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.
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.
See the documentation for more details!
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"
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.
As this reportsrender dependes on both R and Python packages, I recommend to install it through conda. The following command will install reportsrender and all its dependencies in the current conda environment:
conda install -c conda-forge grst::reportsrender
If you prefer not to use conda, you can follow the approach below:
For the Rmarkdown render engine additionally (there is no need to install them if you are not going to use the Rmarkdown rendeirng engine):
R and the following packages:
Install from pip:¶
pip install reportsrender
Install from github:¶
pip install flit flit installfrom github:grst/reportsrender