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🟡 Changes recommended
The level-filtering test fails with a one-row config, and Docker dependency gaps can prevent app startup or leave images without Signac support.
4 open issues
What changed in this PR
This PR prepares CellSight for Bioconductor checks while updating its app-generation pipeline, examples, and documentation.
Changes:
- Migrates generated app metadata to
qs2serialization and updates templates and runtime dependencies. - Adds automated tests, validation fixes, and R CMD check/BiocCheck workflows.
- Makes examples and vignettes executable where data is available, adds session information, and refreshes package documentation.
| File | Description |
|---|---|
| vignettes/templates.Rmd | Updates file names and adds session information. |
| vignettes/modalities.Rmd | Runs PBMC examples and marks illustrative sections. |
| vignettes/docker.Rmd | Adds executable session information. |
| vignettes/deployment.Rmd | Documents qs2 files and serving dependencies. |
| vignettes/credits.Rmd | Updates contributor details and session information. |
| vignettes/configuration.Rmd | Adapts executable configuration examples to PBMC data. |
| vignettes/cellsight.Rmd | Enables cached-data examples and documents new file names. |
| tools/render-and-lint.R | Migrates template fixtures to qs2. |
| tools/docker/CellSight/install_packages.R | Expands container dependencies. |
| tests/testthat/test-write_df_chunked_hdf5r.R | Tests HDF5 column writing and rewriting. |
| tests/testthat/test-show-functions.R | Tests configuration display helpers. |
| tests/testthat/test-scTrim.R | Tests template whitespace handling. |
| tests/testthat/test-makeShinyFiles-pipeline.R | Tests app generation and error handling. |
| tests/testthat/test-getRefGeneGTF.R | Tests genome validation and cache creation. |
| tests/testthat/test-createConfig.R | Tests configuration creation and validation. |
| tests/testthat/test-config-edit-helpers.R | Tests configuration editing helpers. |
| tests/testthat/test-checkConfig.R | Tests configuration consistency checks. |
| tests/testthat/helper-fixtures.R | Adds a cached synthetic Seurat fixture. |
| tests/testthat.R | Adds the test suite entry point. |
| README.md | Adds heading spacing. |
| R/writeFastH5.R | Removes package attachment and enables a temporary-file example. |
| R/showOrder.R | Adds a self-contained data-backed example. |
| R/showLegend.R | Enables data-backed legend examples. |
| R/reorderMeta.R | Fixes equality validation and enables its example. |
| R/modMetaName.R | Updates the metadata-renaming example. |
| R/modLabels.R | Updates the categorical-label example. |
| R/modDefault.R | Updates the default-selection example. |
| R/modColours.R | Updates the colour-selection example. |
| R/makeShinyFilesSpatial.R | Uses qs2 and inheritance-aware class checks. |
| R/makeShinyFilesGEX.R | Migrates metadata serialization and qualifies reduction lookup. |
| R/makeShinyFilesDEG.R | Migrates defaults serialization and adds a synthetic example. |
| R/makeShinyFilesATACsignac.R | Writes bigWig metadata with qs2. |
| R/makeShinyFilesATACarchr.R | Migrates metadata serialization and class validation. |
| R/makeShinyFiles.R | Improves dispatch validation and missing-file errors. |
| R/makeShinyCodes.R | Reads qs2 metadata and defaults headers to NULL. |
| R/makeH5fromSeurat.R | Adds an example and inheritance-aware assay checks. |
| R/makeH5fromArchR.R | Adds illustrative export guidance. |
| R/makeH5fromAnndata.R | Adds conditional illustrative export guidance. |
| R/jinjaHelpers.R | Adds examples and explicit template imports. |
| R/getRefGeneGTF.R | Updates mouse annotation URLs and cache examples. |
| R/ExportGroupBW.R | Declares parallel-processing and sparse-matrix imports. |
| R/delMeta.R | Enables a self-contained metadata-removal example. |
| R/createConfig.R | Updates class checks and enables its example. |
| R/checkConfig.R | Fixes mismatch checks and updates class handling. |
| R/addMeta.R | Updates class handling and enables its example. |
| NOTICE | Adds an AI-assisted contribution notice. |
| NAMESPACE | Registers newly declared imports. |
| man/write_df_chunked_hdf5r.Rd | Enables the temporary-file example. |
| man/showOrder.Rd | Synchronizes the runnable display example. |
| man/showLegend.Rd | Synchronizes runnable legend examples. |
| man/scTrim.Rd | Adds a whitespace-trimming example. |
| man/scJinjaCfg.Rd | Adds a template-rendering example. |
