external tutorials and cleanup

[giovp]

initial tutorial for tf, pinging @hspitzer for reference, not ready for review yet

[review-notebook-app]

Check out this pull request on 

See visual diffs & provide feedback on Jupyter Notebooks.

---

Powered by ReviewNB

[giovp]

I'll push the fixed tutorials with new imagecontainer api here @hspitzer @michalk8

[michalk8]

Ok, just 2 reminders:

• please put the tutorials in docs/source/external_tutorials - the cannot be on the top-level directory, because of nbshpinx
• please make sure that the legends are not overlapping
• you can specify as_array='some'_key' and it will yield just the array from that key (or as_array=['key1', 'key2], which will yield a tuple at every step)

[giovp]

wll do that!

what do you mean by this?

you can specify as_array='some'_key' and it will yield just the array from that key (or as_array=['key1', 'key2], which will yield a tuple at every step)

[michalk8]

what do you mean by this?

img.generate_equal_crops(as_array=True) will yield {'layer_1': <array_1>, 'layer_2': <array_2>},
img.generate_equal_crops(as_array='layer_1') will yield <array_1>
img.generate_equal_crops(as_array=['layer_1', 'layer_2']) will yield (<array_1>, <array_2>)

[giovp]

I'm gonna merge this is not tests error. I feel Ishould do another round anyway but in another PR

[michalk8]

@giovp the thumbnails were wrong, you must put this info to 'metadata' part of the cell, not inside the 'source' (i.e. where the code is) - should be fixed now (I've added one for Napari from cell 6.
I've also fixed some CSS issues with images, already in scverse/squidpy#237

[hspitzer]

@michalk8 @giovp I'll do a review of tutorials and examples now, checking for typos etc. Could we freeze the tutorial and example text until I'm done with that? Especially important for the external tutorial notebooks, as merging them is a pain. I plan to be done by tomorrow morning.

[hspitzer]

@michalk8 @giovp now finished with review. Looks great (and was already great)! I fixed some spelling errors and captions. I also added a lot of citations to references.bib. There are still some left in the "Morans I" section of the H&E tutorial, but I don't know if we even have to add them. They are only referenced once.

I also added the cropping and image container example from #42 @davidsebfischer .

I could not find how to specify the ordering. At least for the images examples, I'd like to have a different one than the one we have right now.

Draft of contributing guide is in in #46

[michalk8]

@hspitzer thanks a lot for the review!

I could not find how to specify the ordering. At least for the images examples, I'd like to have a different one than the one we have right now.

In docs/source/{examples,tutorials}.rst, you can find the glob pattern - you have to mention each tutorial explicitly - here's an example for external tutorials:

External tutorials
------------------
This section contains tutorials showcasing how squidpy can interface with external libraries.

.. nbgallery::
    :glob:

    external_tutorials/tutorial_tf
    external_tutorials/tutorial_napari
    external_tutorials/tutorial_tangram

Re spelling errors: I ran tox -e check-docs, it still caught a few - do you want to handle this or shall I?
I already did it once (allowed wordlist is in docs/source/spelling_wordlist.txt), though external tutorials have been overwritten and need to be done again. The spellchecker is using EN_US (so visualise is a incorrect spelling), but it can be changed it to EN_UK if you want, just let me know so that I can sync it up with the main repo (will do the sync after the tutorial/examples is done).

[michalk8]

I am going to run the spellchecker and also on the main repo.

[michalk8]

I've opted for EN_US and have made spellcheck part of the linting step, it should pass now (fingers crossed).
I've disabled tox -e check-docs, since some remain are broken since we're private, most likely it will be re-enabled in the main repo only.
Going to run the checker on the main repo so that after the tutorial/examples reoder, the doc stylization can be closed.

[hspitzer]

Thanks for dealing with the automated spellchecking! EN_US is fine and more used in software (I just have a lot of UK collabs, and am getting more and more used to the UK spelling). I will push a reordering of the tutorials now.

[giovp]

awesome, I also need to push an additional tutorial on data format. It's very small and should be able to do it by this morning, thank you both!

[hspitzer]

@michalk8 I just saw that there is another docs/source/examples.rst in the main Squidpy repo? Do I have to add the ordering there or here in squidpy notebooks? Probably in the main repo?

[michalk8]

@michalk8 I just saw that there is another docs/source/examples.rst in the main Squidpy repo? Do I have to add the ordering there or here in squidpy notebooks? Probably in the main repo?

Yes, you can just add it here and I will sync it in scverse/squidpy#237

[hspitzer]

@michalk8 I just saw that there is another docs/source/examples.rst in the main Squidpy repo? Do I have to add the ordering there or here in squidpy notebooks? Probably in the main repo?

Yes, you can just add it here and I will sync it in theislab/squidpy#237

great, thanks a lot! Already added here.

[giovp]

I should be able to submit this last tutorial thsi afternoon,and then we can merge this

[giovp]

ok, added the tutorial, I would merge this as is and ask couple of people to review it his weekedn. But can submit minor PR early next week separate for this. If tests passes: LGTM!!!!!!!!