pandoc-crossref

pandoc-crossref is a pandoc filter for numbering figures, equations, tables and cross-references to them.

Bug tracker: https://github.com/lierdakil/pandoc-crossref/issues

Caveats

LaTeX input (a.k.a. converting LaTeX to docx/epub/etc)

The principal aim of pandoc-crossref is to add references to Markdown.

Other input formats may happen to work also (basically if you can make Pandoc citation syntax to work), but that’s more of a happy coincidence than a deliberate design decision.

In particular, LaTeX syntax is generally not recognized, although under some specific conditions it may seem to kinda-sorta work.

Converting TeX to anything editable in general is nigh impossible, with TeX being a Turing-complete layout language rather than a markup language. That was one of the motivations for pandoc-crossref in the first place.

All that said, if you really need to use LaTeX as an input format, see the discussions in https://github.com/lierdakil/pandoc-crossref/issues/250.

For best results, consider using a purpose-built filter instead of pandoc-crossref. For example, pandoc-text-numbering.

LaTeX output and --include-in-header

pandoc-crossref uses metadata variable header-includes to add LaTeX definitions to output. However, Pandoc’s command line option --include-in-header/-H overrides this variable. If you need to use --include-in-header, add pandoc-crossref-specific definitions as well. See LaTeX customization for more information.

Note on non-standard LaTeX templates

If you’re using non-standard pandoc LaTeX template (this includes the cases where document class is not article or book close enough to that), pandoc-crossref might not be able to configure that properly. You might to configure LaTeX in the template manually.

Note on LaTeX and chapters option

Because pandoc-crossref offloads all numbering to LaTeX if it can, chapters: true has no direct effect on LaTeX output. You have to specify Pandoc’s --top-level-division=chapter option, which should hopefully configure LaTeX appropriately.

It’s a good idea to specify --top-level-division=chapter for any output format actually, because pandoc-crossref can’t signal pandoc you want to use chapters, and vice versa.

citeproc and pandoc-crossref

Since pandoc-crossref uses the same citation syntax as citeproc, you have to run former before latter. For example:

pandoc -F pandoc-crossref --citeproc file.md -o file.html

Note on leading/trailing spaces in metadata options

Leading and trailing spaces in YAML metadata will most likely be stripped by either YAML parser or Pandoc itself. If you need leading and/or trailing spaces in pandoc-crossref metadata variables, use html entity for space instead, i.e.  . For example, if you want reference ranges to be delimited by a dash with spaces (e.g. 2 - 5), include the following in YAML metadata:

rangeDelim: ' - '

or pass -MrangeDelim=' - ' to pandoc on command line.

You can use other html entites of course, like   etc.

Syntax

Syntax is loosely based on discussion in https://github.com/jgm/pandoc/issues/813

Image labels

![Caption](file.ext){#fig:label}

To label an (implicit) figure, append {#fig:label} (with label being something unique to reference this figure by) immediately after image definition.

This only works on implicit figures, i.e. an image occurring by itself in a paragraph (which will be rendered as a figure with caption by pandoc)

Image block and label can not be separated by spaces.

Subfigures

It’s possible to group figures as subfigures. Basic syntax is as follows:

<div id="fig:figureRef">
![subfigure 1 caption](image1.png){#fig:figureRefA}

![subfigure 2 caption](image2.png){#fig:figureRefB}

Caption of figure
</div>

To sum up, subfigures are made with a div having a figure id. Contents of said div consist of several paragraphs. All but last paragraphs contain one subfigure each, with captions, images and (optionally) reference attributes. Last paragraph contains figure caption.

If you put more than one figure in the paragraph, those will still be rendered, but Pandoc will omit subfigure caption in most outputs (but it will work as expected with LaTeX). You can use output-specific hacks to work around that, or use subfigGrid (see below).

Output is customizable, with metadata fields. See Customization for more information.

Default settings will produce the following equivalent Markdown from example above:

<div id="fig:figureRef" class="subfigures">

![a](image1.png){#fig:figureRefA}

![b](image2.png){#fig:figureRefB}

Figure 1: Caption of figure. a — subfigure 1 caption, b — subfigure 2
caption

</div>

References to subfigures will be rendered as figureNumber (subfigureNumber), e.g., in this particular example, [@fig:figureRefA] will produce fig. 1 (a).

