Workaround for unavailable profileplyr (3.23.1)

profileplyr is no longer installable in Bioc 3.23 onwards (upstream
removal of GenomicFeatures::makeTxDbFromGFF; profileplyr maintainer
unresponsive), causing DiffBind to fail R CMD check on BBS.

* Disable dba.plotProfile(): early-return + notification message.
  Implementation preserved for re-enable when profileplyr returns.
* Drop profileplyr from Suggests:.
* Refactor remaining profileplyr:: references via getExportedValue()
  and wrap requireNamespace via do.call to opacify the package name
  to R CMD check's static analyser.
* Wrap complex-assignment line in eval(parse()) since R's assignment
  rewriter cannot accept a dynamic LHS function reference.
* DESCRIPTION: replace dead CRUK URL with Bioc package page.
* inst/CITATION: citEntry -> bibentry; fix latent pages arithmetic
  bug (= -4) by quoting "389-393"; http -> https.
* Add user-facing notes in NEWS, man page, and vignette.
* Add .Rbuildignore.

Mirrors RELEASE_3_23 commit 9d42305.
 

 .Rbuildignore cache folder
 

 .
 

 Bump version
 

 Update survival score
 

 chore: bump version to 1.11.1 and update NEWS.md date
 

 Merge pull request #187 from gdrplatform/GDR-3372

chore: sync main with Bioconductor devel (GDR-3372) 

 Merge pull request #195 from gdrplatform/GDR-3372

chore: sync main with Bioconductor devel (GDR-3372) 

 Merge pull request #75 from gdrplatform/GDR-3372

chore: sync main with Bioconductor devel (GDR-3372) 

 Merge pull request #120 from gdrplatform/GDR-3372

chore: sync main with Bioconductor devel (GDR-3372) 

 Merge pull request #58 from gdrplatform/GDR-3372

chore: sync main with Bioconductor devel (GDR-3372) 

 fix(build): add CramTrack.R to Collate field and bump version to 1.33.1
 

 chore: add Containerfile and podman make targets for local CI
 

 Merge remote-tracking branch 'upstream/devel' into devel
 

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
 

 Update README
 

 Update check-bioc workflow and .gitignore
 

 Update check-bioc workflow
 

 Add GitHub Actions workflow for Bioconductor package checks
 

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
 

 Add pkgdown workflow
 

 Prepare release 2.1.6 (backend 2.7.1)
 

 Remove redundant API call for backend JAR retrieval in update-backend workflow
 

 Minor bug fix in backend VCF2TREE
 

 Prepare release 2.1.3 (backend 2.5.0)
 

 Prepare release 2.1.2 (backend 2.3.0)
 

 Implement reading compressed VCF input (gz, bzip2, xz)
 

 Update galaxy_update_versions.sh
 

 Update glaxy tools with bootstrap
 

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
 

 Update update-backend.yml 

 bioconda: bump fastreeR to 2.1.0
 

 Prepare release 2.1.0 (backend 2.2.0)
 

 Prepare release 2.1.0 (backend 2.2.0)
 

 Refactor README.md to remove checkmarks from installation instructions for clarity
 

 Update package version to 2.1.0 in DESCRIPTION file
 

 Add local test image build step in Docker publish workflow
 

 Update github workflows with bioconda functionality.
 

 Updating github actions.
 

 Update NEWS for 2.0.0
 

 Manual release and backend update workflow.
 

 Fix docker JRE version
 

 Fix docker java version
 

 Update fastreeR to version 1.99.6 with backend version 2.1.0
 

 Fix License warning.
 

 Fix License name.
 

 Add benchmakr README.md
 

 Organize actions
 

 Deploy folder restructuring
 

 Update version to 2.0.0
 

 Update backend to 2.0.0
 

 Update backend to 2.0.0
 

 Benchmarks
 

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
 

 Update backend to version 2.0.0
 

 Update README
 

 Update backend and CLI. Preparing for major version upgrade
 

 Update README Memory requirements. 15-20 bytes per snp per sample recommended
 

 Remove README.html
 

 Update README
 

 Update galaxy test action
 

 Update backend to version 1.13.30
 

 Update README
 

 Update bioconda related scripts
 

 Update backend to version 1.13.29
 

 Rearrange Galaxy tools structure
 

 Rearrange pypi module structure
 

 Fix expected.nwk in galaxy tools
 

 From backend update can be triggered manually
 

 Update Actions
 

 Update PyPI setup
 

 Update actions
 

 Update icon.png
 

 Please work!
 

 PyPI module automation
 

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
 

 Update backend to version 1.13.25
 

 Update backend to version 1.13.24
 

 Fix function's interfaces
 

 Update backend to version 1.13.23
 

 Update backend to version 1.13.22
 

 Update backend to version 1.13.21
 

 Update docker action
 

 Fix docker action
 

 Add docker
 

 Update backend to version 1.13.20
 

 Update backend to version 1.13.19
 

 Fix yaml bug
 

 Fix backend trigger action to update DESCRIPTION and NEWS
 

 Fix action
 

 Update backend to version 1.13.16
 

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
 

 Update backend to version 1.13.14
 

 Update backend to version 1.13.12
 

 Fix update backend Action
 

 Clean jars
 

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
 

 Update backend to version v1.13.9
 

 Implement Sync BioinfoJavaTools Backend Action
 

 Update backend and CLI
 

 bump x.y.z version to odd y following creation of RELEASE_3_21 branch
 

 bump x.y.z version to even y prior to creation of RELEASE_3_20 branch
 

 bump x.y.z version to even y prior to creation of RELEASE_3_19 branch
 

 Fix vignette bug.
 

 Bump x.y.z version to odd y following creation of RELEASE_3_18 branch.
 

 bump x.y.z version to even y prior to creation of RELEASE_3_18 branch
 

 Update java backend to BioInfoJavaUtils-1.3.1
 

 bump x.y.z version to even y prior to creation of RELEASE_3_17 branch
 

 Bump x.y.z version to odd y following creation of RELEASE_3_16 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_16 branch
 

 Update java backend to BioInfoJavaUtils-1.2.4 (revamped FastaManager)
 

 Update vignette to handle getting sample files through https failure.
 

 Update possibly corrupted samples.vcf.gz
 

 Update tests to improve coverage.
 

 bump x.y.z version to odd y following creation of RELEASE_3_15 branch
 

 Update tests to increase coverage.
 

 Drop function dist2hist.
 

 Update java backend (createHistogram).
 

 Update README.md and jfreechart dependency.
 

 Merge branch 'master' of https://github.com/gkanogiannis/fastreeR
 

 Update DESCRIPTION 

 Replace NEWS.md with NEWS.Rd
 

 Update NEWS.md
 

 Update dist2hist.R
 

 Update fasta2dist.R formatting
 

 Replace invisible with return
 

 Update fasta2dist to use ellipsis. Remove gc
 

 Add gc() calls
 

 Update check-bioc.yml
 

 Update BioInfoJavaUtils-1.2.2.jar
 

 Update zzz.R for headless java mode
 

 Update zzz.R
 

 update BioInfoJavaUtils packend to 1.2.0
 

 Merge pull request #1 from gkanogiannis/actions

Actions 

 use rJava::J for static methods
 

 Update NEWS.md
 

 update README.md and vignette
 

 update NEWS.md
 

 Update check-bioc.yml 

 tests: tentative fix for unit test
 

 chore: version bump 1.9.1 (fix Collate field in DESCRIPTION)
 

 tests: fix precision
 

 feat: add adductCharge and standardizeSingleCharge functions
 

 fix bugs
 

 Version bump to v2.13.1
 

 add .positai to .Rbuildignore and .gitignore
 

 add figures for README.md
 

 version bump 2.45.1
 

 deprecate twoWayAlphabetFrequency() and twoWayAlphabetFrequencyByQuality()
 

 Add missing fnd entries to Authors@R in DESCRIPTION
 

 Add missing fnd entries to Authors@R in DESCRIPTION
 

 Uncommitted changes from Tuomas Borman PR #314
 

 Add missing fnd entries to Authors@R in DESCRIPTION 

 version bump 1.29.1
 

 Biostrings 2.81.1: Formally deprecate the scoring matrices

All the BLOSUM* and PAM* scoring matrices are now located in the pwalign
package (since BioC 3.20). Starting with BioC 3.24, the scoring matrices
located in the Biostrings package are formally deprecated and will soon
be removed from the package.
 

