Add support for citations

Manifest.toml

@@ -0,0 +1,161 @@
+# This file is machine-generated - editing it directly is not advised
+
+[[Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[BibTeX]]
+git-tree-sha1 = "f434dde47e2c755c7cf9472bd394d1c074d7f475"
+repo-rev = "master"
+repo-url = "https://github.com/mpastell/BibTeX.jl.git"
+uuid = "0c132655-f423-5f6f-9a5a-d55cfa15b9d7"
+version = "0.0.0"
+
+[[Codecs]]
+deps = ["Test"]
+git-tree-sha1 = "70885e5e038cba1c4c17a84ad6c40756e10a4fb5"
+uuid = "19ecbf4d-ef7c-5e4b-b54a-0a0ff23c5aed"
+version = "0.5.0"
+
+[[Compat]]
+deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
+git-tree-sha1 = "49269e311ffe11ac5b334681d212329002a9832a"
+uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
+version = "1.5.1"
+
+[[Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[DelimitedFiles]]
+deps = ["Mmap"]
+uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+
+[[Distributed]]
+deps = ["Random", "Serialization", "Sockets"]
+uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+
+[[DocStringExtensions]]
+deps = ["LibGit2", "Markdown", "Pkg", "Test"]
+git-tree-sha1 = "1df01539a1c952cef21f2d2d1c092c2bcf0177d7"
+uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+version = "0.6.0"
+
+[[Highlights]]
+deps = ["DocStringExtensions", "InteractiveUtils", "REPL", "Test"]
+git-tree-sha1 = "286ff83d696dd92748e603a3219618d9e407e872"
+uuid = "eafb193a-b7ab-5a9e-9068-77385905fa72"
+version = "0.3.1"
+
+[[InteractiveUtils]]
+deps = ["Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[IteratorInterfaceExtensions]]
+deps = ["Test"]
+git-tree-sha1 = "5484e5ede2a4137b9643f4d646e8e7b87b794415"
+uuid = "82899510-4779-5014-852e-03e436cf321d"
+version = "0.1.1"
+
+[[JSON]]
+deps = ["Dates", "Distributed", "Mmap", "Sockets", "Test", "Unicode"]
+git-tree-sha1 = "1f7a25b53ec67f5e9422f1f551ee216503f4a0fa"
+uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+version = "0.20.0"
+
+[[LibGit2]]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+
+[[Libdl]]
+uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+
+[[LinearAlgebra]]
+deps = ["Libdl"]
+uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
+[[Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[Mmap]]
+uuid = "a63ad114-7e13-5084-954f-fe012c677804"
+
+[[Mustache]]
+deps = ["Printf", "Tables", "Test"]
+git-tree-sha1 = "3cc9a0b673519c5c39186e636d747facb12bf075"
+uuid = "ffc61752-8dc7-55ee-8c37-f3e9cdd09e70"
+version = "0.5.11"
+
+[[Pkg]]
+deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+
+[[Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[[REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[Random]]
+deps = ["Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[Requires]]
+deps = ["Test"]
+git-tree-sha1 = "f6fbf4ba64d295e146e49e021207993b6b48c7d1"
+uuid = "ae029012-a4dd-5104-9daa-d747884805df"
+version = "0.5.2"
+
+[[SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+
+[[Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
+[[SharedArrays]]
+deps = ["Distributed", "Mmap", "Random", "Serialization"]
+uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
+
+[[Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
+
+[[SparseArrays]]
+deps = ["LinearAlgebra", "Random"]
+uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[[Statistics]]
+deps = ["LinearAlgebra", "SparseArrays"]
+uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+
+[[TableTraits]]
+deps = ["IteratorInterfaceExtensions", "Test"]
+git-tree-sha1 = "eba4b1d0a82bdd773307d652c6e5f8c82104c676"
+uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
+version = "0.4.1"
+
+[[Tables]]
+deps = ["IteratorInterfaceExtensions", "LinearAlgebra", "Requires", "TableTraits", "Test"]
+git-tree-sha1 = "5aa45584645393c1717e0cc1f0362c2ea81470a9"
+uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
+version = "0.1.17"
+
+[[Test]]
+deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[UUIDs]]
+deps = ["Random", "SHA"]
+uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+
+[[Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
+
+[[YAML]]
+deps = ["Codecs", "Compat"]
+git-tree-sha1 = "3bde77cee95cce0c0b9b18813d85e18e8ed4f415"
+uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
+version = "0.3.2"

Project.toml

@@ -1,30 +1,31 @@
 name = "Weave"
 uuid = "44d3d7a6-8a23-5bf8-98c5-b353f8df5ec9"
-version="0.7.2"
+version = "0.7.2"
 
