fix: allow error in render

[maxkarlsson]

Description

• The ES now tolerates chunk errors and will in most cases render a report even if some chunks fail.

Fixes: PNA-1765

Type of change

• Bug fix

How Has This Been Tested?

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

[Copilot]

Pull request overview

This PR enables error tolerance in Quarto report rendering by adding error: true to execution options across multiple report template files. This allows reports to render successfully even when individual code chunks encounter errors, addressing issue PNA-1765.

Key Changes:

• Added YAML front matter with execution options to 5 child template files
• Set error: true in the main template file to propagate error tolerance
• Standardized execution configuration (ragg_png device, suppressed warnings/messages/echo) across all templates

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
inst/quarto/spatial.qmd	Added YAML front matter with error tolerance enabled
inst/quarto/quality_metrics.qmd	Added YAML front matter with error tolerance enabled
inst/quarto/preprocessing.qmd	Added YAML front matter with error tolerance enabled
inst/quarto/pixelatorES.qmd	Added error: true to existing execution options
inst/quarto/cell_annotation.qmd	Added YAML front matter with error tolerance enabled
inst/quarto/abundance.qmd	Added YAML front matter with error tolerance enabled

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[Copilot]

[nitpick] The value 'dir' for execute-dir is ambiguous. Consider using a more descriptive name like 'project' or documenting what this refers to, as it's unclear whether this is a placeholder or an actual directory name.

Suggested change

	execute-dir: dir
	execute-dir: project