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

ctb · 2019-01-14T18:16:01Z

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?

codecov · 2019-01-14T18:21:41Z

Codecov Report

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

@@           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 · 2019-01-14T18:24:46Z

w00t the basic config seems to work! https://sourmash.readthedocs.io/en/add-nbsphinx/test-notebook.html

ctb · 2019-02-17T17:44:12Z

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

ctb · 2019-02-23T15:06:18Z

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.

taylorreiter · 2019-03-01T18:58:02Z

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!

ctb · 2019-03-03T17:52:52Z

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)

luizirber

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

binder/environment.yml

ctb · 2019-03-06T23:42:22Z

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

ctb · 2019-03-06T23:42:41Z

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

luizirber · 2019-03-07T00:29:16Z

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

ctb · 2019-03-07T01:35:48Z

thx all!

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

Updates the requirements on [pytest-cov](https://github.com/pytest-dev/pytest-cov) to permit the latest version. <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst">pytest-cov's changelog</a>.</em></p> <blockquote> <h2>5.0.0 (2024-03-24)</h2> <ul> <li>Removed support for xdist rsync (now deprecated). Contributed by Matthias Reichenbach in <code>[#623](pytest-dev/pytest-cov#623) <https://github.com/pytest-dev/pytest-cov/pull/623></code>_.</li> <li>Switched docs theme to Furo.</li> <li>Various legacy Python cleanup and CI improvements. Contributed by Christian Clauss and Hugo van Kemenade in <code>[#630](pytest-dev/pytest-cov#630) <https://github.com/pytest-dev/pytest-cov/pull/630></code><em>, <code>[#631](pytest-dev/pytest-cov#631) <https://github.com/pytest-dev/pytest-cov/pull/631></code></em>, <code>[#632](pytest-dev/pytest-cov#632) <https://github.com/pytest-dev/pytest-cov/pull/632></code>_ and <code>[#633](pytest-dev/pytest-cov#633) <https://github.com/pytest-dev/pytest-cov/pull/633></code>_.</li> <li>Added a <code>pyproject.toml</code> example in the docs. Contributed by Dawn James in <code>[#626](pytest-dev/pytest-cov#626) <https://github.com/pytest-dev/pytest-cov/pull/626></code>_.</li> <li>Modernized project's pre-commit hooks to use ruff. Initial POC contributed by Christian Clauss in <code>[#584](pytest-dev/pytest-cov#584) <https://github.com/pytest-dev/pytest-cov/pull/584></code>_.</li> </ul> <h2>4.1.0 (2023-05-24)</h2> <ul> <li>Updated CI with new Pythons and dependencies.</li> <li>Removed rsyncdir support. This makes pytest-cov compatible with xdist 3.0. Contributed by Sorin Sbarnea in <code>[#558](pytest-dev/pytest-cov#558) <https://github.com/pytest-dev/pytest-cov/pull/558></code>_.</li> <li>Optimized summary generation to not be performed if no reporting is active (for example, when <code>--cov-report=''</code> is used without <code>--cov-fail-under</code>). Contributed by Jonathan Stewmon in <code>[#589](pytest-dev/pytest-cov#589) <https://github.com/pytest-dev/pytest-cov/pull/589></code>_.</li> <li>Added support for JSON reporting. Contributed by Matthew Gamble in <code>[#582](pytest-dev/pytest-cov#582) <https://github.com/pytest-dev/pytest-cov/pull/582></code>_.</li> <li>Refactored code to use f-strings. Contributed by Mark Mayo in <code>[#572](pytest-dev/pytest-cov#572) <https://github.com/pytest-dev/pytest-cov/pull/572></code>_.</li> <li>Fixed a skip in the test suite for some old xdist. Contributed by a bunch of people in <code>[#565](pytest-dev/pytest-cov#565) <https://github.com/pytest-dev/pytest-cov/pull/565></code>_.</li> </ul> <h2>4.0.0 (2022-09-28)</h2> <p><strong>Note that this release drops support for multiprocessing.</strong></p> <ul> <li> <p><code>--cov-fail-under</code> no longer causes <code>pytest --collect-only</code> to fail Contributed by Zac Hatfield-Dodds in <code>[#511](pytest-dev/pytest-cov#511) <https://github.com/pytest-dev/pytest-cov/pull/511></code>_.</p> </li> <li> <p>Dropped support for multiprocessing (mostly because <code>issue 82408 <https://github.com/python/cpython/issues/82408></code>_). This feature was mostly working but very broken in certain scenarios and made the test suite very flaky and slow.</p> <p>There is builtin multiprocessing support in coverage and you can migrate to that. All you need is this in your <code>.coveragerc</code>::</p> <p>[run] concurrency = multiprocessing</p> </li> </ul>  </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/5295ce01c84262cec88f31255e9ac538718f3047"><code>5295ce0</code></a> Bump version: 4.1.0 → 5.0.0</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/1181b067972bf94569f8011f3b18f271690f9ab1"><code>1181b06</code></a> Update changelog.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/9757222e2e044361e70125ebdd96e5eb87395983"><code>9757222</code></a> Fix a minor grammar error (<a href="https://redirect.github.com/pytest-dev/pytest-cov/issues/636">#636</a>)</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/9f5cd81a0dbe3fe41681efdbef516c08988fe8ff"><code>9f5cd81</code></a> Cleanup releasing instructions. Closes <a href="https://redirect.github.com/pytest-dev/pytest-cov/issues/616">#616</a>.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/93b5047ec5050d63c10a6fe16a09b671a7a03df8"><code>93b5047</code></a> Add test for pyproject.toml loading without explicit --cov-config. Ref <a href="https://redirect.github.com/pytest-dev/pytest-cov/issues/508">#508</a>.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/ff50860d7c67b920503745d92a3f0944cf41f982"><code>ff50860</code></a> docs: add config instructions for pyproject.toml.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/4a5a4b5fa4b1c63ddcab5cbc1813798c9b6f1d36"><code>4a5a4b5</code></a> Keep GitHub Actions up to date with GitHub's Dependabot</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/1d7f55963d5138f41c452a946f7cca7e0b6ee8b2"><code>1d7f559</code></a> Fix or remove URLs that are causing docs tests to fail</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/6a5af8e85b8242ac815f33e26adf9068f5f0ebc3"><code>6a5af8e</code></a> Update changelog.