pip install dissertate

In nb_config.py,

import dissertate

c = get_config()

c.Exporter.preprocessors = ['dissertate.preprocessors.CellElider',
                            'dissertate.preprocessors.EmptyCellElider']

c.Exporter.template_file = dissertate.markdown_template_path()

then,

jupyter nbconvert --config nb_config.py --to markdown your_nb.ipynb

If you don't want a cell in the output, edit the cell metadata to include,

{"tags": ["private"]}

Alternatively, you can use

{"tags": ["todo"]}

or,

{"tags": ["setup"]}

for semantic differences that have no effect on dissertate processing.

If you want to retain the output of the cell but not the code (e.g., for an emitted matplotlib graph),

{"tags": ["output-generator"]}