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+---
+title: "Pangler: literate programming in Pandoc"
+author: Federico Igne
+date: \today
+---
+
+This documents describes the logic and design of `pangler`, a minimal tangler for literate programming using the [Pandoc Markdown syntax](https://pandoc.org/MANUAL.html#pandocs-markdown).
+
+[Literate Programming](https://en.wikipedia.org/wiki/Literate_programming) (LP) is a programming paradigm that emphasize the natural flow of thoughts that the programmer experiences when writing software.
+The paradigm can be seen as "documentation first" and the focus is on "human-to-human" communication.
+The produced document is a text-based prose document describing the logic and the design of the program, interspersed with snippets of code that form the final software.
+
+Given an LP document, one can either extract the *tangled* code (with a "tangler") or generate its documentation, "woven" from the literate input source (with a "weaver").
+
+In this case, [Pandoc](https://pandoc.org) is a very good weaver, supporting the generation of different document formats from a Markdown source.
+This document is an attempt at providing a tangler working alongside Pandoc.
+`pangler` is itself written in Pandoc Markdown format and can be generated from this document using itself.
+
+# Literate programming with `pangler`
+
+`pangler` uses two main features provided by the Pandoc Markdown syntax, which are not necessarily present in other Markdown flavours:
+
+1. [`backtick_code_blocks`](https://pandoc.org/MANUAL.html#extension-backtick_code_blocks) for writing fenced snippets of code, and
+2. [`fenced_code_attributes`](https://pandoc.org/MANUAL.html#extension-fenced_code_attributes) for adding arbitrary HTML attributes, classes and ID to a snippet of code.
+
+## Writing programs
+
+In the following, we indicate a *literate program* as a markdown file written in Pandoc Markdown syntax.
+
+A minimal block of code, recognized by `pangler`, with ID `identifier` is
+
+~~~
+```{#identifier}
+[code snippet]
+```
+~~~
+
+Code blocks can contain **code macros** of the form `<<identifier>>` where `identifier` is a valid code block ID.
+Code macros will be recursively substituted by the corresponding code snippet during [code generation][Tangling: generating the source files].
+A code macro needs to be placed in its own line, with an optional (whitespace) indentation, used during code generation to indent the code snippet.
+
+Additional attributes and classes can be added to a code block, as well;
+the language of the code snippet can be provided and is useful to enable correct syntax highlighting.
+
+~~~
+```{#identifier .python}
+[python code snippet]
+```
+~~~
+
+An identifier can also be a file name matching the following regex
+
+```{#regex_path .rust}
+static ref PATH: Regex =
+  Regex::new(
+    r"^(?:[[:word:]\.-]+/)*[[:word:]\.-]+\.[[:alpha:]]+$"
+  ).unwrap();
+```
+
+In that case the code block is considered a valid **entry point** for the generation of a file with that name.
+The code block defines the content of the new file.
+
+~~~
+```{#file.py .python}
+[python main file]
+```
+~~~
+
+File names can be generated in subfolders using the `path` attribute.
+The following code block determines the content of file `path/to/file.py`.
+
+~~~
+```{#file.py .python path="path/to/"}
+[python main file]
+```
+~~~
+
+This path is relative to the current working directory, unless [the `-o`/`--output` flag is used][Command Line Interface].
+
+Code blocks without an ID are ignored.
+
+```{#code_block_gathering .rust}
+if !id.is_empty() {
+  let key = {
+    let path = attrs.iter().find(|(k,_)| k == "path");
+    if let Some(path) = path {
+      format!("{}{}", path.1, id) 
+    } else {
+      id.to_string()
+    }
+  };
+  <<code_block>>
+} else {
+  eprintln!("Ignoring code block without ID:");
+  eprintln!("{}", indent(Cow::from(code),4));
+}
+```
+
+Code blocks are processed in order.
+By default, if an identifier is already defined, the code block is appended to the current corresponding value.
+
+Use the `override` class in the code block definition to cause the block to override the previous entry with the same key, if this exists.
+
+~~~
+```{#identifier .python .override}
+[Python code snippet]
+```
+~~~
+
+This is handled in code as follows
+
+```{#code_block .rust}
+if clss.iter().any(|c| c == "override") {
+  blocks.insert(key, Cow::from(code));
+} else {
+  blocks.entry(key)
+        .and_modify(|s| {
+          *s += "\n";
+          *s += Cow::from(code)
+        })
+        .or_insert(Cow::from(code));
+}
+```
+
+## Tangling: generating the source files
+
+To bootstrap the tangling process, an early version of `pangler` is provided under `bin/` in this repository.
+
+You can generate the code for the current version of the program, in the current working directory, with
+
+```sh
+./bin/pangler-v0.1.0 README.md
+```
+
+and compile it with
+
+```sh
+cargo build --release
+```
+
+From now on you can make changes to the `README.md` file and use the latest version of `pangler` to tangle and compile it.
