Add a (failing) --execute example

The example fails because Jupytext rewrites the ipynb file:
[jupytext] Updating 'test.ipynb' with this change:
E               @@ -5,10 +5,10 @@
E                   "execution_count": 1,
E                   "metadata": {
E                    "execution": {
E               -     "iopub.execute_input": "2021-01-26T22:24:31.954956Z",
E               -     "iopub.status.busy": "2021-01-26T22:24:31.949570Z",
E               -     "iopub.status.idle": "2021-01-26T22:24:31.979381Z",
E               -     "shell.execute_reply": "2021-01-26T22:24:31.978412Z"
E               +     "iopub.execute_input": "2021-01-26T22:24:34.617791Z",
E               +     "iopub.status.busy": "2021-01-26T22:24:34.614232Z",
E               +     "iopub.status.idle": "2021-01-26T22:24:34.619679Z",
E               +     "shell.execute_reply": "2021-01-26T22:24:34.619940Z"
E                    }
E                   },
E                   "outputs": [

tests/conftest.py

@@ -60,7 +60,7 @@ def python_notebook():
             "kernelspec": {
                 "display_name": "Python 3",
                 "language": "python",
-                "name": "python3",
+                "name": "python_kernel",
             }
         },
     )
@@ -86,7 +86,7 @@ def notebook_with_outputs():
             "kernelspec": {
                 "display_name": "Python 3",
                 "language": "python",
-                "name": "python3",
+                "name": "python_kernel",
             }
         },
     )

tests/test_pre_commit_4_sync_execute.py

@@ -0,0 +1,68 @@
+import pytest
+from git.exc import HookExecutionError
+from nbformat.v4.nbbase import new_code_cell
+from pre_commit.main import main as pre_commit
+
+from jupytext import read, write
+
+from .utils import requires_user_kernel_python3, skip_pre_commit_tests_on_windows
+
+
+@requires_user_kernel_python3
+@skip_pre_commit_tests_on_windows
+def test_pre_commit_hook_sync_execute(
+    tmpdir,
+    cwd_tmpdir,
+    tmp_repo,
+    capsys,
+    jupytext_repo_root,
+    jupytext_repo_rev,
+    notebook_with_outputs,
+):
+    """Here we sync the ipynb notebook with a py:percent file and execute it (this is probably not a very
+    recommendable hook!)"""
+    pre_commit_config_yaml = f"""
+repos:
+- repo: {jupytext_repo_root}
+  rev: {jupytext_repo_rev}
+  hooks:
+  - id: jupytext
+    args: [--sync, --execute, --diff]
+    additional_dependencies:
+    - nbconvert
+"""
+    tmpdir.join(".pre-commit-config.yaml").write(pre_commit_config_yaml)
+
+    tmp_repo.git.add(".pre-commit-config.yaml")
+    pre_commit(["install", "--install-hooks", "-f"])
+
+    # simple notebook with kernel 'user_kernel_python3'
+    nb = notebook_with_outputs
+    nb.cells = [new_code_cell("3+4")]
+
+    # pair it to a py file and write it to disk
+    nb.metadata["jupytext"] = {"formats": "ipynb,py:percent"}
+    write(nb, "test.ipynb")
+
+    # try to commit it, should fail because
+    # 1. the py version hasn't been added
+    # 2. the outputs are missing
+    tmp_repo.git.add("test.ipynb")
+    with pytest.raises(
+        HookExecutionError,
+        match="files were modified by this hook",
+    ):
+        tmp_repo.index.commit("failing")
+
+    # Add the two files
+    tmp_repo.git.add("test.ipynb")
+    tmp_repo.git.add("test.py")
+
+    # now the commit will succeed
+    tmp_repo.index.commit("passing")
+    assert "test.ipynb" in tmp_repo.tree()
+    assert "test.py" in tmp_repo.tree()
+
+    # the first cell has the expected output
+    nb = read("test.ipynb")
+    assert nb.cells[0].outputs[0]["test/plain"] == "7"

tests/utils.py

@@ -61,6 +61,10 @@ def isort_version():
     not any(get_kernel_spec(name).language == "R" for name in find_kernel_specs()),
     reason="irkernel is not installed",
 )
+requires_user_kernel_python3 = pytest.mark.skipif(
+    "python_kernel" not in find_kernel_specs(),
+    reason="Please run 'python -m ipykernel install --name python_kernel --user'",
+)
 requires_myst = pytest.mark.skipif(
     not is_myst_available(), reason="myst_parser not found"
 )