From 4d6f3ddd2a0e7acebabfcd89a66af6da56cf5d94 Mon Sep 17 00:00:00 2001
From: hguturu <hguturu@gmail.com>
Date: Tue, 18 Mar 2025 10:07:18 -0700
Subject: [PATCH 01/14] feature: Add support for qmd, need to fix handling of
 leading #| and tests

---
 nbqa/__main__.py   |  6 ++++--
 nbqa/path_utils.py | 12 +++++++++---
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/nbqa/__main__.py b/nbqa/__main__.py
index 087eb1d3..06b3006c 100644
--- a/nbqa/__main__.py
+++ b/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"))
diff --git a/nbqa/path_utils.py b/nbqa/path_utils.py
index 3a5b37d8..de58f1bf 100644
--- a/nbqa/path_utils.py
+++ b/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
 

From 4e59da246abbb8cea6810891d0b6f7bbba94fbd9 Mon Sep 17 00:00:00 2001
From: hguturu <hguturu@gmail.com>
Date: Tue, 18 Mar 2025 14:38:05 -0700
Subject: [PATCH 02/14] feature: add _restore_quarto_cell_options to support
 preserving cell options

---
 nbqa/replace_source.py | 36 ++++++++++++++++++++++++++++++++++--
 1 file changed, 34 insertions(+), 2 deletions(-)

diff --git a/nbqa/replace_source.py b/nbqa/replace_source.py
index 94588f63..cf13c30e 100644
--- a/nbqa/replace_source.py
+++ b/nbqa/replace_source.py
@@ -28,6 +28,37 @@
 SEPARATOR = {True: MARKDOWN_SEPARATOR, False: CODE_SEPARATOR}
 
 
+def _restore_quarto_cell_options(source: str) -> str:
+    """
+    Restore the cell option comments #| at the start of the cell.
+
+    This comment like is typically changed to '# |' by third party tools.
+
+    This is for the cell options in quarto format as described at
+    https://quarto.org/docs/reference/cells/cells-jupyter.html.
+
+    Parameters
+    ----------
+    source
+        Portion of Python file between cell separators.
+
+    Returns
+    -------
+    str
+        New source with leading '# |' restored to '#!'.
+    """
+    new_lines = []
+    lines = source.splitlines()
+    i = 0
+    for i, line in enumerate(lines):
+        if not line.startswith("# |"):
+            break  # only leading '#!' are cell options
+        new_lines.append("#|" + line[3:])
+    if i < len(lines):
+        new_lines.extend(lines[i:])
+    return "\n".join(new_lines)
+
+
 def _restore_semicolon(
     source: str,
     cell_number: int,
@@ -123,6 +154,7 @@ def _get_new_source(
     source = _restore_semicolon(
         pycell, code_cell_number, notebook_info.trailing_semicolons
     )
+    source = _restore_quarto_cell_options(source)
     return _reinstate_magics(
         source,
         notebook_info.temporary_lines.get(code_cell_number, []),
@@ -216,7 +248,7 @@ 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 +358,7 @@ 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

From 7de848381204f28bf3e37c370a5d1d97948925a4 Mon Sep 17 00:00:00 2001
From: hguturu <hguturu@gmail.com>
Date: Tue, 18 Mar 2025 15:02:42 -0700
Subject: [PATCH 03/14] fixed typo in docstring

---
 nbqa/replace_source.py | 2 +-
 tests/test_jupytext.py | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/nbqa/replace_source.py b/nbqa/replace_source.py
index cf13c30e..38a825a7 100644
--- a/nbqa/replace_source.py
+++ b/nbqa/replace_source.py
@@ -45,7 +45,7 @@ def _restore_quarto_cell_options(source: str) -> str:
     Returns
     -------
     str
-        New source with leading '# |' restored to '#!'.
+        New source with leading '# |' restored to '#|'.
     """
     new_lines = []
     lines = source.splitlines()
diff --git a/tests/test_jupytext.py b/tests/test_jupytext.py
index 7702ea85..8b9afdda 100644
--- a/tests/test_jupytext.py
+++ b/tests/test_jupytext.py
@@ -296,11 +296,11 @@ 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(

