Bibtex citations does not work

[a-cellofan]

Hi,

I have tried to get citations work with pandown in ST2 but it does not work. I have a configuration file: pandoc-config.json int the same directory than the source file:
{
"pandoc_arguments":
{
//////////////////////////////////////////////////////////////////////
// Arguments are explained in Pandoc's documentation: //
// http://johnmacfarlane.net/pandoc/README.html . //
// The contents of this file will be merged with the package's //
// Pandown.sublime-settings file, the user's Pandown.sublime-settings/
// file, and local project settings, with what's specified here //
// taking precedence. For more information about how to use this //
// file, please see the Pandown README. //
//////////////////////////////////////////////////////////////////////
"markdown_extensions":
{
/////////////////////////
// MARKDOWN EXTENSIONS //
/////////////////////////
// A backslash followed by a newline is also a line break.
"escaped_line_breaks": true,

        // Require a blank line before a header.
        "blank_before_header": true,

        // Headers can be assigned attributes using this syntax at the end of
        // the line containing the header text:
        // {#identifier .class .class key=value key=value}
        "header_attributes": true,

        // A header without specified attributes will automatically be assigned
        // a unique identifier based on the header text.
        "auto_identifiers": true,

        // Pandoc assumes header references have been defined for each header.
        "implicit_header_references": true,

        // Require a blank line before block quotes. In nested blockquotes,
        // require:
        // > Quotation
        // >
        // > > Quotation within quotation.
        "blank_before_blockquote": true,

        // Fence code blocks off with tildes or backticks.
        "fenced_code_blocks": true,

        // Start lines with pipe characters to and the division into lines and
        // leading whitespace will be preserved. Useful for setting verse and
        // addresses.
        "line_blocks": true,

        // Pandoc allows fancier numbering using uppercase letters, lowercase
        // letters and Roman numerals. List markers may be enclosed in parentheses
        // or followed by a single right-parenthesis or period, then two spaces.
        "fancy_lists": true,

        // Pandoc will pay attention to the starting number for each list.
        "startnum": true,

        // Pandoc supports definition lists; see documentation here for the
        // correct syntax: http://johnmacfarlane.net/pandoc/README.html#definition-lists
        "definition_lists": true,

        // The list marker (@) can be used to sequentially number examples in
        // a way that persists throughout the document.
        "example_lists": true,

        // Pandoc supports four kinds of tables, the syntax for which is given at:
        // http://johnmacfarlane.net/pandoc/README.html#tables.
        "simple_tables": true,
        "multiline_tables": true,
        "grid_tables": true,
        "pipe_tables": true,

        // A table caption is a paragraph beginning with the string "Table:" or a
        // colon alone. It may be placed at the beginning or end of a table.
        "table_captions": true,

        // Pandoc allows the inclusion of a title block that will not appear in
        // the body of the document:
        // % Title
        // % Author(s) (separated by semicolons)
        // % Date
        "pandoc_title_block": true,

        // A backslash may be used to escape any Markdown symbol.
        "all_symbols_escapable": true,

        // Using underscores within a word for emphasis is disabled by
        // default. Use * instead.
        "intraword_underscores": false,

        // To strike letters in your text, surround them with ~~two tildes~~.
        "strikeout": true,

        // Superscripts may be written by surrounding text with ^ characters,
        // subscripts by surrounding text with ~ characters. Escape spaces within
        // scripts using \ .
        "superscript": true,
        "subscript": true,

        // Add attribtues, including syntax highlighting, to inline code.
        "inline_code_attributes": true,

        // Text between two $ characters will be rendered as LaTeX math.
        "tex_math_dollars": true,

        // The default behavior in Markdown allows you to insert raw HTML
        // anywhere in a document.
        "raw_html": true,

        // By default, Pandoc interprets Markdown in blocks of HTML as Markdown.
        // This deviates from Markdown.pl's default behavior.
        "markdown_in_html_blocks": true,

