Skip to content

Bioc revisions#242

Closed
HelenaLC wants to merge 998 commits into
mainfrom
devel
Closed

Bioc revisions#242
HelenaLC wants to merge 998 commits into
mainfrom
devel

Conversation

@HelenaLC

@HelenaLC HelenaLC commented Jul 5, 2026

Copy link
Copy Markdown
Owner

No description provided.

HelenaLC and others added 30 commits April 23, 2026 17:34
Former-commit-id: 72aabc1
Former-commit-id: 022727cb2e516000e1e353fe55fee621b1d66c5f
Former-commit-id: 6025414
Former-commit-id: 226887d1aaeb78f9af2920b947ddac1387360304
Former-commit-id: 73f2a1e
Former-commit-id: 68d07cef7e3dc88c0a4506094b3331a9ddc411fe
Former-commit-id: 028952a
Former-commit-id: b42ca0cc02891cc7e6a04ddcabf7005a79de0c8d
Former-commit-id: a0c797e
Former-commit-id: 97b19b4cc7e3ac402b7b75f158ac437f42a85a02
Former-commit-id: 45b4f01
Former-commit-id: 051a8f6747d5e0cfaa3754b849e27d5ed17d471f
Former-commit-id: 5a5e2a3
Former-commit-id: 67b784d7de077180d580ede35244385dc9f6a811
Former-commit-id: 1838911
Former-commit-id: 30a0217c22c249584ae2aca73b4dddaf4a1bc15c
Former-commit-id: 6c58eff
Former-commit-id: 296271378f92e5d16ed5ac02bb0ec545e986509b
Former-commit-id: b20135b
Former-commit-id: 911588db70dcfbe6ba7d3c585416696af6896d38
Use dedicated base R functions to simplify some code patterns

Former-commit-id: 3c4d422
Former-commit-id: 72f971c507daf37a960fdfb97a793d1372c7c1d4
Former-commit-id: d756d86
Former-commit-id: 6910d446c8515f09a1c669bfbe5b456225c62b4c
Former-commit-id: 0ad831f
Former-commit-id: cd01138d3d77e593e66a0eff04ef1947d8ef79e5
Former-commit-id: 4a34743
Former-commit-id: a8a00d75e71ee9d107a7d52da25a05436294ef95
Former-commit-id: ee064f2
Former-commit-id: 1445576f4079487cbad28bf06af23afcb2e0652f
Former-commit-id: a13efa9
Former-commit-id: ab2a07666052457edc1cb8a1293563daa5da27a0
Former-commit-id: 3b012db
Former-commit-id: 944fbfa2bee44e61fa45f702d9c0c627222463a1
Former-commit-id: 54d09ce
Former-commit-id: b8fc6b8e2f6ed08ea6ff58e96b1a84c26cd56bfa
Former-commit-id: 898b167
Former-commit-id: cea4e920aa5447277a8b08f4de6ca5bd289257ec
Former-commit-id: d93ffcb
Former-commit-id: dd122a379d4f47e1b2c638cb0b9a3f7c19f6a333
+combine

Former-commit-id: bacee93
Former-commit-id: 375d2c9c6643f5f21ffa331818b9257afdb87ba1
Former-commit-id: c00da7d
Former-commit-id: e793744c551f692b59c42573c0ec27b479ed70ee
simplified point/shape subsetting

Former-commit-id: 3c155de
Former-commit-id: 099394ec4f90c1027be169ca71bc2867964db0e7
Former-commit-id: 3398e65
Former-commit-id: e4b296267d932275e6b8a2d6737b750afa786d36
Former-commit-id: 6dbeebf
Former-commit-id: 333ddd408113c54a9285d787673cb22f379e9ced
Former-commit-id: f693aaf
Former-commit-id: e32ca588fd123d76da6fe2c939076f6179b07cb6
Former-commit-id: 6fd8b83
Former-commit-id: 8154c2dfa928091b477e84c348e617a4fcc96524
Former-commit-id: 6d7d036
Former-commit-id: bd8c17224c91eb36129bfaade718617255271283
Former-commit-id: 2290dfd
Former-commit-id: 13feafc8a97152e7c949d9fbdc28f2ca2c86a6f1
Former-commit-id: 7181865
Former-commit-id: e85e4bf4f70dd8bf6b299ed69927e61999f25768
Bisaloo and others added 26 commits May 28, 2026 09:32
Former-commit-id: 09a9477
Former-commit-id: 77a7f5a2193c9f7734ecd63ed820367398c2e690
Former-commit-id: 175f1d8
Former-commit-id: 09b53224cc8263c93bef5964382dcdee359d473e
Former-commit-id: 8fafb05
Former-commit-id: 97041c53b7a12f57d65ae98b9bc866c4be80abf1
Former-commit-id: 772f956
Former-commit-id: 24d083d7c0151dbf62de78ee46ea78082ea2fb77
Former-commit-id: f64b557
Former-commit-id: ea1a7da6af724c1f161c413371e5190bb682248d
* 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

