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S3 reading support - #198

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Bisaloo wants to merge 999 commits into
HelenaLC:mainfrom
Bisaloo:s3-read
Closed

S3 reading support#198
Bisaloo wants to merge 999 commits into
HelenaLC:mainfrom
Bisaloo:s3-read

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@Bisaloo

@Bisaloo Bisaloo commented May 15, 2026 •
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  • Enable reading on S3 (excepted for the tables element, as this needs to be implemented separately in anndataR. Prerequisite: Consolidated Zarr metadata at the root of the anndata zarr store scverse/anndataR#461)
  • Warn when trying to read a folder which is not a spatialdata folder. Currently, we just return an empty spatialdata object, which is not helpful.
  • Improve performance on local spatialdata folders which already provide consolidated metadata.

HelenaLC and others added 30 commits April 23, 2026 17:36
@HelenaLC
stash
6025414
@HelenaLC
merge query
73f2a1e
@Bisaloo
Use dedicated lengths() function where possible
028952a
@Bisaloo
Mark some regexes as fixed
a0c797e
@Bisaloo
Use anyNA() where relevant
45b4f01
@Bisaloo
Use dedicated endsWith() base R function
5a5e2a3
@Bisaloo
Use seq_len() where relevant
1838911
@Bisaloo
Use seq_along() where relevant
6c58eff
@Bisaloo
Use vectorized sprintf() calls instead of for loops
b20135b
@HelenaLC
Merge pull request HelenaLC#159 from Bisaloo/misc-cleanup
3c4d422 
Use dedicated base R functions to simplify some code patterns
@HelenaLC
fix unit tests
d756d86
@HelenaLC
track changes
0ad831f
@HelenaLC
+hugo,charlotte,michael as authors
4a34743
@HelenaLC
valTable -> getTable
ee064f2
@HelenaLC
simplify methods dispatch
a13efa9
@HelenaLC
+Imports: rlang
3b012db
@HelenaLC
+@importFrom rlang git add R/trans.R
54d09ce
@HelenaLC
+samuel
898b167
@HelenaLC
add missing imports; fiix examples
d93ffcb
@HelenaLC
Merge pull request HelenaLC#155 from HelenaLC/combine
bacee93 
+combine
@HelenaLC
simplified point/shape subsetting
c00da7d
@HelenaLC
Merge pull request HelenaLC#161 from HelenaLC/combine
3c155de 
simplified point/shape subsetting
@HelenaLC
fix PointFrame transformations
3398e65
@HelenaLC
refactorize point/shape transformations & unit testing
6dbeebf
@HelenaLC
.zattrs constructor
f693aaf
@HelenaLC
split table vs. spatial query; added object-wide query
6fd8b83
@HelenaLC
fix unit tests
6d7d036
@HelenaLC
+crop
2290dfd
@HelenaLC
update docs
7181865
@HelenaLC
v0.99.31
15394c7
Bisaloo and others added 26 commits May 28, 2026 09:32
@Bisaloo
Run devtools::document()
175f1d8
@HelenaLC
fix generics: labels, transform
8fafb05
@Bisaloo
Use BiocGenerics::transform()
772f956
@Bisaloo
Install from r-universe in pkgdown workflow
f64b557
@HelenaLC
new BiocGenerics, minimal 3d support
f2189ec 
* revise validity to accept >2/3D
* revise ome(ro) version retrieval
* make use of new BiocGenerics
* move EBImage to Suggests:, remove paws
* minimal list of authors until further discussion
@HelenaLC
SimpleList, path()
a2cbcda 
* use prototyped S4Vectors::SimpleList as slots
* new path() method to retrieve on-disk file paths
* more tests & validity
* bump to v0.99.39
@HelenaLC @Bisaloo
v0.99.40
a49b09b 
* simplify code bits using seq_along(), lengths(), .data, etc.
* assure layer lists are fully named (updated validity, tests, setters)
* make SpatialDataImage/Label() accept single-arary (HelenaLC#216)
* v0.99.40

---------

Co-authored-by: Hugo Gruson <git@hugogruson.fr>
@HelenaLC
revise combine() to accept (named) list (HelenaLC#229)
9d08d86
@HelenaLC
address r-universe reports (v.99.40 -> .41) (HelenaLC#230)
cffa06f 
* fix URL: and BugReports:
* fix R CMD check warnings
* in vignette, call spatialdataR::transform() explicitly
* v0.99.41
@HelenaLC
>2/3D array subsetting (HelenaLC#231)
95343c1 
* sda sub revision for >2/3 dims
* crop multi-scale adjustment
* divert badge to r-uni action
* v0.99.42
@HelenaLC
scale matching in mask(); fix channels() (HelenaLC#232)
ce16614 
* match scales in mask()
* channels() bug fix
* fix [,sdArray docs
@HelenaLC
axes() arg to get name/type/unit; centroids,label: >2D, multiscale ad…
110e8e7 
…justment

* add axes() arg to return name/type/unit
* >2D & multi-scale adjustment in centroids,label
@HelenaLC
init support for time dim.
4276392 
* update sdArray validity & tests to allow time dim.
* mask,image/label returns one assay per timepoint
@HelenaLC
tests & refactoring
00782e7 
* refactor: identifier validation, multiscales & spatial axiis accession
* SpatialDataAttrs() with >2/3d support
* tests for show(), SpatialDataAttrs()
* axes() arg to return name/type/unit
* v0.99.43
@HelenaLC
refactoring (HelenaLC#236)
0753bd4 
* factor out + test .sync_tables_on_crop
* restructure utils
* test 4D masking
* v0.99.43
@HelenaLC
fix vignette hyperlink
5765abc
@HelenaLC
drop unneeded import
fb652db
@HelenaLC
factor out fun .to_sf() to convert crop,frame input to sf
c81bd49
@Bisaloo
S3 reading support
48d9321
@Bisaloo
Restore validation on local paths to avoid regression
a1da313
@Bisaloo
Set minimum Rarr version
cfec396
@Bisaloo
Ensure ds is defined for remote stores
53da9b7
@Bisaloo
Improve v2 handling
6f58e37
@Bisaloo
Remove extra messages
c7a43e8
@Bisaloo
Make sure trailing slash is present in paths
1c6d852
@Bisaloo
Create store_meta if missing
aebc8c1
@HelenaLC HelenaLC closed this Jul 5, 2026
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3 participants

@Bisaloo @HelenaLC @Artur-man