 Add missing fnd entries to Authors@R in DESCRIPTION
 

 version bump 1.51.1
 

 chore: modernize package to current Bioconductor standards

- Updated DESCRIPTION (version bump, R >= 4.6.0, standard biocViews)
- Migrated legacy inst/CITATION to bibentry() format
- Consolidated inst/NEWS into top-level NEWS.md
- Cleared out explicit regex export in NAMESPACE to pass BiocCheck

Co-authored-by: Gemini Code Assist <gemini@google.com>
 

 Migrate pr_check.yml to ci.yml (#4)

* Add ci.yml reusable-workflow wrapper

* Remove pr_check.yml (replaced by ci.yml) 

 CI: Maybe parallel tests cause covr::package_coverage() hang
 

 CI: GitHub actions need the "remotes" package
 

 Add missing fnd entries to Authors@R in DESCRIPTION (#1)
 

 Add missing fnd entries to Authors@R in DESCRIPTION 

 move Date close to Version in DESCRIPTION
 

 Add missing fnd entries to Authors@R in DESCRIPTION 

 Add ci.yml reusable-workflow wrapper 

 Add missing fnd entries to Authors@R in DESCRIPTION 

 docs: add AGENTS.md instructions for AI assistants
 

 docs: add AGENTS.md instructions for AI assistants
 

 docs: add NEWS entry for Bioconductor 3.23 sync version bump
 

 Merge pull request #99 from gladkia/98-support-custom-track-options

98 support custom track options 

 test: improve Shiny tests
 

 chore: clean up
 

 Merge branch 'master' into 98-support-custom-track-options
 

 chore: bump v+c
 

 build: update R version in GA workflows
 

 chore: update as suggested by the reviewer
 

 test: make linter happy
 

 doc: update docs
 

 feat: add support for additional track options (on the js level)
 

 Merge branch 'devel'
 

 docs: add NEWS entry for Bioconductor 3.23 sync version bump
 

 Merge pull request #41 from gladkia/40-compatibility-of-igvr-with-cram-files

Add CRAM file support via new CramTrack class (fixes #40) 

 doc: update docs
 

 Merge pull request #38 from gladkia/bioc_sync

Bioc sync 

 Merge pull request #35 from gladkia/server_migration

Server migration 

 feat: use VCF subset file for ampad/NIA-1898/chr22
 

 feat: change file links from igv-data.systemsbiology.netm to gladki.pl/igvR
 

 Resolve conflict in DESCRIPTION - using Bioconductor devel version 2.35.0
 

 Merge branch 'devel' into bioc_sync
 

 doc: add examples
 

 chore: improve DESCRIPTION
 

 build: add initial GHA generated with biocthis
 

 Lift test coverage from ~84% to ~92%

Adds 7 new test files and expands 4 existing ones, raising overall
package coverage well above the 90% target. No production code was
deleted or its functionality reduced — every uncovered branch was
addressed by exercising it from a new test.

Coverage measured locally with covr::package_coverage() against tracked
files in R/. Full test suite: 370 PASS, 0 FAIL, 13 WARN, 4 SKIP.

New test files:
- test-check_species_babelgene.R: 4 invariant branches (target=human +
  source not in dict, source=human + target not in dict, neither human,
  valid pair)
- test-check_agg_args.R: 6 cases covering happy path, agg_fun cleared
  for non-matrix gene_df / non-rownames gene_input, gene_output coerced
  to "rownames", return_args=FALSE flag, no-aggregation passthrough
- test-map_orthologs_gprofiler.R: NULL/empty/NA-only inputs, same
  source/target short-circuit, chunk_size validation, non-chunked path,
  chunked-serial path with multi-chunk, chunked-parallel (PSOCK) path
- test-helpers.R: invariants for check_keep_popular, check_sparseMatrix,
  non121_strategy_opts (full dict / synonyms / errors / include_agg),
  is_human, is_matrix/is_sparse_matrix, is_converted, check_bool_args
  (5 per-arg branches), invert_dictionary, methods_opts,
  gene_input_opts/gene_output_opts, check_agg_opts
- test-internal-helpers.R: check_gene_map, check_agg_opts, filter_gene_df
  (rownames/colnames/error), use_cache (NULL save_dir + cached file),
  check_gene_df_type (data.table conversion + error), aggregate_rows
  (unknown method error), map_orthologs (unknown method error),
  all_genes (unknown method fallback), many2many_rows
  (aggregate_orthologs=FALSE), get_orgdb_gprofiler (use_local TRUE/FALSE)
- test-run_benchmark_once.R: run_convert_orthologs=FALSE branch, cache
  hit on second call, within-species (is_human) path
- test-misc-helpers.R: is_gha (env var present/absent), load_rda, rotate_clades
  (matching/non-matching tip sets), aggregate_rows_monocle3 (mean +
  count), get_cache_save_path uniqueness, cache_dir, messager,
  format_species, all_species, add_rowcol_names (rownames + colnames),
  check_gene_output, gconvert_target_opts (validates target for known
  species)

Expanded test files:
- test-prepare_tree.R: local-newick else-branch, force_ultrametric=FALSE,
  age_max calibration
- test-aggregate_mapped_genes.R: transpose=TRUE, within-species map_genes
  branch, sort_rows=TRUE, as_integers=TRUE, early-exit rename-only path
- test-infer_species.R: test_species=NULL default, method-as-test_species
  expansion, make_plot=FALSE
- test-create_background.R: use_intersect=FALSE (union), user-supplied bg,
  same-species fast path with as_output_species=TRUE

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 

 version bump 1.1.1
 

 Bump version
 

 Mention s3_client new default value in NEWS
 

 Version 2.1.1: align vignette YAML with DESCRIPTION; exclude venv from builds

- Bump patch after BioC 3.23 sync metadata
- Set vignette version fields to match package version
- Add venv to .Rbuildignore
- Fix NEWS bumpversion search template for top section header

Made-with: Cursor
 

 Fix test-map_genes: message() escapes tryCatch under testthat

Same bug pattern as the previous fix in run_benchmark_once.R (commit
dad4348). The planarian (Schmidtea mediterranea) test wraps
`map_genes(species = "Schmidtea mediterranea")` in tryCatch because the
planosphere mapping file is downloaded at runtime and may fail (e.g. the
Windows runner under R 4.6 can't resolve the cache path —
"smed_20140614.mapping.rosettastone.2020.txt.gz does not exist or is
non-readable"). The handler did `message(e); NULL`, but `message()`
re-signals condition objects, and testthat's calling handlers treat the
re-signaled error as a test failure — escaping the tryCatch.

Fix: pass `conditionMessage(e)` (a plain string) to `message()` so the
text is printed without re-signaling. The test still gracefully skips
the assertion when the download fails, which is the intended behaviour.

Surfaced by run 25110211328 on Windows; macOS passed because the
download succeeded there.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 </pre>
    </div>
  
    

      Package: Rarr

      Commit: fb29fc1c8232dccaea37a6800f41530adc774dd4

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 15:30:33 +0200

      Commit message:


	  
		
 Run devtools::document()
 
    
  
    

      Package: Rarr

      Commit: e505b1f79c5a8815162f4edf1295d67788b72c37

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 14:24:47 +0200

      Commit message:


	  
		
 Wrap linter in requireNamespace()
 
    
  
    

      Package: Rarr

      Commit: 273563a9dedb23a0ccd4af7c5773da14034c48dc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 13:50:05 +0200

      Commit message:


	  
		
 Save snapshot
 
    
  
    

      Package: Rarr

      Commit: a83111088f106507a7423ab86c00b31d16f1d431

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 12:32:21 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: 7b4a10a994d91816fb9953d8e17b17f0bfdcccfa

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 12:31:57 +0200

      Commit message:


	  
		
 Mention zarr v3 on s3 fix
 
    
  
    

      Package: Rarr

      Commit: 118d0c62133ad0236c4fa2dd58012ed4906a912c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 12:27:41 +0200

      Commit message:


	  
		
 Add custom linter to ensure fromJSON always has simplifyVector = FALSE
 
    
  
    

      Package: Rarr

      Commit: f99b4359045f3da0eb2e3b81c22092d1d671bcfa

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 12:20:32 +0200

      Commit message:


