def test_two_raw_cells_are_preserved(
nb=new_notebook(cells=[new_raw_cell("---\nX\n---"),
new_raw_cell("Y")])):
"""Test the pattern described at https://github.com/mwouts/jupytext/issues/466"""
py = jupytext.writes(nb, "py")
nb2 = jupytext.reads(py, "py")
compare_notebooks(nb2, nb)
def test_read_simple_file(script="""# ---
# title: Simple file
# ---
# %% [markdown]
# This is a markdown cell
# %% [md]
# This is also a markdown cell
# %% [raw]
# This is a raw cell
# %%% sub-cell title
# This is a sub-cell
# %%%% sub-sub-cell title
# This is a sub-sub-cell
# %% And now a code cell
1 + 2 + 3 + 4
5
6
# %%magic # this is a commented magic, not a cell
7
"""):
nb = jupytext.reads(script, 'py:percent')
compare_notebooks(
new_notebook(cells=[
new_raw_cell('---\ntitle: Simple file\n---'),
new_markdown_cell('This is a markdown cell'),
new_markdown_cell('This is also a markdown cell',
metadata={'region_name': 'md'}),
new_raw_cell('This is a raw cell'),
new_code_cell('# This is a sub-cell',
metadata={
'title': 'sub-cell title',
'cell_depth': 1
}),
new_code_cell('# This is a sub-sub-cell',
metadata={
'title': 'sub-sub-cell title',
'cell_depth': 2
}),
new_code_cell('''1 + 2 + 3 + 4
5
6
%%magic # this is a commented magic, not a cell
7''',
metadata={'title': 'And now a code cell'})
]), nb)
script2 = jupytext.writes(nb, 'py:percent')
compare(script2, script)
def test_read_raw_cell_markdown_version_1_1_with_mimetype(header="""---
jupyter:
jupytext:
text_representation:
extension: .md
format_name: markdown
format_version: '1.1'
jupytext_version: 1.1.0-rc0
kernelspec:
display_name: Python 3
language: python
name: python3
---
""", markdown_11="""```raw_mimetype="text/restructuredtext"
.. meta::
:description: Topic: Integrated Development Environments, Difficulty: Easy, Category: Tools
:keywords: python, introduction, IDE, PyCharm, VSCode, Jupyter, recommendation, tools
```
""", markdown_12="""<!-- #raw raw_mimetype="text/restructuredtext" -->
.. meta::
:description: Topic: Integrated Development Environments, Difficulty: Easy, Category: Tools
:keywords: python, introduction, IDE, PyCharm, VSCode, Jupyter, recommendation, tools
<!-- #endraw -->
"""):
nb = jupytext.reads(header + '\n' + markdown_11, 'md')
compare(nb.cells[0], new_raw_cell(source=""".. meta::
:description: Topic: Integrated Development Environments, Difficulty: Easy, Category: Tools
:keywords: python, introduction, IDE, PyCharm, VSCode, Jupyter, recommendation, tools""",
metadata={'raw_mimetype': 'text/restructuredtext'}))
md2 = jupytext.writes(nb, 'md')
assert "format_version: '1.1'" not in md2
nb.metadata['jupytext']['notebook_metadata_filter'] = '-all'
md2 = jupytext.writes(nb, 'md')
compare(md2, markdown_12)
def test_raise_on_different_cell_type():
ref = new_notebook(cells=[new_markdown_cell('Cell one'),
new_code_cell('Cell two')])
test = new_notebook(cells=[new_markdown_cell('Cell one'),
new_raw_cell('Cell two')])
with pytest.raises(AssertionError):
compare_notebooks(ref, test)
def test_raw_with_metadata(no_jupytext_version_number, text="""# + key="value" active=""
# Raw cell
# # Commented line
""", notebook=new_notebook(cells=[new_raw_cell('Raw cell\n# Commented line', metadata={'key': 'value'})])):
nb2 = jupytext.reads(text, 'py')
compare_notebooks(nb2, notebook)
text2 = jupytext.writes(notebook, 'py')
compare(text2, text)
def test_raw_cell_with_metadata(markdown="""<!-- #raw key="value" -->
raw content
<!-- #endraw -->
"""):
nb = jupytext.reads(markdown, 'md')
compare(nb.cells[0], new_raw_cell(source='raw content', metadata={'key': 'value'}))
markdown2 = jupytext.writes(nb, 'md')
compare(markdown2, markdown)
def test_raw_cell_with_metadata(markdown="""<!-- #raw key="value" -->
raw content
<!-- #endraw -->
""", ):
nb = jupytext.reads(markdown, "md")
compare(nb.cells[0],
new_raw_cell(source="raw content", metadata={"key": "value"}))
markdown2 = jupytext.writes(nb, "md")
compare(markdown2, markdown)
def test_raw_cell_with_metadata(markdown="""```key="value"
raw content
```
"""):
nb = jupytext.reads(markdown, 'md')
compare(nb.cells[0],
new_raw_cell(source='raw content', metadata={'key': 'value'}))
markdown2 = jupytext.writes(nb, 'md')
compare(markdown, markdown2)
def get_test_notebook(name):
"""
Make a test notebook for the given name.