| man/reorderMeta.Rd | Synchronizes the runnable ordering example. |
| man/refGeneCache.Rd | Documents reference cache creation. |
| man/modMetaName.Rd | Synchronizes the renaming example. |
| man/modLabels.Rd | Synchronizes the label-editing example. |
| man/modDefault.Rd | Synchronizes the default-selection example. |
| man/modColours.Rd | Synchronizes the colour-editing example. |
| man/makeShinyFilesSpatial.Rd | Clarifies spatial example requirements. |
| man/makeShinyFilesGEX.Rd | Documents qs2 outputs and runnable usage. |
| man/makeShinyFilesDEG.Rd | Documents serialization changes and synthetic usage. |
| man/makeShinyFilesATACsignac.Rd | Updates output names and example requirements. |
| man/makeShinyFilesATACarchr.Rd | Updates output names and example requirements. |
| man/makeShinyFiles.Rd | Synchronizes the runnable app-data example. |
| man/makeShinyCodes.Rd | Documents optional headers and runnable generation. |
| man/makeH5fromSeurat.Rd | Adds a synthetic HDF5 export example. |
| man/makeH5fromArchR.Rd | Adds illustrative ArchR export guidance. |
| man/makeH5fromAnndata.Rd | Adds illustrative AnnData export guidance. |
| man/getRefGeneGTF.Rd | Documents cached reference downloads. |
| man/delMeta.Rd | Synchronizes the metadata-removal example. |
| man/createConfig.Rd | Synchronizes the configuration example. |
| man/checkConfig.Rd | Synchronizes the configuration-checking example. |
| man/addMeta.Rd | Synchronizes the metadata-addition example. |
| inst/templates/ui.R.jinja | Loads generated app metadata with qs2. |
| inst/templates/server.R.jinja | Loads server-side metadata with qs2. |
| inst/templates/partials/ui/violin-box.R.jinja | Uses native pipes for input helpers. |
| inst/templates/partials/ui/trackplot.R.jinja | Updates the file-name comment only. |
| inst/templates/partials/ui/spatial-zoom.R.jinja | Uses a native pipe for the metadata helper. |
| inst/templates/partials/ui/spatial-zoom-multislide.R.jinja | Uses a native pipe for the metadata helper. |
| inst/templates/partials/ui/spatial-sidebyside.R.jinja | Uses native pipes for metadata helpers. |
| inst/templates/partials/ui/spatial-sidebyside-multislide.R.jinja | Uses native pipes for metadata helpers. |
| inst/templates/partials/ui/spatial-sidebyside-extra.R.jinja | Uses native pipes for metadata helpers. |
| inst/templates/partials/ui/proportion.R.jinja | Uses native pipes for grouping helpers. |
| inst/templates/partials/ui/module-score.R.jinja | Uses a native pipe for the gene-list helper. |
| inst/templates/partials/ui/dimred-zoom.R.jinja | Uses a native pipe for the feature helper. |
| inst/templates/partials/ui/dimred-split.R.jinja | Uses a native pipe for the split helper. |
| inst/templates/partials/ui/dimred-sidebyside.R.jinja | Uses native pipes for feature helpers. |
| inst/templates/partials/ui/dimred-coexpression.R.jinja | Uses native pipes for feature helpers. |
| inst/templates/partials/ui/bubble-heatmap.R.jinja | Uses native pipes for input helpers. |
| inst/templates/partials/server/trackplot.R.jinja | Updates the file-name comment only. |
| inst/templates/partials/server/spatial-zoom.R.jinja | Uses a native pipe for table formatting. |
| inst/templates/partials/server/dimred-zoom.R.jinja | Uses a native pipe for table formatting. |
| inst/templates/partials/server/dimred-coexpression.R.jinja | Uses a native pipe for table formatting. |
| inst/templates/partials/server/deg-dimred.R.jinja | Uses native pipes for DEG table formatting. |
| DESCRIPTION | Updates dependencies, authorship, testing, and Bioconductor metadata. |
| .github/workflows/r-cmd-check.yml | Adds an R CMD check workflow. |
| .github/workflows/pr-gate.yml | Updates the builder image and dependency installation. |
| .github/workflows/pkgdown.yml | Installs declared dependencies before website generation. |
| .github/workflows/lint-templates.yml | Updates the builder image and dependency installation. |
| .github/workflows/bioccheck.yml | Adds a BiocCheck workflow. |
| .github/scripts/rcmdcheck-summary.R | Runs package checks and summarizes results. |
| .github/scripts/bioccheck-summary.R | Builds, runs BiocCheck, and summarizes results. |
| _pkgdown.yml | Adds reference-data helpers to website navigation. |
Review effort: Balanced
redekarnr
approved these changes
Oct 29, 2026
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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Commits extending the feature set, documentation, and configuration to be aligned with the Bioconductor standard.