Quarto deletes the original `index.ipynb` file when rendering a different notebook (`index.render.ipynb`) with `output-file: index`, despite the original file being explicitly ignored in the project configuration.

Create the files described in _quarto.yml, including index.ipynb and index.render.ipynb, then run quarto render with ipynb: default enabled. Verify that index.render.ipynb produces index.html, index.pdf, and the output index.ipynb while the ignored original index.ipynb remains untouched.

Bug description

Quarto unexpectedly deletes the original index.ipynb file when rendering a different notebook (index.render.ipynb) with output-file: index, despite the original file being explicitly ignored in the project configuration.

_quarto.yml

project:
  type: website
  render:
   - '*.ipynb'
   - '!index.ipynb'
website:
  title: "Test"
format:
  html: default
  pdf: default
  # When the following line is uncommented, the "index.ipynb" file is deleted upon render
  # ipynb: default

index.ipynb

{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "---\n",
        "title: \"Test - index.ipynb\"\n",
        "---\n",
        "\n",
        "## Test - index.ipynb\n",
        "\n",
        "This is a Quarto website.\n",
        "\n",
        "To learn more about Quarto websites visit <https://quarto.org/docs/websites>."
      ]
    }
  ],
  "metadata": {
    "kernelspec": {
      "display_name": "Python 3",
      "language": "python",
      "name": "python3"
    }
  },
  "nbformat": 4,
  "nbformat_minor": 4
}

index.render.ipynb

{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "---\n",
        "title: \"Test - index.render.ipynb\"\n",
        "output-file: index\n",
        "---\n",
        "\n",
        "## Test - index.render.ipynb\n",
        "\n",
        "This is a Quarto website.\n",
        "\n",
        "To learn more about Quarto websites visit <https://quarto.org/docs/websites>."
      ]
    }
  ],
  "metadata": {
    "kernelspec": {
      "display_name": "Python 3",
      "language": "python",
      "name": "python3"
    }
  },
  "nbformat": 4,
  "nbformat_minor": 4
}

Note: The bug appears to be triggered when the ipynb: default format is uncommented in _quarto.yml. When this line is commented out, the original index.ipynb is not deleted.

Steps to reproduce

1. Create a Quarto project with the following files:

   • index.ipynb: A standard Quarto notebook
   • index.render.ipynb: A notebook with output-file: index in its YAML front matter
   • _quarto.yml: A project configuration file with !index.ipynb in the render options

2. Ensure _quarto.yml contains:

   project:
     type: website
     render:
      - '*.ipynb'
      - '!index.ipynb'
   website:
     title: "Test"
   format:
     html: default
     pdf: default
     ipynb: default
   

3. Run quarto render to build the project.

Note: The bug appears to be triggered when the ipynb: default format is uncommented in _quarto.yml. When this line is commented out, the original index.ipynb is not deleted.

Expected behavior

• index.render.ipynb should be rendered as index.html, index.pdf and index.ipynb in the output directory.
• The original index.ipynb should remain untouched, as it's specified to be ignored in _quarto.yml.

Actual behavior

• index.render.ipynb is correctly rendered as index.html, index.pdf and index.ipynb in the output directory.
• The original index.ipynb is unexpectedly deleted, despite being specified as ignored in the project configuration.

Your environment

Distributor ID:	Ubuntu
Description:	Ubuntu 22.04.5 LTS
Release:	22.04
Codename:	jammy

Quarto check output

Quarto 1.5.57
[✓] 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: 1.5.57
      Path: /opt/quarto/bin

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

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /home/anon-b/.TinyTeX/bin/aarch64-linux
      Version: 2024

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

[✓] Checking Python 3 installation....OK
      Version: 3.10.12
      Path: /usr/bin/python3
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter

[✓] Checking R installation...........(None)

      Unable to locate an installed version of R.
      Install R from https://cloud.r-project.org/