Extension project pre-release script not found

Bug description

Not sure if this is related to #9889, but a user of the Sverto extension has reported that it no longer works:

https://github.com/jimjam-slam/sverto/issues/27

It appears that on the latest pre-release, the pre-render script provided by the Sverto extension is not found, causing render or preview to fail. On the older pre-release v.1.5.30, it's found without a problem.

Note that unlike #9889, Sverto provides a single string for the contributed prerender script, not a list:

title: Sverto
author: James Goldie
version: 1.0.1
quarto-version: ">=1.4.0"
contributes:
  filters:
    - sverto.lua
  project:
    project:
      type: website
      pre-render: sverto-prerender.lua

Steps to reproduce

quarto create project website test-sverto-2
cd test-sverto-2
quarto preview   # Works
quarto use template jimjam-slam/sverto    # do NOT create a subdirectory
npm install

Set in _quarto.yml:

project:
  type: sverto

Then:

quarto preview   # Produces error above

Expected behavior

On v1.5.30:

Preparing to preview
_extensions/jimjam-slam/sverto/sverto-prerender.lua

> svelte-app@1.0.0 build
> rollup -c ./_extensions/jimjam-slam/sverto/rollup.config.js --configQuartoOutPath=/Users/jgol0005/Code/tests/test-sverto-2/_site --configSvelteInPaths=

No Svelte filtes found; skipping Svelte compilation
Sverto pre-render finished!

Watching files for changes
Browse at http://localhost:3577/

GET: /

And then when navigating to example.html:

And then when navigating to example.html:

Circles.svelte → _site...
created _site in 271ms

GET: /example.html

Actual behavior

On v1.5.43:

Preparing to preview
sverto-prerender.lua
Error running filter sverto-prerender.lua:
cannot open sverto-prerender.lua: No such file or directory
ERROR: Error
    at runScripts (file:///Users/jgol0005/Code/quarto-cli/src/command/render/project.ts:916:15)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async runPreRender (file:///Users/jgol0005/Code/quarto-cli/src/command/render/project.ts:880:3)
    at async renderProject (file:///Users/jgol0005/Code/quarto-cli/src/command/render/project.ts:328:5)
    at async serveProject (file:///Users/jgol0005/Code/quarto-cli/src/project/serve/serve.ts:269:20)
    at async Command.actionHandler (file:///Users/jgol0005/Code/quarto-cli/src/command/preview/cmd.ts:398:7)
    at async Command.execute (file:///Users/jgol0005/Code/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)
    at async Command.parseCommand (file:///Users/jgol0005/Code/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1780:14)
    at async quarto (file:///Users/jgol0005/Code/quarto-cli/src/quarto.ts:159:5)
    at async file:///Users/jgol0005/Code/quarto-cli/src/quarto.ts:180:5

Your environment

OS: macOS 14.4.1
IDE: VSCode 1.90.0

Quarto check output

quarto check
Quarto 99.9.9
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.2.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 99.9.9
      commit: 98b7fec8d3daf0c549d91785d4afa104eb899748
      Path: /Users/jgol0005/Code/quarto-cli/package/dist/bin

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

[✓] Checking LaTeX....................OK
      Tex:  (not detected)

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

[✓] Checking Python 3 installation....OK
      Version: 3.9.7 (Conda)
      Path: /Users/jgol0005/miniforge3/bin/python
      Jupyter: 4.9.2
      Kernels: python3

(|) Checking Jupyter engine render....Traceback (most recent call last):
  File "/Users/jgol0005/Code/quarto-cli/src/resources/jupyter/jupyter.py", line 21, in <module>
    from notebook import notebook_execute, RestartKernel
  File "/Users/jgol0005/Code/quarto-cli/src/resources/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

ERROR: Error
    at renderFiles (file:///Users/jgol0005/Code/quarto-cli/src/command/render/render-files.ts:350:23)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async render (file:///Users/jgol0005/Code/quarto-cli/src/command/render/render-shared.ts:102:18)
    at async checkJupyterRender (file:///Users/jgol0005/Code/quarto-cli/src/command/check/check.ts:325:18)
    at async file:///Users/jgol0005/Code/quarto-cli/src/command/check/check.ts:285:11
    at async withSpinner (file:///Users/jgol0005/Code/quarto-cli/src/core/console.ts:81:12)
    at async checkJupyterInstallation (file:///Users/jgol0005/Code/quarto-cli/src/command/check/check.ts:281:9)
    at async check (file:///Users/jgol0005/Code/quarto-cli/src/command/check/check.ts:64:7)
    at async Command.actionHandler (file:///Users/jgol0005/Code/quarto-cli/src/command/check/cmd.ts:33:5)
    at async Command.execute (file:///Users/jgol0005/Code/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)