Former-commit-id: f2189ec
Former-commit-id: ca8904705621e30a292924ecac16fda8555af314
* use prototyped S4Vectors::SimpleList as slots
* new path() method to retrieve on-disk file paths
* more tests & validity
* bump to v0.99.39

Former-commit-id: a2cbcda
Former-commit-id: 2ac682d78bbd2348d9837d34154ac9d9b16b5205
* 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 (#216)
* v0.99.40

---------

Co-authored-by: Hugo Gruson <git@hugogruson.fr>
Former-commit-id: a49b09b
Former-commit-id: 6576415293f70f15c73ebaf4521d5d4462455ca3
Former-commit-id: 9d08d86
Former-commit-id: 6080e4c6a547e0dedb8c09b1822e0ecdcdc990b5
* fix URL: and BugReports:
* fix R CMD check warnings
* in vignette, call spatialdataR::transform() explicitly
* v0.99.41

Former-commit-id: cffa06f
Former-commit-id: 5834adfcca72e389b24ac14d25ecb21d1aa743a0
* sda sub revision for >2/3 dims
* crop multi-scale adjustment
* divert badge to r-uni action
* v0.99.42

Former-commit-id: 95343c1
Former-commit-id: dd5651ea94ff829c4123e891078c5e56fd5f5f30
* match scales in mask()
* channels() bug fix
* fix [,sdArray docs

Former-commit-id: ce16614
Former-commit-id: ba54630a2332e224c1b9b4da5f0a7216ecb7c599
…justment

* add axes() arg to return name/type/unit
* >2D & multi-scale adjustment in centroids,label

Former-commit-id: 110e8e7
Former-commit-id: 1fe92907f9ede257c0a98508d979a6e03afb3d46
* update sdArray validity & tests to allow time dim.
* mask,image/label returns one assay per timepoint

Former-commit-id: 4276392
Former-commit-id: 04e8420a6b5f827812d330252e291d75a68502c6
* 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

Former-commit-id: 00782e7
Former-commit-id: 9e868cf3be784cc2034cc157ef7b8aa8c9c2bdaf
* factor out + test .sync_tables_on_crop
* restructure utils
* test 4D masking
* v0.99.43

Former-commit-id: 0753bd4
Former-commit-id: 4ae0e4dc71933004b99f659ad273cd12f4dad797
Former-commit-id: 5765abc
Former-commit-id: a00121fc4cd5bef634ca3fbfdcd1f36f0c7307b9
Former-commit-id: fb652db
Former-commit-id: a999782253c70c0c4b2d96bdadaac2f0533cd6c2
Former-commit-id: c81bd49
Former-commit-id: c3a0f63cd685f8c84898ff2e669eddbf29388c54
Former-commit-id: a8540be
Former-commit-id: d7f6d90fb7c6cfb757033f1913022da6908dadee
Former-commit-id: 8fb03de
Former-commit-id: c555f59b106b26fda9a5a0207f0dfc1ffb0c6558
Former-commit-id: cc4a877
Former-commit-id: da47d2977104f147bbd0b3b4bbab858ed07a36bc
Former-commit-id: 9943534
Former-commit-id: 20d2a20b8cddb947bebffe81e8afcc4d010f4a63
Former-commit-id: 4619888
Former-commit-id: 5737710a25cff0ccb72853eb88816ff1637e21ca
Former-commit-id: c7fc33d
Former-commit-id: 73330201c9358f458105d100405436a4c618c7ec
Former-commit-id: 98349d9
Former-commit-id: 92810ef367e1fe2fc6d8a2db64ad4f0709d233c8
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

3 participants