A programming story

This is the story of a small program that parses source code. It converts comments into HTML (via Markdown) and nicely highlights code (using SyntaxHighlighter).

  story "0.0.3-SNAPSHOT"

  :description "A literate programming tool."

The program is written in the Clojure language and uses the pegdown implementation of Markdown with a number of its extensions enabled.

It uses clojure 1.2.1 for now because that is what [Leiningen] 1.x uses and at some stage there will be a lein-story plugin.

  [[org.clojure/clojure "1.2.1"]
   [org.pegdown/pegdown "1.1.0"]
   [fs "0.11.0"]

A modified org.clojure/tools.cli is used (for repeated options). To be merged with upstream by 0.1.0.

   [me.panzoo/tools.cli "0.2.2"]]
  :main story.main)

Check out the sources at https://github.com/jedahu/story


To use this program you need to know four things: the single-line comment syntax of your source-code, Markdown, the story syntax for anchors, and the story syntax for includes.

Comment blocks that are flush with the left margin are parsed and rendered using Markdown, those prefixed with whitespace are ignored. Anchors are comment lines whose content is ‘@<anchor-id>’. To include another source file add a comment line whose content is ‘%include <file-path>’.

By default this program is set up to process a Lisp like language with single semi-colon comment tokens. A small source example with anchors, includes, and wiki links might look like this:

;;<. Copyright (c) 2012, Me 
;; Boring license notice.
;; Blah blah blah.
;; This section will not show in the documentation.

;; # My awesome program
;; Introductory paragraph, uses *Markdown*. Fast forward to the
;; [[last paragraph]].
;; Blah blah blah.

;;. This comment will not show in the documentation.
(defn hello []
  (println "Hello world!"))

(assert (= (hello) "Hello world!"))

;;%require config.xml

;;%include fibonacci.clj
;;%include fibonacci.js // javascript
;;@last paragraph
;; This is the last paragraph. Go back to the [[hello]] function. Go to the
;; [[fibonacci.clj/fib]] function.


As you can see, files written in different languages can be included. In this example fibonacci.js is followed by the comment syntax and language name to use with SyntaxHighlighter. For a number of languages (including javascript) this information can be obtained from the file extension and the appropriate brush file pulled in automatically; those languages are listed in the Language map.

Test code and production

Test code can be included inline using <? and ?>, and commented out for production. The %require directive marks a file or directory for production use without including it in the documentation. See Testing for more detail.

Internal links

Wiki style links ([[link]]) point to explicit anchors (;@<id>) or to implicit anchors (the names of definitions). Implicit anchors are created for Markdown headings (#-style only) and definitions in code (only for languages with methods for story.core/code-anchor-id; be aware, not all methods have been well tested).

Wiki links to anchors in other files must be qualified by the file’s path. The markup for the link to code-anchor-id looks like this: [[src/story/core.clj/code-anchor-id]].

If any anchors for code definitions are created, an alphabetical TOC like list of links to those anchors will appear on the right side of the page.

Build instructions

To build story.jar make sure Leiningen is installed and run the following commands in the story project directory:

lein deps
lein uberjar

If all goes well a file named something like story-x.x.x-standalone.jar will have magically appeared in the project directory. Rename it to story.jar if you like.

Command line usage

java -jar story.jar input-files output

If output is absent, the program’s output is streamed to standard-out. For more detail run the program with the --help option or have a look at the Commandline section.

This HTML document (assuming you are not reading the source file) was created by the command: java -jar story.jar project.clj index.html.

Programmatic usage

Call story.core/process-files with a list of file paths and an output stream or file-path. It may be necessary to set up bindings for one or more of the dynamic variables described in the Top level variables section depending on whether the file suffixes are in the Language map or not.

The equivalent of the above commandline invocation is: (process-files ["project.clj"] "index.html").

The code

The code is Copyright (c) Jeremy Hughes 2011 and is available under the ISC license, except for the cond-let, read-lines, and write-lines functions which are Copyright (c) Rich Hickey and are under the EPL. These licenses are in the root of this source distribution in the files LICENSE and epl-v10.html.

The usual stuff comes first. This code needs to read and write to files, manipulate strings, and parse Markdown.

(ns story.core
  (:refer-clojure :exclude [comment])
    [clojure.java.io :as io]
    [clojure.string :as string]
    [java.util.regex Pattern]
    [java.io BufferedReader BufferedWriter]
    [org.pegdown PegDownProcessor Extensions

Internal links (to element ids) are nice to have. These imports will be used to create a modified LinkRenderer.

