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[MRG] update documentation & add notebooks to docs #631

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merged 25 commits into from Mar 7, 2019

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ctb commented Jan 14, 2019

This reorganizes the documentation and adds Jupyter notebooks + binder links. See

for the major points of reorg.

Rendered notebooks are under the add-nbsphinx branch on readthedocs. Direct links:

both tutorials are also now updated to work, and to use bioconda:

Fixes #430 #552. See #628 for related discussions. Includes cleanup from #607.

TODO:

  • link these into the rest of the documentation :)
  • add binder integration so that from the documentation, you can directly click to execute notebooks
  • add relative links between notebooks so that once in binder, you don't have to start up an independent binder
  • before merge, check to make sure that we're pointing binder at the right branch (master, presumably)

Checklist:

  • Is it mergeable?
  • make test Did it pass the tests?
  • make coverage Is the new code covered?
  • Did it change the command-line interface? Only additions are allowed
    without a major version increment. Changing file formats also requires a
    major version number increment.
  • Was a spellchecker run on the source code and documentation after
    changes were made?
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codecov bot commented Jan 14, 2019

Codecov Report

Merging #631 into master will not change coverage.
The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #631   +/-   ##
=======================================
  Coverage   89.47%   89.47%           
=======================================
  Files          27       27           
  Lines        4238     4238           
  Branches       39       39           
=======================================
  Hits         3792     3792           
  Misses        446      446

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ctb commented Jan 14, 2019

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ctb commented Feb 17, 2019

This is ready for initial commentary @luizirber @taylorreiter - thoughts very welcome!

@ctb ctb referenced this pull request Feb 23, 2019

Closed

[WIP] Remove outdated files in preparation for a 2.0.0 release. #607

0 of 5 tasks complete

@ctb ctb changed the title [WIP] add notebooks to readthedocs site [WIP] update documentation & add notebooks to docs Feb 23, 2019

@ctb ctb changed the title [WIP] update documentation & add notebooks to docs [MRG] update documentation & add notebooks to docs Feb 23, 2019

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ctb commented Feb 23, 2019

Ready for review @luizirber @taylorreiter @bluegenes - once this is reviewed and OKed, I will update all the references to the add/nbsphinx branch to point to master, and then merge.

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taylorreiter commented Mar 1, 2019

  • I don't see the "Notebooks" section at sourmash.readthedocs.io
  • I like that you link to other notebooks at the bottom of each notebook
  • "sourmash: working with private collections of signatures" In[2] currently has output that indicates the signatures are already present, so the calculations do not occur. I can't find the big_genomes directory to see whether this is expected behavior (did big_genomes get switched to genomes?). If it is, maybe we should make a note of it in the notebook?

Otherwise, LGTM!

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ctb commented Mar 3, 2019

Thanks @taylorreiter!

Curious - why are you looking for the Notebooks section? :) (I had that in earlier, but then I refactored.) Do I have a reference to it somewhere?

Thanks for the catch re big_genomes! It's created in the top of the notebook (mkdir -p ...) so that's no problem; I've redone the signature calculation and pushed updates.

If it looks good, I think it's ready to be approved (and then I'll go update all of the URLs before merging)

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luizirber left a comment

Fix the binder/environment.yml channel order, and good to go!

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ctb commented Mar 6, 2019

ok. maybe I didn't do this right? but it should be ready.

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ctb commented Mar 6, 2019

(that is, ready to be approved. I'll need to do the branch name editing before merging.)

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luizirber commented Mar 7, 2019

@ctb it's approved now. MacOS wheel building seems to be failing on Travis, probably related to joerick/cibuildwheel#122 (will check)

@ctb ctb merged commit 8797eb6 into master Mar 7, 2019

@ctb ctb deleted the add/nbsphinx branch Mar 7, 2019

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ctb commented Mar 7, 2019

thx all!

luizirber added a commit that referenced this pull request Mar 19, 2019

[MRG] update documentation & add notebooks to docs (#631)
This reorganizes the documentation and adds Jupyter notebooks + binder links. 

* remove out of date notebooks

* remove outdated scripts

* configure nbsphinx and add a test notebook

* add nbsphinx to reqs

* add 2019-upr-kmers notebooks and example files

* add/update notebooks

* add binder configuration

* remove dockerfile

* update notebooks, link into documentation

* fix formatting issue that looks like a typo

* update basic sourmash tutorial commands to work, mostly

* fix sourmash_databases link

* updated tutorials

* fix spacing

* significant documentation reorganization and (hopefully) simplification

* add tutorial master index back in

* add dashing and hulk refs

* add bigsi

* fix branch reference for notebook so that it works

* update notebook with signature recalculation

* fix order of bioconda channels

* fix URLs
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