        // Pandoc allows raw TeX to be passed in addition to raw HTML.
        "raw_tex": true,

        // If set to `true`, Pandoc will use \newcommand and \renewcommand
        // definitions in all LaTeX math blocks.
        "latex_macros": true,

        // An image occurring by itself in a paragraph will be rendered as a
        // figure with a caption: ![This is the caption](path/to/image.jpg)
        "implicit_figures": true,

        // Pandoc will parse footnotes in the syntax listed here:
        // http://johnmacfarlane.net/pandoc/README.html#footnotes
        "footnotes": true,
        "inline_notes": true,

        // Use the syntax given here for citations:
        // http://johnmacfarlane.net/pandoc/README.html#citations
        "citations": true,

        // All newlines within a paragraph will be interpreted as linebreaks
        // rather than spaces.
        "hard_line_breaks": false,

        // Anything between \( and \) will be interpreted as TeX inline math,
        // and anything between \[ and \] as TeX display math.
        "tex_math_single_backslash": false,

        // Same as above, but escaped with two backslashes.
        "tex_math_double_backslash": false,

        // Markdown is only parsed within block-level tags if `markdown=1` is
        // set in their attributes.
        "markdown_attribute": false,

        // Enables a MultiMarkdown-style title block:
        // Title:    My Title
        // Author:   Arthur Author
        // Date:     January 1, 2013
        // Comment:  This is a mmd title block, and it even includes
        //           a field spanning multiple lines.
        "mmd_title_block": false,

        // Skip PHP Markdown Extra abbreviation keys instead of parsing them
        // as paragraphs if set to `true`.
        "abbreviations": false,

        // Makes all absolute URLs into links, even when not enclosed in <...>.
        "autolink_bare_uris": false,

        // Parse (but ignore, at the moment) MMD-style key--value attribtues
        // in image and link references.
        "link_attributes": false,

        // Parses MMD-style header identifiers (in square brackets between header
        // text and closing ATX #s.
        "mmd_header_identifiers": false
    },




    "command_arguments":
    {
        ////////////////////////////
        // COMMAND-LINE ARGUMENTS //
        ////////////////////////////
        // Modify this setting to tell Pandoc to look for any of the following
        // in the specified directory rather than ~/.pandoc or Pandoc's default
        // directory tree. Note that this is not an all-purpose includes
        // directory---Pandoc will only look for these files and folders.
        //      data_dir/
        //          reference.odt
        //          reference.docx
        //          default.csl
        //          epub.css
        //          slidy/
        //          slideous/
        //          s5/
        //          templates/
        // Anything placed under templates and will be found by the "template"
        // setting; otherwise, to set an include directory, use the "includes_paths"
        // option above.
        "data-dir": "",

        // "Parse untranslatable HTML codes and LaTeX environments as
        // raw HTML or LaTeX, instead of ignoring them."
        "parse-raw": true,

        // Straight quotes into curly quotes, --- to em-dash, -- to en-dash,
        // ... to ellipsis, nonbreaking spaces after certain abbreviations.
        "smart": true,

        // - before a numeral to en-dash, -- to em-dash
        "old-dashes": false,

        // "Speficy the base level for headers"
        // Specify a number or "false" to disable.
        "base-header-level": false,

        // Apply code classes to all indented code blocks. N.B.:
        // does not apply to fenced code, which must still be
        // configured inline.
        // MUST BE DEFINED AS A LIST, EVEN IF EMPTY. This is correct:
        //      "indented-code-classes": [],
        // and so is this:
        //      "indented-code-classes": [ "numberLines" ],
        // but this is not:
        //      "indented-code-classes": "numberLines"
        "indented-code-classes":
        [
        ],

        // When image paths or URLs have no extension, this one
        // will be used.
        "default-image-extension": "",

        // Merge adjacent elements, remove repeated spaces, etc.
        "normalize": true,

        // Set the number of spaces per tab. Should be set to
        // "false" (for default behavior) or a number.
        "tab-stop": false,