     LinkRenderer LinkRenderer$Rendering]
    [org.pegdown.ast WikiLinkNode]))

A few of the top level variables use these utility functions.

(declare normalize-anchor)
(declare html-escape)

Top level variables

A few objects need to be accessed by a number of functions: regular expressions that match the beginning of lines, SyntaxHighlighter options, a PegDownProcessor, and a modified LinkRenderer.


This dynamic variable is bound once in the commandline -main method and is never subsequently altered by the code in this namespace. The variable is bound to a map containing the following settings: which SyntaxHighlighter theme to use; which SyntaxHighlighter brushes to include to start with (other brushes may be added automatically by the program); what CSS file to include if any; and whether to log messages to std-err or not.

(def ^{:dynamic true} *settings*
  {:theme "shThemeEclipse.css"
   :static-brushes []
   :stylesheet nil
   :verbose? false})

Per input file

These variables are rebound for every input file.

(def ^{:dynamic true} *single-comment*
  ; "A string containing a single comment token."
(def ^{:dynamic true} *language*
  ; "A language string for use with SyntaxHighlighter."
(def ^{:dynamic true} *path*
  ; "The path of the file currently being processed."

Per output stream

These variables are given bindings only in the render-files function.

Brushes can be added by the program whenever a new file is processed.

(def ^{:dynamic true} *brushes* nil)
(def ^{:dynamic true} *code-anchors* nil)

Language map

Including SyntaxHighlighter brush files automatically based on file suffix or the language argument to an include directive is preferrable to explicitly listing brushes on the commandline or in a program that calls this one. Comment syntax is listed here too for the same reason.

Don’t use languages and language-aliases directly. Use lang-info, lang-brush, and lang-comment instead. Those three functions route their input through canonical-lang which resolves any aliases to their canonical equivalent.

(def languages
  ; "A map of language names to a pairs of comment syntax and SyntaxHighlighter
  ; brush file names."
  {:clojure [";;" "shBrushClojure.js"]
   :applescript ["--" "shBrushAppleScript.js"]
   :as3 ["//" "shBrushAS3.js"]
   :bash ["#" "shBrushBash.js"]
   :shell ["#" "shBrushBash.js"]
   :sh ["#" "shBrushBash.js"]
   :cpp ["//" "shBrushCpp.js"]
   :c++ ["//" "shBrushCpp.js"]
   :cxx ["//" "shBrushCpp.js"]
   :c ["//" "shBrushCpp.js"]
   :c# ["//" "shBrushCSharp.js"]
   :c-sharp ["//" "shBrushCSharp.js"]
   :csharp ["//" "shBrushCSharp.js"]
   :delphi ["//" "shBrushDelphi.js"]
   :pascal ["//" "shBrushDelphi.js"]
   :erlang ["%" "shBrushErlang.js"]
   :erl ["%" "shBrushErlang.js"]
   :groovy ["//" "shBrushGroovy.js"]
   :java ["//" "shBrushJava.js"]
   :javafx ["//" "shBrushJavaFX.js"]
   :jfx ["//" "shBrushJavaFX.js"]
   :javascript ["//" "shBrushJScript.js"]
   :js ["//" "shBrushJScript.js"]
   :perl ["#" "shBrushPerl.js"]
   :pl ["#" "shBrushPerl.js"]
   :php ["#" "shBrushPhp.js"]
   :python ["#" "shBrushPython.js"]
   :py ["#" "shBrushPython.js"]
   :ruby ["#" "shBrushRuby.js"]
   :rb ["#" "shBrushRuby.js"]
   :sass ["//" "shBrushSass.js"]
   :scss ["//" "shBrushSass.js"]
   :scala ["//" "shBrushScala.js"]
   :sql ["--" "shBrushSql.js"]
   :vim ["\"" "shBrushVimscript.js"]
   :vimscript ["\"" "shBrushVimscript.js"]
   :vb ["'" "shBrushVb.js"]
   :vbnet ["'" "shBrushVb.js"]
   :markdown ["" nil]
(def language-aliases
  ; "A map of aliases to canonical language names."
  {:clj :clojure
   :cljs :clojure
   :actionscript3 :as3
   :sh :bash
   :shell :bash
   :c :cpp
   :c++ :cpp
   :cxx :cpp
   :c# :csharp
   :c-sharp :csharp
   :erl :erlang
   :jfx :javafx
   :js :javascript
   :pl :perl
   :py :python
   :rb :ruby
   :sass :scss
   :vimscript :vim
   :vbnet :vb
   :md :markdown})

Pegdown instances

The same pegdown processor and link renderer are used for each program execution.