+
+## Weaving: generating the documentation
+
+As explained above we use [`pandoc`](https://pandoc.org/) as a weaver.
+Run the following command to generate a PDF file for this document
+
+```sh
+pandoc --to latex \
+       --listings \
+       --number-sections \
+       --lua-filter=util/weaver.lua \
+       --output pangler.pdf \
+       README.md
+```
+
+The Lua filter `util/weaver.lua` is provided to handle custom `pangler` attributes during the PDF generation via the \LaTeX\ engine.
+
+## Integration with (Neo)Vim
+
+(Neo)Vim supports code highlighting inside Markdown blocks, when the programming language is provided among its attributes.
+Add the following to your config file to enable code highlighting for a specific set of languages
+
+```vimscript
+let g:markdown_fenced_languages =
+  ['python','rust','scala']
+```
+
+# Command Line Interface
+
+`pangler` offers a very simple command line interface.
+For an overview of the functionalities offered by the tool run
+
+```sh
+pangler --help
+```
+
+`pangler` uses the `clap` library to parse command line arguments
+
+```{#dependencies .toml}
+clap = { version = "3.1", features = ["derive"] }
+```
+
+```{#uses .rust}
+use clap::Parser;
+```
+
+using the [Derive API](https://github.com/clap-rs/clap/blob/v3.1.18/examples/tutorial_derive/README.md) to define the exposed functionalities.
+The `struct` holding the CLI information is defined as follow
+
+```{#config .rust}
+/// A tangler for Literate Programming in Pandoc
+#[derive(Parser, Debug)]
+#[clap(author, version, about, long_about = None)]
+struct Config {
+  <<config_depth>>
+  <<config_output>>
+  <<config_input>>
+}
+```
+
+and the arguments are parsed as
+
+```{#config_parse .rust}
+let config = Config::parse();
+```
+
+`pangler` accepts a sequence of files that will be parsed, code will be collected and used to build the final program.
+Note that the order of the file provided on the CLI is important when using the [overriding functionality][Writing programs].
+
+```{#config_input .rust}
+/// Input files
+input: Vec<PathBuf>,
+```
+
+By default, files are generated in the current working directory.
+
+```{#constants .rust}
+const BASE: &str = "./";
+```
+
+This behaviour can be overridden using the `-o`/`--output` flag.
+
+```{#config_output .rust}
+/// Base output directory [default: './']
+#[clap(short, long)]
+output: Option<PathBuf>,
+```
+
+Finally, recursive substitution of blocks can lead to an infinite loop.
+By default, `pangler` will stop after 10 substitution iterations, but this parameter can be changed with the `-d`/`--depth` flag.
+
+```{#config_depth .rust}
+/// Maximum substitution depth
+#[clap(short, long, default_value_t = 10)]
+depth: u32,
+```
+
+# The program
+
+The program is structured as a single Rust file with the following being the main entry point of the program
+
+```{#main.rs .rust path="src/"}
+<<uses>>
+
+<<constants>>
+
+<<config>>
+
+<<types>>
+
+<<functions>>
+
+fn main() -> Result<()> {
+  <<config_parse>>
+  <<pandoc_setup>>
+  Ok(())
+}
+```
+
+## Pandoc
+
+We are using [`rust-pandoc`](https://github.com/oli-obk/rust-pandoc) and [`pandoc-ast`](https://github.com/oli-obk/pandoc-ast) to interact with `pandoc` from Rust.
+
+```{#dependencies .toml}
+pandoc = "0.8"
+pandoc_ast = "0.8"
+```
+
+```{#uses .rust}
+use pandoc::{
+  InputFormat,InputKind,OutputFormat,OutputKind,Pandoc
+};
+use pandoc_ast::Block;
+```
+
+First we need to initialize a new `Pandoc` struct
+
+```{#pandoc_setup .rust}
+let mut pandoc = Pandoc::new();
+```
+
+and set up the input parameters.
+The input is a sequence of Markdown files passed as config options from the CLI.
+
+```{#pandoc_setup .rust}
+pandoc.set_input(InputKind::Files(config.input));
+pandoc.set_input_format(InputFormat::Markdown, vec![]);
+```
+
+The output is piped to stdout in JSON format.
+
+```{#pandoc_setup .rust}
+pandoc.set_output(OutputKind::Pipe);
+pandoc.set_output_format(OutputFormat::Json, vec![]);
+```
+
+In this way, we will be able to pipe the output into a Pandoc filter that will collect the code snippets and build the codebase for us.