 [deps]
-Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
-Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
-Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
-REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+BibTeX = "0c132655-f423-5f6f-9a5a-d55cfa15b9d7"
 Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
-Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
-JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Highlights = "eafb193a-b7ab-5a9e-9068-77385905fa72"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
 Mustache = "ffc61752-8dc7-55ee-8c37-f3e9cdd09e70"
-YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
+Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
 [compat]
 Highlights = ">=0.3.1"
+Mustache = ">=0.4.1"
 Plots = ">=0.19.0"
 YAML = ">=0.3.0"
-Mustache = ">=0.4.1"
 
 [extras]
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
 test = ["Test", "Plots"]

REQUIRE

@@ -5,3 +5,4 @@ Mustache
 YAML
 Compat 0.25.0
 Requires
+BibTeX

src/Weave.jl

@@ -103,6 +103,11 @@ function weave(source ; doctype = :auto,
     css != nothing && (doc.css = css)
     template != nothing && (doc.template = template)
 
+    WeaveMarkdown.reset_parser()
+    if haskey(doc.header, "bibliography")
+        WeaveMarkdown.init_parser(joinpath(dirname(source), doc.header["bibliography"]))
+    end
+
     try
       doc = run(doc, doctype = doctype,
               mod = mod,
@@ -130,7 +135,7 @@ function weave(source ; doctype = :auto,
           rm(mdname)
       elseif doc.doctype == "md2pdf"
           success = run_latex(doc, outname, latex_cmd)
-          success && rm(doc.fig_path, force = true, recursive = true)
+          rm(doc.fig_path, force = true, recursive = true)
           success || return
           outname = get_outname(out_path, doc, ext = "pdf")
       end
@@ -141,6 +146,7 @@ function weave(source ; doctype = :auto,
     #    @warn("Something went wrong during weaving")
     #    println(e)
     finally
+        WeaveMarkdown.reset_parser()
         doctype == :auto && (doctype = detect_doctype(doc.source))
         if occursin("pandoc2pdf", doctype) && cache == :off
             rm(doc.fig_path, force = true, recursive = true)

src/WeaveMarkdown/bibliography.jl

@@ -0,0 +1,25 @@
+import Mustache
+
+function list_references(m::MIME"text/html")
+    tpl = Mustache.template_from_file(joinpath(@__DIR__, "../../templates/html_citations.tpl"))
+    refs = Dict()
+    for key in keys(CITATIONS[:refnumbers])
+        refs[CITATIONS[:refnumbers][key]] = key
+    end
+    io = IOBuffer()
+    write(io, "<ol>")
+    for i in 1:length(refs)
+        ref = CITATIONS[:references][refs[i]]
+        ref[ref["type"]] = "true"
+        ref["author"] = replace(ref["author"], r"\sand\s"i => ", ")
+        for key in keys(ref)
+            ref[key] = replace(ref[key], r"\{|\}" => "")
+            ref[key] = replace(ref[key], "--" => "&ndash;")
+        end
+        write(io, "<li>")
+        write(io, Mustache.render(tpl, ref))
+        write(io, "</li>")
+    end
+    write(io, "</ol>")
+    return String(take!(io))
+end

src/WeaveMarkdown/html.jl

@@ -1,4 +1,3 @@
-#module Markdown2HTML
 # Markdown to HTML writer, Modified from Julia Base.Markdown html writer
 using Markdown: MD, Header, Code, Paragraph, BlockQuote, Footnote,
       Admonition, List, HorizontalRule, Bold, Italic, Image, Link, LineBreak,
@@ -230,10 +229,21 @@ function htmlinline(io::IO, comment::Comment)
     write(io, "<!-- $(comment.text) -->")
 end
 
+function htmlinline(io::IO, citations::Citations)
+    withtag(io, :span, :class => "citation") do
+        cites = []
+        for c in citations.content
+            if c.no == 0
+                push!(cites, "<span class=\"missing\">?</span>")
+            else
+                push!(cites, c.no)
+            end
+        end
+    write(io, string("[", join(cites, ","), "]"))
+    end
+end
+
 htmlinline(io::IO, x) = tohtml(io, x)
 
 # API
-
 html(md) = sprint(html, md)
-
-#end

src/WeaveMarkdown/latex.jl

@@ -9,12 +9,20 @@ function latex(io::IO, tex::Markdown.LaTeX)
 end
 
 #Remove comments that can occur inside a line
-function latexinline(io, comment::WeaveMarkdown.Comment)
+function latexinline(io, comment::Comment)
     write(io, "")
 end
 
-function latex(io::IO, comment::WeaveMarkdown.Comment)
+function latex(io::IO, comment::Comment)
     for line in split(comment.text, r"\r\n|\n")
         write(io, "% $line\n")
     end
 end
+
+function latexinline(io, citations::Citations)
+    cites = []
+    for c in citations.content
+        push!(cites, c.key)
+    end
+    write(io, string("\\citep{", join(cites, ", "), "}"))
+end