From 4728e771aa81c029c41e248cd9d34588a678b729 Mon Sep 17 00:00:00 2001
From: hguturu <hguturu@gmail.com>
Date: Wed, 19 Mar 2025 11:43:03 -0700
Subject: [PATCH 04/14] tests: Add test_qmd for new jupytext qmd feature

---
 tests/data/notebook_for_testing.qmd | 33 +++++++++++++++
 tests/test_jupytext.py              | 63 +++++++++++++++++++++++++++++
 2 files changed, 96 insertions(+)
 create mode 100644 tests/data/notebook_for_testing.qmd

diff --git a/tests/data/notebook_for_testing.qmd b/tests/data/notebook_for_testing.qmd
new file mode 100644
index 00000000..f8cfc842
--- /dev/null
+++ b/tests/data/notebook_for_testing.qmd
@@ -0,0 +1,33 @@
+---
+title: "Quarto Basics"
+format:
+  html:
+    code-fold: true
+jupyter: python3
+---
+
+```{python}
+#| label: fig-polar
+#| fig-cap: A line plot on a polar axis
+# This is a comment
+# | Looks like a cell option, but treat like
+# comment since not at top
+
+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])
diff --git a/tests/test_jupytext.py b/tests/test_jupytext.py
index 8b9afdda..75202be9 100644
--- a/tests/test_jupytext.py
+++ b/tests/test_jupytext.py
@@ -198,6 +198,69 @@ 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"""
+        """      jupytext_version: 1.16.7\n"""
+        """  kernelspec:\n"""
+        """    display_name: Python 3\n"""
+        """    language: python\n"""
+        """    name: python3\n"""
+        """---\n"""
+        """\n"""
+        """```{python}\n"""
+        """#| label: fig-polar\n"""
+        """#| fig-cap: A line plot on a polar axis\n"""
+        """# This is a comment\n"""
+        """# | Looks like a cell option, but treat like\n"""
+        """# comment since not at top\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"])

From 55fd296a4ada49aa3377395a13812266540fe3cc Mon Sep 17 00:00:00 2001
From: hguturu <hguturu@gmail.com>
Date: Wed, 19 Mar 2025 11:44:21 -0700
Subject: [PATCH 05/14] tests: fixing test_qmd to work with white space
 stripping of precommit

---
 tests/test_jupytext.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/test_jupytext.py b/tests/test_jupytext.py
index 75202be9..cf9a9217 100644
--- a/tests/test_jupytext.py
+++ b/tests/test_jupytext.py
@@ -252,11 +252,11 @@ def test_qmd(tmp_test_data: Path) -> None:
         """```\n"""
         """\n"""
         """# Other Markdown\n"""
-        """This content should not change in any way. \n"""
+        """This content should not change in any way.\n"""
         """#| cell option like line\n"""
-        """#comment like line \n"""
+        """#comment like line\n"""
         """code that won't get formatted\n"""
-        """ax.set_rticks([0.5,1,1.5,2]) \n"""
+        """ax.set_rticks([0.5,1,1.5,2])\n"""
     )
     assert result == expected
 

From ed08156f646ef6527c9a2183da32f899aea09a95 Mon Sep 17 00:00:00 2001
From: hguturu <hguturu@gmail.com>
Date: Wed, 19 Mar 2025 12:14:18 -0700
Subject: [PATCH 06/14] docs: Added reference to qmd in README.md

---
 README.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/README.md b/README.md
index 53e6088b..f61e111a 100644
--- a/README.md
+++ b/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/).
 

From 37a39905fc75d6cd25b67ac1f7e472f561374559 Mon Sep 17 00:00:00 2001
From: hguturu <hguturu@gmail.com>
Date: Wed, 19 Mar 2025 12:26:32 -0700
Subject: [PATCH 07/14] build: added quarto-cli to requirements-dev and
 toolchain extra

---
 requirements-dev.txt | 1 +
 setup.cfg            | 1 +
 2 files changed, 2 insertions(+)

diff --git a/requirements-dev.txt b/requirements-dev.txt
index 45632468..96b1aafb 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -16,5 +16,6 @@ pytest
 pytest-cov
 pytest-randomly
 pyupgrade
+quarto-cli
 ruff
 yapf
diff --git a/setup.cfg b/setup.cfg
index f7be9f59..02bea3c3 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -53,6 +53,7 @@ toolchain =
     mypy
     pylint
     pyupgrade
+    quarto-cli
     ruff
 
