Merge pull request #160 from akhmerov/script_outputs

use nbconvert to write scripts

Author: akhmerov

.github/workflows/tests.yml

@@ -27,6 +27,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
+        python -m bash_kernel.install  # For testing a non-standard kernel
         pip install .
 
     - name: Run tests

jupyter_sphinx/execute.py

@@ -1,7 +1,9 @@
 """Execution and managing kernels."""
 
 import os
+import warnings
 from pathlib import Path
+from logging import Logger
 
 from sphinx.transforms import SphinxTransform
 from sphinx.errors import ExtensionError
@@ -18,6 +20,22 @@
 else:
      from nbclient.client import execute as executenb
 
+import traitlets
+# Workaround of https://github.com/ipython/traitlets/issues/606
+if traitlets.version_info < (5, 1):
+    class LoggerAdapterWrapper(Logger):
+        """Wrap a logger adapter, while pretending to be a logger."""
+        def __init__(self, wrapped):
+            self._wrapped = wrapped
+
+        def __getattribute__(self, attr):
+            if attr == "_wrapped":
+                return object.__getattribute__(self, attr)
+            return self._wrapped.__getattribute__(attr)
+else:
+    def LoggerAdapterWrapper(logger_adapter):
+        return logger_adapter
+
 import nbformat
 
 import jupyter_sphinx as js
@@ -262,20 +280,19 @@ def write_notebook_output(notebook, output_dir, notebook_name, location=None):
         resources,
         os.path.join(output_dir, notebook_name + ".ipynb"),
     )
-    # Write a script too.  Note that utf-8 is the de facto
-    # standard encoding for notebooks. 
-    ext = notebook.metadata.get("language_info", {}).get("file_extension", None)
-    if ext is None:
-        ext = ".txt"
-        js.logger.warning(
-            "Notebook code has no file extension metadata, " "defaulting to `.txt`",
-            location=location,
-        )
-    contents = "\n\n".join(cell.source for cell in notebook.cells)
 
-    notebook_file = notebook_name + ext
+    exporter = nbconvert.exporters.ScriptExporter(
+        log=LoggerAdapterWrapper(js.logger)
+    )
+    with warnings.catch_warnings():
+        # See https://github.com/jupyter/nbconvert/issues/1388
+        warnings.simplefilter('ignore', DeprecationWarning)
+        contents, resources = exporter.from_notebook_node(notebook)
+
+    notebook_file = notebook_name + resources['output_extension']
     output_dir = Path(output_dir)
-    (output_dir / notebook_file).write_text(contents, encoding = "utf8")
+    # utf-8 is the de-facto standard encoding for notebooks.
+    (output_dir / notebook_file).write_text(contents, encoding="utf8")
 
 
 def contains_widgets(notebook):

requirements.txt

@@ -7,3 +7,6 @@ nbformat
 # For documentation building and testing
 matplotlib
 pytest
+
+# A non-standard kernel
+bash_kernel

tests/test_execute.py

@@ -2,6 +2,7 @@
 import shutil
 import os
 import sys
+import warnings
 from io import StringIO
 from unittest.mock import Mock
 from pathlib import Path
@@ -35,7 +36,7 @@ def doctree():
     def doctree(
         source,
         config=None,
-        return_warnings=False,
+        return_all=False,
         entrypoint="jupyter_sphinx",
         buildername='html'
     ):
@@ -59,9 +60,8 @@ def doctree(
         app.build()
 
         doctree = app.env.get_and_resolve_doctree("index", app.builder)
-
-        if return_warnings:
-            return doctree, warnings.getvalue()
+        if return_all:
+            return doctree, app, warnings.getvalue()
         else:
             return doctree
 