(def processor
  ; "A PegDownProcessor set up with the following extensions:
    (reduce bit-or
            [(. Extensions AUTOLINKS)
             (. Extensions SMARTYPANTS)
             (. Extensions FENCED_CODE_BLOCKS)
             (. Extensions DEFINITIONS)
             (. Extensions WIKILINKS)])))

Pegdown’s link rendering is overriden for the wiki link case. Un-qualified links are given a qualified href, and qualified links are given an unqualified value. normalize-anchor is used to normalize the href. For example, in the file path/to/foo.c, these wiki links:

[[one link]]
[[path/to/bar.c/another link]]

create this output:

<a href='#path/to/foo.c/one-link'>one link</a>
<a href='#path/to/bar.c/another-link'>another link</a>
(def link-renderer
  ; "A pegdown LinkRenderer that renders wiki links as links to internal
  ; document fragments rather than external HTML pages."
  (letfn [(def-name [s] (re-find #"(?<=/)[^/]+$" s))
          (anchor-name [s]
            (html-escape (or (def-name s) s)))]
    (proxy [LinkRenderer] []
         (if-let [text (and (instance? WikiLinkNode node)
                            (.getText node))]
                             (normalize-anchor text))
                           (anchor-name text))
             (catch java.io.UnsupportedEncodingException _
               (throw (IllegalStateException.))))
           (proxy-super render node)))
        ([node text]
         (proxy-super render node text))
        ([node url title text]
         (proxy-super render node url title text))))))


A few utility functions to make it easier to print messages to the console, iterate side-effects through a collection, access resources, encode a string for use as an id or fragment identifier, and bind an output stream to *out* over a lexical scope.

(defmacro cond-let
  "Takes a binding-form and a set of test/expr pairs. Evaluates each test one
  at a time. If a test returns logical true, cond-let evaluates and returns
  expr with binding-form bound to the value of test and doesn't evaluate any of
  the other tests or exprs. To provide a default value either provide a literal
  that evaluates to logical true and is binding-compatible with binding-form,
  or use :else as the test and don't refer to any parts of binding-form in the
  expr. (cond-let binding-form) returns nil."
  [bindings & clauses]
  (let [binding (first bindings)]
    (when-let [[test expr & more] clauses]
      (if (= test :else)
        `(if-let [~binding ~test]
           (cond-let ~bindings ~@more))))))
(defn message
  "Write s to standard error."
  [& s]
  (when (:verbose? *settings*)
    (binding [*out* (io/writer System/err)]
      (println (apply str s)))))
(defn each
  "Apply f to each item of coll in order for side effects only. Evaluates coll
  strictly, unlike for. Returns nil."
  [f coll]
  (doseq [c coll]
    (f c)))
(defn lazy-each
  [f coll]
    (when (seq coll)
      (cons (f (first coll)) (lazy-each f (rest coll))))))
(defn slurp-resource
  "Get the complete contents of a Java resource. Throws an exception on
  failure unless continue-on-failure? is truthy."
  [resource-name & continue-on-failure?]
    (-> (.getContextClassLoader (Thread/currentThread))
      (.getResourceAsStream resource-name)
    (catch Exception e
      (message "Failed to read resource " resource-name)
      (if continue-on-failure?
        (message "    continuing anyway...")
        (do (message "    aborting...")
          (throw e))))))
(defn slurp-file|resource
  "Get the contents of the file at path, or failing that, the contents of a
  Java resource. Throws an exception on failure unless continue-on-failure? is
  [path & continue-on-failure?]
  (try (slurp path)
    (catch java.io.FileNotFoundException _
      (message "Using internal " path)
      (slurp-resource path continue-on-failure?))))
(defn encode-anchor
  "Encode s for use as a fragment identifier."
    (if (some #{\/} s) s (str *path* "/" s))
    "\\s" "-"))
(defn normalize-anchor
  "Encode s using encode-anchor and ensure it is qualified by file path."
  (encode-anchor (if (some #{\/} s) s (str *path* "/" s))))
(defn html-escape
  "Escape s for inclusion in HTML."
    {\< "&lt;"
     \> "&gt;"
     \& "&amp;"}))

