opt-in to cell magics

docs/configuration.rst

@@ -63,19 +63,20 @@ or you can put the following in your :code:`pyproject.toml` file
 Ignore cells
 ~~~~~~~~~~~~
 
-By default, :code:`nbQA` will ignore line magics (e.g. :code:`%matplotlib inline`), and :code:`%%bash` and :code:`%%script` cell magics.
-To ignore extra cells, you can use the :code:`--nbqa-ignore-cells` CLI argument, e.g.
+By default, :code:`nbQA` will ignore line magics (e.g. :code:`%matplotlib inline`), as well as most cell magics.
+To process code in cells with cell magics, you can use the :code:`--nbqa-process-cells` CLI argument, e.g. to process
+code within :code:``%%add_to`` cell magics, use
 
 .. code-block:: bash
 
-    nbqa black my_notebook.ipynb --nbqa-ignore-cells %%html,%%cython
+    nbqa black my_notebook.ipynb --nbqa-process-cells add_to
 
-or the :code:`ignore_cells` option in your :code:`pyproject.toml` file, e.g.
+or the :code:`process_cells` option in your :code:`pyproject.toml` file, e.g.
 
 .. code-block:: toml
 
-    [tool.nbqa.ignore_cells]
-    black = "%%html,%%cython"
+    [tool.nbqa.process_cells]
+    black = add_to
 
 Include / exclude
 ~~~~~~~~~~~~~~~~~

nbqa/__main__.py

@@ -559,7 +559,7 @@ def _run_on_one_root_dir(
                 nb_info_mapping[notebook] = save_source.main(
                     notebook,
                     temp_python_file,
-                    configs.nbqa_ignore_cells,
+                    configs.nbqa_process_cells,
                     cli_args.command,
                 )
             except Exception as exc:

nbqa/cmdline.py

@@ -46,7 +46,9 @@ class CLIArgs:  # pylint: disable=R0902,R0903
     nbqa_config
         Config file for 3rd party tool (e.g. :code:`.mypy.ini`)
     nbqa_ignore_cells
-        Ignore cells whose first line starts with the input token
+        Deprecated.
+    nbqa_process_cells
+        Process code within these cell magics.
     nbqa_addopts
         Any additional flags passed to third-party tool (e.g. :code:`--quiet`).
     nbqa_files
@@ -60,6 +62,7 @@ class CLIArgs:  # pylint: disable=R0902,R0903
     nbqa_addopts: Sequence[str]
     nbqa_mutate: bool
     nbqa_ignore_cells: Optional[str]
+    nbqa_process_cells: Optional[str]
     nbqa_config: Optional[str]
     nbqa_diff: bool
     nbqa_files: Optional[str]
@@ -82,6 +85,7 @@ def __init__(self, args: argparse.Namespace, cmd_args: Sequence[str]) -> None:
         self.nbqa_mutate = args.nbqa_mutate or False
         self.nbqa_config = args.nbqa_config or None
         self.nbqa_ignore_cells = args.nbqa_ignore_cells or None
+        self.nbqa_process_cells = args.nbqa_process_cells or None
         self.nbqa_diff = args.nbqa_diff or False
         self.nbqa_files = args.nbqa_files or None
         self.nbqa_exclude = args.nbqa_exclude or None
@@ -136,8 +140,17 @@ def parse_args(argv: Optional[Sequence[str]]) -> "CLIArgs":
             required=False,
             help=dedent(
                 r"""
-                Ignore cells whose first line starts with this. You can pass multiple options,
-                e.g. `nbqa black my_notebook.ipynb --nbqa-ignore-cells %%%%cython,%%%%html`
+                Deprecated, do not use.
+                """
+            ),
+        )
+        parser.add_argument(
+            "--nbqa-process-cells",
+            required=False,
+            help=dedent(
+                r"""
+                Process code within these cell magics. You can pass multiple options,
+                e.g. `nbqa black my_notebook.ipynb --nbqa-process-cells add_to,write_to`
                 by placing commas between them.
                 """
             ),

