reportsrender 0.2

Execute and Render notebooks as HTML reports.

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 rmd my_notebook.Rmd report.html

• Execute a parametrized jupyter notebook with papermill

reportsrender 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.

Usage:
  reportsrender <notebook> <out_file> [options]
  reportsrender --help

Options:
  -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]

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       User `papermill` to execute the notebook. Works for every
                    kernel available in the jupyter installation.

Installation

Conda (recommended):

As this package dependes on both R and Python packages, I recommend to install the package through conda.

I yet need to create a conda package and upload it on conda-forge, but you can create the following environment and install the package:

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

Manual install:

Get dependencies:

• Python

• pandoc

For the Rmarkdown render engine additionally:

• R and the following packages:

rmarkdown
reticulate

Install from github:

pip install flit
flit installfrom github:grst/reportsrender