IO helpers

(defmacro with-out-stream
  "Wrap an output stream using clojure.java.io/writer bind it to *out*, then
  execute body."
  [out & body]
  `(with-open [w# (io/writer ~out)]
     (binding [*out* w#]
(defn read-lines
  "Like clojure.core/line-seq but opens r with reader.  Automatically
  (let [read-line (fn this [^BufferedReader rdr]
                      (if-let [line (.readLine rdr)]
                        (cons line (this rdr))
                        (.close rdr))))]
    (read-line (io/reader r))))
(defn write-lines
  "Writes lines (a seq) to f, separated by newlines.  f is opened with
  writer, and automatically closed at the end of the sequence."
  [w lines]
  (with-open [^BufferedWriter writer (io/writer w)]
    (loop [lines lines]
      (when-let [line (first lines)]
        (.write writer (str line))
        (.newLine writer)
        (recur (rest lines))))))
(defn map-lines
  [r w f]
  (write-lines w (map f (read-lines r))))

SyntaxHighlighter language helpers

(defn canonical-lang
  "Given a language keyword, return its canonical equivalent."
  (let [k (keyword l)]
    (get language-aliases k k)))
(defn lang-info
  "Given a language keyword, return its information as a vector pair of
  comment syntax and SyntaxHighlighter brush name."
  (languages (canonical-lang l)))
(defn lang-comment
  "Given a language keyword, return its comment syntax."
  (first (lang-info l)))
(defn lang-brush
  "Given a language keyword, return its default SyntaxHighlighter brush name."
  (second (lang-info l)))

Regular expression helpers

(defn ?match [s reg]
  (when-let [m (re-find (reg) s)]
    (.substring s (count m))))
(defn comment
  "A regular expression matching the beginning of a commented line."
  (re-pattern (str "^\\s*" (Pattern/quote *single-comment*))))
(defn markdown*
  (if (= :markdown (canonical-lang *language*))
    (re-pattern (str (comment) " "))))
(defn markdown
  (re-pattern (str (markdown*) "|" (comment) "$")))
(defn hidden-comment
  "A regular expression matching the beginning of a commented line that will
  not appear in the output."
  (re-pattern (str (comment) ".")))
(defn anchor
  "A regular expression matching the beginning of an anchor line."
  (re-pattern (str (comment) "@ *")))
(defn heading
  "A regular expression matching the beginning of a heading line."
  (re-pattern (str (markdown*) "\\#+ *")))
(defn include
  "A regular expression matching the beginning of an include line."
  (re-pattern (str (comment) "%include +")))
(defn required
  "A regular expression matching the beginning of a require line."
  (re-pattern (str (comment) "%require +")))
(defn begin-test
  "A regular expression matching the beginning of a test section."
  (re-pattern (str (comment) "<\\?")))
(defn end-test
  "A regular expression matching the end of a test section."
  (re-pattern (str (comment) "\\?>")))
(defn begin-hidden
  "A regular expression matching the beginning of a hidden section."
  (re-pattern (str (comment) "<\\.")))
(defn end-hidden
  "A regulare expression matching the end of a hidden section."
  (re-pattern (str (comment) "\\.>")))


Parsing is done by looping through a lazy list of lines. A character stream backed by that lazy list is used when reading across lines is necessary. See the :else case in classify-line and code-anchor-id :clojure for an example.

The entry-point for parsing is the gather-lines function at the end of this section.

(defn lines-reader [lines]
  (let [lines-left (atom (interpose "\n" (filter seq lines)))]
      (proxy [java.io.Reader] []
        (close [])

The clojure reader only calls the zero arity read method. Punting on implementing the other arities for now.

           (let [ll @lines-left
                 line (first ll)
                 c (first line)]
             (reset! lines-left
                     (if (seq (rest line))
                       (cons (subs line 1) (rest ll))
                       (rest ll)))
             (if c (int c) -1))))))))

Anchors for definitions are generated using the current line and a reader from the current line. Methods are expected to return a string identifying the definition, or nil if there is no definition beginning at the current line. The default method unconditionally returns nil.

(defmulti code-anchor-id
  "If the current line (or reader) begins a definition, return the definition
  name, otherwise return nil."
  (fn [line reader] *language*)
  :default :default)
(defmethod code-anchor-id :default [_ _] nil)

The clojure method uses the clojure reader, which should be more robust than methods which use regular expressions.

(defmethod code-anchor-id :clojure [line reader]
  (when (re-find #"^\(" line)
    (let [code (read reader)]
        (= 'defmethod (first code))
        (str (second code) " " (nth code 2))

        (re-find #"^def" (str (first code)))
        (name (second code))

        :else nil))))

Not all of these methods are well tested, like this javascript one.