+
+```{#pandoc_setup .rust}
+pandoc.add_filter(
+  move |json| pandoc_ast::filter(json,
+    |pandoc| {
+      <<pandoc_filter>>
+    }
+  )
+);
+pandoc.execute().unwrap();
+```
+
+## Pandoc filters
+
+Pandoc allows for the definition of [custom filters](https://pandoc.org/filters.html) to change the abstract syntax tree of a document.
+
+In this case we use a filter to collect code snippets from the input Markdown text into a `HashMap`, mapping code block identifiers to code block snippets.
+
+```{#uses .rust}
+use std::borrow::Cow;
+use std::collections::HashMap;
+```
+
+```{#types .rust}
+type Blocks<'a> = HashMap<String,Cow<'a,str>>;
+```
+
+Code blocks are wrapped into a [`Cow`](https://doc.rust-lang.org/stable/std/borrow/enum.Cow.html), i.e., a "copy-on-write" smart pointer, to avoid string duplication, unless strictly necessary.
+
+We iterate over all code blocks, along with their IDs, classes and attributes, collecting them
+
+```{#pandoc_filter .rust}
+let mut blocks: Blocks = HashMap::new();
+pandoc.blocks.iter().for_each(|block|
+  if let Block::CodeBlock((id,clss,attrs), code) = block {
+    <<code_block_gathering>>
+  }
+);
+```
+
+And then we build the source code, making sure to cut off recursive code generation with depth larger than `config.depth`.
+
+```{#pandoc_filter .rust}
+build(&config.output, &blocks, config.depth);
+```
+
+The filter returns the Pandoc JSON unchanged.
+
+```{#pandoc_filter .rust}
+pandoc
+```
+
+## Source code generation
+
+In order to build the source code from the gathered code block snippets, we need to recursively substitute *code macros* of the form `<<identifier>>` with the corresponding code block.
+
+Code macros are matched with the following regex
+
+```{#regex_macro .rust}
+static ref MACRO: Regex =
+  Regex::new(
+    r"(?m)^([[:blank:]]*)<<([^>\s]+)>>"
+  ).unwrap();
+```
+
+Note that, when matching the code macro, we keep track of its indentation as well, in order to properly indend code.
+
+Given a code macro, the following closure will compute the substituting block of code, properly indented.
+The input `Captures` structure is a vector with the regex capture groups, i.e., indentation and macro identifier, along with the full match in the first position.
+
+In case we reach the maximum allowed depth we truncate code block substitution and notify the user that something might not have been generated as expected.
+
+```{#macro_closure .rust}
+|caps: &Captures| {
+  if current_depth < max_depth {
+    let block = blocks
+      .get(&caps[2])
+      .expect("Block not present")
+      .clone();
+    indent(block, caps[1].len())
+  } else {
+    eprintln!("Reached maximum depth, \
+               output might be truncated.\n\
+               Increase `--depth` accordingly.");
+    Cow::Owned(String::from(""))
+  }
+}
+```
+
+As explained above, the building process iterates over all collected blocks and detects relevant entry points (files to generate) to start the recursive macro substitution.
+
+```{#functions .rust}
+fn build(
+  base: &Option<PathBuf>,
+  blocks: &Blocks,
+  max_depth: u32
+) {
+  <<regex_definition>>
+  blocks
+    .iter()
+    .for_each(|(path,code)| if PATH.is_match(path) { 
+      <<code_generation>>
+    })
+}
+
+```
+
+### Recursive macro substitution
+
+The code generating algorithm went through multiple iterations and showed some interesting details of using `Cow`s.
+
+```{#code_generation .rust}
+let mut current_depth = 0;
+let mut code = code.clone();
+while MACRO.is_match(&code) {
+  code = MACRO.replace_all(
+    &code,
+    <<macro_closure>>
+  );
+  current_depth += 1;
+}
+```
+
+The problem with this version is that, due to how `Cow` works, the value returned by `replace_all` cannot live longer than the borrowed `code` passed as a parameter.
+This is because the function returns a reference to `code` (`Cow::Borrowed`) if no replacement takes place, so for the returned value to be valid, `code` still needs to be available.
+But here, `code` gets overridden right away, so, in principle, if no replacement takes place `code` gets overridden by a reference to itself (losing data).
+
+However, note that this doesn't happen in practice (but the compiler doesn't know about this) because the `replace_all` function is applied as long as some replacement is possible (`while`
+condition).
+In other words, all calls to `replace_all` always return an `Cow::Owned` value.
+
+The problem is solved by a clever use of pattern matching
+
+```{#code_generation .rust .override}
+let mut current_depth = 0;
+let mut code = code.clone();
+while let Cow::Owned(new_code) = MACRO.replace_all(
+  &code,
+  <<macro_closure>>
+) {
+  code = Cow::from(new_code);
+  current_depth += 1;
+}
+```
+
+In this case, the matched `Cow::Owned` is not concerned by any lifetime (the type is `Cow<'_,str>`) of the borrowed value `code`.
