Update tutorials

[Marius1311]

This updates the two tutorials we already had and adds new one, focused on using CellRank when no RNA velocity information is present.

[review-notebook-app[bot]]

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[Marius1311]

@michalk8, the updating of our two old tutorials is done and waiting for your review. In the meantime, I will start with the new tutorial.

[michalk8]

Thanks @Marius1311 , I've left some comments in ReviewNB. Also, since the files were renamed, you should modify the test function names in tests

[Marius1311]

Thanks Mike! I added a putative link to the external page https://cellrank.readthedocs.io/en/latest/external.html - is that correct? Links are checked automatically anyway, aren't they?

[Marius1311]

I've left my comments in ReviewNB.

Thanks! That's a really helpful tool I find.

[michalk8]

Thanks Mike! I added a putative link to the external page https://cellrank.readthedocs.io/en/latest/external.html - is that correct? Links are checked automatically anyway, aren't they?

Not really, because you're still using latest, not stable. Links are not checked automatically, not is spell-checking.

[Marius1311]

Okay, I re-directed all links to stable, but probably missed a few.

[Marius1311]

I'm done with all your comments in ReviewNB.

[Marius1311]

Just need your help with surpressing these ugly warnings, can't figure out how to do it.

[michalk8]

Just need your help with surpressing these ugly warnings, can't figure out how to do it.

Ok, I will handle it.

[michalk8]

Warnings are being filtered now (I've fixed some that we produce), note to self MatplotlibDeprecationWarning is a subclass of UserWarning.

[michalk8]

@Marius1311 please could you stick to using cellrank Jupyter kernel? otherwise, tests are broken, see

kernel_name = 'py38_devel'

    def get_kernel_spec(self, kernel_name):
        """Returns a :class:`KernelSpec` instance for the given kernel_name.

        Raises :exc:`NoSuchKernel` if the given kernel name is not found.
        """
        if not _is_valid_kernel_name(kernel_name):
            self.log.warning("Kernelspec name %r is invalid: %s", kernel_name,
                             _kernel_name_description)

        resource_dir = self._find_spec_directory(kernel_name.lower())
        if resource_dir is None:
>           raise NoSuchKernel(kernel_name)
E           jupyter_client.kernelspec.NoSuchKernel: No such kernel named py38_devel

[Marius1311]

Ok, got it, thanks!

[Marius1311]

Hi @michalk8, the beyond_rna_velocity tutorial is ready for a final round of your review!

[michalk8]

Thanks @Marius1311 , will review it shortly.

[michalk8]

I've fixed some typos, but apart from that, it's really great, I have no objections. I will go over the rest of the tutorials as well and fix latest -> stable.

[Marius1311]

Fantastic work, thanks a lot @michalk8