"""
nb = new_notebook()
nb.cells.append(new_code_cell("'code_' + '{}'".format(name)))
nb.cells.append(new_raw_cell("raw_{}".format(name)))
nb.cells.append(new_markdown_cell('markdown_{}'.format(name)))
return nb
def test_raise_on_different_cell_type():
ref = new_notebook(
cells=[new_markdown_cell('Cell one'),
new_code_cell('Cell two')])
test = new_notebook(
cells=[new_markdown_cell('Cell one'),
new_raw_cell('Cell two')])
with pytest.raises(NotebookDifference):
compare_notebooks(ref, test, ext='.md')
def test_notebook(name):
"""
Make a test notebook for the given name.
"""
nb = new_notebook()
nb.cells.append(new_code_cell("'code_' + '{}'".format(name)))
nb.cells.append(new_raw_cell("raw_{}".format(name)))
nb.cells.append(new_markdown_cell("markdown_{}".format(name)))
return nb
def test_inactive_cell(text='''```python active="md"
# This becomes a raw cell in Jupyter
```
''', expected=new_notebook(
cells=[new_raw_cell('# This becomes a raw cell in Jupyter',
metadata={'active': 'md'})])):
nb = jupytext.reads(text, 'md')
compare_notebooks(nb, expected)
text2 = jupytext.writes(nb, 'md')
compare(text2, text)
def test_inactive_cell_using_tag(text='''```python tags=["active-md"]
# This becomes a raw cell in Jupyter
```
''', expected=new_notebook(
cells=[new_raw_cell('# This becomes a raw cell in Jupyter',
metadata={'tags': ['active-md']})])):
nb = jupytext.reads(text, 'md')
compare_notebooks(nb, expected)
text2 = jupytext.writes(nb, 'md')
compare(text2, text)
def test_raise_on_different_cell_type(raise_on_first_difference):
ref = new_notebook(
cells=[new_markdown_cell("Cell one"),
new_code_cell("Cell two")])
test = new_notebook(
cells=[new_markdown_cell("Cell one"),
new_raw_cell("Cell two")])
with pytest.raises(NotebookDifference):
compare_notebooks(test,
ref,
"md",
raise_on_first_difference=raise_on_first_difference)
def test_raw_with_metadata_2(
no_jupytext_version_number,
text="""# + [raw] key="value"
# Raw cell
# # Commented line
""",
notebook=new_notebook(cells=[
new_raw_cell("Raw cell\n# Commented line", metadata={"key": "value"})
]),
):
nb2 = jupytext.reads(text, "py")
compare_notebooks(nb2, notebook)
def test_metadata_and_cell_to_header():
nb = new_notebook(metadata=dict(mainlanguage='python'),
cells=[
new_raw_cell(source="---\ntitle: Sample header\n---",
metadata={'noskipline': True})
])
header = writer().metadata_and_cell_to_header(nb)
assert '\n'.join(header) == """---
title: Sample header
jupyter:
mainlanguage: python
---"""
assert nb.cells == []
def test_active_tag(
text='''# + tags=["active-py"]
interpreter = 'python'
# + tags=["active-ipynb"]
# interpreter = 'ipython'
''', ref=new_notebook(cells=[
new_raw_cell("interpreter = 'python'", metadata={'tags': ['active-py']}),
new_code_cell("interpreter = 'ipython'", metadata={'tags': ['active-ipynb']})])):
nb = jupytext.reads(text, 'py')
compare_notebooks(nb, ref)
py = jupytext.writes(nb, 'py')
compare(py, text)