@@ -295,8 +295,6 @@ def test_emphasize_lines(doctree):
     """
     tree = doctree(source)
     cell0, cell1 = tree.traverse(JupyterCellNode)
-    (cellinput0, celloutput0) = cell0.children
-    (cellinput1, celloutput1) = cell1.children
 
     assert cell0.attributes["emphasize_lines"] == [1, 3, 4, 5]
     assert cell1.attributes["emphasize_lines"] == [2, 4]
@@ -314,9 +312,8 @@ def test_execution_environment_carries_over(doctree):
         a
     """
     tree = doctree(source)
-    cell0, cell1 = tree.traverse(JupyterCellNode)
-    (cellinput0, celloutput0) = cell0.children
-    (cellinput1, celloutput1) = cell1.children
+    _, cell1 = tree.traverse(JupyterCellNode)
+    (_, celloutput1) = cell1.children
     assert celloutput1.children[0].rawsource.strip() == "2"
 
 
@@ -336,9 +333,8 @@ def test_kernel_restart(doctree):
         a
     """
     tree = doctree(source)
-    cell0, cell1 = tree.traverse(JupyterCellNode)
-    (cellinput0, celloutput0) = cell0.children
-    (cellinput1, celloutput1) = cell1.children
+    _, cell1 = tree.traverse(JupyterCellNode)
+    (_, celloutput1) = cell1.children
     assert "NameError" in celloutput1.children[0].rawsource
 
 
@@ -359,7 +355,7 @@ def test_raises(doctree):
     """
     tree = doctree(source)
     (cell,) = tree.traverse(JupyterCellNode)
-    (cellinput, celloutput) = cell.children
+    (_, celloutput) = cell.children
     assert "ValueError" in celloutput.children[0].rawsource
 
     source = """
@@ -370,7 +366,7 @@ def test_raises(doctree):
     """
     tree = doctree(source)
     (cell,) = tree.traverse(JupyterCellNode)
-    (cellinput, celloutput) = cell.children
+    (_, celloutput) = cell.children
     assert "ValueError" in celloutput.children[0].rawsource
 
 
@@ -407,7 +403,7 @@ def test_stdout(doctree):
     """
     tree = doctree(source)
     (cell,) = tree.traverse(JupyterCellNode)
-    (cellinput, celloutput) = cell.children
+    (_, celloutput) = cell.children
     assert len(cell.children) == 2
     assert celloutput.children[0].rawsource.strip() == "hello world"
 
@@ -420,7 +416,7 @@ def test_stderr(doctree):
         print('hello world', file=sys.stderr)
     """
 
-    tree, warnings = doctree(source, return_warnings=True)
+    tree, _, warnings = doctree(source, return_all=True)
     assert "hello world" in warnings
     (cell,) = tree.traverse(JupyterCellNode)
     (_, celloutput) = cell.children
@@ -556,7 +552,7 @@ def test_latex(doctree):
     for start, end in delimiter_pairs:
         tree = doctree(source.format(start, end))
         (cell,) = tree.traverse(JupyterCellNode)
-        (cellinput, celloutput) = cell.children
+        (_, celloutput) = cell.children
         assert celloutput.children[0].astext() == r"\int"
 
 
@@ -619,3 +615,42 @@ def test_download_role(text, reftarget, caption, tmp_path):
     assert_node(ret[0][0], [literal, caption])
     assert msg == []
 
+
+def test_save_script(doctree):
+    source = """
+    .. jupyter-kernel:: python3
+      :id: test
+
+    .. jupyter-execute::
+
+      a = 1
+      print(a)
+    """
+    tree, app, _ = doctree(source, return_all=True)
+    outdir = Path(app.outdir)
+    saved_text = (outdir / '../jupyter_execute/test.py').read_text()
+    assert saved_text.startswith('#!/usr/bin/env python')
+    assert 'print(a)' in saved_text
+
+
+def test_bash_kernel(doctree):
+    pytest.importorskip('bash_kernel')
+    if sys.platform == 'win32':
+        pytest.skip("Not trying bash on windows.")
+
+    source = """
+    .. jupyter-kernel:: bash
+      :id: test
+
+    .. jupyter-execute::
+
+      echo "foo"
+    """
+    with warnings.catch_warnings():
+        # See https://github.com/takluyver/bash_kernel/issues/105
+        warnings.simplefilter('ignore', DeprecationWarning)
+        _, app, _ = doctree(source, return_all=True)
+
+    outdir = Path(app.outdir)
+    saved_text = (outdir / '../jupyter_execute/test.sh').read_text()
+    assert 'echo "foo"' in saved_text