Use align for ```math blocks (#143)

* Use align for ```math blocks
* Fix deprecation from inline parsing
* Update tests

src/Markdown2HTML.jl

@@ -157,7 +157,7 @@ end
 
 function html(io::IO, tex::LaTeX)
     withtag(io, :p, :class => "math") do
-        write(io, string("\\[", tex.formula, "\\]"))
+        write(io, string("\\[\n\\begin{align}\n", tex.formula, "\n\\end{align}\n\\]"))
     end
 end
 

src/format.jl

@@ -4,6 +4,7 @@ using Compat
 using Dates
 using Markdown
 using REPL.REPLCompletions: latex_symbols
+import Markdown.latex
 
 function format(doc::WeaveDoc)
     formatted = AbstractString[]
@@ -301,7 +302,6 @@ function indent(text, nindent)
                     string(repeat(" ", nindent), x), split(text, "\n")), "\n")
 end
 
-
 function wraplines(text, line_width=75)
     result = AbstractString[]
     lines = split(text, "\n")
@@ -324,3 +324,7 @@ result = ""
     end
 result *= text
 end
+
+function latex(io::IO, tex::Markdown.LaTeX)
+    write(io, string("\n\\begin{align}\n", tex.formula, "\n\\end{align}\n"))
+end

src/pandoc.jl

@@ -111,6 +111,7 @@ function run_latex(doc::WeaveDoc, outname, latex_cmd = "xelatex")
   @info("Weaved code to $outname. Running $latex_cmd")
   textmp = mktempdir(".")
   try
+    out = read(`$latex_cmd -shell-escape $xname -aux-directory $textmp -include-directory $(doc.cwd)`, String)
     out = read(`$latex_cmd -shell-escape $xname -aux-directory $textmp -include-directory $(doc.cwd)`, String)
     rm(xname)
     rm(textmp, recursive=true)

src/readers.jl

@@ -303,7 +303,7 @@ function parse_inline(text::AbstractString, inline_ex::Regex)
         doc = InlineText(text[e:(s-1)], e, s-1, textno)
         textno += 1
         push!(res, doc)
-        e = s + endof(ic.match)
+        e = s + lastindex(ic.match)
         push!(res, InlineCode(ic.captures[1], s, e, codeno))
         codeno += 1
     end

test/markdown_test.jl

@@ -30,7 +30,7 @@ Some **text** with different [^note] *formatting* and \$math\$ and text.
 2. List two
 
 ```julia
-x = 3 
+x = 3
 ```
 
 !!! note "Something"
@@ -49,7 +49,11 @@ ref_html = """<h1>H1</h1>
 <div class=\"footnote\" id=\"footnote-note\"><p class=\"footnote-title\">note</p><p>test note</p>
 </div>
 <hr />
-<p class=\"math\">\\[more math\\]</p>
+<p class=\"math\">\\[
+\\begin{align}
+more math
+\\end{align}
+\\]</p>
 <ul>
 <li><p>List one</p>
 </li>
@@ -62,7 +66,7 @@ ref_html = """<h1>H1</h1>
 <li><p>List two</p>
 </li>
 </ol>
-<pre><code class=\"language-julia\">x &#61; 3 </code></pre>
+<pre><code class=\"language-julia\">x &#61; 3</code></pre>
 <div class=\"admonition note\"><p class=\"admonition-title\">Something</p><p>Test admonition with <img src=\"link/to/image.png\" alt=\"Image\" /></p>
 </div>
 <blockquote>