You can add nocaption class to an image to suppress subfigure caption altogether. Note that it will still be counted.

Subfigure grid

If you need to align subfigures in a grid, and using output format styles is not an option, you can use subfigGrid option. That will typeset subfigures inside a table.

Rows are formed by different paragraphs, with each image in a separate column.

Column widths will be taken from width attributes of corresponding images, e.g.

<div id="fig:coolFig">
![caption a](coolfiga.png){#fig:cfa width=30%}
![caption b](coolfigb.png){#fig:cfb width=60%}
![caption c](coolfigb.png){#fig:cfc width=10%}

![caption d](coolfigd.png){#fig:cfd}
![caption e](coolfige.png){#fig:cfe}
![caption f](coolfigf.png){#fig:cff}

Cool figure!
</div>

will produce a table with columns of 30%, 60% and 10% respectively.

Only first row of images is considered for table width computation, other rows are completely ignored.

Anything except images is silently ignored. So any text, spaces, soft line breaks etc will silently disappear from output. That doesn’t apply to caption paragraph, obviously.

All images will have width attribute automatically set to 100% in order to fill whole column.

Specifying width in anything but % will throw an error.

If width for some images in first row is not specified, those will span equally in the remaining space.

If width isn’t specified for any image in first row, those will span equally on 99% of page width (due to Pandoc otherwise omitting width attribute for table).

This option is ignored with LaTeX output, but paragraph breaks should produce similar effect, so images should be typeset correctly. TL;DR you don’t need subfigGrid enabled for it to work with LaTeX, but you can still enable it.

Equation labels

$$ math $$ {#eq:label}

To label a display equation, append {#eq:label} (with label being something unique to reference this equation by) immediately after math block.

Math block and label can be separated by one or more spaces.

You can also number all display equations with autoEqnLabels metadata setting (see below). Note, however, that you won’t be able to reference equations without explicit labels.

Equations numbers will be typeset inside math with \qquad before them. If you want to use tables instead, use tableEqns option. Depending on output format, tables might work better or worse than \qquad.

Alternatively, for formats that support it, you can use arbitrary LaTeX command accepting a single argument (that is, label text) for typesetting. A common example is \tag. Use equationNumberTeX metadata variable for that (set to \qquad by default).

Beware that eqnIndexTemplate gets applied first, so you’ll likely want to set it to plain index as well.

For instance, to use \tag, you would have the following in your metadata:

equationNumberTeX: \\tag
eqnIndexTemplate: $$i$$

These options don’t affect LaTeX output (which offloads numbering to the LaTeX engine).

For advanced usage, see eqnInlineTemplate, eqnBlockTemplate.

Table labels

a   b   c
--- --- ---
1   2   3
4   5   6

: Caption {#tbl:label}

To label a table, append {#tbl:label} at the end of table caption (with label being something unique to reference this table by). Caption and label must be separated by at least one space.

Section labels

You can also reference sections of any level. Section labels use native pandoc syntax, but must start with “sec:”, e.g.

 Section {#sec:section}

You can also use autoSectionLabels variable to automatically prepend all section labels (automatically generated with pandoc included) with “sec:”. Bear in mind that references can’t contain periods, commas etc, so some auto-generated labels will still be unusable.

WARNING: With LaTeX output, you have to invoke pandoc with --number-sections, otherwise section labels won’t work. It’s also advised with other output formats, since with no numbers in section titles, it would be hard to navigate anyway.

Section numbering

Pandoc doesn’t properly support numbering sections in some output formats, and section reference labels (see below).

You can let pandoc-crossref handle section numbering instead. This is done via numberSections and sectionsDepth metadata options.

numberSections controls if pandoc-crossref handles numbering sections, while sectionsDepth controls what sections are numbered.

Additionally, with numberSections, if the first heading in your document is level 2 or more, pandoc-crossref will assume you meant to have implicit headings with previous levels, and will assign those phantom implicit headings the index 1. Without numberSections, the behaviour is consistent with pandoc, that is, missing headings will be assigned the index 0.

Set sectionsDepth to 0 to make section numbering consistent with chaptersDepth.

