reconcile master-only changes into dev after bioconductor release#189
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- Fix _pkgdown.yml to include accessible colors for dev site version - Update citation in CITATION, README.md, and DESCRIPTION - Change installation information to reflect Bioconductor - Update URLs for links - Update NEWS.md to match stable release versioning - Add workflow notes for bioconductor and github sync - Remove out of date GHAs (pulled from commit 86b9188; syncs changes from commits 069cd9, d5c2e57, 3780907, 9c3c131)
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Pull request overview
This PR reconciles changes that landed only on master (during the Bioconductor release process) back into the dev branch, syncing bug fixes for gene_network(), vignette/documentation polish, pkgdown configuration, family/seealso roxygen tags, and version/citation metadata updates.
Changes:
- Backports
gene_network()fixes (per-cluster ligand-sum accumulation, restricting receptors/TFs to those downstream of included ligands) and other minor R changes. - Sweeping documentation updates:
@family/@seealsotags, typo/wording fixes, vignette links updated to.htmlURLs, NEWS.md rewrite, README/index install instructions. - Repository housekeeping: removes legacy Bioconductor sync workflow, adds
.github/workflow_notes.md, updates DESCRIPTION (version, authors/emails, deps),_pkgdown.ymlnavbar/development mode, and addspkgdown/extra.css.
Reviewed changes
Copilot reviewed 60 out of 64 changed files in this pull request and generated 7 comments.
Show a summary per file
| File | Description |
|---|---|
| R/plot_network.R | Backports gene_network() ligand/receptor accumulation fixes |
| R/access_functions.R | Adds @family accessors and reworks dom_linkages parameter docs |
| R/build_domino.R, R/create_domino.R, R/create_rl_map.R, R/cor_scatter.R, R/gene_conversion.R, R/data.R, R/linkage_summary_class.R, R/plot_circos.R, R/plot_heatmaps.R, R/plot_differential_linkages.R, R/summarize_linkages.R, R/test_differential_linkages.R, R/count_linkage.R | Roxygen documentation polish, family/seealso tags, typo fixes |
| man/*.Rd | Regenerated docs reflecting roxygen changes |
| man/roxygen/meta.R | New roxygen metadata defining family titles |
| vignettes/.Rmd, vignettes/articles/.Rmd | Link/typo corrections, alt text, loomR setup note |
| README.md, index.Rmd, index.md | Install instructions, citation/version updates |
| NEWS.md | Rewritten changelog reflecting v1.6.0 release notes |
| DESCRIPTION, inst/CITATION | Version, author email, dependency updates |
| _pkgdown.yml, pkgdown/extra.css | pkgdown navbar/development mode/theme tweaks |
| .github/workflows/bioc_branch.yml, .github/copy_to_branch.sh, .github/workflows/pull_request_template.md | Removed legacy Bioconductor sync workflow and PR template |
| .github/workflow_notes.md | New developer guide for GitHub/Bioconductor sync |
Files not reviewed (4)
- man/CellPhoneDB.Rd: Language not supported
- man/PBMC.Rd: Language not supported
- man/build_domino.Rd: Language not supported
- man/circos_ligand_receptor.Rd: Language not supported
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Summary
This pull request brings master-only changes back into the dev branch after the divergence that occurred during the Bioconductor release process. Ideally, this should ensure all relevant master updates are represented in the dev branch and keep a clear mapping from each master-only commit to how it was handled in the dev branch
During bioconductor release prep, select bug fixes and documentation updates had to be manually backported from dev to master and additional master updates were made for release operations. Given the filename changes on the dev branch, this divergence requires manual reconciliation.
Mapping master-only commits
Intentionally not moved from master to dev
Pulled/patched from master to dev
Manually applied from master to dev
gene_network()function, bringing dev in sync with master commits b3e8b65 and 0c864dd