scrolling="no" s... style of links uses wiki links which are problematic for ot... converts text files into different formats. I'm hoping to use it to convert Markdown files to:

• PDF
• Word doc
• HTML

Installation (WSL2)

1. Install Ubuntu packages.

    sudo apt install texlive-full pandoc
   

2. Create a conda environment.

    mamba create -n pandoc -y python=3.7 pandoc nodejs click
    conda activate pandoc
   

Links

The ObsidianObsidian
Obsidian

Tasks

Pending

table tags
from ""
where project=[[Obsidian]] and status!="done"


Completed

table tags
from ""
where project=[[Obsidian]] and status="done"


Summary

Obsidian is software that performs…

HTML

For future reference, the following HTML tags work:

<iframe>
<figure>
<figcaption>
<table>
<div>
<progress>


[[div]]

<div style="page-break-after: always;"></div>


[[iframe]]

<iframe id="igraph" scrolling="no" s... style of links uses wiki links which are problematic for other software. A crude way is to convert the links to plain text before publishing.

python3 convert_wikilinks.py -i pandoc-example.md -o pandoc-example-convert.md 
pandoc -s pandoc-example-convert.md -o pandoc-example.html

CrossRef

mamba install -c conda-forge pandoc-crossref

Citations

npm install -g pandoc-doi2bib

Using a bibliography as a relative path causes the error (node:1331) UnhandledPromiseRejectionWarning: TypeError [ERR_INVALID_ARG_TYPE]: The "path" argument must be of type string or an instance of Buffer or URL. Received undefined

Citation Style

Download a CSL style from https://www.zotero.org/styles. Ex. https://www.zotero.org/styles/apa-numeric-superscript-brackets

Convert

Markdown

PDF

• Default:

    pandoc pandoc-example.md -o pandoc-example_default.pdf
  

  !Pandoc Example Default.png

• Eisvogel Latex Template:

    pandoc pandoc-example.md -o pandoc-example_eisvogel.pdf --template templates/Eisvogel/eisvogel.latex 
  

  !Pandoc Example Style.png

• PLOS Pathogens LaTeX Template:

    pandoc pandoc-example.md -o pandoc-example_plos.pdf --template templates/PLOS/plos_latex_template.pdf 
  

• Can you use css with a pdf output? NOPE.

  pandoc \
      -s pandoc-example-convert.md \
      -c templates/github.css \
      -o pandoc-example_github.pdf
  

LaTeX

• Default latex template.

    pandoc -f markdown -t latex -o pandoc-example.tex pandoc-example.md
  

Word doc

• Default word template.

    pandoc  -s -o pandoc-example.docx pandoc-example.md 
  

The styling looks 'okay', but the aesthetics can be drastically improved with templates.

• Save the default template.

    pandoc --print-default-data-file default.docx > templates/default.docx
  

  Customize the formatting, for example, change the title to font size 50.

    bash
    pandoc --reference-doc templates/default.docx -o pandoc-example_custom.docx pandoc-example.md
  

• IEEE Template:

    pandoc pandoc-example.md --reference-docx=templates/IEEE-A4.docx -o pandoc-example_IEEE-A4.docx
  

• With Cross-Ref:

    pandoc mydoc.tex --filter pandoc-crossref --bibliography=myref.bib --reference-docx=IEEE_template.doc -o mydoc.docx
  

Beamer Slides

• Default beamer template

    pandoc -t beamer slides/2021-03-23_pandoc.md -o slides/2021-03-23_pandoc.pdf
  

reveal.js Slides

• Run the reveal.js server

    reveal-md path/to/my/slides.md
  

Standalone HTML

HTML with table of contents, CSS, and custom footer:

pandoc -s Chromosome\ Resequencing.md -o Chromosome\ Resequencing.html

• killercup css (looks great)

    pandoc \
      -s pandoc-example.md \
      -c templates/killercup.css \
      -o pandoc-example_killercup.html
  
    pandoc \
      -s 'Chromosome Resequencing Convert.md' \
      -c templates/killercup.css \
      -F mermaid-filter \
      -o 'Chromosome Resequencing killercup.html'
  
  

• MVP css:

    ./convert_wikilinks.py --input pandoc-example.md --output pandoc-example_convert.md;
    pandoc \
      -s pandoc-example_convert.md \
      -c templates/pandoc-mvp-css/css/mvp.css \
      --template templates/pandoc-mvp-css/template.html \
      --toc \
      --toc-depth=2 \
      -o pandoc-example_convert_mvp.html
  

• GitHub css from @dashed (looks super good!)

    pandoc \
      -s pandoc-example-convert.md \
      -c templates/github.css \
      -o pandoc-example_github.html
  	  
    pandoc \
      -s 'Chromosome Resequencing Convert.md' \
      -c templates/github.css \
      -F mermaid-filter \
      -o 'Chromosome Resequencing Github.html'