Support for running nbqa on quatro format (.qmd) markdown files

README.md

@@ -126,6 +126,12 @@ reformatted my_notebook.md
 All done! ✨ 🍰 ✨
 1 files reformatted.
 ```
+Quarto format markdown ``.qmd`` files are also supported via [quarto-cli](https://github.com/quarto-dev/quarto-cli) (requires `jupytext` and `quarto-cli` to be installed):
+
+```console
+$ nbqa "ruff check --select=I --fix" my_notebook.qmd
+Found 1 error (1 fixed, 0 remaining).
+```
 
 See [command-line examples](https://nbqa.readthedocs.io/en/latest/examples.html) for examples involving [doctest](https://docs.python.org/3/library/doctest.html), [flake8](https://flake8.pycqa.org/en/latest/), [mypy](http://mypy-lang.org/), [pylint](https://github.com/PyCQA/pylint), [autopep8](https://github.com/hhatto/autopep8), [pydocstyle](http://www.pydocstyle.org/en/stable/), [yapf](https://github.com/google/yapf), and [ruff](https://github.com/charliermarsh/ruff/).
 

nbqa/__main__.py

@@ -126,7 +126,7 @@ def _get_notebooks(root_dir: str) -> Iterator[Path]:
         jupytext_installed = True
     if os.path.isfile(root_dir):
         _, ext = os.path.splitext(root_dir)
-        if (jupytext_installed and ext in (".ipynb", ".md")) or (
+        if (jupytext_installed and ext in (".ipynb", ".md", ".qmd")) or (
             not jupytext_installed and ext == ".ipynb"
         ):
             return iter((Path(root_dir),))
@@ -138,7 +138,9 @@ def _get_notebooks(root_dir: str) -> Iterator[Path]:
 
     if jupytext_installed:
         iterable = itertools.chain(
-            Path(root_dir).rglob("*.ipynb"), Path(root_dir).rglob("*.md")
+            Path(root_dir).rglob("*.ipynb"),
+            Path(root_dir).rglob("*.md"),
+            Path(root_dir).rglob("*.qmd"),
         )
     else:  # pragma: nocover
         iterable = itertools.chain(Path(root_dir).rglob("*.ipynb"))

nbqa/path_utils.py

@@ -88,7 +88,7 @@ def read_notebook(notebook: str) -> Tuple[Optional[Dict[str, Any]], Optional[boo
     if ext == ".ipynb":
         trailing_newline = content.endswith("\n")
         return json.loads(content), trailing_newline
-    assert ext == ".md"
+    assert ext in (".md", ".qmd")
     try:
         import jupytext  # pylint: disable=import-outside-toplevel
         from markdown_it import MarkdownIt  # pylint: disable=import-outside-toplevel
@@ -133,8 +133,14 @@ def read_notebook(notebook: str) -> Tuple[Optional[Dict[str, Any]], Optional[boo
     parsed = MarkdownIt("commonmark").disable("inline", True).parse(content)
     lexer = None
     for token in parsed:
-        if token.type == "fence" and token.info.startswith("{code-cell}"):
-            lexer = remove_prefix(token.info, "{code-cell}").strip()
+        if token.type == "fence" and (
+            token.info.startswith("{code-cell}") or token.info.startswith("{python}")
+        ):
+            lexer = (
+                remove_prefix(token.info, "{code-cell}").strip()
+                if not token.info.startswith("{python}")
+                else "python"
+            )
             md_content["metadata"]["language_info"] = {"pygments_lexer": lexer}
             break
 

nbqa/replace_source.py

@@ -216,7 +216,7 @@ def _write_notebook(
                     f"{json.dumps(notebook_json, indent=1, ensure_ascii=False)}"
                 )
     else:
-        assert ext == ".md"
+        assert ext in (".md", ".qmd")
         import jupytext  # pylint: disable=import-outside-toplevel
         from jupytext.config import (  # pylint: disable=import-outside-toplevel
             load_jupytext_config,
@@ -326,7 +326,7 @@ def _print_diff(code_cell_number: int, cell_diff: Iterator[str]) -> bool:
 
     if line_changes:
         header = f"Cell {code_cell_number}"
-        headers = [f"{BOLD}{header}{RESET}\n", f"{'-'*len(header)}\n"]
+        headers = [f"{BOLD}{header}{RESET}\n", f"{'-' * len(header)}\n"]
         sys.stdout.writelines(headers + line_changes + ["\n"])
         return True
     return False

requirements-dev.txt

@@ -16,5 +16,6 @@ pytest
 pytest-cov
 pytest-randomly
 pyupgrade
+quarto-cli
 ruff
 yapf

setup.cfg

@@ -53,6 +53,7 @@ toolchain =
     mypy
     pylint
     pyupgrade
+    quarto-cli
     ruff
 
 [flake8]

tests/data/notebook_for_testing.qmd

@@ -0,0 +1,44 @@
+---
+title: Quarto Basics
+format:
+  html:
+    code-fold: true
+jupyter:
+  jupytext:
+    text_representation:
+      extension: .qmd
+      format_name: quarto
+      format_version: '1.0'
+      jupytext_version: 1.16.7
+  kernelspec:
+    display_name: Python 3
+    language: python
+    name: python3
+---
+
+```{python}
+#| label: fig-polar
+# | fig-cap: A line plot on a polar axis
+#|  Additional content
+# This is a comment that stops cell options
+#| fig-subcap: A line plot on a polar axis
+# |  Additional content
+
+import numpy as np
+import matplotlib.pyplot as plt
+
+r = np.arange(0, 2, 0.01)
+theta = 2 * np.pi * r
+fig, ax = plt.subplots(subplot_kw={"projection": "polar"})
+ax.plot(theta, r)
+ax.set_rticks([0.5, 1, 1.5, 2])
+ax.grid(True)
+plt.show()
+```
+
+# Other Markdown
+This content should not change in any way.