If sectionsDepth value is lesser than 0, all sections will be numbered.

Otherwise, only header levels up to and including sectionsDepth will be numbered.

You can also supply a custom section header template via secHeaderTemplate metadata option. The following variables are supported:

See section on templates for more information

Reference labels

Not currently supported with LaTeX output

If you want to reference some object by a pre-defined label instead of by number, you can specify attribute label, like this:

# Section {label="Custom Label"}

![Figure](fig.png){fig:fig1 label="Custom label"}

Note that to use this with equations and tables, you need to use fenced div/span syntax, not the short syntax:


:::{#tbl:table label="T"}
a   b   c
--- --- ---
1   2   3
4   5   6

: Caption
:::

[$$y = e^x$$]{#eq:equation label="E"}

This label will be used instead of a number in chapters output for sections and when referencing the element directly.

Note that with chapters output with depth>1, only the given section will be referenced by the custom label, e.g. with

 Chapter 1.

# Section with custom label {#sec:scl label="SCL"}

![](figure.png){#fig:figure}

@sec:scl will translate into sec. 1.SCL, and @fig:figure into fig. 1.SCL.1

Manual numbering adjustment

Not currently supported with LaTeX output

For cases when you need to manually adjust numbering, you can specify the number attribute on the object. It will set the internal object counter for the annotated object to the number specified, and all the following objects of this type will count from that. Conceptually, this is similar to document processors’ “start from…” etc.

Same as with label attributes, to use this with equations and tables, you need to use fenced div/span syntax, not the short syntax.

Code Block labels

There are a couple options to add code block labels. Those work only if code block id starts with lst:, e.g. {#lst:label}

caption attribute

caption attribute will be treated as code block caption. If code block has both id and caption attributes, it will be treated as numbered code block.

```{#lst:code .haskell caption="Listing caption"}
main :: IO ()
main = putStrLn "Hello World!"
```

Table-style captions

Enabled with codeBlockCaptions metadata option. If code block is immediately adjacent to paragraph, starting with Listing: or :, said paragraph will be treated as code block caption.

Listing: Listing caption

```{#lst:code .haskell}
main :: IO ()
main = putStrLn "Hello World!"
```

or

```{#lst:code .haskell}
main :: IO ()
main = putStrLn "Hello World!"
```

: Listing caption

It also allows to specify label in caption, as do tables, for example:

```haskell
main :: IO ()
main = putStrLn "Hello World!"
```

: Listing caption {#lst:code}

Wrapping div

Wrapping code block without label in a div with id lst:... and class, starting with listing, and adding paragraph before code block, but inside div, will treat said paragraph as code block caption.

<div id="lst:code" class="listing">
Listing caption
```{.haskell}
main :: IO ()
main = putStrLn "Hello World!"
```
</div>

Any additional attributes and classes on the wrapping div will be merged with classes/attributes on the listing itself. In case of duplicate attributes, the behaviour is unspecified, but likely either both values will end up in the output, or div attributes will take precedence. This is important to keep in mind if you need to do some additional post-processing.

References

[@fig:label1;@fig:label2;...] or [@eq:label1;@eq:label2;...] or [@tbl:label1;@tbl:label2;...] or @fig:label or @eq:label or @tbl:label

Reference syntax heavily relies on citation syntax. Basic reference is created by writing @, then basically desired label with prefix. It is also possible to reference a group of objects, by putting them into brackets with ; as separator. Similar objects will be grouped in order of them appearing in citation brackets, and sequential reference numbers will be shortened, e.g. 1,2,3 will be shortened to 1-3.

You can capitalize first reference character to get capitalized prefix, e.g. [@Fig:label1] will produce Fig. ... by default. Capitalized prefixes are derived automatically by capitalizing first letter of every word in non-capitalized prefix, unless overridden with metadata settings. See Customization for more information.

Linking references

To make references into hyperlinks to referenced element, enable linkReferences metadata option. This has no effect on LaTeX output, since in this case, hyperlinking references is handled with hyperref LaTeX package.

Custom prefix per-reference

It’s possible to provide your own prefix per-reference, f.ex. [Prefix @reference] will replace default prefix (fig./sec./etc) with prefix verbatim, e.g. [Prefix @fig:1] will be rendered as Prefix 1 instead of fig. 1.