(defmethod code-anchor-id :javascript [line reader]
  (or (second (re-find #"^\s*function\s+([^\s\(]+)" line))
      (second (re-find #"^var\s+([A-Za-z_][A-Za-z_0-9]*)\s*=\s*function[\s\(]" line))
      (second (re-find #"^\s*'?([A-Za-z_][A-Za-z_0-9]*)'?\s*:\s*function[\s\(]" line))))
(defmethod code-anchor-id :vim [line reader]
  (second (re-find #"^function!?\s+([a-zA-Z_][a-zA-Z_0-9]*)" line)))

The line parser emits a list of [<classification> <data>] pairs. This function calls code-anchor-id and returns an [:anchor <id>] pair. It also stores the anchor information for future use by code-anchor-toc, which generates a table of contents for definitions with anchors.

(defn maybe-code-anchor
  "If the current line (or reader) begins a definition, store the definition
  name in *code-anchors* with the current file path as its key. Return the
  path qualified id, or return nil."
  [line reader]
  (if-let [id (code-anchor-id line reader)]
      (swap! *code-anchors*
             (fn [old]
               (update-in old [*path*] #(conj (or % []) id))))
      [[:anchor (str *path* "/" id)]])
(defn include-info
  (let [[path & [token lang]] (string/split s #"\s+")
        lang (canonical-lang (or lang
                                 (re-find #"(?<=\.)[^/.]+$" path)
        comment (or token
                    (lang-comment (or lang *language*))
    [path comment lang]))

Each line of a source file will be either code, comment, anchor, include, or test code. Headings are treated as both anchors and comments.

(defn classify-line
  "Classify the first line in lines. Commented lines prefixed by white space
  are ignored. Returns a vector containing a single pair of the form
  [<classification> <data>], where <data> is a string except in the case of an
  include where it is a vector of [<path> & [<comment-syntax> <language>]]."
  [[line :as lines]]
  (let [m (partial ?match line)]
      (m include) [[:include (include-info text)]]
      (m required) []
      (m begin-test) [[:begin-test text]]
      (m end-test) [[:end-test text]]
      (m begin-hidden) [[:begin-hidden text]]
      (m end-hidden) [[:end-hidden text]]
      (m anchor) [[:anchor text]]
      (m heading) [[:anchor text]
                   [:comment (m markdown)]]
      (m markdown) [[:comment text]]
      (m hidden-comment) []
      :else (conj (maybe-code-anchor line (lines-reader lines))
                  [:code line]))))

Each line is classified lazily.

(defn classify-lines
  "Classify each line in lines as :code, :comment, :anchor, or :include.
  Returns a lazy list of [<classification> <data>] pairs. See classify-line for
  more detail."
    (when (seq lines)
      (concat (classify-line lines) (classify-lines (rest lines))))))

Adjacent lines of the same classification need to be gathered together into a single string (except for anchors and includes).

(defn gather-lines-
    (when-let [classfn (first (first lines))]
        (#{:comment :code} classfn)
        (let [[same tail] (split-with #(= classfn (first %)) lines)
              text (string/join "\n" (map second same))]
          (cons [classfn text] (gather-lines- tail)))

        (= :begin-hidden classfn)
          (rest (drop-while
                  #(not= :end-hidden (first %))
                  (rest lines))))

        (cons (first lines) (gather-lines- (rest lines)))))))

The entry-point for parsing is this gather-lines function.

(defn gather-lines
  "Join adjacent strings of the same classification together (except :anchor
  and :include). Return a lazy list of [<classification> <data>] pairs. See
  classify-line for more detail."
  (gather-lines- (classify-lines lines)))


The method that transforms each classified chunk into HTML, dispatches on the classification of each item in the list returned by gather-lines.

(defmulti html<- first)

SyntaxHighlighter brushes are associated with files if the language is supplied or can be worked out from the file suffix.

(defn maybe-associate-brush [path lang]
  (when-let [b (and lang (lang-brush lang))]
    (when-not (@*brushes* b)
      (message "Associating "path " with brush " b)
      (swap! *brushes* conj b))))

The output of each file is wrapped in article or section tags. Article tags for top-level files and section tags for included ones.

