Fix extra_files paths for subfolder Quarto documents

[anders-wiggers]

Intent

Fix incorrect file paths in the manifest when rendering standalone Quarto documents whose .qmd file and extra_files are located in a subdirectory. Previously, the subdirectory name could be duplicated when joining base_dir and rel_path, causing extra files to be resolved to non-existent paths (e.g. subdir/subdir/file.ext).

Type of Change

• Bug Fix
• New Feature
• Breaking Change

Approach

For standalone Quarto documents (the else branch where file_or_directory is not a directory):

• Compute a common base directory across the main .qmd file and all extra_files:

  all_files = [file_or_directory] + extra_files
  abs_paths = [os.path.abspath(p) for p in all_files]
  base_dir = os.path.commonpath(abs_paths)

• Convert all relevant file paths to be relative to this common base_dir:

  relevant_files = [os.path.relpath(p, base_dir) for p in abs_paths]

• Keep the directory-based Quarto project branch (isdir(file_or_directory)) unchanged, still delegating to _create_quarto_file_list.

This ensures:

• When both the .qmd and extra_files live in the same subfolder (e.g. subdir/report.qmd and subdir/data.csv) and extra_files is specified with the subfolder component (["subdir/data.csv"]), the manifest now uses:

  • base_dir = <common root>
  • rel_path = "subdir/data.csv"
    avoiding the duplicated subdir/subdir path.

• Extra files located outside the .qmd’s subdirectory continue to work: the common path becomes the deepest shared parent directory, and all paths are consistently relative to that parent.

Directions for Reviewers

To validate manually:

1. Create a structure like:

   project-root/
     subdir/
       report.qmd
       test/
         data.csv
   

2. From project-root, invoke the packaging logic with:

   • file_or_directory="subdir/report.qmd"
   • extra_files=["subdir/test/data.csv"]

3. Inspect the generated manifest (or log / debug around manifest_add_file) and verify:

   • data.csv is added once.
   • The final path used to locate data.csv contains subdir/test/data.csv (not subdir/subdir/test/data.csv).

Checklist

• I have updated CHANGELOG.md to cover notable changes.
• I have updated all related GitHub issues to reflect their current state.
• I have run the rsconnect-python-tests-at-night workflow in Connect against this feature branch.

[jonkeane]

Thank you so much for submitting a PR for this. Overall this looks ok, but would you mind also adding some tests to confirm this behavior?

I suspect using something like

rsconnect-python/tests/test_bundle.py

Lines 1018 to 1067 in 323223d

	def test_make_quarto_manifest_project_with_extra_files(self):
	temp_proj = tempfile.mkdtemp()
	# include extra_files parameter
	fp = open(join(temp_proj, "a"), "w")
	fp.write("This is file a\n")
	fp.close()
	fp = open(join(temp_proj, "b"), "w")
	fp.write("This is file b\n")
	fp.close()
	fp = open(join(temp_proj, "c"), "w")
	fp.write("This is file c\n")
	fp.close()
	manifest, _ = make_quarto_manifest(
	temp_proj,
	{
	"quarto": {"version": "0.9.16"},
	"engines": ["jupyter"],
	"config": {"project": {"title": "quarto-proj-py"}, "editor": "visual", "language": {}},
	},
	AppModes.SHINY_QUARTO,
	None,
	["a", "b", "c"],
	[],
	None,
	)
	if sys.platform == "win32":
	a_hash = "f4751c084b3ade4d736c6293ab8468c9"
	b_hash = "4976d559975b5232cf09a10afaf8d0a8"
	c_hash = "09c56e1b9e6ae34c6662717c47a7e187"
	else:
	a_hash = "4a3eb92956aa3e16a9f0a84a43c943e7"
	b_hash = "b249e5b536d30e6282cea227f3a73669"
	c_hash = "53b36f1d5b6f7fb2cfaf0c15af7ffb2d"
	self.assertEqual(
	manifest,
	{
	"version": 1,
	"metadata": {"appmode": "quarto-shiny"},
	"quarto": {"version": "0.9.16", "engines": ["jupyter"]},
	"files": {
	"a": {"checksum": a_hash},
	"b": {"checksum": b_hash},
	"c": {"checksum": c_hash},
	},
	},
	)

as inspiration would be a good starting point.

[jonkeane]

Am I reading this correctly that this is using absolute paths at first then shifts them to relative paths (relative to the base_dir)? Is there a way to avoid that back and forth and just go directly to paths relative to the base_dir? It's not the end of the world if not, just seems like a bit of extra back and forth that is slightly distracting.

[jonkeane]

These are just whitespace changes, yeah?