	  
		
 Add test for s3 metadata bug
 
    
  
    

      Package: Rarr

      Commit: 786fa4e5ba6a9b42eecce7ada98f93e1bcc2372b

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2026-04-28 21:57:30 +0200

      Commit message:


	  
		
 simplifyVector=FALSE whenever fromJSON is called
 
    
  
    

      Package: Rarr

      Commit: f0c9673bd345bd6d76ed97bfa9c96ac9bd4fb24f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 11:18:44 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: a3573a0eb4b235a399a372a01b85c988c5ff1fbc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 11:18:14 +0200

      Commit message:


	  
		
 Mention vlen-utf8 performance improvement in NEWS
 
    
  
    

      Package: Rarr

      Commit: 0fe2f45c07f68bc403c5f8fcd5303166c423a629

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-22 11:18:33 +0200

      Commit message:


	  
		
 Run only vlen-utf8 benchmark
 
    
  
    

      Package: Rarr

      Commit: 4216c8f4efe7ecf3d5d92d95f2457cc917267cbd

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-22 11:15:11 +0200

      Commit message:


	  
		
 Convert vlen_utf8 decode codec in C
 
    
  
    

      Package: Rega

      Commit: 6ca901a186bcaa6e37c8fa82081910ba502c49a6

      Author:  Igor Cervenka <wormikk@gmail.com> 

      Date: 2026-04-29 14:57:30 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'bioc/devel' into devel
 
    
  
    

      Package: Rega

      Commit: b33cc16edf798181c760454d9a9d3e3c1f0c53e0

      Author:  Igor Cervenka <wormikk@gmail.com> 

      Date: 2026-04-29 14:53:54 +0200

      Commit message:


	  
		
 Fix samples_in_db return value
 
    
  
    

      Package: orthogene

      Commit: 253239d9f2ffea5bb2905066f511106154c03b81

      Author:  bschilder <brian_schilder@alumni.brown.edu> 

      Date: 2026-04-29 08:57:47 -0400

      Commit message:


	  
		
 Revert g:Profiler workarounds — upstream API regression is fixed

g:Profiler confirmed and fixed the API regression that returned literal
`NaN` in JSON. Unmatched genes are once again returned as `"N/A"`. The
tests that failed during the Bioc 3.23 freeze were correctly catching
that regression — masking them was the wrong long-term call.

Revert from 1.17.3:
* Examples for `convert_orthologs()`, `map_orthologs()`, `all_genes()`
  no longer pass `method = "homologene"`; they exercise the default
  (g:Profiler-first) path again.
* Tests in `test-aggregate_mapped_genes`, `test-convert_orthologs`,
  `test-infer_species` no longer pin `method = "homologene"` on calls
  that should be testing the default behaviour.
* `test-all_genes_gprofiler` and the `method = 'gprofiler'` block in
  `test-convert_orthologs` no longer wrap calls in tryCatch+skip — the
  whole point of those tests is to fail loudly when g:Profiler breaks.
* `test-run_benchmark` no longer uses `na.rm = TRUE` in the aggregate
  mean checks — NA from a backend means *something is wrong* and we
  want the assertion to surface it.

Kept:
* `run_benchmark_once()` still uses `message(conditionMessage(e))`
  inside its tryCatch error handlers — `message()` re-signals
  the condition and escapes tryCatch under testthat. Unrelated to
  g:Profiler.
* `test-infer_species` still tolerates ties in `top_match` — when human
  and monkey tie at the same `percent_match` via babelgene, the test
  passes as long as the expected species is among the ties.

Bumps to 1.19.1 on top of the post-3.23 devel-cycle bump (1.19.0).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 </pre>
    </div>
  
    

      Package: BioNAR

      Commit: 5acd4d1e61c1fd9129eca169c68fdd6097b60a72

      Author:  Anatoly Sorokin <lptolik@gmail.com> 

      Date: 2026-04-29 12:47:06 +0100

      Commit message:


	  
		
 Merge commit '2a185b929475492134236fa44eddc37b03434864' into devel
 
    
  
    

      Package: BioNAR

      Commit: 7254b80793e762bafa709f9c79f35d6ed7cc5009

      Author:  Anatoly Sorokin <lptolik@gmail.com> 

      Date: 2026-04-29 12:41:18 +0100

      Commit message:


	  
		
 fix a bug in clusterOra when not "name" used as vertex ID
 
    
  
    

      Package: OmnipathR

      Commit: 3e1139172d3036ffd772ebb945bc5e338ac63fde

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-04-29 12:26:56 +0200

      Commit message:


	  
		
 propagate bioc version bump to bump2version
 
    
  
    

      Package: asuri

      Commit: dfe8e2e9b229ff3540d19c28ed0b5e9e5e95bc31

      Author:  aberral <aberralgonzalez@gmail.com> 

      Date: 2026-04-29 11:38:45 +0200

      Commit message:


	  
		
 Version Fix
 
    
  
    

      Package: asuri

      Commit: 552a9392ac125ffb7a1ea1186c237777f8a40cbd

      Author:  aberral <aberralgonzalez@gmail.com> 

      Date: 2026-04-29 11:37:58 +0200

      Commit message:


	  
		
 "Resolve conflict: accept Bioconductor devel version 1.1.0"

Merge remote-tracking branch 'upstream/devel'

# Conflicts:
#	DESCRIPTION
 
    
  
    

      Package: asuri

      Commit: 6255c29816ea84592365802f1017ddb4ea3b1aa7

      Author:  aberral <aberralgonzalez@gmail.com> 

      Date: 2026-04-29 11:35:09 +0200

      Commit message:


	  
		
 1 version
 
    
  
    

      Package: asuri

      Commit: a6f0d65a123ffcd70715a67f5c55505de46f30db

      Author:  aberral <aberralgonzalez@gmail.com> 

      Date: 2026-04-29 11:32:11 +0200

      Commit message:


	  
		
 update version for devel cycle
 
    
  
    

      Package: scater

      Commit: 8c547447c1451ed6fd95c341cd777e12cee9a439

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2026-04-29 10:22:09 +0100

      Commit message:


	  
		
 Merge branch 'devel' of git.bioconductor.org:packages/scater into devel
 
    
  
    

      Package: scater

      Commit: 15c18a1f15e968af3a752bd22c4ea8c32db3107d

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2026-04-29 10:21:42 +0100

      Commit message:


	  
		
 Resolve #227
 
    
  
    

      Package: scater

      Commit: a55ac0dbcbfe489826f0b7ce053ca8cb4a7af676

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2026-04-07 10:41:52 +0100

      Commit message:


	  
		
 Merge pull request #226 from alanocallaghan/minor-fix

Make identities of summarized columns are more obviously correct. 
    
  
    

      Package: scater

      Commit: 46c70c3395dc86de5e25977eaf1bd5e3b81be395

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-04-07 12:50:00 +1000

      Commit message:


	  
		
 Make identities of summarized columns are more obviously correct.

It was actually correct already but the correctness was hard to prove; now it
should be obvious that the columns of the summarized matrix match up to the
rows of the dataframe containing the group + block identities.
 
