John MacFarlane
fd99fe4d7e
Linkification of URLs in the bibliography is now done in the citeproc library, depending on the setting of an option. We set that option depending on the value of the metadata field `link-bibliography` (defaulting to true, for consistency with earlier behavior, though the new behavior includes the CSL draft recommendation of hyperlinking the title or the whole entry if a DOI, PMID, PMCID, or URL field is present but not explicitly rendered). These changes implement the following recommendations from the draft CSL v1.0.2 spec (Appendix VI): > The CSL syntax does not have support for configuration of links. > However, processors should include links on bibliographic references, > using the following rules: > If the bibliography entry for an item renders any of the following > identifiers, the identifier should be anchored as a link, with the > target of the link as follows: > - url: output as is > - doi: prepend with "`https://doi.org/`" > - pmid: prepend with "`https://www.ncbi.nlm.nih.gov/pubmed/`" > - pmcid: prepend with "`https://www.ncbi.nlm.nih.gov/pmc/articles/`" > If the identifier is rendered as a URI, include rendered URI components > (e.g. "`https://doi.org/`") in the link anchor. Do not include any other > affix text in the link anchor (e.g. "Available from: ", "doi: ", "PMID: "). > If the bibliography entry for an item does not render any of > the above identifiers, then set the anchor of the link as the item > title. If title is not rendered, then set the anchor of the link as the > full bibliography entry for the item. Set the target of the link as one > of the following, in order of priority: > > - doi: prepend with "`https://doi.org/`" > - pmcid: prepend with "`https://www.ncbi.nlm.nih.gov/pmc/articles/`" > - pmid: prepend with "`https://www.ncbi.nlm.nih.gov/pubmed/`" > - url: output as is > > If the item data does not include any of the above identifiers, do not > include a link. > > Citation processors should include an option flag for calling > applications to disable bibliography linking behavior. Thanks to Benjamin Bray for getting this all working.
Pandoc
The universal markup converter
Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library. It can convert from
bibtex(BibTeX bibliography)biblatex(BibLaTeX bibliography)commonmark(CommonMark Markdown)commonmark_x(CommonMark Markdown with extensions)creole(Creole 1.0)csljson(CSL JSON bibliography)csv(CSV table)docbook(DocBook)docx(Word docx)dokuwiki(DokuWiki markup)epub(EPUB)fb2(FictionBook2 e-book)gfm(GitHub-Flavored Markdown), or the deprecated and less accuratemarkdown_github; usemarkdown_githubonly if you need extensions not supported ingfm.haddock(Haddock markup)html(HTML)ipynb(Jupyter notebook)jats(JATS XML)jira(Jira/Confluence wiki markup)json(JSON version of native AST)latex(LaTeX)markdown(Pandoc’s Markdown)markdown_mmd(MultiMarkdown)markdown_phpextra(PHP Markdown Extra)markdown_strict(original unextended Markdown)mediawiki(MediaWiki markup)man(roff man)muse(Muse)native(native Haskell)odt(ODT)opml(OPML)org(Emacs Org mode)rst(reStructuredText)t2t(txt2tags)textile(Textile)tikiwiki(TikiWiki markup)twiki(TWiki markup)vimwiki(Vimwiki)
It can convert to
asciidoc(AsciiDoc) orasciidoctor(AsciiDoctor)beamer(LaTeX beamer slide show)bibtex(BibTeX bibliography)biblatex(BibLaTeX bibliography)commonmark(CommonMark Markdown)commonmark_x(CommonMark Markdown with extensions)context(ConTeXt)csljson(CSL JSON bibliography)docbookordocbook4(DocBook 4)docbook5(DocBook 5)docx(Word docx)dokuwiki(DokuWiki markup)epuborepub3(EPUB v3 book)epub2(EPUB v2)fb2(FictionBook2 e-book)gfm(GitHub-Flavored Markdown), or the deprecated and less accuratemarkdown_github; usemarkdown_githubonly if you need extensions not supported ingfm.haddock(Haddock markup)htmlorhtml5(HTML, i.e. HTML5/XHTML polyglot markup)html4(XHTML 1.0 Transitional)icml(InDesign ICML)ipynb(Jupyter notebook)jats_archiving(JATS XML, Archiving and Interchange Tag Set)jats_articleauthoring(JATS XML, Article Authoring Tag Set)jats_publishing(JATS XML, Journal Publishing Tag Set)jats(alias forjats_archiving)jira(Jira/Confluence wiki markup)json(JSON version of native AST)latex(LaTeX)man(roff man)markdown(Pandoc’s Markdown)markdown_mmd(MultiMarkdown)markdown_phpextra(PHP Markdown Extra)markdown_strict(original unextended Markdown)mediawiki(MediaWiki markup)ms(roff ms)muse(Muse),native(native Haskell),odt(OpenOffice text document)opml(OPML)opendocument(OpenDocument)org(Emacs Org mode)pdf(PDF)plain(plain text),pptx(PowerPoint slide show)rst(reStructuredText)rtf(Rich Text Format)texinfo(GNU Texinfo)textile(Textile)slideous(Slideous HTML and JavaScript slide show)slidy(Slidy HTML and JavaScript slide show)dzslides(DZSlides HTML5 + JavaScript slide show),revealjs(reveal.js HTML5 + JavaScript slide show)s5(S5 HTML and JavaScript slide show)tei(TEI Simple)xwiki(XWiki markup)zimwiki(ZimWiki markup)- the path of a custom Lua writer, see Custom writers below
Pandoc can also produce PDF output via LaTeX, Groff ms, or HTML.
Pandoc’s enhanced version of Markdown includes syntax for tables, definition lists, metadata blocks, footnotes, citations, math, and much more. See the User’s Manual below under Pandoc’s Markdown.
Pandoc has a modular design: it consists of a set of readers, which parse text in a given format and produce a native representation of the document (an abstract syntax tree or AST), and a set of writers, which convert this native representation into a target format. Thus, adding an input or output format requires only adding a reader or writer. Users can also run custom pandoc filters to modify the intermediate AST (see the documentation for filters and Lua filters).
Because pandoc’s intermediate representation of a document is less expressive than many of the formats it converts between, one should not expect perfect conversions between every format and every other. Pandoc attempts to preserve the structural elements of a document, but not formatting details such as margin size. And some document elements, such as complex tables, may not fit into pandoc’s simple document model. While conversions from pandoc’s Markdown to all formats aspire to be perfect, conversions from formats more expressive than pandoc’s Markdown can be expected to be lossy.
Installing
Here’s how to install pandoc.
Documentation
Pandoc’s website contains a full User’s Guide. It is also available here as pandoc-flavored Markdown. The website also contains some examples of the use of pandoc and a limited online demo.
Contributing
Pull requests, bug reports, and feature requests are welcome. Please make sure to read the contributor guidelines before opening a new issue.
License
© 2006-2021 John MacFarlane (jgm@berkeley.edu). Released under the GPL, version 2 or greater. This software carries no warranty of any kind. (See COPYRIGHT for full copyright and warranty notices.)