 [flake8]

From 5e9cb65eea0c1b637a2a598e71cdc8c225d14106 Mon Sep 17 00:00:00 2001
From: hguturu <hguturu@gmail.com>
Date: Mon, 24 Mar 2025 11:36:35 -0700
Subject: [PATCH 08/14] fix: change qmd lines back without breaking other tools

---
 nbqa/replace_source.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/nbqa/replace_source.py b/nbqa/replace_source.py
index 38a825a7..87bed9c7 100644
--- a/nbqa/replace_source.py
+++ b/nbqa/replace_source.py
@@ -28,7 +28,7 @@
 SEPARATOR = {True: MARKDOWN_SEPARATOR, False: CODE_SEPARATOR}
 
 
-def _restore_quarto_cell_options(source: str) -> str:
+def _restore_quarto_cell_options(lines: list[str]) -> list[str]:
     """
     Restore the cell option comments #| at the start of the cell.
 
@@ -39,16 +39,15 @@ def _restore_quarto_cell_options(source: str) -> str:
 
     Parameters
     ----------
-    source
-        Portion of Python file between cell separators.
+    lines
+        Lines after all pre-processing restored.
 
     Returns
     -------
-    str
-        New source with leading '# |' restored to '#|'.
+    list[str]
+        Lines with leading '# |' restored to '#|'.
     """
     new_lines = []
-    lines = source.splitlines()
     i = 0
     for i, line in enumerate(lines):
         if not line.startswith("# |"):
@@ -56,7 +55,7 @@ def _restore_quarto_cell_options(source: str) -> str:
         new_lines.append("#|" + line[3:])
     if i < len(lines):
         new_lines.extend(lines[i:])
-    return "\n".join(new_lines)
+    return new_lines
 
 
 def _restore_semicolon(
@@ -154,7 +153,6 @@ def _get_new_source(
     source = _restore_semicolon(
         pycell, code_cell_number, notebook_info.trailing_semicolons
     )
-    source = _restore_quarto_cell_options(source)
     return _reinstate_magics(
         source,
         notebook_info.temporary_lines.get(code_cell_number, []),
@@ -257,6 +255,8 @@ def _write_notebook(
         config = load_jupytext_config(os.path.abspath(temp_notebook))
 
         for cell in notebook_json["cells"]:
+            if ext == ".qmd":
+                cell["source"] = _restore_quarto_cell_options(cell["source"])
             cell["source"] = "".join(cell["source"])
         jupytext.jupytext.write(notebook_json, temp_notebook, config=config)
 

From fb9b38339d564b342a62e86bb8afabf2f63485ff Mon Sep 17 00:00:00 2001
From: hguturu <hguturu@gmail.com>
Date: Mon, 24 Mar 2025 12:44:20 -0700
Subject: [PATCH 09/14] fix: _restore_quarto_cell_options so that existing
 non-cell options don't get turned into cell options

---
 nbqa/replace_source.py              | 34 +++++++++++++++++++----------
 tests/data/notebook_for_testing.qmd |  1 +
 tests/test_jupytext.py              |  1 +
 3 files changed, 25 insertions(+), 11 deletions(-)

diff --git a/nbqa/replace_source.py b/nbqa/replace_source.py
index 87bed9c7..3a0448a3 100644
--- a/nbqa/replace_source.py
+++ b/nbqa/replace_source.py
@@ -28,7 +28,7 @@
 SEPARATOR = {True: MARKDOWN_SEPARATOR, False: CODE_SEPARATOR}
 
 
-def _restore_quarto_cell_options(lines: list[str]) -> list[str]:
+def _restore_quarto_cell_options(og_lines: list[str], lines: list[str]) -> list[str]:
     """
     Restore the cell option comments #| at the start of the cell.
 
@@ -39,23 +39,33 @@ def _restore_quarto_cell_options(lines: list[str]) -> list[str]:
 
     Parameters
     ----------
+    og_lines
+        Original input lines.
     lines
-        Lines after all pre-processing restored.
+        Lines after all formatting and magics restored.
 