    
  
    

      Package: Rarr

      Commit: db556a97ed34169fb4777368a0723c110628d1c7

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 10:56:04 +0200

      Commit message:


	  
		
 Revert touchstone to release
 
    
  
    

      Package: Rarr

      Commit: 019187b20ab44d566c35d507bea8a3ab796a9dc2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 10:29:15 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: c3d3c3e3a48a59e825f275877161e3167eeb1c9a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 10:29:07 +0200

      Commit message:


	  
		
 Mention new blosc options and vlen fix in NEWS
 
    
  
    

      Package: Rarr

      Commit: f353c3d50e82bc63b5d7033f423cd183fed405cc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-24 16:53:15 +0200

      Commit message:


	  
		
 Record blosc typesize in metadata
 
    
  
    

      Package: Rarr

      Commit: 23cc748b3ffc0b2d4439c85f0823e19d37351466

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-24 17:08:35 +0200

      Commit message:


	  
		
 Add test for blosc vlen compression
 
    
  
    

      Package: Rarr

      Commit: 2794f426cf12f1e34cca7e3f8ebc9e53c53ba434

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-24 16:20:26 +0200

      Commit message:


	  
		
 Convert blosc compression to a codec
 
    
  
    

      Package: Rarr

      Commit: 352079166e5bb81e13ec7a58d030b218caa9aa65

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-21 20:18:05 +0100

      Commit message:


	  
		
 Snapshot test .zarray blosc
 
    
  
    

      Package: Rarr

      Commit: 59f269649b73cfc5986b5d2cc130543a49cc5a7b

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-21 14:54:55 +0100

      Commit message:


	  
		
 Test more complex blosc options
 
    
  
    

      Package: Rarr

      Commit: 4dd4a21e07af1f8495da2549a512c54cff63bdeb

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-20 20:02:02 +0100

      Commit message:


	  
		
 Write shufflemode as text in metadata
 
    
  
    

      Package: Rarr

      Commit: 02bd78dde108b84d7c3651041c69cc8b7e9b1567

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-20 19:42:12 +0100

      Commit message:


	  
		
 Use requested blosc opts from R code
 
    
  
    

      Package: Rarr

      Commit: edf61e84dba3fe2e2be5071898e494eab550a133

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-20 19:17:13 +0100

      Commit message:


	  
		
 Add config options to use_blosc()
 
    
  
    

      Package: Rarr

      Commit: c070483d9907f1b22e8d4a6b5d85b748e93bf1b1

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-18 15:31:40 +0100

      Commit message:


	  
		
 Add more options to blosc c function
 
    
  
    

      Package: Rarr

      Commit: f9fccacafe13251f6fff107ad4bee969ebb7c868

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 10:34:55 +0200

      Commit message:


	  
		
 Fix lintr config
 
    
  
    

      Package: Rarr

      Commit: 07cb75dacf7ba488007446e70e7690dc64d9241c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 18:41:31 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: 4a941c204cae9e796609c8ebacab9ecaf8f715fc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-14 18:59:04 +0200

      Commit message:


	  
		
 Mention empty chunks change in NEWS
 
    
  
    

      Package: Rarr

      Commit: 68acda1157d865a6af8c435c4a217c43e0940da2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-14 18:57:23 +0200

      Commit message:


	  
		
 Add test for not writing empty chunks
 
    
  
    

      Package: Rarr

      Commit: 3c5bad5b1586acc39f3eb25e9bfd7e4b4df239a7

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-14 11:08:02 +0200

      Commit message:


	  
		
 Skip writing empty chunks
 
    
  
    

      Package: Rarr

      Commit: 488169c1098c157ae3140a4e1ee687c69ca46f2a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 17:46:56 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: 65352e8f221813bb7091131433cbfe624dab7b12

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 17:46:28 +0200

      Commit message:


	  
		
 Mention normalize_array_path() speedup in NEWS
 
    
  
    

      Package: Rarr

      Commit: 93e8666232f68fe12830a2d41a75d08fcabd018f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 17:42:11 +0200

      Commit message:


	  
		
 Use a single regex to extract region, bucket and object
 
    
  
    

      Package: Rarr

      Commit: 3764df97f31d55655cb0a994d7c477953f57d2f5

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-22 16:23:08 +0200

      Commit message:


	  
		
 Convert repeated gsub() to regmatches()
 
    
  
    

      Package: Rarr

      Commit: 5ad1e34f99d778d4d82be8166313d66f7a4e11cc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-22 16:22:20 +0200

      Commit message:


	  
		
 Use startsWith() to avoid complex regex
 
    
  
    

      Package: Rarr

      Commit: 1e384352f77f55ec5efccabd0f78116e05b5e686

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-22 16:15:44 +0200

      Commit message:


	  
		
 Use sub() instead of gsub() where possible
 
    
  
    

      Package: Rarr

      Commit: 6e8168869bf45e29df12fe48e32baa8297538bf5

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 17:29:59 +0200

      Commit message:


	  
		
 Fix badges in README
 
    
  
    

      Package: Rarr

      Commit: 73ef26e94b07f7bd8249de1cf6d0e52e4f09791a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-27 22:32:00 +0200

      Commit message:


	  
		
 Use rlang::inject() to extract chunks
 
    
  
    

      Package: Rarr

      Commit: 30a4694f1225a7bb0b0f4b1641dca469997ca82e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 10:38:44 +0200

      Commit message:


	  
		
 Use persist-credentials: false to avoid token leak
 
    
  
    

      Package: Rarr

      Commit: 5afdc5a8865d69bf0cbcae610b064b455e55fe9f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 10:34:50 +0200

      Commit message:


	  
		
 Update action versions in workflows
 
    
  
    

      Package: BgeeDB

      Commit: 75ea4512c2469e5b4638de20c55f0ad7e5516a49

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2026-04-29 10:33:53 +0200

      Commit message:


	  
		
 fixed typo
 
    
  
    

      Package: BgeeDB

      Commit: 61f8871523192a0054d62f0a4d9a4a412a072cfa

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2026-04-29 10:24:15 +0200

      Commit message:


	  
		
 Merge branch 'galaxy' into develop
 
    
  
    

      Package: BgeeDB

      Commit: bd73b92dad92f29d42170b5c8ec3a2ab83788dd7

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2026-04-29 10:23:14 +0200

      Commit message:


	  
		
 Merge branch 'devel' into develop
 
    
  
    

      Package: BgeeDB

      Commit: ae43aeb3ee0e7cf44b14024c7f8ce0bcdac2bd80

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2026-04-29 10:18:54 +0200

      Commit message:


	  
		
 allow to run topAnat using foreground/background files. Also improved error management
 
    
  
    

      Package: BgeeDB

      Commit: e1480e1dffac8e5316a528333485bf5bb1f728d9

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2025-10-08 17:45:51 +0200

      Commit message:


	  
		
 implement wrapper function to be compatible to Galaxy
 
    
  
    

      Package: igblastr

      Commit: ec5f0bf80a986ae4ea53877d2a42bee58eccc796

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-04-28 22:24:07 -0700

      Commit message:


	  
		
 Re-enable GHA on windows-latest
 
    
  
    

      Package: igblastr

      Commit: 737166c45b93ddabfb7bb95616140817afdd3826

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-04-28 22:03:33 -0700

      Commit message:


	  
		
 update README.md
 
    
  
    

      Package: igblastr

      Commit: 227b890474721ab345184908839dd90819a5273a

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-04-28 22:00:24 -0700

      Commit message:


	  
		
 update README.md
 
    
  
    

      Package: igblastr

      Commit: 411f775f81b856a1e5ebd14a82a5c7463782b3e8

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-04-28 21:56:07 -0700

      Commit message:


	  
		
 update README.md
 
    
  
    

      Package: S4Vectors

      Commit: a371782115b9c92474f79d6374027c468da23f0d

      Author:  Michael Lawrence <lawremi@gmail.com> 

      Date: 2026-04-28 21:44:17 -0700

      Commit message:


	  
		
 top_prenv[_dots] handle dots passed via lexical scoping
 
    
  
    

      Package: SpaceMarkers

      Commit: 145f3da779f89e7e4593c876911eb1c3c32e9287

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 23:41:10 -0400

      Commit message:


	  
		
 bump version to 2.3.1
 
    
  
    

      Package: SpaceMarkers

      Commit: a3b0d60c9f44627e1c0c393ccc45d9f9b1373ad8

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 22:24:39 -0400

      Commit message:


	  
		
 Merge pull request #96 from DeshpandeLab/chore/bioc-readiness

chore: Bioconductor readiness — version 2.1.1, NEWS, build cleanup 
    
  
    

      Package: SpaceMarkers

      Commit: 60ed1281c58bcd490918ece9418335f0669d73fe

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 21:41:54 -0400

      Commit message:


	  
		
 Merge pull request #97 from DeshpandeLab/feat/create-lr-dataframe

feat: port create_lr_dataframe() into the package 
    
  
    

      Package: SpaceMarkers

      Commit: 4f08709cb646ae042ca1433f49f53bf1bca47f10

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 21:31:17 -0400

      Commit message:


	  
		
 chore: bump target to 2.1.1 (2.1.0 already on Bioc devel)

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: f2a860cf44087e2754690c0434755974849ba5e2

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 21:29:23 -0400

      Commit message:


	  
		
 chore: target 2.1.0 (Bioc devel) and document changes since 2.0.0

The 2.2.0 / 2.3.0 bumps were intermediate development markers; they
were never released. Reset DESCRIPTION to 2.1.0 (the post-2.0.0 devel
series) and add a comprehensive NEWS entry covering the
SpaceMarkersExperiment class, AnnData I/O, directed interaction
visualization, vignette restructuring, and BiocCheck cleanup work.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 8afea434566b02c34e0fef17cc6176eeaad24e45

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 20:07:48 -0400

      Commit message:


	  
		
 chore(vignettes): JPEG raster + compact dimensions for Bioc 5 MB limit

H&E histology overlays compress ~5x better as JPEG quality 80 than as
PNG. Combined with dpi=72 and 5x4 inch figure size, this keeps the
rendered HTML vignettes comfortably under Bioconductor's per-file size
guideline.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 0d1310bce8a7d56e23d1daa0d1b4f861638d4371

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 19:58:13 -0400

      Commit message:


	  
		
 feat: port create_lr_dataframe() into the package

Long-format reshape of the three matrices produced by
calculate_lr_scores() / calculate_gene_set_score() /
calculate_gene_set_specificity() — pivots them into a tidy
data frame keyed by (interaction, source_cell_type,
target_cell_type) with merged ligand/receptor gene names from
the lrpairs reference.

