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Formalize spec #882

Merged
merged 16 commits into from
Jan 30, 2023
Merged

Formalize spec #882

merged 16 commits into from
Jan 30, 2023

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ivirshup
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@ivirshup ivirshup commented Jan 17, 2023

Adding formal language and more details to the on disk specification for anndata.

The goal of this PR is to be more clear about what we expect to see from an AnnData formatted object on disk.

Eventually it would make sense to add some formatting to allow multiple versions of specifications, and to potentially separate prose and spec to separate documents.

TODO

  • Remaining specifications
    • AnnData shape restrictions
    • String arrays
    • Scalar types
    • Nullable types
  • Check specifications against code
  • Get second pair of eyes for careful review

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codecov bot commented Jan 17, 2023

Codecov Report

Merging #882 (55dd77d) into master (3c5f63d) will increase coverage by 0.06%.
The diff coverage is n/a.

Additional details and impacted files
@@            Coverage Diff             @@
##           master     #882      +/-   ##
==========================================
+ Coverage   83.64%   83.70%   +0.06%     
==========================================
  Files          34       34              
  Lines        4487     4498      +11     
==========================================
+ Hits         3753     3765      +12     
+ Misses        734      733       -1     
Impacted Files Coverage Δ
anndata/_io/specs/registry.py 95.23% <0.00%> (+0.55%) ⬆️
anndata/_io/utils.py 73.83% <0.00%> (+0.93%) ⬆️

@ivirshup ivirshup marked this pull request as ready for review January 23, 2023 12:03
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@giovp giovp left a comment

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mostly typos

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@ivirshup ivirshup requested a review from giovp January 26, 2023 18:59
@ivirshup ivirshup merged commit 38e3325 into scverse:master Jan 30, 2023
ivirshup added a commit that referenced this pull request Jan 30, 2023
Added release note for #882, and used the user tag for PR authors
@ivirshup ivirshup mentioned this pull request Jan 30, 2023
ivirshup added a commit that referenced this pull request Jan 30, 2023
* Update release notes

Added release note for #882, and used the user tag for PR authors

* typo fix
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4 participants