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Update docs to generalize from DANDI Archive to DANDI instance #1548

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merged 6 commits into from
Dec 19, 2024

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@kabilar kabilar commented Dec 10, 2024

cc @aaronkanzer

@kabilar kabilar requested a review from yarikoptic December 10, 2024 19:01
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codecov bot commented Dec 10, 2024

Codecov Report

Attention: Patch coverage is 0% with 1 line in your changes missing coverage. Please review.

Project coverage is 88.57%. Comparing base (38409e8) to head (3d175a7).
Report is 19 commits behind head on master.

Files with missing lines Patch % Lines
dandi/files/__init__.py 0.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master    #1548      +/-   ##
==========================================
+ Coverage   88.44%   88.57%   +0.13%     
==========================================
  Files          78       78              
  Lines       10742    10742              
==========================================
+ Hits         9501     9515      +14     
+ Misses       1241     1227      -14     
Flag Coverage Δ
unittests 88.57% <0.00%> (+0.13%) ⬆️

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This is great! See some minor comments, but major thing I think is to look either to make testing there more flexible (allow for regex matching?) or just remove those changes from this PR and coordinate later with similar changes to dandi-archive

README.md Outdated Show resolved Hide resolved
@@ -13,13 +13,13 @@
],
"version": "draft",
"@context": "https://raw.githubusercontent.com/dandi/schema/master/releases/0.6.4/context.json",
"citation": "Aguillon-Rodriguez, Valeria; Angelaki, Dora E.; Bayer, Hannah M.; Bonacchi, Niccol\u00f2; Carandini, Matteo; Cazettes, Fanny; Chapuis, Gaelle A.; Churchland, Anne K.; Dan, Yang; Dewitt, Eric E. J.; Faulkner, Mayo; Forrest, Hamish; Haetzel, Laura M.; Hausser, Michael; Hofer, Sonja B.; Hu, Fei; Khanal, Anup; Krasniak, Christopher S.; Laranjeira, In\u00eas; Mainen, Zachary F.; Meijer, Guido T.; Miska, Nathaniel J.; Mrsic-Flogel, Thomas D.; Murakami, Masayoshi; Noel, Jean-Paul; Pan-Vazquez, Alejandro; Rossant, Cyrille; Sanders, Joshua I.; Socha, Karolina Z.; Terry, Rebecca; Urai, Anne E.; Vergara, Hernando M.; Wells, Miles J.; Wilson, Christian J.; Witten, Ilana B.; Wool, Lauren E.; Zador, Anthony (2023) Standardized and reproducible measurement of decision-making in mice (Version draft) [Data set]. DANDI archive. http://localhost:8085/dandiset/000001/draft",
"citation": "Aguillon-Rodriguez, Valeria; Angelaki, Dora E.; Bayer, Hannah M.; Bonacchi, Niccol\u00f2; Carandini, Matteo; Cazettes, Fanny; Chapuis, Gaelle A.; Churchland, Anne K.; Dan, Yang; Dewitt, Eric E. J.; Faulkner, Mayo; Forrest, Hamish; Haetzel, Laura M.; Hausser, Michael; Hofer, Sonja B.; Hu, Fei; Khanal, Anup; Krasniak, Christopher S.; Laranjeira, In\u00eas; Mainen, Zachary F.; Meijer, Guido T.; Miska, Nathaniel J.; Mrsic-Flogel, Thomas D.; Murakami, Masayoshi; Noel, Jean-Paul; Pan-Vazquez, Alejandro; Rossant, Cyrille; Sanders, Joshua I.; Socha, Karolina Z.; Terry, Rebecca; Urai, Anne E.; Vergara, Hernando M.; Wells, Miles J.; Wilson, Christian J.; Witten, Ilana B.; Wool, Lauren E.; Zador, Anthony (2023) Standardized and reproducible measurement of decision-making in mice (Version draft) [Data set]. DANDI Archive. http://localhost:8085/dandiset/000001/draft",
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those are coming from dandi-archive

❯ git grep 'DANDI archive'
dandiapi/api/models/version.py:        citation = f'{name} ({year}). (Version {version}) [Data set]. DANDI archive. {url}'
dandiapi/api/models/version.py:                    f'{cl} ({year}) {name} (Version {version}) [Data set]. DANDI archive. {url}'
...

there should be a "satellite" PR there to likely preceed these changes or we should improve testing here to allow for flexibility (didn't look ATM) but these are the cause of failing tests ATM e.g. https://github.com/dandi/dandi-cli/actions/runs/12262974763/job/34213512790?pr=1548#step:8:25905

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do you think you could remove those changes in the tests for now so we could not delay accepting major portion of the changes @kabilar to not breed conflicts etc?

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it was merged now, so we should be all set here. I will retrigger tests to see if all good (frankly I don't remember if we need release of archive first) and then we could proceed

dandi/dandiapi.py Outdated Show resolved Hide resolved
kabilar and others added 2 commits December 12, 2024 22:27
Co-authored-by: Yaroslav Halchenko <[email protected]>
Co-authored-by: Yaroslav Halchenko <[email protected]>
@yarikoptic yarikoptic added release Create a release when this pr is merged internal Changes only affect the internal API labels Dec 19, 2024
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oh that codecov

codecov/patch — 0.00% of diff hit (target 88.44%)

;-)

@yarikoptic yarikoptic merged commit 811c835 into dandi:master Dec 19, 2024
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🚀 PR was released in 0.66.3 🚀

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