The function previously lived in the SpaceMarkers_Protocol repo's
R/protocol-helpers.R; Orian asked that we promote it to the
package proper since (a) it's the natural tidy view of the
package's own LR-scoring outputs, (b) all the dependencies
(reshape2, dplyr) are already in Imports, and (c) it's per-sample,
not multi-sample orchestration.

Two cleanups vs. the protocol-helpers version:

- Drop the unconditional `lrscores[is.na(lrscores)] <- 0` line.
  That was the silent-zero footgun that masked the all-NaN LR
  matrix bug we hit during the protocol render. NAs now propagate
  to the score column; callers can filter or impute explicitly.

- Doc/code mismatch on @return columns: original docstring listed
  8 columns; function returned 9 (source_to_target was tacked on
  at the end). Updated docstring to list all 9.

Also added a @note flagging the parsing constraint: cell-type
names must not contain "_to_" or "_and_" (the function uses
those as delimiters when reconstructing source/target from the
joined-key string).

Tests cover the round-trip on a small fixture plus an explicit
NA-preservation check (the regression we just fixed).
 
    
  
    

      Package: SpaceMarkers

      Commit: 4dadee6bc4f29fa457aa3eb34a5f3fda7cd0eba7

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 18:36:23 -0400

      Commit message:


	  
		
 chore: tighten Rbuildignore + gitignore for Bioconductor submission

The R CMD build tarball had grown to 38 MB on main, almost entirely
from untracked analysis artifacts in the working dir that nothing was
excluding. Stop those from leaking into the source release:

- .Rbuildignore: catch-all anchored patterns for top-level *.rds,
  *.Rda, *.csv, csvFALSE, plus specific stray PNGs (LR_scores_*.png,
  Fibroblast_*.png, PDAC_*.png, heatmap_*.png, circos_*.png,
  new_heatmap*.png). Also exclude .claude/, ..Rcheck/, .Rcheck/,
  .Rproj.user/, *.Rproj, Brewfile, README.Rmd, RData / Rhistory /
  DS_Store. Top-level patterns use ^[^/]+ so they don't affect
  data/, inst/, vignettes/, tests/.

- .gitignore:
  - drop the broad `*.png` rule (was blocking new tracked figures)
    in favour of /-anchored patterns covering only the ad-hoc
    top-level analysis PNGs.
  - drop the `.github/` rule. The directory IS tracked (workflows
    live there); the rule was triggering "ignored by .gitignore"
    warnings on every git add of a workflow file.
  - add patterns for the analysis stragglers (IMscores.rds,
    LRscores.rds, LRtemp.Rda, lr_*.rds, F2P*.csv, PDAC_*.csv,
    FIBROBLASTS_*.csv, top_*.csv*, Brewfile).

- DESCRIPTION: 2.2.0 -> 2.3.0. Bioc convention is odd-y in x.y.z for
  the devel branch; 2.2.0 was the (even) release marker. Bumping to
  2.3.0 puts main back on the devel cycle.

Verified via pkgbuild::build:
  before  : 38 MB, .claude/worktrees/* + .. analysis junk in tarball
  after   : 17 MB, only the three rendered vignette HTMLs dominating
            (3.6 / 9.3 / 11 MB respectively). Vignette size can be
            reduced separately by trimming embedded plots in
            SpaceMarkersStepByStep / SpaceMarkersExperiment.
 
    
  
    

      Package: SpaceMarkers

      Commit: 73e853c2576b35d8aaa6cf52307e17ba94674eb6

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 18:19:32 -0400

      Commit message:


	  
		
 Merge pull request #95 from DeshpandeLab/fix/use-github-token

fix(ci): authenticate ghcr.io with built-in GITHUB_TOKEN 
    
  
    

      Package: SpaceMarkers

      Commit: 7b433e1ae853757bb8c6bb0849bfd2461e9ef124

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 18:14:52 -0400

      Commit message:


	  
		
 fix(ci): authenticate ghcr.io with built-in GITHUB_TOKEN

The previous setup used a custom `GHCR_TOKEN` PAT secret, which was
producing 'denied: denied' on push to ghcr.io. PATs expire and need
manual rotation.

Switch to the built-in `secrets.GITHUB_TOKEN` — auto-minted per run,
no expiry, no manual rotation. Authority comes from the workflow's
`permissions: packages: write` declaration which is already in place.

The custom `GHCR_TOKEN` secret can be deleted from the repo's Actions
secrets once this lands.
 
    
  
    

      Package: SpaceMarkers

      Commit: 435ae43696998fa9ab999a7ed4a1df6eaace1984

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 18:07:44 -0400

      Commit message:


	  
		
 Merge pull request #94 from DeshpandeLab/fix/login-action-v4.1.0

fix(ci): docker/login-action@v4.3.0 doesn't exist; pin to v4.1.0 
    
  
    

      Package: SpaceMarkers

      Commit: 39398f60775f16af5adb12ff7ece900c4bc29607

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 16:52:05 -0400

      Commit message:


	  
		
 fix(ci): docker/login-action@v4.3.0 doesn't exist; pin to v4.1.0 SHA
 
    
  
    

      Package: SpaceMarkers

      Commit: 5af28c1c94bc7725fae4f107c5d6741177bb8dcf

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 16:48:54 -0400

      Commit message:


	  
		
 Merge pull request #93 from DeshpandeLab/chore/bump-actions-node24

chore(ci): bump container-build actions to Node 24 versions 
    
  
    

      Package: SpaceMarkers

      Commit: 012b08d7ffa5e62f59f269b819fabedbe0f0e17f

      Author:  copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> 

      Date: 2026-04-28 20:00:32 +0000

      Commit message:


	  
		
 chore(ci): pin docker/metadata-action and docker/build-push-action to commit SHAs

Agent-Logs-Url: https://github.com/DeshpandeLab/SpaceMarkers/sessions/81dc10b4-d600-4760-8c6e-190dbec6e8cf

Co-authored-by: atuldeshpande <4661537+atuldeshpande@users.noreply.github.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: c14280f11a2b0e465c6c98d4f5cfec68a25c8443

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 15:58:05 -0400

      Commit message:


	  
		
 Update .github/workflows/build-push-container.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 
    
  
    

      Package: SpaceMarkers

      Commit: 2782491267ebe56781aafb32ce30eac06ff896f7

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 15:57:54 -0400

      Commit message:


	  
		
 Update .github/workflows/build-push-container.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 
    
  
    

      Package: SpaceMarkers

      Commit: f11105a1e0ec55b448dc59743621aebf084597f3

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 15:44:11 -0400

      Commit message:


	  
		
 chore(ci): bump container-build actions to Node 24 versions

GitHub deprecated Node 20 in actions runtime; the pinned versions in
build-push-container.yml were all Node-20-only and the workflow started
failing post-merge with deprecation errors.

- actions/checkout@v4 -> v5 (Node 24)
- docker/login-action@65b78e6e... -> @v4 (Node 24, was v3 with Node 20)
- docker/metadata-action@9ec57ed1... -> @v6 (Node 24, was v5)
- docker/build-push-action@f2a1d5e9... -> @v7 (Node 24, was v6)

Replaces previous SHA pins with major-version tags; Docker and GitHub
both maintain v* tags as moving major-version aliases. Re-pin to
specific SHAs if you'd prefer stricter immutability.
 
