integration with jupyter?

[Benfeitas]

Awsome job on this! I am wondering if you see this being used in jupyter md? Thanks a lot in advance!

[diallobakary4]

A Jupiter notebook can be converted such that only the markdown cell are outputted. This following command is exhaustive in doing and you may find more details in the documentation.
jupiter nbconvert --to markdown --no-prompt --no-input --TemplateExporter.exclude_raw=True TemplateExporter.exclude_output=True --MarkdownExporter.exclude_code_cell=True --MarkdownExporter.exclude_input=True --MarkdownExporter.exclude_input_prompt=True --MarkdownExporter.exclude_output=True --MarkdownExporter.exclude_output_prompt=True --MarkdownExporter.exclude_raw=True --MarkdownExporter.exclude_unknown=True output.md
The notebook is exported into markdown.
So following the markdown syntax here while writing in your notebook and the markdown file can easily be converted to a manuscript using pandoc. Obviously, pandoc cross-ref and pandoc cite-proc will be doing the majority of the conversion for crossreferencing and citations. Pandoc-csv2table and pandoc-placetable are two interesting filters to automatically refer to a csv file in the markdown (import the csv as a markdown table).
It allows also some formatting flexibility when submitting to journals with different formatting. Pandoc has the --reference-doc=reference_doc.docx option, "reference_doc.docx" can be any journal word template. Some minor manual adjustment may be required. In a similar when exporting to pdf you can use a latex template,

[Benfeitas]

@diallobakary4 thank you so much, this is very useful! I am only getting started at using jupyter for this function. Perhaps a bit unrelated to this thread, but do you have any reference guide for the pandoc filters?

[diallobakary4]

There is the pandoc website https://pandoc.org/filters.html
Also most filters have a github page on which there is the related documentation:
https://github.com/jgm/pandoc-citeproc
https://github.com/lierdakil/pandoc-crossref
https://github.com/baig/pandoc-csv2table
Some interesting reading here:
https://pandoc-scholar.github.io/
https://blog.kdheepak.com/downloads/writing-papers-with-markdown.ieee.pdf
It will really be great to have all of integrated into the Jupyter lab and notebook by default as the format is popular in teaching and academia. It can really speed up the formatting process and the attached notebook to publications will make research reproducible and facilitate access to raw data.

[diallobakary4]

Another interesting approach here https://github.com/chrisjsewell/ipypublish

[Benfeitas]

Linked