dont run on invalid notebooks

Author: MarcoGorelli

docs/history.rst

@@ -2,6 +2,11 @@
 Changelog
 =========
 
+1.5.2 (2022-09-28)
+~~~~~~~~~~~~~~~~~~
+Fixed bug in which, when running ``nbqa`` on a directory,
+it wasn't ignoring invalid files (thanks @francesco-ballarin for the report!)
+
 1.5.1 (2022-09-20)
 ~~~~~~~~~~~~~~~~~~
 Built-in hooks now have ``types_or: [jupyter, markdown]``, so that

nbqa/__main__.py

@@ -120,7 +120,6 @@ def _get_notebooks(root_dir: str) -> Iterator[Path]:
         jupytext_installed = False
     else:
         jupytext_installed = True
-
     if os.path.isfile(root_dir):
         _, ext = os.path.splitext(root_dir)
         if (jupytext_installed and ext in (".ipynb", ".md")) or (
@@ -306,7 +305,6 @@ def _run_command(
     else:
         python_module = COMMAND_TO_PYTHON_MODULE.get(main_command, main_command)
         cmd = [sys.executable, "-m", python_module, *sub_commands]
-
     output = subprocess.run(
         [*cmd, *args, *cmd_args],
         capture_output=True,
@@ -660,7 +658,11 @@ def _main(cli_args: CLIArgs, configs: Configs) -> int:
             [
                 i.file
                 for key, i in nb_to_tmp_mapping.items()
-                if key not in saved_sources.failed_notebooks
+                if key
+                not in (
+                    *saved_sources.failed_notebooks,
+                    *saved_sources.non_python_notebooks,
+                )
             ],
             shell=configs["shell"],
         )

tests/test_jupytext.py

@@ -275,3 +275,21 @@ def test_invalid_config_file(tmpdir: "LocalPath") -> None:
         match=r"Passing unrecognized arguments to super\(JupytextConfiguration\)",
     ):
         main(["black", os.path.join(tmpdir, "foo.md")])
+
+
+def test_jupytext_on_folder(capsys: "CaptureFixture") -> None:
+    """Check invalid files aren't checked."""
+    path = os.path.join("tests", "invalid_data")
+    main(
+        [
+            "flake8",
+            path,
+        ]
+    )
+    out, _ = capsys.readouterr()
+    expected = (
+        f'{os.path.join(path, "invalid_syntax.ipynb")}:cell_1:0:1: D100 Missing docstring in public module\n'
+        f'{os.path.join(path, "assignment_to_literal.ipynb")}:cell_1:0:1: D100 Missing docstring in public module\n'
+        f'{os.path.join(path, "automagic.ipynb")}:cell_1:0:1: D100 Missing docstring in public module\n'
+    )
+    assert out == expected