        // Generate "an appropriate header and footer"
        "standalone": true,

        // Use a template file other than the default to
        // generate output. Pandoc will look for a template in the
        // working directory, then data_dir/templates/, then its
        // built-in directory tree.
        // See Pandoc's README for information about templates:
        // http://johnmacfarlane.net/pandoc/README.html#templates
        "template": "",

        // Supply a dict of keys and values to be passed to
        // the template file. Values may be lists
        // if your template includes loops; see this plugin's README.
        "variables":
        {
        },

        // By default, text is wrapped for the output format.
        "no-wrap": false,

        // If wrapping text, wrap to "columns" columns.
        // Specify a number or "false" to disable.
        "columns": false,

        // Generate and include a table of contents.
        "table-of-contents": false,

        // The number of section levels to include in the table of contents.
        // Specify a number or "false" for default (3).
        "toc-depth": false,

        // Disable syntax highlighting globally.
        "no-highlight": false,

        // Style to use for syntax highlighting.
        // Valid highlight_style values:
        // "pygments" (default), "kate", "monochrome",
        // "espresso", "zenburn", "haddock", "tango"
        "highlight-style": "pygments",


        // Supply lists of files---NOT single file names---to include verbatim in the output.
        // This is correct:
        //          "include_in_header": [ "myfile" ]
        // and this is not:
        //          "include_in_header": "myfile"
        // Default templates support multiple includes.
        // Insert just before </head>
        "include-in-header": [],
        // Insert just after <body>
        "include-before-body": [],
        // Insert includes just before </body>
        "include-after-body": [],

        // Convert includes to 'data:' URIs so that the
        // output can be viewed offline.
        "self-contained": false,

        // Use <q> tags for quotes in HTML5 output
        "html-q-tags": false,

        // In HTML output ONLY, restrict to ASCII characters
        // with numerical HTML entities.
        "ascii": false,

        // When outputting Markdown, use reference-style links (e.g. [go here!][1])
        // rather than inline (e.g. [go here!](http://place.the) ).
        "reference-links": false,

        // Force use of ATX-style headers ("# H1", "## H2", etc.) in output.
        // The default is to use a combination, with setext-style headers:
        // H1
        // ===
        //
        // for H1 and H2, then ATX.
        "atx-headers": false,

        // Top-level headers become TeX/Docbook chapters.
        "chapters": false,

        // Generate section numbers.
        "number-sections": false,

        // Sections in HTML output can be offset by a fixed number.
        // The first number is added to the output for top-level
        // headings, the second number to second-level headings,
        // etc. Must be specified as a list.
        "number-offset":
        [
        ],

        // "Do not convert quotation marks, apostrophes, and dashes to the TeX ligatures"
        "no-tex-ligatures": false,

        // Use listings package for TeX code
        "listings": false,

        // In slideshow output, display list items one slide at a time.
        "incremental": false,

        // Header level at which to break slides. Above breaks sections, below
        // creates subheads. Normally set based on context of document.
        // See: http://johnmacfarlane.net/pandoc/README.html#structuring-the-slide-show
        // Set to a number or "false" to disable.
        "slide-level": false,

        // Enclose sections in <div> or <section> tags, attach "id" attributes based on
        // the section name.
        "section-divs": false,

        // Conceal mailto: links from robots.
        // Acceptable values: "none", "javascript", "references"
        "email-obfuscation": "references",

        // "Specify a prefix to be added to all automatically generated identifiers
        // in HTML output. This is useful for preventing duplicate identifiers when
        // generating fragments to be included in other pages."
        "id-prefix": "",

        // Insert a string before the header title tag but not the body title
        "title-prefix": "",

        // Link to any number of CSS stylesheets
        // without triggering the standalone include features.
        "css":
        [
            "github.css"
        ],