+#| cell option like line
+#comment like line
+code that won't get formatted
+ax.set_rticks([0.5,1,1.5,2])

tests/test_jupytext.py

@@ -198,6 +198,71 @@ def test_md(tmp_test_data: Path) -> None:
     assert result == expected
 
 
+def test_qmd(tmp_test_data: Path) -> None:
+    """
+    Notebook in qmd format.
+
+    Parameters
+    ----------
+    tmp_test_data
+        Temporary copy of test data.
+    """
+    notebook = tmp_test_data / "notebook_for_testing.qmd"
+
+    main(["black", str(notebook)])
+
+    with open(notebook, encoding="utf-8") as fd:
+        result = fd.read()
+    expected = (
+        """---\n"""
+        """title: Quarto Basics\n"""
+        """format:\n"""
+        """  html:\n"""
+        """    code-fold: true\n"""
+        """jupyter:\n"""
+        """  jupytext:\n"""
+        """    text_representation:\n"""
+        """      extension: .qmd\n"""
+        """      format_name: quarto\n"""
+        """      format_version: '1.0'\n"""
+        f"      jupytext_version: {jupytext.__version__}\n"
+        """  kernelspec:\n"""
+        """    display_name: Python 3\n"""
+        """    language: python\n"""
+        """    name: python3\n"""
+        """---\n"""
+        """\n"""
+        """```{python}\n"""
+        """#| label: fig-polar\n"""
+        """#| fig-cap: |-\n"""
+        """#|   A line plot on a polar axis\n"""
+        """#|   Additional content\n"""
+        """# This is a comment that stops cell options\n"""
+        """# | fig-subcap: A line plot on a polar axis\n"""
+        """# |  Additional content\n"""
+        """\n"""
+        """import numpy as np\n"""
+        """import matplotlib.pyplot as plt\n"""
+        """\n"""
+        """r = np.arange(0, 2, 0.01)\n"""
+        """theta = 2 * np.pi * r\n"""
+        """fig, ax = plt.subplots(subplot_kw={"projection": "polar"})\n"""
+        """ax.plot(theta, r)\n"""
+        """ax.set_rticks([0.5, 1, 1.5, 2])\n"""
+        """ax.grid(True)\n"""
+        """plt.show()\n"""
+        """```\n"""
+        """\n"""
+        """# Other Markdown\n"""
+        """This content should not change in any way.\n"""
+        """#| cell option like line\n"""
+        """#comment like line\n"""
+        """code that won't get formatted\n"""
+        """ax.set_rticks([0.5,1,1.5,2])\n"""
+    )
+    assert result == expected
+
+
 def test_non_jupytext_md() -> None:
     """Check non-Python markdown will be ignored."""
     ret = main(["black", "README.md"])
@@ -296,11 +361,11 @@ def test_jupytext_on_folder(capsys: "CaptureFixture") -> None:
     )
     out, _ = capsys.readouterr()
     expected = (
-        f'{os.path.join(path, "invalid_syntax.ipynb")}:cell_1:0 at module level:\n'
+        f"{os.path.join(path, 'invalid_syntax.ipynb')}:cell_1:0 at module level:\n"
         "        D100: Missing docstring in public module\n"
-        f'{os.path.join(path, "assignment_to_literal.ipynb")}:cell_1:0 at module level:\n'
+        f"{os.path.join(path, 'assignment_to_literal.ipynb')}:cell_1:0 at module level:\n"
         "        D100: Missing docstring in public module\n"
-        f'{os.path.join(path, "automagic.ipynb")}:cell_1:0 at module level:\n'
+        f"{os.path.join(path, 'automagic.ipynb')}:cell_1:0 at module level:\n"
         "        D100: Missing docstring in public module\n"
     )
     assert "\n".join(sorted(out.splitlines())) == "\n".join(