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/d9fe8dfed15023d3410dd299c5092e755b8981c2"><code>d9fe8df</code></a> Switch to furo. Closes <a href="https://redirect.github.com/pytest-dev/pytest-cov/issues/618">#618</a>.</li> <li>Additional commits viewable in <a href="https://github.com/pytest-dev/pytest-cov/compare/v4.0.0...v5.0.0">compare view</a></li> </ul> </details> <br /> Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. 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Updates the requirements on [pytest-cov](https://github.com/pytest-dev/pytest-cov) to permit the latest version. <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst">pytest-cov's changelog</a>.</em></p> <blockquote> <h2>6.0.0 (2024-10-29)</h2> <ul> <li>Updated various documentation inaccuracies, especially on subprocess handling.</li> <li>Changed fail under checks to use the precision set in the coverage configuration. Now it will perform the check just like <code>coverage report</code> would.</li> <li>Added a <code>--cov-precision</code> cli option that can override the value set in your coverage configuration.</li> <li>Dropped support for now EOL Python 3.8.</li> </ul> <h2>5.0.0 (2024-03-24)</h2> <ul> <li>Removed support for xdist rsync (now deprecated). Contributed by Matthias Reichenbach in <code>[#623](pytest-dev/pytest-cov#623) <https://github.com/pytest-dev/pytest-cov/pull/623></code>_.</li> <li>Switched docs theme to Furo.</li> <li>Various legacy Python cleanup and CI improvements. Contributed by Christian Clauss and Hugo van Kemenade in <code>[#630](pytest-dev/pytest-cov#630) <https://github.com/pytest-dev/pytest-cov/pull/630></code><em>, <code>[#631](pytest-dev/pytest-cov#631) <https://github.com/pytest-dev/pytest-cov/pull/631></code></em>, <code>[#632](pytest-dev/pytest-cov#632) <https://github.com/pytest-dev/pytest-cov/pull/632></code>_ and <code>[#633](pytest-dev/pytest-cov#633) <https://github.com/pytest-dev/pytest-cov/pull/633></code>_.</li> <li>Added a <code>pyproject.toml</code> example in the docs. Contributed by Dawn James in <code>[#626](pytest-dev/pytest-cov#626) <https://github.com/pytest-dev/pytest-cov/pull/626></code>_.</li> <li>Modernized project's pre-commit hooks to use ruff. Initial POC contributed by Christian Clauss in <code>[#584](pytest-dev/pytest-cov#584) <https://github.com/pytest-dev/pytest-cov/pull/584></code>_.</li> </ul> <h2>4.1.0 (2023-05-24)</h2> <ul> <li>Updated CI with new Pythons and dependencies.</li> <li>Removed rsyncdir support. This makes pytest-cov compatible with xdist 3.0. Contributed by Sorin Sbarnea in <code>[#558](pytest-dev/pytest-cov#558) <https://github.com/pytest-dev/pytest-cov/pull/558></code>_.</li> <li>Optimized summary generation to not be performed if no reporting is active (for example, when <code>--cov-report=''</code> is used without <code>--cov-fail-under</code>). Contributed by Jonathan Stewmon in <code>[#589](pytest-dev/pytest-cov#589) <https://github.com/pytest-dev/pytest-cov/pull/589></code>_.</li> <li>Added support for JSON reporting. Contributed by Matthew Gamble in <code>[#582](pytest-dev/pytest-cov#582) <https://github.com/pytest-dev/pytest-cov/pull/582></code>_.</li> <li>Refactored code to use f-strings. Contributed by Mark Mayo in <code>[#572](pytest-dev/pytest-cov#572) <https://github.com/pytest-dev/pytest-cov/pull/572></code>_.</li> <li>Fixed a skip in the test suite for some old xdist. Contributed by a bunch of people in <code>[#565](pytest-dev/pytest-cov#565) <https://github.com/pytest-dev/pytest-cov/pull/565></code>_.</li> </ul> <h2>4.0.0 (2022-09-28)</h2> <p><strong>Note that this release drops support for multiprocessing.</strong></p> <ul> <li><code>--cov-fail-under</code> no longer causes <code>pytest --collect-only</code> to fail</li> </ul>  </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/95404375a0e436178e012e20b8865c23c54c8a50"><code>9540437</code></a> Bump version: 5.0.0 → 6.0.0</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/9f8175467afc67db9001fb364ad1f2dfe79b51f1"><code>9f81754</code></a> Further trim down envs and drop Python 3.8.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/b12b5ec65da4c66bbc0c35918957f9f875f465c3"><code>b12b5ec</code></a> Update conf.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/23f4b27b432a54fcc3b6df7363f0e73e568233fb"><code>23f4b27</code></a> Update changelog.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/291a04f49566054bb19644aba27c3799ac8b7f42"><code>291a04f</code></a> Bump test deps and trim config.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/08f1101455ba293dda388fdb3b61e62fd95a827d"><code>08f1101</code></a> Add <code>--cov-precision</code> option. Close <a href="https://redirect.github.com/pytest-dev/pytest-cov/issues/655">#655</a>.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/76fe2a7e48e5c9c53644994c5ba5a421c84286f5"><code>76fe2a7</code></a> Move the warnings/errors in a place that doesn't import anything.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/a9ea7b71711479d4c5ccc5e21e2eb1694b259cb0"><code>a9ea7b7</code></a> Implement error/warning for the bad dynamic_context being set in config.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/c299e01b6422284a6a7f7322e6b9bf8f44aa3c25"><code>c299e01</code></a> Add explicit suffixing to make it easier to see the identify the sources/usag...</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/c87e54643ef696ed2b0e2b9a4209581da8467fcb"><code>c87e546</code></a> Add reproducer for weird xdist dynamic_context interaction. Ref <a href="https://redirect.github.com/pytest-dev/pytest-cov/issues/604">#604</a>.</li> <li>Additional commits viewable in <a href="https://github.com/pytest-dev/pytest-cov/compare/v4.0.0...v6.0.0">compare view</a></li> </ul> </details> <br /> Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. 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ctb added 4 commits January 7, 2019 13:20

