Add delete mode by jp-dark · Pull Request #4125 · single-cell-data/TileDB-SOMA

jp-dark · 2025-06-13T20:03:34Z

Issue and/or context:

Closes SOMA-168
Closes SOMA-170
Closes SOMA-180

Changes:

C++ Changes:

Make SOMAArray copy constructor the default copy constructor.
Add soma_mode_ as a private variable to SOMAArray and SOMAGroup.
Add new OpenMode::soma_delete option to OpenMode enum (the soma_ prefix was added since delete is a special keyword.
Add soma_ prefix to existing OpenMode values for consistency.

Python Changes:

Update to a new version of somacore (adds 'd' mode to somacore.options.OpenMode)
Add verify_open_for_deleting to SOMA objects
Rename _verify_open_for_reading to verify_open_for_reading
Add d as a valid mode for opening/reopening SOMA objects
Deprecate deleting elements from a Collection in write mode
Add support for deleting elements from a Collection in delete mode

R Changes:

Deprecate deleting elements from a Collection in write mode
Add support for deleting elements from a Collection in delete mode

Before Merging:

Update changelogs
Release and update somacore version

Also add method that converts OpenMode to string

This is to create a new delete mode. The name `delete` is reserved in C++ and `del` is reserved in Python.

codecov · 2025-06-13T20:07:12Z

Codecov Report

Attention: Patch coverage is 78.13333% with 82 lines in your changes missing coverage. Please review.

Project coverage is 65.96%. Comparing base (143ffb2) to head (b40ac21).
Report is 4 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4125      +/-   ##
==========================================
+ Coverage   65.89%   65.96%   +0.06%     
==========================================
  Files         158      160       +2     
  Lines       20988    21150     +162     
  Branches     1237     1248      +11     
==========================================
+ Hits        13830    13951     +121     
- Misses       6745     6782      +37     
- Partials      413      417       +4

Flag	Coverage Δ
libtiledbsoma	`54.08% <78.36%> (+0.21%)`	⬆️
python	`89.32% <75.75%> (-0.09%)`	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Components	Coverage Δ
python_api	`89.32% <75.75%> (-0.09%)`	⬇️
libtiledbsoma	`44.89% <64.38%> (+0.50%)`	⬆️

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bkmartinjr

A bunch of small stuff, but nothing of major concern. Preemptively approving

Co-authored-by: Paul Hoffman <[email protected]>

mojaveazure

LGTM; please remember to bump the R develop version in DESCRIPTION

jp-dark added 11 commits June 11, 2025 11:58

Add delete mode to OpenMode enum

24b2ae7

Also add method that converts OpenMode to string

Add delete mode to C++ SOMAArray and SOMAGroup

9ab1e4a

Make SOMAArray copy constructor default

4e748f3

Move C++ tests

690a7e9

Rename OpenMode enums to include soma_ prefix

d035168

This is to create a new delete mode. The name `delete` is reserved in C++ and `del` is reserved in Python.

Add delete mode to rcpp

24b2cc3

Add C++ delete mode to Python clib

724a002

Add delete mode to R

9ff177b

Add delete mode to python

5f172a8

Add delete mode to array state machine

3988d17

Fix mode in test

d8f7f61

jp-dark added 4 commits June 13, 2025 16:46

Fix tests

9eae4e0

Run clang-format-18

2fc20c4

Update changelogs

9dde4c0

Fix deleter

b95f6ee

jp-dark requested review from bkmartinjr and mojaveazure June 13, 2025 22:13

jp-dark changed the title ~~Dark/add delete mode~~ Add delete mode Jun 14, 2025