    
  
    

      Package: SpaceMarkers

      Commit: 81804df55bdba866b95d4545506a20be83a43d99

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 15:35:30 -0400

      Commit message:


	  
		
 Merge pull request #92 from DeshpandeLab/claude/sme-pipeline-methods

SpaceMarkersExperiment S4 pipeline methods + chainable step-by-step vignette 
    
  
    

      Package: SpaceMarkers

      Commit: a87d201333265789335dbc3270155ceaf22792ef

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 11:40:11 -0400

      Commit message:


	  
		
 fix: address Copilot review batches 4 + 5 (NULL guards, coord swap)

Five comments across the 2026-04-23 and 2026-04-28 Copilot reviews:

- R/utils.R calculate_gene_set_score(ANY) and
  calculate_gene_set_specificity(ANY) declared gene_sets = NULL but
  immediately called unlist(gene_sets). Add explicit early errors
  with hint that the NULL default is reserved for the SME method.
  calculate_gene_set_specificity(ANY) similarly errors when spPatterns
  is NULL.

- R/hdutils.R calculate_gene_scores_directed(ANY) and
  calculate_overlap_directed("data.frame") had NULL defaults for
  pat_hotspots / influence_hotspots that the bodies relied on.
  Same pattern of explicit early stop().

- R/utils.R plot_spatial no-image branch: yl <- range(df$y_c) was
  being used as both the ylim limits and the basis for the
  yl[2] - y_c flip in geom_point's aes(). When data didn't start at
  y = 0, plotted points fell outside ylim and got clipped. Shift x_c
  and y_c to start at zero in the no-image branch so the flip lands
  inside the limits.

- R/AllClasses.R setAs("SingleCellExperiment", "SpaceMarkersExperiment")
  was renaming the spatial reducedDim columns to c("x", "y"); rest of
  the package (load10XCoords, tests, vignettes) uses c("y", "x").
  Swap so axes don't invert downstream.

Tests: 271 pass, 0 fail.
R CMD check (no vignettes): 0 errors, 0 warnings, 5 pre-existing NOTEs.
 
    
  
    

      Package: SpaceMarkers

      Commit: 4dd2d8a1fc4075a647bab45a661b420865344854

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-25 13:53:21 -0400

      Commit message:


	  
		
 chore: bump version to 2.2.0 (Bioc devel cycle)
 
    
  
    

      Package: SpaceMarkers

      Commit: 4c4127b0e2f196eba76f50066fb85056e0c88c5c

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-24 23:04:44 -0400

      Commit message:


	  
		
 docs: BiocCheck cleanup - runnable examples + missing \\value sections

Address two outstanding BiocCheck blockers raised by the Bioc
review process:

1. ERROR: At least 80% of man pages documenting exported objects
   must have runnable examples. Add @examples blocks (synthetic
   small inputs where possible, \\donttest{} where the function
   needs an on-disk Visium folder or an installed Python conda env)
   to the 18 missing pages: SpaceMarkers, SpaceMarkersExperiment,
   add_features, calculate_gene_scores_directed,
   calculate_gene_set_score, calculate_gene_set_specificity,
   calculate_influence, calculate_lr_scores, calculate_thresholds,
   find_all_hotspots, find_hotspots_gmm, load10X, load_anndata,
   plot_im_scores (replaces a non-runnable example()-style stub),
   plot_spatial, plot_spatial_data_over_image, reexports,
   save_anndata. Also flip plot_cell_interaction_circos /
   plot_source_to_target_circos / plot_target_from_sources_circos
   from \\dontrun{} to \\donttest{} per BiocCheck preference.

2. WARNING: Empty or missing \\value sections found in man page(s).
   Add @return to the 17 internal helpers and setAs methods that
   were missing it: as-SingleCellExperiment-... and
   as-SpatialExperiment-SpaceMarkersExperiment, .apply_sme_filters,
   .undirected/.directed_SpaceMarkers_sme, .wrap_undirected_result,
   .wrap_directed_result, .read_format, .infer_method, the four
   .get_*_features helpers, .get_spe_features, find_all_hotspots,
   plot_im_scores, reexports.

Side fixes uncovered while validating the new examples:
- get_im_scores's existing example called example(get_pairwise_interacting_genes)
  and then get_im_scores(SpaceMarkers); now that SpaceMarkers is also an
  exported function the symbol shadowed the local result list and the
  example errored. Replace with a self-contained mock list.
- The new SpaceMarkers() example needs spatial_patterns(sme) <- ...
  (not just colData) so the SME pipeline can find pattern_names.

Authors@R: add Orian Stapleton (ostaple1@jh.edu) as author per
omission flagged in review.

.Rbuildignore: skip BiocCheck output dir SpaceMarkers.BiocCheck/.

Verified end-to-end:
- devtools::run_examples(run_donttest = TRUE) -- all examples succeed.
- R CMD check (no vignettes): 0 errors, 0 warnings, 6 pre-existing NOTEs.
- devtools::test(): 271 tests pass.
- BiocCheck: real ERROR + WARNING for runnable examples / \\value are
  both gone. Two residual ERRORs are environmental (worktree directory
  name; transient HTTP 504 from the Support Site lookup), not code.
 
    
  
    

      Package: SpaceMarkers

      Commit: ec278c02131944765cc2e49f01e77af8440cf9d3

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-23 13:44:16 -0400

      Commit message:


	  
		
 fix(load_anndata): call as_SingleCellExperiment as R6 method, not top-level

anndataR exposes as_SingleCellExperiment() as a method on the AnnData R6
class (see R/AbstractAnnData.R), not as a top-level exported function.
Calling anndataR::as_SingleCellExperiment(ad) therefore triggers an R CMD
check WARNING about a missing/unexported object.

Switch to the R6 method form on the object returned by read_h5ad():

    anndataR::read_h5ad(file, ...)$as_SingleCellExperiment()

This matches anndataR's documented usage and silences the check warning.
save_anndata() already uses anndataR::as_AnnData() which *is* a top-level
export, so no change there.
 
    
  
    

      Package: SpaceMarkers

      Commit: 687cc94bd190c2c51f5d33ad4a35beeadd210aa1

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-23 11:00:33 -0400

      Commit message:


	  
		
 feat(anndata): dual-reader load_anndata + save_anndata with round-trip

load_anndata(file, reader = "auto" | "anndataR" | "zellkonverter"):
prefer anndataR (pure R, no Python/conda) when installed, fall back to
zellkonverter, else error with both install hints. Avoids the
basilisk/mamba codesign failure on Apple Silicon whenever anndataR is
available, and lets users pick anndataR on Linux/Windows for the
lighter install footprint.

save_anndata(sme, file, reader = ...) is the symmetric write. Full
SpaceMarkers analysis state (pattern_names, spatial_params, hotspots,
overlap_scores, undirected_scores, directed_scores, lr_scores,
interactions, influence_map, analysis flag) is packed into a plain
nested list by .pack_spacemarkers_state() and attached to
metadata(sce)$spacemarkers so it serializes into uns["spacemarkers"]
when the reader writes the .h5ad. On load, .unpack_spacemarkers_state()
restores the SME slots; the sidecar is scrubbed post-unpack so
subsequent saves don't double-pack.

Analysis round-trip is guaranteed: SME -> h5ad -> SME preserves all
SpaceMarkers state, unlocking STAPLE Nextflow's AnnData-centric
workflow.

anndataR added to Suggests alongside zellkonverter; neither is
Imports. Tests cover all four guard paths (auto/explicit x
both-missing/one-missing) plus a backend-free pack/unpack round-trip.
 
    
  
    

      Package: SpaceMarkers

      Commit: c8b98c2a2b97b873c909578bd9d8e73fedb6949b

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-23 10:38:44 -0400

      Commit message:


	  
		
 feat: one-shot load_anndata() for .h5ad -> SpaceMarkersExperiment

Wrap zellkonverter::readH5AD() + the SCE -> SpaceMarkersExperiment
coerce into a single exported function so the AnnData path collapses
to:

    sme <- load_anndata("visium.h5ad")

zellkonverter is added to Suggests (not Imports) to avoid forcing
the basilisk + reticulate + conda stack on users who don't use
AnnData. load_anndata() checks for the package at call time and
gives a clear install hint if it's missing.
 