     Returns
     -------
     list[str]
         Lines with leading '# |' restored to '#|'.
     """
-    new_lines = []
+    restored_lines = []
     i = 0
+    # iteration logic should be safe since all cell options are at the start
+    # and single lines so shouldn't suffer multi-line formatting before
+    # breaking out
     for i, line in enumerate(lines):
-        if not line.startswith("# |"):
-            break  # only leading '#!' are cell options
-        new_lines.append("#|" + line[3:])
-    if i < len(lines):
-        new_lines.extend(lines[i:])
-    return new_lines
+        if not line.startswith("# |") or not og_lines[i].startswith("#|"):
+            # only leading '#|' are cell options
+            # if we encounter a line without, then all following are not
+            # we also skip if the formatting tool hasn't changed '#|' to '# |'
+            # since that means the formatter is handling qmd lines properly
+            i -= 1  # rolling back so the logic below works without branching
+            break
+        restored_lines.append("#|" + line[3:])
+
+    restored_lines.extend(lines[i + 1 :])
+    return restored_lines
 
 
 def _restore_semicolon(
@@ -255,8 +265,6 @@ def _write_notebook(
         config = load_jupytext_config(os.path.abspath(temp_notebook))
 
         for cell in notebook_json["cells"]:
-            if ext == ".qmd":
-                cell["source"] = _restore_quarto_cell_options(cell["source"])
             cell["source"] = "".join(cell["source"])
         jupytext.jupytext.write(notebook_json, temp_notebook, config=config)
 
@@ -310,6 +318,8 @@ def mutate(  # pylint: disable=too-many-locals,too-many-arguments
         )
         if not new_source:
             cells_to_remove.append(cell_number)
+        if notebook.endswith(".qmd"):
+            new_source = _restore_quarto_cell_options(new_source)
         cell["source"] = new_source
 
