Report section dispatch system

[maxkarlsson]

Description

This adds the report argument to the workflow registration so that it is possible to associate tabs with a workflow. The Quarto main file has been downgraded to a preamble + section dispatcher to follow the recipe in the registered workflow.

Added

• Workflows register a Quarto report recipe (preamble + sections) via register_es_data_workflow(), retrieved with get_es_workflow_report().

Changed

• The Quarto shell dispatches report sections from the registered workflow recipe. Shared children live under inst/quarto/shared/; workflow-owned children live under inst/quarto/workflows/<id>/.

Type of change

• New feature

How Has This Been Tested?

Tests have been added and manual tests.

PR checklist:

• I have run R CMD check on the package and it passes.
• I have made changes to the documentation.
• I have added tests.
• I have documented any significant changes in CHANGELOG.md

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Note

Medium Risk
Breaking change to register_es_data_workflow() and report assembly path; misconfigured extension workflows fail at registration or render time, though built-in paths are covered by tests.

Overview
Workflows now own the HTML report layout, not only data extractors. register_es_data_workflow() takes a required report factory that returns a recipe (preamble child paths + tab sections with id, title, child). Recipes are validated at registration (structure, unique section ids, on-disk child paths). get_es_workflow_report() retrieves the recipe; amplicon_demux registers .amplicon_demux_report() on load.

pixelatorES.qmd is a thin shell: it loads the recipe for params$workflow, knits preamble children, then builds the panel tabset from sections. Section .qmd files move under inst/quarto/shared/ (cross-workflow) and inst/quarto/workflows/<id>/ (workflow-specific).

Also adds exported test_es_data() for aligned test fixtures and switches tests away from hand-built structure(..., class = "es_data"). Breaking for anyone who registered workflows in 0.12.0 without a report argument.

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[Copilot]

Pull request overview

Adds workflow-specific Quarto report recipes and dynamically assembles reports from registered workflow definitions.

Changes:

• Extends workflow registration with validated report factories.
• Reorganizes Quarto content into shared and workflow-specific sections.
• Adds tests and documentation for report recipes.

Reviewed changes

Copilot reviewed 8 out of 17 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
R/workflow_registry.R	Adds report registration, validation, and retrieval.
R/es_data.R	Defines the amplicon-demux report recipe.
R/zzz.R	Registers the built-in report factory.
NAMESPACE	Exports the report getter.
tests/testthat/test_es_data.R	Tests report recipes and validation.
inst/quarto/pixelatorES.qmd	Dynamically dispatches report children.
inst/quarto/shared/preprocessing.qmd	Provides shared report setup.
inst/quarto/shared/samples.qmd	Provides the shared samples section.
inst/quarto/shared/run_settings.qmd	Provides shared run metadata.
inst/quarto/workflows/amplicon_demux/quality_metrics.qmd	Adds workflow quality metrics.
inst/quarto/workflows/amplicon_demux/cell_annotation.qmd	Adds cell annotation content.
inst/quarto/workflows/amplicon_demux/abundance.qmd	Adds abundance content.
inst/quarto/workflows/amplicon_demux/spatial.qmd	Adds spatial metrics content.
man/register_es_data_workflow.Rd	Documents the report parameter.
man/get_es_workflow_report.Rd	Documents report retrieval.
DEVELOPERS.md	Explains workflow report development.
CHANGELOG.md	Records the report-recipe feature.

Files not reviewed (2)

• man/get_es_workflow_report.Rd: Generated file
• man/register_es_data_workflow.Rd: Generated file

Suppressed comments (1)

R/workflow_registry.R:218

• The factory output is validated only during registration, but this public getter invokes the factory again and returns that later result unchecked. A stateful or environment-dependent factory can therefore register successfully and then supply a malformed recipe that fails unpredictably inside the Quarto dispatcher. Validate each produced recipe before returning it.

get_es_workflow_report <- function(name) {
  return(.get_es_workflow_definition(name)$report())
}

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