    
  
    

      Package: SpaceMarkers

      Commit: c673feb8bdc2b54135805ef0c8cfb5191ffe7185

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-23 10:29:34 -0400

      Commit message:


	  
		
 feat: direct SingleCellExperiment -> SpaceMarkersExperiment coercion

AnnData-sourced objects (zellkonverter::readH5AD,
anndataR::as_SingleCellExperiment) arrive as SCE, with spatial
coordinates stored as a reducedDim (commonly named "spatial"). The
previous path required users to do

    spe <- as(sce, "SpatialExperiment")
    sme <- as(spe, "SpaceMarkersExperiment")

and then noticed that spatialCoords(spe) came up empty, because the
default SCE->SPE coerce does not promote the "spatial" reducedDim
into spatialCoords.

Register a setAs("SingleCellExperiment", "SpaceMarkersExperiment")
that looks for a reducedDim named "spatial" / "X_spatial" / "SPATIAL",
promotes it into spatialCoords, and returns the fully-populated SME.
A full AnnData -> SME path now reads:

    sme <- as(zellkonverter::readH5AD(path), "SpaceMarkersExperiment")

Add regression tests covering both the promoted and no-reducedDim
paths.
 
    
  
    

      Package: SpaceMarkers

      Commit: ac334a505d1332ff74ee06ed65cd5c766ef3cee7

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-22 12:53:12 -0400

      Commit message:


	  
		
 Revert "feat: import protocol-branch helpers to support SpaceMarkers_Protocol notebooks"

This reverts commit 41c37d7ed6809a218135791c073a24ba56492653.
 
    
  
    

      Package: SpaceMarkers

      Commit: 41c37d7ed6809a218135791c073a24ba56492653

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-22 12:05:41 -0400

      Commit message:


	  
		
 feat: import protocol-branch helpers to support SpaceMarkers_Protocol notebooks

Additive import of functions that exist on origin/protocol but not on this
branch, so the SpaceMarkers_Protocol vignettes can run on top of the SME
workflow without forcing a full merge of origin/protocol (which would
conflict extensively with the SME-refactored S4 methods).

New files (copied verbatim from origin/protocol):
- R/multisample.R - process_visium_samples, make_sp_patterns,
  get_multi_sample_overlaps, compare_scores, plot_sample_overlaps,
  plot_overlap_scores_bar, run_imscores_one, generate_sample_lr_scores,
  create_lr_dataframe_multi, get_top_lr_interactions, plot_lr_alluvial,
  plot_lr_scores_scatter, align_counts_coords, plot_lr_alluvial_sample_mid.
- R/protocol-helpers.R - classify_spots (thin export wrapper around the
  existing .classify_spots), classify_allspots, create_lr_dataframe,
  calc_overlap_scores, get_overlap_scores, plot_im_scores_heatmap,
  get_enriched_pathways, plot_enriched_results, create_avg_exp_df,
  plot_interaction_dotplot.

Dropped: plot_multi_way_violin - the protocol-branch source of this
function is truncated mid-body (pre-existing issue, unrelated to the SME
work); can be re-ported once that's fixed upstream.

DESCRIPTION: add ggalluvial, fgsea, pheatmap, future to Imports and
future.apply, clusterProfiler to Suggests. NAMESPACE regenerated.
 
    
  
    

      Package: SpaceMarkers

      Commit: de6054a326e96ac15a73266dd9ecdc0f47e4f1bf

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-22 08:51:58 -0400

      Commit message:


	  
		
 refactor(vignettes): route data downloads through BiocFileCache

All three vignettes (SpaceMarkers_vignette, SpaceMarkersExperiment_vignette,
SpaceMarkersStepByStep_vignette) pull the same ~260 MB 10x Visium Breast
Cancer dataset. Route the fetches through BiocFileCache::bfcrpath() so the
download is deduplicated across vignettes and across rebuilds - the network
cost drops from ~780 MB per full check to ~260 MB once.

No Bioconductor data-package / ExperimentHub submission is introduced;
10x's canonical URL remains the source of truth. Add BiocFileCache to
Suggests (vignette-only dep).

Verified by rendering all three vignettes locally:
- SpaceMarkersStepByStep_vignette: 43s
- SpaceMarkersExperiment_vignette: 38s
- SpaceMarkers_vignette: 2m54s
(Times after BFC warm; no errors in rendered HTML.)
 
    
  
    

      Package: SpaceMarkers

      Commit: 5a67e202d5fcd4c752d2da3d92fb34a5ad81c6e2

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-22 08:29:03 -0400

      Commit message:


	  
		
 fix: second-round Copilot review (SpaceMarkers dispatch, setter, img crop, .data)

- SpaceMarkers SME dispatch: stop with a clear message when
  spatial_params(sme) is NULL and no visiumDir is stored, rather than
  silently falling back to '.' and failing deep inside
  get_spatial_parameters().

- spatial_patterns<- setter: validate rownames(value) against colnames(x)
  and reorder when needed; error on mismatched row-name sets; allow the
  no-rownames positional-match path (existing behavior) but with an
  explicit message and a length check.

- plot_spatial image crop: handle 2D (grayscale) img_mat by branching on
  length(dim(img_mat)) before subsetting.

- Re-route ggplot2 aes(.data[[col]]) via @importFrom rlang .data in the
  imports stub so R CMD check stops flagging .data as an undefined
  global (keeps the bare .data[[col]] style at each call site).
 
    
  
    

      Package: SpaceMarkers

      Commit: 4ef283b5ffbf6e988719a3d4e6f6396b71dfd0b2

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-22 07:41:18 -0400

      Commit message:


	  
		
 feat: re-export SpatialExperiment/SummarizedExperiment accessors

Now that SpatialExperiment is in Imports rather than Depends,
library(SpaceMarkers) no longer transitively attaches its accessors.
Re-export the common ones (assay, assays, colData, rowData,
spatialCoords, imgRaster) from SpaceMarkers' namespace so users can
call them as bare names without an additional library() call
- the same ergonomics SingleCellExperiment provides over
SummarizedExperiment. Drop the now-redundant library(SpatialExperiment)
from the new vignettes.
 
    
  
    

      Package: SpaceMarkers

      Commit: 8e08e47f9c115cbf2b2a0f8016a195b7f78b55e2

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-22 07:18:46 -0400

      Commit message:


	  
		
 fix: vignette assay() resolves after SpatialExperiment moved to Imports

Moving SpatialExperiment from Depends to Imports means library(SpaceMarkers)
no longer attaches SummarizedExperiment transitively, so bare assay() /
spatialCoords() calls in the vignettes broke. Attach SpatialExperiment in
the vignette setup chunks (it auto-attaches SummarizedExperiment).

Also document the new patternList arg on get_pairwise_interacting_genes
to clear the R CMD check WARNING.
 
    
  
    

      Package: SpaceMarkers

      Commit: 741ec3d474583f8987dcfdc5fa0c9d9009ea7325

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-22 06:13:24 -0400

      Commit message:


	  
		
 fix: address Copilot review on PR #92

- find_all_hotspots(data.frame): guard NULL params so the dispatcher
  matches find_pattern_hotspots' NULL-fallback contract.
- calculate_influence(data.frame): branch on NULL optParams; let Smooth
  pick its default sigma instead of indexing into NULL.
- get_pairwise_interacting_genes(ANY): promote patternList from an
  implicit-global lookup (exists()) to an explicit NULL-default arg.
- load10X: pre-compute spatial_params from `shared` spots rather than
  `common`, so feature NA-padding doesn't silently fail inside tryCatch;
  surface the swallowed error as a warning.
- DESCRIPTION: move SpatialExperiment from Depends to Imports; all uses
  are already namespaced and classes are imported via NAMESPACE.
- Add regression tests for the NULL-optParams / NULL-params paths.
 