(defmacro wrap-in-tags [tag & body]
     (print ~tag)
     (print (str "</" (re-find #"(?<=^<)[^\s>]+" ~tag) ">"))))
(defn render-file [tag path & [token lang]]

For each file, new bindings are made for comment syntax and language. If the language or comment syntax (token) are not supplied, they are guessed from the path suffix, and if that fails they are set to the values they have in the enclsing dynamic scope (i.e., from the commandline or the including file).

  (binding [*language* (canonical-lang
                         (or lang
                             (re-find #"(?<=\.)[^/.]+$" path)
    (binding [*single-comment* (or token
                                   (lang-comment *language*)
      (binding [*path* path]
          (when-not (= :markdown (canonical-lang *language*))
            (maybe-associate-brush path *language*))

Lines of source code are read lazily by line-seq and gathered lazily by gather-lines, Along with printing each chunk of comment or code to an output stream, this ensures that the maximum memory used by this program will be determined by the largest comment or code chunk and not the total size of the source file.

          (each html<- (gather-lines (read-lines path))))))))

Code chunks are wrapped in a pre with the correct incantation for SyntaxHighlighter in its class attribute; comments are run through the Markdown processor; anchors become hrefless HTML anchors; and includes wrap the result of parsing and rendering the file they point to in section tags.

(defmethod html<- :code [[_ text]]
  (when-not (string/blank? text)
    (println (str "<pre class='brush: " (name *language*) "'>"
                  (html-escape text)
(defmethod html<- :comment [[_ text]]
  (println (.markdownToHtml processor text link-renderer)))
(defmethod html<- :anchor [[_ text]]
  (println (str "<a id='" (normalize-anchor text) "'></a>")))
(defmethod html<- :include [[_ [path comment lang] :as args]]
  (render-file "<section>" path comment lang))
(defmethod html<- :begin-test [_]
  (println "<div class='test'>"))
(defmethod html<- :end-test [_]
  (println "</div>"))

Look and feel

A TOC is created for code anchors.

(defn code-anchor-toc []
  (wrap-in-tags "<div id='code-anchors'>"
    (wrap-in-tags "<ul>"
      (doseq [[path ids] (reverse @*code-anchors*)]
        (wrap-in-tags "<li>"
          (print (str path "<br>"))
          (wrap-in-tags "<ul>"
            (doseq [id (sort ids)]
              (wrap-in-tags "<li>"
                (wrap-in-tags (str "<a href='#"
                                   (encode-anchor (str path "/" id))
                  (print (html-escape id)))))))))))

All javascript and CSS are inlined in the output.

(defn inline-js [s]
  (println "<script>" s "</script>"))
(defn inline-css [s]
  (println "<style>" s "</style>"))

SyntaxHighlighter brushes can be set and the default theme (shThemeEclipse.css) overridden on the commandline. An additional stylesheet can also be set.

Because lack of brush or theme will not materially affect the structure of the output page, failure to load one or more of them will not cause the program to halt, though it will be logged to standard-error.

(defn inline-brushes []
  (message "Adding the following brushes to output:")
  (each (partial message "    ") @*brushes*)
  (each inline-js
        (filter identity
                (map #(slurp-file|resource % :continue-on-failure)
(defn inline-theme []
  (when-let [s (and (:theme *settings*)
                      (:theme *settings*)
    (inline-css s)))
(defn inline-stylesheet []
  (when-let [s (and (:stylesheet *settings*)
                      (:stylesheet *settings*)
    (inline-css s)))

The resulting look-and-feel resources are included together.

(defn look-and-feel []
  (inline-js (slurp-resource "XRegExp.js"))
  (inline-js (slurp-resource "shCore.js"))
  (inline-js (slurp-resource "outliner."))
  (inline-css (slurp-resource "page.css"))

Javascript configuration and entry-point for SyntaxHighlighter and TOC outline are included from an external resource.

(defn javascript-setup []
  (inline-js (slurp-resource "page.js")))


The output is HTML5 which is why no html, head, or body tags are present. The order of things in the output file is fairly normal for HTML: style and behaviour information first, followed by visible content, followed by the javascript entry-point.

(defn render-files- [paths]
    "<!doctype html>"
    "<meta charset=utf-8>")

Multiple input files are rendered to a single stream. The content of each file’s rendering is wrapped in its own article tags.

  (each (partial render-file "<article>") paths)
(defn render-files [paths]

*brushes* and *code-anchors* are rebound on every invocation of render-files to prevent unneeded brushes and anchors accumulating across calls.

