Filter extensions can't be specified in combination with processing phases

[multimeric]

Bug description

The AST processing phases feature doesn't seem compatible with packaged extensions.

This works:

filters:
  - path: lifecycle.lua
    at: pre-ast

Whereas this fails:

filters:
  - path: lifecycle
    at: pre-ast

With the error ERROR (/opt/quarto/share/filters/main.lua:3832) cannot open lifecycle: No such file or directory. I assume this is supposed to work, since otherwise extensions have no access to the lifecycle hooks.

Steps to reproduce

I've made a super simple reprex of this here: https://github.com/multimeric/quarto-lifecycle:

1. git clone https://github.com/multimeric/quarto-lifecycle
2. cd quarto-lifecycle
3. quarto render example.qmd.

Expected behavior

The document to render without error.

Actual behavior

ERROR (/opt/quarto/share/filters/main.lua:3832) cannot open lifecycle: No such file or directory

Your environment

Ubuntu 22.04.

Quarto check output

Quarto 1.6.39
[✓] Checking environment information...
      Quarto cache location: /home/migwell/.cache/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.4.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.46.3: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.6.39
      Path: /opt/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: v2024.12
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /home/migwell/.TinyTeX/bin/x86_64-linux
      Version: 2024

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.12.8 (Conda)
      Path: /home/migwell/micromamba/envs/bash-kernel/bin/python
      Jupyter: 5.7.2
      Kernels: python3, bash, rust

(|) Checking Jupyter engine render....Traceback (most recent call last):
  File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module>
    from notebook import notebook_execute, RestartKernel
  File "/opt/quarto/share/jupyter/notebook.py", line 15, in <module>
    from yaml import safe_load as parse_string
ModuleNotFoundError: No module named 'yaml'
[✓] Checking Jupyter engine render....OK

[cderv]

I wanted to check an idea, and I believe this happens because we are not resolving filter looking in extension.

Filters are resolved in

quarto-cli/src/command/render/defaults.ts

Lines 46 to 53 in f7e913e

	// resolve filters
	const resolvedFilters = await resolveFilters(
	[
	...(allDefaults[kFilters] || []),
	],
	options,
	allDefaults,
	);

and resolved looking in extension

quarto-cli/src/command/render/filters.ts

Lines 733 to 734 in f7e913e

	// Resolve any filters that are provided by an extension
	filters = await resolveFilterExtension(options, filters);

but we only resolve filter of type string (so not { path: 'lifecycle', at: 'pre-ast'} at this part.

quarto-cli/src/command/render/filters.ts

Lines 855 to 861 in f7e913e

	const getFilter = async (filter: QuartoFilter) => {
	// Look for extension names in the filter list and result them
	// into the filters provided by the extension
	if (
	filter !== kQuartoFilterMarker && filter !== kQuartoCiteProcMarker &&
	typeof filter === "string"
	) {

So the full filter path is not resolved, and on Lua side the filter can be loaded.

BTW @multimeric, with your example repo, this does not work for me either.

This works:

filters:
 - path: lifecycle.lua
   at: pre-ast

Extension or not it fails 🤔 same cause to me: we don't resolve filter of the form path / at in extensions as you found.

We should just tweak resolveFilters() to resolve filter path in extension also for entry point filter.