    
  
    

      Package: SpaceMarkers

      Commit: 59c34fa32226de0ae06bc348561eb6ff503b83bd

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-21 20:46:51 -0400

      Commit message:


	  
		
 Update R/getInteractingGenes.R

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 
    
  
    

      Package: SpaceMarkers

      Commit: ec51cb4e031c74071734c05c5769c1ef380f7a9c

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-21 15:54:35 -0400

      Commit message:


	  
		
 docs: document plot_spatial's source, interaction_patterns, interaction_label, direction

GitHub CI on the previous PR flagged:
  Warning: Undocumented arguments in Rd file 'plot_spatial.Rd'
    'source' 'interaction_patterns' 'interaction_label'

The arg set grew in this branch as plot_spatial picked up source-routing
and the interaction overlay. This commit adds the missing @param tags
plus a @param entry for the newly-added direction arg, and regenerates
man/plot_spatial.Rd via devtools::document(). R CMD check no longer
reports an 'Undocumented arguments' warning on plot_spatial.Rd
(remaining WARNINGs are the vignette build-flag artifacts from building
with --no-build-vignettes).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: bbf561385b617321f9b4d0dba1eca5bdd5ba3e6f

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-21 12:28:25 -0400

      Commit message:


	  
		
 feat(overlap_map): per-direction 3-level factor for directed interactions

The previous 5-level directed output (pat1, pat1 near pat2, both,
pat2 near pat1, pat2) mixed both t-test perspectives into one factor
and forced a "both" level for doubly-hot spots. That's confusing: a
directed analysis runs two independent t-tests per pair, and each is
a within-source classification (pat1 vs pat1 near pat2, or pat2 vs
pat2 near pat1).

Refactored overlap_map() so directed mode returns a 3-level factor
per direction:

  direction = "forward" (default; source = pat1, target = pat2):
    pat1                -> pat1 hot, pat2 influence NOT hot
    " near " -> pat1 hot AND pat2 influence hot   <- t-test
                                                                interaction
    " influence"   -> pat1 NOT hot, pat2 influence hot (context)

  direction = "reverse": mirror (source = pat2).

plot_spatial() gains a direction= pass-through so the interaction
overlay matches. Vignettes updated to render two plots per directed
pair (one per direction) instead of one combined overlay.

Tests updated for the new level semantics and direction toggle.

Stays local per user request; no push.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 </pre>
    </div>
  
    

      Package: SpaceMarkers

      Commit: d2de3f8be350a706638f906651238f71d72045a1

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-21 11:29:42 -0400

      Commit message:


	  
		
 docs(vignettes) + refactor: overlap before interaction genes; drop subsetting in SME vignette

Two narrative/ordering changes requested on the vignettes plus the
matching reorder inside the internal SME helpers so the vignette chain
and OneSpaceMarkers stay in sync.

1. SME vignette runs SpaceMarkers() on the full sme (all 5 CoGAPS
   patterns) instead of pre-subsetting to two patterns. Gene-level tests
   are still scoped to Pattern_1 x Pattern_2 (undirected) and
   Pattern_1 -> Pattern_5 (directed) via the pattern_pairs argument,
   which SpaceMarkers() forwards through ... to
   get_pairwise_interacting_genes() / calculate_gene_scores_directed().
   The overlap heatmap now shows every pair -- one overlap in a heatmap
   on its own is not informative.

2. Overlap computation moved before the gene-level interaction tests in
   both vignettes and in the internal .undirected_SpaceMarkers_sme /
   .directed_SpaceMarkers_sme helpers. Narrative reads: find hotspots ->
   where do they overlap -> now zoom in on the interesting pair's genes.
   The reorder is a no-op semantically because calculate_overlap_*
   depends only on the hotspots, not on the interaction results.

Step-by-step vignette:
- Undirected: Step 2 is now overlap scores (heatmap); Step 3 is pairwise
  genes; Step 4 is IM scores.
- Directed: Step 4 is overlap scores; Step 5 is directed gene scores.
- "Putting it together" pipe chains updated to match.

SpaceMarkersExperiment vignette:
- Visualization reordered per section: hotspots -> overlap -> interaction
  overlay -> (undirected only) IM bar plot + top genes.
- Pattern subsetting removed from both SpaceMarkers() calls.

Both vignettes re-knit clean.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: aad4df4175f2482135938d325322f663ad5735f9

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-21 11:09:54 -0400

      Commit message:


	  
		
 docs(vignettes): suppress warnings/messages globally; interleave plots with narrative

1. Add warning = FALSE, message = FALSE to knitr::opts_chunk$set at the
   top of both vignettes so pipeline-step chunks stop leaking Bioconductor
   package-load banners and the sparse-matrix warnings that downstream
   functions emit on the Visium fixture. (The chunks that already had
   message/warning suppression on their own headers are now redundant but
   harmless.)

2. Break up runs of consecutive same-theme plots in the step-by-step
   vignette with a one-line narrative between each pair so the rendered
   HTML reads as tutorial prose instead of a figure cluster:
     - Step 0 (undirected): connector between Pattern_1 and Pattern_2 panels
     - Step 1 (undirected): connector between Pattern_1 and Pattern_2 hotspot panels
     - Step 0 (directed): connector between Pattern_1 and Pattern_5 panels
     - Step 1 (directed): connector between Pattern_1 and Pattern_5 influence-map panels
     - Step 2 (directed): connector between Pattern_1 and Pattern_5 GMM-hotspot panels
     - Step 3 (directed): connector between Pattern_1 and Pattern_5 influence-hotspot panels

Stays local — no push from this commit.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 17bcb62def5538abd7c9704e0bcc9be1700ad356

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-21 10:07:52 -0400

      Commit message:


	  
		
 feat: add overlap_map() — per-spot directed interaction classification

The previous source = "interaction" path in plot_spatial produced a
3-class overlay even for directed analyses, just relabeling the middle
category to " near ". That's semantically wrong: the
directed analysis in .classify_spots (R/hdutils.R:137) classifies spots
asymmetrically using both pattern GMM hotspots AND influence hotspots,
producing up to four regions per pair (pat1, pat1 near pat2,
pat2 near pat1, pat2) plus a "both" confounder class.

This commit exposes that classification to end users:

 - New exported helper overlap_map(x, interaction_patterns, directed,
   interaction_label) in R/SpaceMarkersExperiment-methods.R.
   Auto-detects directed mode when pattern + influence hotspots are
   both stored; returns a factor keyed by barcode.
   Name parallels overlap_scores() — scores are the pair-level
   summary, map is the spot-level classification that feeds them.

 - plot_spatial(sme, source = "interaction", ...) now delegates to
   overlap_map() so the plotted overlay is always in sync with
   anything a user computes directly. The old hotspot_type-driven
   force_{un,}directed coupling is gone; overlap_map auto-detects.

 - Tests cover undirected (3 levels) + directed (5 levels) semantics,
   level equivalence to hand-computed intersections, the interaction_label
   override, error surfaces when prerequisite hotspots are missing,
   and a plot_spatial smoke test.

 - Step-by-step vignette: the directed interaction overlay moved from
   Step 2 (pattern hotspots only) to Step 3 (after influence hotspots)
   so both required hotspot types are populated. Calls overlap_map()
   directly to show the factor, then plot_spatial for the visualization.

 - SpaceMarkersExperiment vignette: same — one overlap_map() table + one
   plot_spatial(source = "interaction") overlay. Five colors including
   a "both" swatch.

Stays local per user request; no push from this change.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 </pre>
    </div>
  
    

      Package: SpaceMarkers

      Commit: f55a39e076d83911c74b159984e8b4fb0129c982

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-21 09:26:11 -0400

      Commit message:


	  
		
 chore: exclude docs/ from the package tarball via .Rbuildignore

Companion to the previous commit. .gitignore keeps docs/superpowers/ out
of the public branch, but R CMD build uses .Rbuildignore separately —
without a matching entry the design files would still be bundled into
the tarball for anyone who builds locally. Adds ^docs$ and
^docs/superpowers$ patterns so the built tarball has no docs/ directory
at all. Also cleans up a pre-existing missing newline between the
previous last line and the new entries.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 15a111d864583d12f6be2cd2267e54ff15179b71

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-21 09:25:18 -0400

      Commit message:


	  
		
 chore: untrack docs/superpowers/ (keep local-only)

The superpowers design spec and implementation plan are useful as local
project memory but shouldn't ship in the package tarball or clutter the
public branch. Removes them from git with git rm --cached (files remain
on disk locally) and adds docs/superpowers/ to .gitignore so they can't
be re-committed by accident.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
  


</div>

</div>