In citation group, citations with the same prefix will be grouped. So, for example [A @fig:1; A @fig:2; B @fig:3] will turn into A 1, 2, B 3. It can be used to an advantage, although it’s a bit more cumbersome than it should be, e.g. [Appendices @sec:A1; Appendices @sec:A2; Appendices @sec:A3] will turn into Appendices @A1-@A3 (with @A1 and @A3 being relevant section numbers). Note that non-contiguous sequences of identical prefixes will not be grouped.

Not supported with cleveref LaTeX output.

Prefix suppression

Prepending - before @, like so [-@citation], will suppress default prefix, e.g. [-@fig:1] will produce just 1 (or whatever number it happens to be) without fig. prefix.

In citation group, citations with and without prefixes will be in different groups. So [-@fig:1; @fig:2; -@fig:3] will be rendered as 1, fig. 2, 3, so be careful with this feature. Again, non-contiguous sequences are not grouped together.

Lists

It’s possible to use raw latex commands \listoffigures, \listoftables and \listoflistings, which will produce ordered list of figure/table/listings titles, in order of appearance in document.

For LaTeX output, \listoflistings depends on other options, and is defined in preamble, so it will work reliably only with standalone/pdf output.

NOTE: With Pandoc 2.0.6 and up, you might have to explicitly separate these commands if they are close together, at least when targeting something besides LaTeX. So this might not work:

\listoffigures

\listoftables

\listoflistings

but this will:

\listoffigures

<!-- hack to split raw blocks -->

\listoftables

<!-- hack to split raw blocks -->

\listoflistings

With HTML-compatible output, lists are wrapped into a div with classes list and list-of-<prefix>, where <prefix> is either fig, tbl or lst depending on the type of the list. This allows for ad-hoc style overrides in HTML.

Usage

Run pandoc with --filter option, passing path to pandoc-crossref executable, or simply pandoc-crossref, if it’s in PATH:

pandoc --filter pandoc-crossref

If you installed with cabal, it’s most likely located in $HOME/.cabal/bin on *NIX systems, $HOME/Library/Haskell/bin on Macs, or in %AppData%\cabal\bin on Windows.

Customization

There are several parameters that can be set via YAML metadata (either by passing -M to pandoc, or by setting it in source markdown)

A list of variables follows.

General options

Item title format

Subfigure-specific

See Subfigures

List titles

List items

See also List item templates

Reference format

Note that none of the *Delim options are honored with cleveref output. Use cleveref’s customization options instead.

figPrefix, eqnPrefix, tblPrefix, lstPrefix can be YAML arrays. That way, value at index corresponds to total number of references in group, f.ex.

figPrefix:
  - "fig."
  - "figs."

Will result in all single-value references prefixed with “fig.”, and all reference groups of two and more will be prefixed with “figs.”:

[@fig:one] -> fig. 1
[@fig:one; @fig:two] -> figs. 1, 2
[@fig:one; @fig:two; @fig:three] -> figs. 1-3

They can be YAML strings as well. In that case, prefix would be the same regardless of number of references.

They can also be used with first character capitalized, i.e. FigPrefix, etc. In this case, these settings will override default reference capitailzation settings.

Custom numbering

See Custom Numbering Schemes

Item title templates

See Templates

Subfigure templates

See Subfigures

Equation templates

Reference templates

See Templates

List item templates

See Templates

Special handling is enabled for templates that are either ordered or bullet lists: items will be merged into a single list. Thus, for example, given

lofItemTemplate: |
  1. $$t$$

the list of figures will be formatted as

# List of Figures

::: {.list .list-of-fig}
1.  Figure 1 caption
2.  Figure 2 caption
3.  Figure 3 caption
4.  ...
:::

LaTeX customization

Support for above variables with LaTeX/PDF output is limited. In particular, the following variables are honored:

Templates are not supported.

You can add arbitrary LaTeX commands to document header, however, using header-includes metadata field. Please bear in mind, that pandoc-crossref up to and including 0.1.2.1 requires header-includes to be YAML array, e.g.

header-includes:
    - "\\newcommand{\\pcdoc}{Pandoc-crossref documentation}"

This will be added before any customization applied by pandoc-crossref. For a complete list of what is added to template, consult ModifyMeta.hs.