  (binding [*brushes* (atom (or (set (:static-brushes *settings*)) #{})
                            :validator #(not (some (comp not string?) %)))
            *code-anchors* (atom (array-map))]
    (render-files- paths)))

The program entry-point takes a list of paths to input files and a single output stream which can also be a file path or anything clojure.java.io/writer can handle.

(defn process-files
  "Take a list of file paths and an output stream, and render each file to the
  stream as HTML."
  [in-paths out]
  (when-let [d (and
                 (or (string? out)
                     (instance? java.io.File out))
                 (fs/dirname out))]
    (fs/mkdirs d))
  (with-out-stream out
    (render-files in-paths)))


Code that is wrapped in test tags ;<? and ;?>, where ; is the comment syntax for the file, will be included in the output by default and wrapped in a div with the class test. To get a production tree without tests, run this program with the --production flag with a directory argument, or call write-production-tree.

To include files in the production tree but not in the documentation, use ;%require <file or directory>, replacing ; with the correct comment token.

(defn write-production-file
  "Write in-file to outdir with all test code commented (thus preserving line
  [in-file outdir]
  (let [out-file (io/file outdir in-file)
        in-test? (atom false)]
    (.. out-file (getParentFile) (mkdirs))
      in-file out-file
      (fn [line]
        (let [m (partial ?match line)]
            (m begin-test)
            (do (reset! in-test? true)

            (m end-test)
            (do (reset! in-test? false)

            (if @in-test?
              (str *single-comment* line)
                (m include)
                (let [[path comment lang] (include-info text)]
                  (binding [*path* path]
                    (binding [*single-comment* comment]
                      (binding [*language* lang]
                        (write-production-file path outdir))))

                (m required)
                (do (if (fs/directory? text)
                      (fs/copy-tree text (io/file outdir (or (fs/dirname text) "")))
                      (fs/copy+ text (io/file outdir text)))

                :else line))))))))

Entry points

There are two entry functions and one -main function for commandline use.

The first entry function is for writing a production tree (all required files sans test sections).

(defn write-production-tree
  "Write the contents of in-paths with recursive included and required files
  and directories to outdir, with any test code commented."
  [in-paths outdir]
  (when (fs/exists? outdir)
    (fs/deltree outdir))
  (fs/mkdirs outdir)
  (doseq [p in-paths]
    (write-production-file p outdir)))

The second entry function is for building documentation. It takes a map of options, an output file, and a list of files to process. The options are all optional but at least one input file must be provided.

The options are:

:comment     String           single line comment syntax
:brushes     ISeq of Strings  paths to SyntaxHighlighter brush files
:theme       String           path to a SyntaxHighlighter theme file
:language    String           SyntaxHighlighter language name
:stylesheet  String           path to a CSS file
:verbose     boolean          whether to use verbose output

For the brush, theme, and stylesheet options the program first tries to read from the filesystem and if that fails because the file is not found then an attempt is made to read from the program’s resources. The resources contain the standard SyntaxHighlighter brushes and themes under their normal file names including an additional shBrushClojure.js and shThemeClojure.css.

Additional brushes may be added by the program as a result of file includes and file suffixes.

(defn story [opts out-file & in-files]
  (binding [*settings* {:theme (or (:theme opts) (:theme *settings*))
                        :stylesheet (:stylesheet opts)
                        :static-brushes (:brush opts)
                        :verbose? (:verbose opts)}]
    (binding [*single-comment* (or (:comment opts) *single-comment*)]
      (binding [*language* (canonical-lang (or (:language opts) *language*))]
          (process-files in-files out-file)))))


(ns story.main
  (:refer-clojure :exclude (comment))
    [clojure.tools.cli :as cli])

To run from the commandline this namespace must be compiled with a -main method.


Use this program from the commandline like so.

(def usage "Usage: java -jar story.jar [options] <input-files>")
(defn -main [& args]
  (let [[amap tail banner]
        (cli/cli args

Here is a list of the options this program can take when run from the commandline.

                 ["-c" "--comment" "Comment syntax"]
                 ["-b" "--brush" "SyntaxHighlighter brush file" :multi true]
                 ["-t" "--theme" "SyntaxHighlighter theme file"]
                 ["-l" "--language" "SyntaxHighlighter language"]
                 ["-s" "--stylesheet" "A stylesheet file to include"]
                 ["-p" "--production" "Production directory."]
                 ["-v" "--verbose" "Turn on verbose output"
                  :default false :flag true]
                 ["-h" "--help" "Show this help" :default false :flag true])]

Multiple brushes can be used by repeating the -b or --brush options.

