reportsrender 0.3.1

Generate reproducible reports from Rmarkdown or jupyter notebooks

Reportsrender allows to create reproducible, consistently looking HTML reports from both jupyter notebooks and Rmarkdown files. It makes use of papermill and Rmarkdown to execute notebooks and uses Pandoc to convert them to HTML.

Features:

• two execution engines: papermill and Rmarkdown.

• support any format supported by jupytext.

• create self-contained HTML that can be shared easily.

• hide inputs and/or outputs of cells.

• parametrized reports

See the documentation for more details!

Getting started

• Execute an rmarkdown document to HTML using the Rmarkdown engine

reportsrender --engine=rmd my_notebook.Rmd report.html

• Execute a parametrized jupyter notebook with papermill

reportsrender --engine=papermill jupyter_notebook.ipynb report.html --params="data_file=table.tsv"

TODO add example notebooks.

Usage from command line

reportsrender

Execute and render a jupyter/Rmarkdown notebook.
The `index` subcommand generates an index html
or markdown file that links to html documents.

Usage:
  reportsrender <notebook> <out_file> [--cpus=<cpus>] [--params=<params>] [--engine=<engine>]
  reportsrender index [--index=<index_file>] [--title=<title>] [--] <html_files>...
  reportsrender --help

Arguments and options:
  <notebook>            Input notebook to be executed. Can be any format supported by jupytext.
  <out_file>            Output HTML file.
  -h --help             Show this screen.
  --cpus=<cpus>         Number of CPUs to use for Numba/Numpy/OpenBLAS/MKL [default: 1]
  --params=<params>     space-separated list of key-value pairs that will be passed
                        to papermill/Rmarkdown.
                        E.g. "input_file=dir/foo.txt output_file=dir2/bar.html"
  --engine=<engine>     Engine to execute the notebook. [default: auto]

Arguments and options of the `index` subcommand:
  <html_files>          List of HTML files that will be included in the index. The tool
                        will generate relative links from the index file to these files.
  --index=<index_file>  Path to the index file that will be generated. Will be
                        overwritten if exists. Will auto-detect markdown (.md) and
                        HTML (.html) format based on the extension. [default: index.html]
  --title=<title>       Headline of the index. [default: Index]

Possible engines are:
  auto                  Use `rmd` engine for `*.Rmd` files, papermill otherwise.
  rmd                   Use `rmarkdown` to execute the notebook. Supports R and
                        python (through reticulate)
  papermill             Use `papermill` to execute the notebook. Works for every
                        kernel available in the jupyter installation.

Installation

conda create -c bioconda -c conda-forge -n reportsrender \
      "python>=3.6" \
      "r-base>=3.5" \
      r-rmarkdown \
      r-reticulate \
      r-bookdown \
      flit \
      pandoc

conda activate reportsrender
flit installfrom github:grst/reportsrender

rmarkdown
reticulate

pip install flit
flit installfrom github:grst/reportsrender