remove out of date notebooks

940e3b5

remove outdated scripts

b0803ec

Merge branch 'rm/notebooks' of /tmp/sourmash into rm/outdated

d743472

configure nbsphinx and add a test notebook

e925aa3

add nbsphinx to reqs

a0b7c8b

ctb added 6 commits February 16, 2019 22:13

add 2019-upr-kmers notebooks and example files

63b3c36

Merge remote-tracking branch 'origin/master' into add/nbsphinx

c4516bd

add/update notebooks

7eeb9b6

add binder configuration

75b36bb

remove dockerfile

db54a30

update notebooks, link into documentation

d5ec017

ctb added 4 commits February 18, 2019 06:57

fix formatting issue that looks like a typo

bc387ef

update basic sourmash tutorial commands to work, mostly

05bbab3

fix sourmash_databases link

c38ad74

updated tutorials

ff22e2f

This was referenced Feb 23, 2019

genbank-d2 database is too big... #646

Closed

sourmash lca database link in tutorial is wrong #632

Closed

revamp tutorial organization in docs #647

Closed

fix spacing

9ebf714

ctb mentioned this pull request Feb 23, 2019

update docs to conda install? #552

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ctb added 5 commits February 23, 2019 06:51

significant documentation reorganization and (hopefully) simplification

4adad88

add tutorial master index back in

4dff1ec

add dashing and hulk refs

8fa3293

add bigsi

1125d4c

Merge branch 'rm/outdated' into add/nbsphinx

b8679ba

ctb mentioned this pull request Feb 23, 2019

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

Closed

5 tasks

fix branch reference for notebook so that it works

73d3665

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

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

ctb mentioned this pull request Feb 23, 2019

what's needed for a 2.0 release? #174

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update notebook with signature recalculation

61e0640

luizirber requested changes Mar 6, 2019

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fix order of bioconda channels

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luizirber approved these changes Mar 7, 2019

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fix URLs

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ctb merged commit 8797eb6 into master Mar 7, 2019

ctb deleted the add/nbsphinx branch March 7, 2019 01:35

ctb mentioned this pull request Mar 9, 2019

where should we be storing notebooks? #628

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ctb mentioned this pull request Apr 4, 2020

Demo notebook: issue parsing signatures #438

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

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

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ctb commented Mar 6, 2019

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ctb commented Jan 14, 2019 •

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codecov bot commented Jan 14, 2019 •

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