Unify 'defaults' and use of quotations across docstrings #2134

alejoe91 · 2023-10-26T15:51:26Z

inspired by @zm711 :)

The way we defined defaults was very non-homogeneous ((default ...), , by default ..., default=...). Made a first pass to unify this as:

param_name: type, default: ...

Might have missed some, but should have caught most of them!

And still missing a couple of modules (sorters, sortingcomponents)

src/spikeinterface/postprocessing/spike_locations.py

zm711 · 2023-10-26T16:21:54Z

@alejoe91

This is super cool! And tons of work. You're a beast man!

zm711

A few more fixes on my pass through :)

src/spikeinterface/core/waveform_tools.py

src/spikeinterface/extractors/mdaextractors.py

src/spikeinterface/widgets/amplitudes.py

src/spikeinterface/widgets/template_similarity.py

src/spikeinterface/widgets/traces.py

src/spikeinterface/widgets/unit_waveforms.py

Co-authored-by: Zach McKenzie <[email protected]>

alejoe91 · 2023-10-27T10:32:49Z

Thanks @zm711

I did another round! I would say that >95% are fixed and this is mergeable :)

zm711

This looks great! and you even unified the quote marks!

Just one typo I noticed in case you want to hit it while you're at it.

src/spikeinterface/sortingcomponents/motion_interpolation.py

zm711

Couple more, but I need to run for the day.

src/spikeinterface/core/base.py

src/spikeinterface/core/baserecordingsnippets.py

samuelgarcia · 2023-10-30T11:29:26Z

@alejoe91 : thank you so much for this amazing and crutial improvement.

zm711

Just a few more that I saw. Also totally mergeable without these and we can fix them later since every commit runs the whole test suite.

src/spikeinterface/core/baserecordingsnippets.py

src/spikeinterface/core/core_tools.py

src/spikeinterface/core/job_tools.py

src/spikeinterface/curation/curationsorting.py

src/spikeinterface/curation/sortingview_curation.py

Co-authored-by: Zach McKenzie <[email protected]>

Unify 'defaults'

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zm711 reviewed Oct 26, 2023

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zm711 reviewed Oct 26, 2023

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sorters wip and fix imports

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alejoe91 added the documentation Improvements or additions to documentation label Oct 27, 2023

alejoe91 and others added 24 commits October 27, 2023 11:33

Update src/spikeinterface/core/waveform_tools.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/core/waveform_tools.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/core/waveform_tools.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/core/waveform_tools.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/widgets/amplitudes.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/widgets/unit_waveforms.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/extractors/mdaextractors.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/extractors/mdaextractors.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/widgets/traces.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/widgets/template_similarity.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/widgets/traces.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/extractors/mdaextractors.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/extractors/neoextractors/tdt.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/extractors/neoextractors/tdt.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/extractors/neoextractors/spikeglx.py

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Update src/spikeinterface/preprocessing/remove_artifacts.py

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Update src/spikeinterface/extractors/neoextractors/spikeglx.py

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Update src/spikeinterface/extractors/neoextractors/spikegadgets.py

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Update src/spikeinterface/extractors/neoextractors/spikegadgets.py

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Update src/spikeinterface/preprocessing/filter.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/postprocessing/correlograms.py

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Update src/spikeinterface/preprocessing/remove_artifacts.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/postprocessing/isi.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/preprocessing/average_across_direction.py

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alejoe91 and others added 3 commits October 27, 2023 11:40

Update src/spikeinterface/preprocessing/directional_derivative.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/preprocessing/depth_order.py

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Co-authored-by: Zach McKenzie <[email protected]>

sortingcomponents and more fixes

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alejoe91 marked this pull request as ready for review October 27, 2023 10:32

zm711 approved these changes Oct 27, 2023

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More quotation handling (core)

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zm711 reviewed Oct 27, 2023

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Final round of cleaning

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alejoe91 changed the title ~~Unify 'defaults' across docsrtings~~ Unify 'defaults' and use of quotations across docsrtings Oct 27, 2023

alejoe91 added 2 commits October 27, 2023 14:18

Add unsaved files

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Import hdbscan when needed and add ros3 to pytest.markers

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alejoe91 added this to the 0.99.0 milestone Oct 27, 2023

zm711 mentioned this pull request Oct 28, 2023

Add Docstring section to development docs #2138

Merged

alejoe91 added 2 commits October 30, 2023 12:34

Solve conflicts

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Solve conflicts

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zm711 reviewed Oct 30, 2023

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alejoe91 and others added 8 commits October 31, 2023 09:36

Update src/spikeinterface/core/baserecordingsnippets.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/core/baserecordingsnippets.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/core/baserecordingsnippets.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/core/job_tools.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/core/job_tools.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/curation/curationsorting.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/curation/sortingview_curation.py

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Co-authored-by: Zach McKenzie <[email protected]>

Update src/spikeinterface/core/core_tools.py

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alejoe91 changed the title ~~Unify 'defaults' and use of quotations across docsrtings~~ Unify 'defaults' and use of quotations across docstrings Oct 31, 2023

samuelgarcia approved these changes Oct 31, 2023

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samuelgarcia merged commit 886530a into SpikeInterface:main Oct 31, 2023
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alejoe91 deleted the unify-docstrings-defaults branch April 12, 2024 08:59

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Unify 'defaults' and use of quotations across docstrings #2134

Unify 'defaults' and use of quotations across docstrings #2134

alejoe91 commented Oct 26, 2023 •

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Unify 'defaults' and use of quotations across docstrings #2134

Unify 'defaults' and use of quotations across docstrings #2134

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