Notebooks on readthedocs

We want notebooks that automatically run through on readthedocs: https://nbsphinx.readthedocs.io/en/0.3.5. So that the basic tutorial (https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/170505_seurat/seurat.ipynb) can be integrated into the scanpy repository in docs/tutorials as a notebook with all output cleared (no images etc.). It is run on the readthedocs server and will produce exactly the same output, as is guaranteed by this test: https://github.com/theislab/scanpy/blob/master/scanpy/tests/notebooks/pbmc3k.py

[grst]

The only thing I need to make sure is if there is a way that people cannot commit notebooks with output in them to the scanpy repo. The latter is an absolute no go.

Should be easy to have that checked by travis

committing things in sphinx-gallery format could be a new way. I’ll check whether this offers some convenience.

If you have any questions/issues regarding this approach, don’t hesitate to open an issue in the jupytext repo. The maintainer is extremely responsive and willing to help.

[falexwolf]

@flying-sheep and anyone interested: I started putting the notebooks on scanpy-tutorials: https://github.com/theislab/scanpy-tutorials and https://scanpy.readthedocs.io/en/latest/tutorials.html now links to the docs generated from scanpy-tutorials.

I’m doing it like this for now as it’s quite a bit less work than getting everything to run on readthedocs, there might indeed be problems with the runtime for building the docs and I think this updated solution isn’t so bad after all…

Opinions are welcome!