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 (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