knitty 0.4.19

Inrterface wrapper for Stitch/Knotr: reproducible report generation tool via Jupyter, Pandoc and Markdown. Export to Jupyter notebook via Notedown.

Knitty

Knitty is a Pandoc filter and Atom/Hydrogen friendly inrterface wrapper for Stitch/Knotr: reproducible report generation tool via Jupyter, Pandoc and Markdown. Insert python code (or other Jupyter kernel code) to the Markdown document and have code's results in the output document. Exports to Jupyter notebook via Notedown.

See Knitty documentation.

You can use vscode-ipynb-py-converter to convert .ipynb to .py to use with Knitty.

Install

Install as part of Pandoctools - convenient interface and works out of the box.

Needs Python 3.6+ but you can have other versions via Jupyter kernels as Knitty can use any installed kernel.

Via conda:

conda install -c defaults -c conda-forge knitty

Via pip:

pip install knitty

Optional install

If you would like to use knotedown to import from R Markdown you need installed knitr:

conda install r-knitr r-reticulate

Usage

Unix:

export PYTHONIOENCODING=utf-8

input_file="doc.md"
metadata="metadata.yml"
reader_args=(-f markdown)
writer_args=(-t html --standalone --self-contained)

cat "${input_file}" | \
pre-knitty "${input_file}" --yaml "$metadata" | \
pandoc "${reader_args[@]}" -t json | \
knitty "${input_file}" "${reader_args[@]}" "${writer_args[@]}" | \
pandoc -f json "${writer_args[@]}" -o "${input_file}.html"

Windows:

chcp 65001 > NUL
set PYTHONIOENCODING=utf-8

set input_file=doc.md
set metadata=metadata.yml
set reader_args=-f markdown
set writer_args=-t html --standalone --self-contained

type "%input_file%" | ^
pre-knitty "%input_file%" --yaml "%metadata%" | ^
pandoc %reader_args% -t json | ^
knitty "%input_file%" %reader_args% %writer_args% | ^
pandoc -f json %writer_args% -o "%input_file%.html"

Jupyter kernel specification in metadata section:

---
kernelspec:
  display_name: R
  language: R
  name: ir
...

Export to Jupyter notebook with cross-references (using pandoc-crossref: download) and execute it:

export PYTHONIOENCODING=utf-8

input_file="doc.md"
metadata="metadata.yml"
reader_args=(-f markdown)
jupymd="markdown-bracketed_spans-fenced_divs-link_attributes-simple_tables\
-multiline_tables-grid_tables-pipe_tables-fenced_code_attributes\
-markdown_in_html_blocks-table_captions-smart"
writer_args=(-t "$jupymd" --standalone --self-contained --filter pandoc-crossref)

cat "${input_file}" | \
pre-knitty "${input_file}" --yaml "$metadata" | \
pandoc "${reader_args[@]}" -t json | \
knitty "${input_file}" "${reader_args[@]}" "${writer_args[@]}" --to-ipynb | \
pandoc -f json "${writer_args}" | \
post-knitty --to-ipynb | \
jupyter nbconvert --to notebook --execute --stdin --stdout > \
"${input_file}.ipynb"