def test_root_level_metadata_as_raw_cell(
tmpdir,
root_level_metadata_as_raw_cell,
rmd="""---
author: R Markdown document author
title: R Markdown notebook title
---
```{r}
1 + 1
```
""",
):
nb_file = tmpdir.join("notebook.ipynb")
rmd_file = tmpdir.join("notebook.Rmd")
cfg_file = tmpdir.join("jupytext.toml")
cfg_file.write(
"root_level_metadata_as_raw_cell = {}".format(
"true" if root_level_metadata_as_raw_cell else "false"
)
)
rmd_file.write(rmd)
jupytext_cli([str(rmd_file), "--to", "ipynb"])
nb = nbformat.read(str(nb_file), as_version=4)
if root_level_metadata_as_raw_cell:
assert len(nb.cells) == 2
compare(
nb.cells[0],
new_raw_cell(
"""---
author: R Markdown document author
title: R Markdown notebook title
---"""
),
)
compare(nb.cells[1], new_code_cell("1 + 1"))
else:
assert len(nb.cells) == 1
compare(nb.cells[0], new_code_cell("1 + 1"))
assert nb.metadata["jupytext"]["root_level_metadata"] == {
"title": "R Markdown notebook title",
"author": "R Markdown document author",
}
# Writing back to Rmd should preserve the original document
jupytext_cli([str(nb_file), "--to", "Rmd"])
compare(rmd_file.read(), rmd)
def test_raw_cell_with_metadata_json(
markdown="""<!-- #raw {"key": "value"} -->
raw content
<!-- #endraw -->
""",
):
nb = jupytext.reads(markdown, "md")
compare_cells(
nb.cells,
[new_raw_cell(source="raw content", metadata={"key": "value"})],
compare_ids=False,
)
markdown2 = jupytext.writes(nb, "md")
compare(markdown2, markdown)
def test_metadata_and_cell_to_header(no_jupytext_version_number):
metadata = {'jupytext': {'mainlanguage': 'python'}}
nb = new_notebook(
metadata=metadata,
cells=[new_raw_cell(source="---\ntitle: Sample header\n---")])
header, lines_to_next_cell = metadata_and_cell_to_header(nb, metadata, get_format_implementation('.md'), '.md')
assert '\n'.join(header) == """---
title: Sample header
jupyter:
jupytext:
mainlanguage: python
---"""
assert nb.cells == []
assert lines_to_next_cell is None
def test_inactive_cell_using_tag(
text="""```python tags=["active-md"]
# This becomes a raw cell in Jupyter
```
""",
expected=new_notebook(cells=[
new_raw_cell("# This becomes a raw cell in Jupyter",
metadata={"tags": ["active-md"]})
]),
):
nb = jupytext.reads(text, "md")
compare_notebooks(nb, expected)
text2 = jupytext.writes(nb, "md")
compare(text2, text)
def test_inactive_cell(
text="""```python active="md"
# This becomes a raw cell in Jupyter
```
""",
expected=new_notebook(cells=[
new_raw_cell("# This becomes a raw cell in Jupyter",
metadata={"active": "md"})
]),
):
nb = jupytext.reads(text, "md")
compare_notebooks(nb, expected)
text2 = jupytext.writes(nb, "md")
compare(text2, text)
def test_metadata_and_cell_to_header():
metadata = {'jupytext': {'mainlanguage': 'python'}}
nb = new_notebook(
metadata=metadata,
cells=[new_raw_cell(source="---\ntitle: Sample header\n---")])
with mock.patch('jupytext.header.INSERT_AND_CHECK_VERSION_NUMBER', False):