This is indeed probably due to #9890 . I believe the whole point was to support pre-render and post-render in extensions... so I am a bit surprised it was already working for you.

@cscheid Looking in debugging mode to your example, I noticed several things

https://github.com/quarto-dev/quarto-cli/blob/98b7fec8d3daf0c549d91785d4afa104eb899748/src/command/render/project.ts#L228-L234

We look for pre-render in project context, and it happens we find the extension script at this step already, with its full resolved path '_extensions/jimjam-slam/sverto/sverto-prerender.lua'

Then we look into extension https://github.com/quarto-dev/quarto-cli/blob/98b7fec8d3daf0c549d91785d4afa104eb899748/src/command/render/project.ts#L240-L250

and we find the script a second time but without resolving as an extension so we get sverto-prerender.lua only.

So we get in the result of getProjectRenderScripts() two pre-render script.

preRenderScripts
(2) ['_extensions/jimjam-slam/sverto/sverto-prerender.lua', 'sverto-prerender.lua']
0: '_extensions/jimjam-slam/sverto/sverto-prerender.lua'
1: 'sverto-prerender.lua'
length: 2
[[Prototype]]: Object
[[Prototype]]: Object

So it seems we are resolving twice the extensions. I see you added full path resolution at https://github.com/quarto-dev/quarto-cli/blob/98b7fec8d3daf0c549d91785d4afa104eb899748/src/extension/extension.ts#L787-L803 So oddly, it does not get "cached" correctly in renderOptions?.services.extension 🤔

Though, about #9890 it seems we resolve project extension, with project context already https://github.com/quarto-dev/quarto-cli/blob/98b7fec8d3daf0c549d91785d4afa104eb899748/src/project/project-context.ts#L146-L151

and we merge extension contribution and project configuration https://github.com/quarto-dev/quarto-cli/blob/98b7fec8d3daf0c549d91785d4afa104eb899748/src/project/project-context.ts#L608-L612

I was curious so I tested your additional test at https://github.com/quarto-dev/quarto-cli/commit/853728e555046ef9d9e0501df1baad4cc906ba9b#diff-09e6a0dcf7cdc6dc00aa75a7608456aba19402c7849178958ec7cc840a1fd874 with quarto in a state before #9890 by reverting the merge commit (except test change) and it seems to pass.

So I don't know full context of #9889 but there is something to deal with.

Note that unlike https://github.com/quarto-dev/quarto-cli/issues/9889, Sverto provides a single string for the contributed prerender script, not a list:

Using this form somehow solve the rendering issue (no error)

  project:
    project:
      type: website
      pre-render: 
        - sverto-prerender.lua

But the pre-render script is run twice because the observation above still applies