     if original_notebook_json == notebook_json:
@@ -409,6 +419,8 @@ def diff(  # pylint: disable=too-many-arguments
             newlinesbefore[python_file],
             newlinesafter[python_file],
         )
+        if notebook.endswith(".qmd"):
+            new_source = _restore_quarto_cell_options(cell["source"], new_source)
         cell["source"][-1] += "\n"
         if new_source:
             new_source[-1] += "\n"
diff --git a/tests/data/notebook_for_testing.qmd b/tests/data/notebook_for_testing.qmd
index f8cfc842..0f3c80c3 100644
--- a/tests/data/notebook_for_testing.qmd
+++ b/tests/data/notebook_for_testing.qmd
@@ -9,6 +9,7 @@ jupyter: python3
 ```{python}
 #| label: fig-polar
 #| fig-cap: A line plot on a polar axis
+# |  Should not be changed back to #|
 # This is a comment
 # | Looks like a cell option, but treat like
 # comment since not at top
diff --git a/tests/test_jupytext.py b/tests/test_jupytext.py
index cf9a9217..b0121a5c 100644
--- a/tests/test_jupytext.py
+++ b/tests/test_jupytext.py
@@ -235,6 +235,7 @@ def test_qmd(tmp_test_data: Path) -> None:
         """```{python}\n"""
         """#| label: fig-polar\n"""
         """#| fig-cap: A line plot on a polar axis\n"""
+        """# |  Should not be changed back to #|\n"""
         """# This is a comment\n"""
         """# | Looks like a cell option, but treat like\n"""
         """# comment since not at top\n"""

From 5f5836a4749dc6cbfe289ec9ad39b57369e849c6 Mon Sep 17 00:00:00 2001
From: hguturu <hguturu@gmail.com>
Date: Mon, 24 Mar 2025 12:45:38 -0700
Subject: [PATCH 10/14] fix: _restore_quarto_cell_options so that existing
 non-cell options don't get turned into cell options

---
 nbqa/replace_source.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nbqa/replace_source.py b/nbqa/replace_source.py
index 3a0448a3..096c15a2 100644
--- a/nbqa/replace_source.py
+++ b/nbqa/replace_source.py
@@ -319,7 +319,7 @@ def mutate(  # pylint: disable=too-many-locals,too-many-arguments
         if not new_source:
             cells_to_remove.append(cell_number)
         if notebook.endswith(".qmd"):
-            new_source = _restore_quarto_cell_options(new_source)
+            new_source = _restore_quarto_cell_options(cell["source"], new_source)
         cell["source"] = new_source
 
     if original_notebook_json == notebook_json:

From 4bbd7e7e2d0e2b47c3fd94bdb604922e4771053d Mon Sep 17 00:00:00 2001
From: hguturu <hguturu@gmail.com>
Date: Mon, 24 Mar 2025 12:57:15 -0700
Subject: [PATCH 11/14] fix: logic in _restore_quarto_cell_options

---
 nbqa/replace_source.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/nbqa/replace_source.py b/nbqa/replace_source.py
index 096c15a2..34818abb 100644
--- a/nbqa/replace_source.py
+++ b/nbqa/replace_source.py
@@ -60,10 +60,9 @@ def _restore_quarto_cell_options(og_lines: list[str], lines: list[str]) -> list[
             # if we encounter a line without, then all following are not
             # we also skip if the formatting tool hasn't changed '#|' to '# |'
             # since that means the formatter is handling qmd lines properly
-            i -= 1  # rolling back so the logic below works without branching
+            restored_lines.append(line)
             break
         restored_lines.append("#|" + line[3:])
-
     restored_lines.extend(lines[i + 1 :])
     return restored_lines
 

From 93f3d2a00ade6c2fffa759449d98bc09bd20b3e3 Mon Sep 17 00:00:00 2001
From: hguturu <hguturu@gmail.com>
Date: Mon, 24 Mar 2025 13:52:19 -0700
Subject: [PATCH 12/14] refactor: changed how _restore_quarto_cell_options is
 applied to not break other formats

---
 tests/data/notebook_for_testing.qmd | 16 +++++++++++++---
 tests/test_jupytext.py              |  2 +-
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/tests/data/notebook_for_testing.qmd b/tests/data/notebook_for_testing.qmd
index 0f3c80c3..25b02805 100644
--- a/tests/data/notebook_for_testing.qmd
+++ b/tests/data/notebook_for_testing.qmd
@@ -1,15 +1,25 @@
 ---
-title: "Quarto Basics"
+title: Quarto Basics
 format:
   html:
     code-fold: true
-jupyter: python3
+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
-# |  Should not be changed back to #|
+#   Should not be changed back to #|
 # This is a comment
 # | Looks like a cell option, but treat like
 # comment since not at top
diff --git a/tests/test_jupytext.py b/tests/test_jupytext.py
index b0121a5c..936768f8 100644
--- a/tests/test_jupytext.py
+++ b/tests/test_jupytext.py
@@ -235,7 +235,7 @@ def test_qmd(tmp_test_data: Path) -> None:
         """```{python}\n"""
         """#| label: fig-polar\n"""
         """#| fig-cap: A line plot on a polar axis\n"""
-        """# |  Should not be changed back to #|\n"""
+        """#   Should not be changed back to #|\n"""
         """# This is a comment\n"""
         """# | Looks like a cell option, but treat like\n"""
         """# comment since not at top\n"""

From b0cb95d747f2e45b329d1ccee7e9826d419b9c00 Mon Sep 17 00:00:00 2001
From: hguturu <hguturu@gmail.com>
Date: Mon, 24 Mar 2025 16:10:09 -0700
Subject: [PATCH 13/14] refactor: removed special handling of qmd cell options,
 since # | are supported

---
 nbqa/replace_source.py              | 43 -----------------------------
 tests/data/notebook_for_testing.qmd | 20 +++++++-------
 tests/test_jupytext.py              | 11 ++++----
 3 files changed, 16 insertions(+), 58 deletions(-)

diff --git a/nbqa/replace_source.py b/nbqa/replace_source.py
index 34818abb..639c9a81 100644
--- a/nbqa/replace_source.py
+++ b/nbqa/replace_source.py
@@ -28,45 +28,6 @@
 SEPARATOR = {True: MARKDOWN_SEPARATOR, False: CODE_SEPARATOR}
 
 
-def _restore_quarto_cell_options(og_lines: list[str], lines: list[str]) -> list[str]:
-    """
-    Restore the cell option comments #| at the start of the cell.
-
-    This comment like is typically changed to '# |' by third party tools.
-
-    This is for the cell options in quarto format as described at
-    https://quarto.org/docs/reference/cells/cells-jupyter.html.
-
-    Parameters
-    ----------
-    og_lines
-        Original input lines.
-    lines
-        Lines after all formatting and magics restored.
-
-    Returns
-    -------
-    list[str]
-        Lines with leading '# |' restored to '#|'.
-    """
-    restored_lines = []
-    i = 0
-    # iteration logic should be safe since all cell options are at the start
-    # and single lines so shouldn't suffer multi-line formatting before
-    # breaking out
-    for i, line in enumerate(lines):
-        if not line.startswith("# |") or not og_lines[i].startswith("#|"):
-            # only leading '#|' are cell options
-            # if we encounter a line without, then all following are not
-            # we also skip if the formatting tool hasn't changed '#|' to '# |'
-            # since that means the formatter is handling qmd lines properly
-            restored_lines.append(line)
-            break
-        restored_lines.append("#|" + line[3:])
-    restored_lines.extend(lines[i + 1 :])
-    return restored_lines
-
-
 def _restore_semicolon(
     source: str,
     cell_number: int,
@@ -317,8 +278,6 @@ def mutate(  # pylint: disable=too-many-locals,too-many-arguments
         )
         if not new_source:
             cells_to_remove.append(cell_number)
-        if notebook.endswith(".qmd"):
-            new_source = _restore_quarto_cell_options(cell["source"], new_source)
         cell["source"] = new_source
 
     if original_notebook_json == notebook_json:
@@ -418,8 +377,6 @@ def diff(  # pylint: disable=too-many-arguments
             newlinesbefore[python_file],
             newlinesafter[python_file],
         )
-        if notebook.endswith(".qmd"):
-            new_source = _restore_quarto_cell_options(cell["source"], new_source)
         cell["source"][-1] += "\n"
         if new_source:
             new_source[-1] += "\n"
diff --git a/tests/data/notebook_for_testing.qmd b/tests/data/notebook_for_testing.qmd
index 25b02805..d3b5bedf 100644
--- a/tests/data/notebook_for_testing.qmd
+++ b/tests/data/notebook_for_testing.qmd
@@ -18,20 +18,20 @@ jupyter:
 
