RootMD 🩺 👩🏼‍⚕️

Scientific reports/literate programming tool for CERN ROOT and c++. RootMD is a markdown (and other format) processor for mark up with ROOT-flavored c++ code. RootMD can execute c++ code and inject the output (from stdout, stderr) and link or embed image outputs. Provides a format for producing code + result for better documentation / notes. This is by design not a jupyter notebook, e.g. not a REPL-like environment. If you like Jupyter notebooks then use that :).

Features

• execute c++ code blocks via ROOT REPL
• capture stdout, stderr and inject into output
• embed (base64) or link to any image files produced
• output to HTML, Markdown (or obsidian flavored markdown), or as a presentation (via Marp)
• execute html, css, javascript code blocks (for html output) to customize output

usage

usage: rootmd [-h] [--output OUTPUT]
              [--format {html,md,obsidian,json,terminal}] [--embed]
              [--asset-dir ASSET_DIR] [--verbosity VERBOSITY]
              [--watch WATCH] [--run RUN] [--clean] [--no-exec]
              input

Convert Markdown with inline c++ code to ROOT output.

positional arguments:
  input                 input Markdown file to execute and convert

optional arguments:
  -h, --help            show this help message and exit
  --output OUTPUT       output filename default <input>.<ext> where <ext>
                        is determined by the chosen format, default html
  --format {html,md,obsidian,json,terminal}
                        output format
  --embed               embed images as base 64
  --asset-dir ASSET_DIR
                        specify asset output directory, paths are NOTE re-
                        written to support unless using obsidian format
  --verbosity VERBOSITY
                        specify log verbosity
  --watch WATCH         watch a file or directory for changes
  --run RUN             command to run after processing a file. The
                        filename can be substituted into the command string
                        with {{file}}. Example: --run="echo {{file}}"
  --clean               clean artifacts, caution - should only use with
                        embed or asset copy to <asset-dir>
  --no-exec             Do not execute any code blocks, just process file
                        (useful for viewing and testing conversion)

TODO

• make it a python package (so that it can be installed via pip)
  • Look into poetry
  • start versioning
• support output verbosity levels
  • & make output useful
• Add comment for input block identification upon processing
• add watch functionality for reprocessing a file on change
  • Add some additional features
  • Handle watch of multiple files, and how output filename should be named
• Add terminal output using rich pretty output package
  • consider iterm image support? See here
  • Basically, markdown output on the terminal : using rich
• Add prismjs for inline code
• test some failure modes when root code has errors leading to hang
• add mathjax to html output for inline mathematics
• "import" source files into output? So that you can write code in separate file but sow it in the output?
  • add as a block option
• support for other "languages", e.g. shell
• support for ROOTJS in HTML output
  • embed histogram as JSON object in HTML
• clean assets in embed mode or other output path
• download + embed external JS for fully contained, offline ready single file HTML output
• Load HTML / CSS defaults from a file in the package
• Better style HTML output (input / output cells more like Jupyter)
  • Consider adding JS for collapsing headings, output blocks etc.
• add format option to output a ROOT macro with markdown and output converted to comments
• integrate usage of RNUplot for graphical output!
• implement an auto-draw so that you dont have to "Print(...)" every block
• block option: run code block as a "macro"
  • You can already use .L, .x
• move ROOT executor into member not superclass
• auto-draw dont do it for cells without any drawing!
• PDF support
• Better PDF embed (link to file) (for Firefox especially) using canvas : https://stackoverflow.com/questions/2104608/hiding-the-toolbars-surrounding-an-embedded-pdf
• Embed PDF base64 in object tag

Feature wish list

• Cache blocks of code for faster rerun
• server for "sharing" of documents, from command line - use secret links
• Technique for RAW output?
  • i.e. write out HTML Table or markup
• inline code replacement, e.g. "We ran TString::Format("%d",tree->GetEntries()) events."

Improve ROOT?

• Apply some default style options

Known issues

• watch isnt working, especially when input not given
• something is surely broken

ROOT REPL issues

ROOT REPL struggles with multi-line code:

• function definitions with "{" on next line does not work since it doesn't understand

void hello() {
  // this works
}

void world() 
{
  // this DOES NOT work
}

Dependencies

RootMD itself is a pure python package which uses:

• mistletoe : python markdown parser and processor
• rich : Rich for pretty terminal output
• pyyaml : for parsing yaml front matter
• Dependencies for HTML output
  • prismjs for syntax highlighting in HTML output
  • mathjax for rendering mathematics
• ROOT : installed on system and available on PATH

Example : see example_in.md and example.md

This is a simple example of markdown processed by RootMD. You can include any c++ code that ROOT can handle. For instance (using ROOT6) this part of the file was processed with

rootmd example_in.md -f md -o example.md

cout << "Hello from ROOT (stdout)" << endl;
cerr << "Hello from ROOT (stderr)" << endl;

# Block [0]
Hello from ROOT (stdout)
Hello from ROOT (stderr)

TH1 * h1 = new TH1F( "hGaus", ";x;counts", 100, -5, 5 );
h1->FillRandom( "gaus", 10000 );
h1->Draw( "pe" );
h1->Draw( "same hist" );
gPad->Print( "h1.svg" );

# Block [1]
Info in <TCanvas::MakeDefCanvas>:  created default TCanvas with name c1
Info in <TCanvas::Print>: SVG file h1.svg has been created