Sveto rendering log showing it ran twice

````powershell ❯ quarto render .\example.qmd > svelte-app@1.0.0 build > rollup -c ./_extensions/jimjam-slam/sverto/rollup.config.js --configQuartoOutPath=C:\Users\chris\AppData\Local\Temp\quarto\test-website\_site --configSvelteInPaths=Circles.svelte: Circles.svelte → _site... created _site in 796ms Sverto pre-render finished! > svelte-app@1.0.0 build > rollup -c ./_extensions/jimjam-slam/sverto/rollup.config.js --configQuartoOutPath=C:\Users\chris\AppData\Local\Temp\quarto\test-website\_site --configSvelteInPaths=Circles.svelte: Circles.svelte → _site... created _site in 694ms Sverto pre-render finished! ````

Hope it helps, and happy to contribute if needed.

I believe the whole point was to support pre-render and post-render in extensions... so I am a bit surprised it was already working for you.

Interesting! I released the current major version of Sverto about three months ago, and it seemed fine up until the issue was reported this week 😅

We look for pre-render in project context, and it happens we find the extension script at this step already, with its full resolved path '_extensions/jimjam-slam/sverto/sverto-prerender.lua'

Then we look into extension

https://github.com/quarto-dev/quarto-cli/blob/98b7fec8d3daf0c549d91785d4afa104eb899748/src/command/render/project.ts#L240-L250

and we find the script a second time but without resolving as an extension so we get sverto-prerender.lua only.

Ah, that explains why the script was running twice! I wasn't sure why that was happening when I finalised the major version but kind of wrote it off at the time 😂

Regarding using

pre-render: sverto-prerender.lua

pre-render: 
    - sverto-prerender.lua

The glob resolving does expect an array it seems https://github.com/quarto-dev/quarto-cli/blob/98b7fec8d3daf0c549d91785d4afa104eb899748/src/extension/extension.ts#L792-L798

So this finds no file

resolvePathGlobs(
      extensionDir,
      preRender,
      [],
    )
{include: Array(0), exclude: Array(0)}

But using an array works

resolvePathGlobs(
      extensionDir,
      [preRender],
      [],
    )
{include: Array(1), exclude: Array(0)}

It seems like the preRender as string[] does not convert and hide the issue.

Because passing a non array as a glob seems bad in our codebase https://github.com/quarto-dev/quarto-cli/blob/98b7fec8d3daf0c549d91785d4afa104eb899748/src/core/path.ts#L279-L288

for (const glob of globs) will iterate over the letters of the string 😓

Maybe we should make sure that resolveGlobs gets an array as globs - it seems string[] type does not handle this enough... 🤔

I was curious to understand 😅

I'm trying to understand how to reconcile the behavior described on the original report with what I see on our test tests/docs/project/prepost/extension. With 1.5.30, that test project doesn't invoke the pre-render script at all, independently of whether pre-render.ts is in an array or not. On main, the test project successfully invokes the pre-render script, but Quarto crashes when the pre-render field is a single string (that's a bug)

What I don't understand is how this also causes the project scripts to be executed twice.

I was curious so I tested your additional test at 853728e#diff-09e6a0dcf7cdc6dc00aa75a7608456aba19402c7849178958ec7cc840a1fd874 with quarto in a state before #9890 by reverting the merge commit (except test change) and it seems to pass.

I can't reproduce this - the file doesn't execute for me before the fix from 9890.

I went back to triple-check that I was indeed running 1.5.30 when I successfully rendered our test case. (Not to accuse you of not believing us, @cscheid! I just wanted to make absolutely sure I hadn't misled us all by running a different version than I thought I was running.)

I believe I am, but there is one anomaly in the quarto check output. First I reverted to 1.5.30:

# in ~/code/quarto-cli
$ git checkout v1.5.30
$ ./configure.sh

Then I did quarto check from the Quarto CLI directory above. It successfully reports the commit that's checked out, tied to v1.5.30:

$ quarto check
Check file:///Users/jimjamslam/code/quarto-cli/src/quarto.ts
Quarto 99.9.9
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.13: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 99.9.9
      commit: e9d5a9cb82098cae44588c182006b581bb6bf9b4
      Path: /Users/jimjamslam/code/quarto-cli/package/dist/bin

Check file:///Users/jimjamslam/code/quarto-cli/src/resources/vendor/deno-land/x/puppeteer@9-0-2/mod.ts
[✓] Checking tools....................OK
      TinyTeX: (not installed)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Tex:  (not detected)

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

[✓] Checking Python 3 installation....OK
      Version: 3.9.7 (Conda)
      Path: /Users/jimjamslam/miniforge3/bin/python