+Moreover `code` takes ownership of `new_code: String` using the `Cow::from()` function.
+No heap allocation is performed, and the string is not copied.
+
+Finally, we write the code to file
+
+```{#code_generation .rust}
+let file = base
+  .clone()
+  .unwrap_or(PathBuf::from(BASE))
+  .join(path);
+write_to_file(file, &code)
+  .expect("Unable to write to file");
+```
+
+## Additional details
+
+### Code indentation
+
+When (positive) code indentation is required, the processed block of code is indented by `indent`.
+
+```{#indent_prefix .rust}
+let prefix = format!("{:indent$}", "");
+```
+
+Each line is then `prefix`ed separately and the result is returned.
+
+```{#functions .rust}
+fn indent<'a>(
+  input: Cow<'a,str>,
+  indent: usize
+) -> Cow<'a,str> {
+  if indent > 0 {
+    <<indent_prefix>>
+    let size = input.len() + indent*input.lines().count();
+    let mut output = String::with_capacity(size);
+    input.lines().enumerate().for_each(|(i,line)| {
+      if i > 0 {
+        output.push('\n');
+      }
+      if !line.is_empty() {
+        output.push_str(&prefix);
+        output.push_str(line);
+      }
+    });
+    Cow::Owned(output)
+  } else {
+    input
+  }
+}
+
+```
+
+Note that, if no indentation is required (i.e., `indent` is equal to 0), no additional allocation is performed, and the `input` is returned as is.
+
+### RegEx matching
+
+`pangler` uses the `regex` library to perform regular expression matching and substitution.
+Moreover, the library suggests the use of `lazy_static` to ensure that the regexes used are compiled exactly once per execution.
+
+
+```{#dependencies .toml}
+lazy_static = "1.4"
+regex = "1.5"
+```
+
+```{#uses .rust}
+use lazy_static::lazy_static;
+use regex::{Captures,Regex};
+```
+
+We wrap the regex definition in a `lazy_static` macro
+
+```{#regex_definition .rust}
+lazy_static! {
+  <<regex_path>>
+  <<regex_macro>>
+}
+```
+
+### Writing to file
+
+Writing to file is an operation performed using the Rust support for OS operations from the standard library.
+
+```{#uses .rust}
+use std::fs;
+use std::io::Result;
+use std::path::PathBuf;
+```
+
+First, all necessary parent directories of `path` are created
+
+```{#parent_directory_creation .rust}
+fs::create_dir_all(path.parent().unwrap())?;
+```
+
+and then the `content` is written to the file provided by 
+    
+```{#write_to_file .rust}
+fs::write(path, content)?;
+```
+
+We perform a check on `path` and only write the content to the file if the path is relative to the current working directory.
+
+```{#functions .rust}
+fn write_to_file(
+  path: PathBuf, content: &str
+) -> std::io::Result<()> {
+  if path.is_relative() {
+    <<parent_directory_creation>>
+    <<write_to_file>>
+  } else { 
+    eprintln!(
+      "Absolute paths not supported: {}",
+      path.to_string_lossy()
+    )
+  }
+  Ok(())
+}
+
+```
+
+# Credits
+
+`pangler v0.2.0` was created by Federico Igne (git@federicoigne.com) and available at [`https://git.dyamon.me/projects/pangler`](https://git.dyamon.me/projects/pangler).
+
+```{#Cargo.toml .toml}
+[package]
+name = "pangler"
+version = "0.2.0"
+edition = "2021"
+
+[dependencies]
+<<dependencies>>
+```
diff --git a/util/weaver.lua b/util/weaver.lua
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--- /dev/null
+++ b/util/weaver.lua
@@ -0,0 +1,34 @@
+if FORMAT:match 'latex' then
+  -- Setting custom `listings` style
+  function Meta(m)
+    m["header-includes"] = pandoc.MetaBlocks({pandoc.RawBlock("latex",[[
+        \lstdefinestyle{weaver}{
+            basicstyle=\small\ttfamily,
+            backgroundcolor=\color{gray!10},
+            xleftmargin=0.5cm,
+            numbers=left,
+            numbersep=5pt,
+            numberstyle=\tiny\color{gray},
+            captionpos=b
+        }
+        \lstset{style=weaver}
+    ]])})
+    return m
+  end
+  function CodeBlock(b)
+    -- Remove `path` attribute and merge it with `id`
+    if b.attributes.path and b.identifier then
+      b.identifier = b.attributes.path .. b.identifier
+      b.attributes.path = nil
+    end
+    -- Add ID to caption
+    if b.identifier then
+      if b.attributes.caption then
+        b.attributes.caption = b.identifier .. ": " .. b.attributes.caption
+      else
+        b.attributes.caption = b.identifier
+      end
+    end
+    return b
+  end
+end