 ```{python}
 #| label: fig-polar
-#| fig-cap: A line plot on a polar axis
-#   Should not be changed back to #|
-# This is a comment
-# | Looks like a cell option, but treat like
-# comment since not at top
+# | 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
+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'})
+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.set_rticks([0.5, 1, 1.5, 2])
 ax.grid(True)
 plt.show()
 ```
diff --git a/tests/test_jupytext.py b/tests/test_jupytext.py
index 936768f8..818c8319 100644
--- a/tests/test_jupytext.py
+++ b/tests/test_jupytext.py
@@ -234,11 +234,12 @@ def test_qmd(tmp_test_data: Path) -> None:
         """\n"""
         """```{python}\n"""
         """#| label: fig-polar\n"""
-        """#| fig-cap: A line plot on a polar axis\n"""
-        """#   Should not be changed back to #|\n"""
-        """# This is a comment\n"""
-        """# | Looks like a cell option, but treat like\n"""
-        """# comment since not at top\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"""

From 7a8dc82fcab008e30eb635fd307d0cabe5c5cd2e Mon Sep 17 00:00:00 2001
From: hguturu <hguturu@gmail.com>
Date: Fri, 11 Apr 2025 15:09:55 -0700
Subject: [PATCH 14/14] fix: test_jupytext.py::test_qmd to be more robust to
 jupytext version

---
 tests/test_jupytext.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_jupytext.py b/tests/test_jupytext.py
index 818c8319..cdb6591b 100644
--- a/tests/test_jupytext.py
+++ b/tests/test_jupytext.py
@@ -225,7 +225,7 @@ def test_qmd(tmp_test_data: Path) -> None:
         """      extension: .qmd\n"""
         """      format_name: quarto\n"""
         """      format_version: '1.0'\n"""
-        """      jupytext_version: 1.16.7\n"""
+        f"      jupytext_version: {jupytext.__version__}\n"
         """  kernelspec:\n"""
         """    display_name: Python 3\n"""
         """    language: python\n"""