If present, the -p or --production option prevents documentation generation, and instead writes a production tree to the supplied directory using write-production-tree.

    (if (or (not (seq tail)) (:help amap))
      (do (println (str usage "\n" banner))
        (System/exit 1))
      (if-let [dir (:production amap)]
        (write-production-tree tail dir)

When no output file is given, the program renders to standard-out.

        (if (= 1 (count tail))
          (apply story amap *out* tail)
          (apply story amap (last tail) (butlast tail)))))))

Javascript setup

This setup code is placed in a function purely to test/show-off story’s anchor generation.

function me_panzoo_story_setup() {

SyntaxHighlighter’s defaults are not suitable, so they are tweaked.

  SyntaxHighlighter.defaults['toolbar'] = false;
  SyntaxHighlighter.defaults['smart-tabs'] = false;
  SyntaxHighlighter.defaults['gutter'] = false;
  SyntaxHighlighter.defaults['unindent'] = false;
  SyntaxHighlighter.defaults['class-name'] = 'code';

h50, the HTML5 outliner is used to create a table of contents.

  var outline = document.createElement('div');
  outline.setAttribute('id', 'outline');
  outline.innerHTML = HTML5Outline(document.body).asHTML(true);
  var children = outline.firstElementChild.firstElementChild.children;
  for (var i = 1; i < children.length; ++i) {

  var h1s = document.getElementsByTagName('h1');
  if (h1s.length > 0) document.title = h1s[0].innerText;

Test code is hidden by default.

  var makeToggle = function(test) {
    var x = document.createElement('div');
    x.setAttribute('class', 'test-toggle');
    x.style.display = 'block';
    x.innerText = '?';
    x.onclick = function() {
      if (test.style.display == 'none') {
        test.style.display = 'block';
      } else {
        test.style.display = 'none';
    return x;
  var tests = document.querySelectorAll('div.test');
  for (var i = 0; i < tests.length; ++i) {
    console.log('test', i, tests[i]);
    var test = tests[i];
    var tog = makeToggle(test);
    test.style.display = 'none';
    test.parentNode.insertBefore(tog, test);

A master toggle is created if there is more than one test section.

  if (tests.length > 1) {
    var masterTog = document.createElement('div');
    masterTog.setAttribute('id', 'master-toggle');
    masterTog.innerText = '? show all';
    masterTog.onclick = function() {
      var show = masterTog.innerText == '? show all';
      var display = show ? 'block' : 'none';
      masterTog.innerText = show ? '? hide all' : '? show all';
      for (var i = 0; i < tests.length; ++i) {
        tests[i].style.display = display;
    var e = document.querySelector('h1').nextSibling;
    e.parentNode.insertBefore(masterTog, e);


Code folding for Vim

Add this code to your ~/.vimrc to enable folding of Markdown files and source files with Markdown comments.

The fold level is determined by the number of # at the start of each heading. Underlined headings are not supported.

Test code is also made foldable.

function! MarkdownLevel(token)
  if 0 == empty(matchstr(getline(v:lnum), '^'.a:token.'<\(?\|\.\)'))
    return 'a1'
  if 0 == empty(matchstr(getline(v:lnum), '^'.a:token.'\(?\|\.\)>'))
    return 's1'
  let level = strlen(matchstr(getline(v:lnum),
        \                     '\(^'.a:token.' \)\@<=#\+\( \)\@='))
  if level == 0
    return "="
    return ">".level

Different comment tokens are supported.

let g:comment#none = ''
let g:comment#semi = ';;'
let g:comment#slashes = '//'
let g:comment#hash = '#'
let g:comment#dblquote = '"'

au BufEnter *.md,*.clj,*.cljs,*.js,*.sh setlocal foldmethod=expr

I don’t know why passing a string literal to MarkdownLevel doesn’t work here. Vimscript is not my forte.

au BufEnter *.md setlocal foldexpr=MarkdownLevel(comment#none)
au BufEnter *.clj,*.cljs setlocal foldexpr=MarkdownLevel(comment#semi)
au BufEnter *.js setlocal foldexpr=MarkdownLevel(comment#slashes)
au BufEnter *.sh setlocal foldexpr=MarkdownLevel(comment#hash)
au BufEnter *.vim setlocal foldexpr=MarkdownLevel(comment#dblquote)

Key bindings

za toggle current fold
zR open all folds
zM close all folds
zr open one more level of folds
zm close one more level of folds