        // "Use the specified file as a style reference in producing a [desired] file.
        // For best results, the reference [file] should be a modified version of
        // a [desired] file produced using pandoc."
        "reference-odt": "",
        "reference-docx": "",

        // "Use the specified CSS file to style the EPUB. If no stylesheet is specified,
        // pandoc will look for a file epub.css in the user data directory (see --data-dir).
        // If it is not found there, sensible defaults will be used."
        "epub-stylesheet": "",

        // Set cover to a specified image.
        "epub-coverimage": "",

        // Link to an XML file containing EPUB metadata in Dublin Core Elements format.
        // See http://dublincore.org/documents/dces/
        "epub-metadata": "",

        // Use the stylesheet specified to embed fonts. Should contain a series of
        // @font-face elements and CSS describing where they're to be used.
        "epub-embed-font": "",

        // Appropriate values: "pdflatex" (default), "xelatex", "lulalatex"
        "latex-engine": "",

        // Specify bibliography database to be used in resolving citations. The database
        // type will be determined from the extension of FILE, which may be .mods (MODS format),
        // .bib (BibTeX/BibLaTeX format), .ris (RIS format), .enl (EndNote format), .xml (EndNote XML format),
        // .wos (ISI format), .medline (MEDLINE format), .copac (Copac format), or .json (citeproc JSON).
        // If you want to use multiple bibliographies, just use this option repeatedly.
        "bibliography": "paper_rings_multiblob/multiblobbed_rings.bib",

        // Link to a CSL (http://citationstyles.org) file for formatting citations.
        "csl": "american-physics-society.csl",

        // "Specify a file containing abbreviations for journal titles and other
        // bibliographic fields (indicated by setting form="short" in the CSL node
        // for the field). The format is described at
        // http://citationstylist.org/2011/10/19/abbreviations-for-zotero-test-release/"
        "citation-abbreviations": "",

        // Use natbib for LaTeX citations.
        "natbib": false,

        // Use BibLaTeX for LaTeX citations.
        "biblatex": true,


        // Place TeX math between <eq> tags in HTML output.
        "gladtex": false,

        // Each of the following can be false, true, or a URL string.
        // Setting to a URL string implies true.
        // Use http://math.etsu.edu/LaTeXMathML/ to format TeX math. If no URL
        // is specified, Pandoc will insert the code for you.
        "latexmathml": false,
        // Convert TeX math to MathML and include a JavaScript to display.
        "mathml": false,
        // Use http://www.math.union.edu/~dpvc/jsmath/ for TeX math. URL must point
        // to its load script, which will not be automatically added by Pandoc.
        "jsmath": false,
        // Use http://www.mathjax.org/ for TeX math. URL must point to MathJax.jds
        // load script. If no URL is provided, Pandoc script will add one.
        "mathjax": true,
        // Render TeX math with mimetex (http://www.forkosh.com/mimetex.html). If no
        // URL is supplied, /cgi-bin/mimetex.cgi is assumed.
        "mimetex": false,
        // Render TeX formulas using an external script that converts TeX formulas
        // to images. The formula will be concatenated with the URL provided.
        // If URL is not specified, the Google Chart API will be used.
        "webtex": false
    }
}

}

As you can see I have activated biblatex and set the bibtex file (paper_rings_multiblob/multiblobbed_rings.bib) and style (american-physics-society.csl), but seems the command is not right parse. I try on the command line this command:

$ pandoc intro.md --biblio paper_rings_multiblob/multiblobbed_rings.bib --csl american-physics-society.csl -o test.html

and it works quite well, so I think it is a problem of the command construction.

Could you help me?

Thanks in advance.

[fredcallaway]

IIRC, you should not use bib latex: true unless you are outputting to .tex

For pdf or html output, you want to use pandoc proc-cite (built in) for citations. e.g.

`Bayesian inference algorithms have proved to be very effective models of word learning tasks [e.g. @Xu07, @tenenbaum08]. -@ just cites the year if you use the authors name earlier.

[a-cellofan]

Thank you!