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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.
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This deprecates the use of the external pandoc-citeproc
filter; citation processing is now built in to pandoc.
* Add dependency on citeproc library.
* Add Text.Pandoc.Citeproc module (and some associated unexported
modules under Text.Pandoc.Citeproc). Exports `processCitations`.
[API change]
* Add data files needed for Text.Pandoc.Citeproc: default.csl
in the data directory, and a citeproc directory that is just
used at compile-time. Note that we've added file-embed as a mandatory
rather than a conditional depedency, because of the biblatex
localization files. We might eventually want to use readDataFile
for this, but it would take some code reorganization.
* Text.Pandoc.Loging: Add `CiteprocWarning` to `LogMessage` and use it
in `processCitations`. [API change]
* Add tests from the pandoc-citeproc package as command tests (including
some tests pandoc-citeproc did not pass).
* Remove instructions for building pandoc-citeproc from CI and
release binary build instructions. We will no longer distribute
pandoc-citeproc.
* Markdown reader: tweak abbreviation support. Don't insert a
nonbreaking space after a potential abbreviation if it comes right before
a note or citation. This messes up several things, including citeproc's
moving of note citations.
* Add `csljson` as and input and output format. This allows pandoc
to convert between `csljson` and other bibliography formats,
and to generate formatted versions of CSL JSON bibliographies.
* Add module Text.Pandoc.Writers.CslJson, exporting `writeCslJson`. [API
change]
* Add module Text.Pandoc.Readers.CslJson, exporting `readCslJson`. [API
change]
* Added `bibtex`, `biblatex` as input formats. This allows pandoc
to convert between BibLaTeX and BibTeX and other bibliography formats,
and to generated formatted versions of BibTeX/BibLaTeX bibliographies.
* Add module Text.Pandoc.Readers.BibTeX, exporting `readBibTeX` and
`readBibLaTeX`. [API change]
* Make "standalone" implicit if output format is a bibliography format.
This is needed because pandoc readers for bibliography formats put
the bibliographic information in the `references` field of metadata;
and unless standalone is specified, metadata gets ignored.
(TODO: This needs improvement. We should trigger standalone for the
reader when the input format is bibliographic, and for the writer
when the output format is markdown.)
* Carry over `citationNoteNum` to `citationNoteNumber`. This was just
ignored in pandoc-citeproc.
* Text.Pandoc.Filter: Add `CiteprocFilter` constructor to Filter.
[API change] This runs the processCitations transformation.
We need to treat it like a filter so it can be placed
in the sequence of filter runs (after some, before others).
In FromYAML, this is parsed from `citeproc` or `{type: citeproc}`,
so this special filter may be specified either way in a defaults file
(or by `citeproc: true`, though this gives no control of positioning
relative to other filters). TODO: we need to add something to the
manual section on defaults files for this.
* Add deprecation warning if `upandoc-citeproc` filter is used.
* Add `--citeproc/-C` option to trigger citation processing.
This behaves like a filter and will be positioned
relative to filters as they appear on the command line.
* Rewrote the manual on citatations, adding a dedicated Citations
section which also includes some information formerly found in
the pandoc-citeproc man page.
* Look for CSL styles in the `csl` subdirectory of the pandoc user data
directory. This changes the old pandoc-citeproc behavior, which looked
in `~/.csl`. Users can simply symlink `~/.csl` to the `csl`
subdirectory of their pandoc user data directory if they want
the old behavior.
* Add support for CSL bibliography entry formatting to LaTeX, HTML,
Ms writers. Added CSL-related CSS to styles.html.
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