nbqa/config/config.py

@@ -50,6 +50,7 @@ class _ConfigSections(NamedTuple):  # pylint: disable=R0903
     ADDOPTS: str = "addopts"
     CONFIG: str = "config"
     IGNORE_CELLS: str = "ignore_cells"
+    PROCESS_CELLS: str = "process_cells"
     MUTATE: str = "mutate"
     DIFF: str = "diff"
     FILES: str = "files"
@@ -75,7 +76,9 @@ class Configs:
     nbqa_config
         Configuration of the third party tool.
     nbqa_ignore_cells
-        Extra cells which nbqa should ignore.
+        Deprecated.
+    nbqa_process_cells
+        Process code within cells with these cell magics.
     nbqa_addopts
         Additional arguments passed to the third party tool
     nbqa_files
@@ -92,6 +95,9 @@ class Configs:
     _config_section_parsers[CONFIG_SECTIONS.IGNORE_CELLS] = (
         lambda arg: arg.split(",") if isinstance(arg, str) else arg
     )
+    _config_section_parsers[CONFIG_SECTIONS.PROCESS_CELLS] = (
+        lambda arg: arg.split(",") if isinstance(arg, str) else arg
+    )
     _config_section_parsers[CONFIG_SECTIONS.MUTATE] = bool
     _config_section_parsers[CONFIG_SECTIONS.DIFF] = bool
     _config_section_parsers[CONFIG_SECTIONS.FILES] = str
@@ -100,6 +106,7 @@ class Configs:
     _mutate: bool = False
     _config: Optional[str] = None
     _ignore_cells: Sequence[str] = []
+    _process_cells: Sequence[str] = []
     _addopts: Sequence[str] = []
     _diff: bool = False
     _files: Optional[str] = None
@@ -141,9 +148,14 @@ def nbqa_addopts(self) -> Sequence[str]:
 
     @property
     def nbqa_ignore_cells(self) -> Sequence[str]:
-        """Additional cells which nbqa should ignore."""
+        """Don't use, deprecated."""
         return self._ignore_cells
 
+    @property
+    def nbqa_process_cells(self) -> Sequence[str]:
+        """Additional cells which nbqa should process."""
+        return self._process_cells
+
     @property
     def nbqa_files(self) -> Optional[str]:
         """Additional cells which nbqa should ignore."""
@@ -172,6 +184,10 @@ def merge(self, other: "Configs") -> "Configs":
         config.set_config(
             CONFIG_SECTIONS.IGNORE_CELLS, self._ignore_cells or other.nbqa_ignore_cells
         )
+        config.set_config(
+            CONFIG_SECTIONS.PROCESS_CELLS,
+            self._process_cells or other.nbqa_process_cells,
+        )
         config.set_config(CONFIG_SECTIONS.MUTATE, self._mutate or other.nbqa_mutate)
         config.set_config(CONFIG_SECTIONS.DIFF, self._diff or other.nbqa_diff)
         config.set_config(CONFIG_SECTIONS.FILES, self._files or other.nbqa_files)
@@ -193,6 +209,7 @@ def parse_from_cli_args(cli_args: CLIArgs) -> "Configs":
         config.set_config(CONFIG_SECTIONS.ADDOPTS, cli_args.nbqa_addopts)
         config.set_config(CONFIG_SECTIONS.CONFIG, cli_args.nbqa_config)
         config.set_config(CONFIG_SECTIONS.IGNORE_CELLS, cli_args.nbqa_ignore_cells)
+        config.set_config(CONFIG_SECTIONS.PROCESS_CELLS, cli_args.nbqa_process_cells)
         config.set_config(CONFIG_SECTIONS.MUTATE, cli_args.nbqa_mutate)
         config.set_config(CONFIG_SECTIONS.DIFF, cli_args.nbqa_diff)
         config.set_config(CONFIG_SECTIONS.FILES, cli_args.nbqa_files)
@@ -211,7 +228,7 @@ def get_default_config(command: str) -> "Configs":
             CONFIG_SECTIONS.CONFIG, DEFAULT_CONFIG["config"].get(command)
         )
         defaults.set_config(
-            CONFIG_SECTIONS.IGNORE_CELLS, DEFAULT_CONFIG["ignore_cells"].get(command)
+            CONFIG_SECTIONS.PROCESS_CELLS, DEFAULT_CONFIG["process_cells"].get(command)
         )
         defaults.set_config(
             CONFIG_SECTIONS.MUTATE, DEFAULT_CONFIG["mutate"].get(command)
@@ -247,3 +264,8 @@ def validate(self) -> None:
             )
         if self.nbqa_config and not Path(self.nbqa_config).exists():
             raise FileNotFoundError(f"{self.nbqa_config} not found.")
+        if self.nbqa_ignore_cells:
+            raise ValueError(
+                "--nbqa-ignore-cells is deprecated since version 0.6.0, "
+                "most cell magics are now excluded by default."
+            )

nbqa/config/default_config.toml

@@ -5,7 +5,7 @@ isort = ["--treat-comment-as-code", "# %%NBQA-CELL-SEP"]
 