      Jupyter: 4.9.2
      Kernels: python3

Traceback (most recent call last):
  File "/Users/jimjamslam/code/quarto-cli/src/resources/jupyter/jupyter.py", line 21, in <module>
    from notebook import notebook_execute, RestartKernel
  File "/Users/jimjamslam/Code/quarto-cli/src/resources/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

ERROR: Error
    at renderFiles (file:///Users/jimjamslam/code/quarto-cli/src/command/render/render-files.ts:350:23)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async render (file:///Users/jimjamslam/Code/quarto-cli/src/command/render/render-shared.ts:102:18)
    at async checkJupyterRender (file:///Users/jimjamslam/code/quarto-cli/src/command/check/check.ts:320:18)
    at async file:///Users/jimjamslam/code/quarto-cli/src/command/check/check.ts:280:11
    at async withSpinner (file:///Users/jimjamslam/Code/quarto-cli/src/core/console.ts:81:12)
    at async checkJupyterInstallation (file:///Users/jimjamslam/code/quarto-cli/src/command/check/check.ts:276:9)
    at async check (file:///Users/jimjamslam/code/quarto-cli/src/command/check/check.ts:64:7)
    at async Command.actionHandler (file:///Users/jimjamslam/Code/quarto-cli/src/command/check/cmd.ts:33:5)
    at async Command.execute (file:///Users/jimjamslam/Code/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)

Then I rendered the doc successfully and ran quarto check afterward. It had the same output, except for the first line (it didn't specify the TS script at the start of the check), and instead of the commit number, it had an error because the folder isn't a git repo (although the subfolder with the bin in it wouldn't be):

$ quarto render
_extensions/jimjam-slam/sverto/sverto-prerender.lua

> svelte-app@1.0.0 build
> rollup -c ./_extensions/jimjam-slam/sverto/rollup.config.js --configQuartoOutPath=/Users/jimjamslam/Code/tests/test-sverto-2/_site --configSvelteInPaths=Circles.svelte:

Circles.svelte → _site...
created _site in 243ms
Sverto pre-render finished!

[1/3] index.qmd
[2/3] about.qmd
[3/3] example.qmd

Output created: _site/index.html

$ quarto check
Quarto 99.9.9
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.13: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 99.9.9
fatal: not a git repository (or any of the parent directories): .git
      Path: /Users/jimjamslam/code/quarto-cli/package/dist/bin

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

[✓] Checking LaTeX....................OK
      Tex:  (not detected)

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

[✓] Checking Python 3 installation....OK
      Version: 3.9.7 (Conda)
      Path: /Users/jimjamslam/miniforge3/bin/python
      Jupyter: 4.9.2
      Kernels: python3

Traceback (most recent call last):
  File "/Users/jimjamslam/code/quarto-cli/src/resources/jupyter/jupyter.py", line 21, in <module>
    from notebook import notebook_execute, RestartKernel
  File "/Users/jimjamslam/Code/quarto-cli/src/resources/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

ERROR: Error
    at renderFiles (file:///Users/jimjamslam/code/quarto-cli/src/command/render/render-files.ts:350:23)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async render (file:///Users/jimjamslam/Code/quarto-cli/src/command/render/render-shared.ts:102:18)
    at async checkJupyterRender (file:///Users/jimjamslam/code/quarto-cli/src/command/check/check.ts:320:18)
    at async file:///Users/jimjamslam/code/quarto-cli/src/command/check/check.ts:280:11
    at async withSpinner (file:///Users/jimjamslam/Code/quarto-cli/src/core/console.ts:81:12)
    at async checkJupyterInstallation (file:///Users/jimjamslam/code/quarto-cli/src/command/check/check.ts:276:9)
    at async check (file:///Users/jimjamslam/code/quarto-cli/src/command/check/check.ts:64:7)
    at async Command.actionHandler (file:///Users/jimjamslam/Code/quarto-cli/src/command/check/cmd.ts:33:5)
    at async Command.execute (file:///Users/jimjamslam/Code/quarto-cli/src/vendor/deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)

That said, the other parts of the quarto check do confirm that the development version of Quarto is being used (I was worried I might have a release version lurking around somewhere), and I also checked the path afterward too:

$ which quarto
/Users/jimjamslam/bin/quarto

$ ls -hl ~/bin/quarto
lrwxr-xr-x  1 jimjamslam  jimjamslam\admin    55B 12 Jun 09:29 /Users/jimjamslam/bin/quarto -> /Users/jimjamslam/code/quarto-cli/package/dist/bin/quarto

@jimjam-slam https://github.com/quarto-dev/quarto-cli/pull/9953 should be merged soon and will get sverto back into working as it should.

Thanks for giving it a look!

I just tested with the latest prerelease and things look to be working. I'm going to go ahead and close this, but please reopen if something comes up. Thanks!

quarto-dev / quarto-cli