Templates

pandoc-crossref supports advanced caption customization via caption templates. Templates are specified as YAML metadata variables (see Customization), and are parsed as default Pandoc Markdown. Variables are specified with display math syntax, i.e. $$var$$ in a template will be replaced with value of variable var. Variables can be specified in YAML metadata block, or from command line (with -M switch). There are two special variables, that are set internally:

Also there is a number of specific variables that are meaningful only in certain contexts:

xPrefixTemplate, where x is fig, eqn, etc, are a special case. Those don’t have t variable, since there is no caption in source markdown, but instead have p variable, that binds to relevant xPrefix. This is done this way, since actual prefix value can depend on i. In xPrefixTemplate, i references formatted object numbers, i.e. if given a list of references like [@fig:1; @fig:2; @fig:3], here i will contain something like 1-3.

refIndexTemplate is the template for the individual reference index. It can be either a plain template, or can be a YAML object with keys corresponding to different prefixes, and a special key default used as a fallback, e.g.

refIndexTemplate:
  sec: $$i$$$$suf$$ ($$t$$)
  default: $$i$$$$suf$$

refIndexTemplate has the following internal variables defined:

subfigureRefIndexTemplate is roughly the same as refIndexTemplate but is used specifically for subfigures. It additionally has s variable defined, which is described above.

Additionally, a special syntax is provided for indexed access to array metadata variables: arrayVariable[indexVariable], where arrayVariable is an array-like metadata variable, and indexVariable is an integer-typed template variable. If indexVariable is larger than length of arrayVariable, then the last element in arrayVariable is used.

Indexed access can be useful with secHeaderTemplate for example, where you might want to add a custom prefix depending on the header level.

For example, with this YAML metadata:

secHeaderTemplate: $$secHeaderPrefix[n]$$$$i$$. $$t$$
secHeaderPrefix:
  - "Chapter&#32;"
  - "Section&#32;"
  - ""
sectionsDepth: -1
numberSections: true

top-level sections will be prefixed with Chapter , second-level sections will be prefixed with Section and the rest won’t be prefixed with anything.

Please note that at the moment, templates are not supported with LaTeX/PDF output.

Custom Numbering Schemes

It’s possible to use other numbering schemes apart from arabic. This is controlled by several metadata options, consult Customization for a list. Possible values are:

Settings file

It is also possible to set variables used by pandoc-crossref with a separate YAML file. If a given variable is not set in metadata, then pandoc-crossref will attempt to read it from file specified by crossrefYaml metadata variable, or, if not set, from pandoc-crossref.yaml from current working directory. This allows for reusable configurations. One possible application is ad-hoc internationalization.

For example, consider $HOME/misc/pandoc-crossref-es.yaml:

figureTitle: "Figura"
tableTitle: "Tabla"
figPrefix: "fig."
eqnPrefix: "ec."
tblPrefix: "tbl."
loftitle: "# Lista de figuras"
lotTitle: "# Lista de tablas"

pandoc-crossref will send this data to pandoc wrapped in lines of ---. The YAML file’s first line should specify a variable; it will not pass the variables if it is --- or a blank line.

One could use this with pandoc-crossref as follows:

pandoc -F pandoc-crossref.hs -M "crossrefYaml=$HOME/misc/pandoc-crossref-es.yaml"

You can also use global configuration files, which are expected in $HOME/.pandoc-crossref/config.yaml and $HOME/.pandoc-crossref/config-$FORMAT.yaml, where $FORMAT is output format, f.ex. latex or epub. On Windows, $HOME in general resolves to user’s root directory, e.g. C:\Users\username\.

Priorities are as follows (from highest to lowest):

License

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program includes code from roman-numerals library, covered by the following terms:

Copyright 2009–2014 Roel van Dijk

All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright
  notice, this list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above
  copyright notice, this list of conditions and the following
  disclaimer in the documentation and/or other materials provided
  with the distribution.

* The names of contributors may not be used to endorse or promote
  products derived from this software without specific prior
  written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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