 [mutate]
 
-[ignore_cells]
+[process_cells]
 
 [diff]
 

nbqa/handle_magics.py

@@ -29,6 +29,7 @@ class IPythonMagicType(Enum):
     HELP = 1
     LINE = 2
     CELL = 3
+    NO_MAGIC = 4
 
 
 class MagicHandler(ABC):
@@ -191,22 +192,15 @@ def get_ipython_magic_type(ipython_magic: str) -> Optional[IPythonMagicType]:
         -------
         Optional[IPythonMagicType]
             Type of the IPython magic
-
-        Raises
-        ------
-        RuntimeError
-            This shouldn't normally happen, it's just a defensive check.
         """
         python_code = INPUT_SPLITTER.transform_cell(ipython_magic)
         magic_type: Optional[IPythonMagicType] = None
         for magic, prefixes in MagicHandler._MAGIC_PREFIXES.items():
             if any(prefix in python_code for prefix in prefixes):
                 magic_type = magic
                 break
-        else:  # pragma: nocover
-            raise RuntimeError(
-                "Unreachable code reached - please report a bug at https://github.com/nbQA-dev/nbQA"
-            )
+        else:
+            magic_type = IPythonMagicType.NO_MAGIC
 
         return magic_type
 

nbqa/save_source.py

@@ -28,27 +28,7 @@
     from pathlib import Path
 
 CODE_SEPARATOR = "# %%NBQA-CELL-SEP\n"
-MAGIC = [
-    "%%!",
-    "%%bash",
-    "%%cython",
-    "%%HTML",
-    "%%html",
-    "%%javascript",
-    "%%js",
-    "%%latex",
-    "%%markdown",
-    "%%perl",
-    "%%python2",
-    "%%ruby",
-    "%%script",
-    "%%sh",
-    "%%sx",
-    "%%system",
-    "%%SVG",
-    "%%svg",
-    "%%writefile",
-]
+MAGIC = ["time", "timeit", "capture", "pypy", "python", "python3"]
 NEWLINE = "\n"
 NEWLINES = defaultdict(lambda: NEWLINE * 3)
 NEWLINES["isort"] = NEWLINE * 2
@@ -296,7 +276,7 @@ def _get_line_numbers_for_mapping(
 
 
 def _should_ignore_code_cell(
-    source: Sequence[str], ignore_cells: Sequence[str]
+    source: Sequence[str], process_cells: Sequence[str]
 ) -> bool:
     """
     Return True if the current cell should be ignored from processing.
@@ -305,8 +285,8 @@ def _should_ignore_code_cell(
     ----------
     source
         Source from the notebook cell
-    ignore_cells
-        Extra cells which nbqa should ignore.
+    process_cells
+        Extra cells which nbqa should process.
 
     Returns
     -------
@@ -315,14 +295,18 @@ def _should_ignore_code_cell(
     """
     if not source:
         return True
-    ignore = MAGIC + [i.strip() for i in ignore_cells]
-    return any(source[0].lstrip().startswith(i) for i in ignore)
+    process = MAGIC + [i.strip() for i in process_cells]
+    magic_type = MagicHandler.get_ipython_magic_type(source[0])
+    if magic_type != IPythonMagicType.CELL:
+        return False
+    first_line = source[0].lstrip()
+    return first_line.split()[0] not in {f"%%{magic}" for magic in process}
 
 
 def main(
     notebook: "Path",
     temp_python_file: "Path",
-    ignore_cells: Sequence[str],
+    process_cells: Sequence[str],
     command: str,
 ) -> NotebookInfo:
     """
@@ -334,8 +318,8 @@ def main(
         Jupyter Notebook third-party tool is being run against.
     temp_python_file
         Temporary Python file to save converted notebook in.
-    ignore_cells
-        Extra cells which nbqa should ignore.
+    process_cells
+        Extra cells which nbqa should process.
     command
         The third-party tool being run.
 
@@ -358,7 +342,7 @@ def main(
         if cell["cell_type"] == "code":
             cell_number += 1
 
-            if _should_ignore_code_cell(cell["source"], ignore_cells):
+            if _should_ignore_code_cell(cell["source"], process_cells):
                 code_cells_to_ignore.add(cell_number)
                 continue
 

tests/data/default_magic.ipynb

@@ -0,0 +1,36 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%timeit\n",
+    "\n",
+    "a = 2 "
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}

tests/data/non_default_magic.ipynb

@@ -0,0 +1,36 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%javascript\n",
+    "\n",
+    "a = 2 "
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}