header, lines_to_next_cell = metadata_and_cell_to_header(nb, metadata, get_format_implementation('.md'), '.md')
assert '\n'.join(header) == """---
title: Sample header
jupyter:
jupytext:
mainlanguage: python
---"""
assert nb.cells == []
assert lines_to_next_cell is None
def test_metadata_and_cell_to_header(no_jupytext_version_number):
metadata = {"jupytext": {"mainlanguage": "python"}}
nb = new_notebook(
metadata=metadata,
cells=[new_raw_cell(source="---\ntitle: Sample header\n---")])
header, lines_to_next_cell = metadata_and_cell_to_header(
nb, metadata, get_format_implementation(".md"), ".md")
assert ("\n".join(header) == """---
title: Sample header
jupyter:
jupytext:
mainlanguage: python
---""")
assert nb.cells == []
assert lines_to_next_cell is None
def test_invalid_raw_cell():
cell = new_raw_cell()
cell["source"] = 5
with pytest.raises(ValidationError):
validate4(cell, "raw_cell")
cell = new_raw_cell()
del cell["metadata"]
with pytest.raises(ValidationError):
validate4(cell, "raw_cell")
cell = new_raw_cell()
del cell["source"]
with pytest.raises(ValidationError):
validate4(cell, "raw_cell")
cell = new_raw_cell()
del cell["cell_type"]
with pytest.raises(ValidationError):
validate4(cell, "raw_cell")
def test_read_mostly_py_rmd_file(rmd="""---
title: Simple file
---
```{python, echo=TRUE}
import numpy as np
x = np.arange(0, 2*math.pi, eps)
```
```{python, echo=TRUE}
x = np.arange(0,1,eps)
y = np.abs(x)-.5
```
```{r}
ls()
```
```{r, results="asis", magic_args="-i x"}
cat(stringi::stri_rand_lipsum(3), sep='\n\n')
```
""", ):
nb = jupytext.reads(rmd, "Rmd")
compare_cells(
nb.cells,
[
new_raw_cell("---\ntitle: Simple file\n---"),
new_code_cell(
"import numpy as np\n"
"x = np.arange(0, 2*math.pi, eps)",
metadata={"echo": True},
),
new_code_cell("x = np.arange(0,1,eps)\ny = np.abs(x)-.5",
metadata={"echo": True}),
new_code_cell("%%R\nls()"),
new_code_cell(
"%%R -i x\ncat(stringi::"
"stri_rand_lipsum(3), sep='\n\n')",
metadata={"results": "asis"},
),
],
compare_ids=False,
)
rmd2 = jupytext.writes(nb, "Rmd")
rmd2 = re.sub(r"```{r ", "```{r, ", rmd2)
rmd2 = re.sub(r"```{python ", "```{python, ", rmd2)
compare(rmd2, rmd)
def test_metadata_and_cell_to_header():
nb = new_notebook(metadata={'jupytext': {
'mainlanguage': 'python'
}},
cells=[
new_raw_cell(source="---\ntitle: Sample header\n---",
metadata={'noskipline': True})
])
header = metadata_and_cell_to_header(nb, get_format('.md'), '.md')
assert '\n'.join(header) == """---
title: Sample header
jupyter:
jupytext:
mainlanguage: python
---"""
assert nb.cells == []
def test_active_tag(
text="""# + tags=["active-py"]
interpreter = 'python'
# + tags=["active-ipynb"]
# interpreter = 'ipython'
""",
ref=new_notebook(cells=[
new_raw_cell("interpreter = 'python'",
metadata={"tags": ["active-py"]}),
new_code_cell("interpreter = 'ipython'",
metadata={"tags": ["active-ipynb"]}),
]),
):
nb = jupytext.reads(text, "py")
compare_notebooks(nb, ref)
py = jupytext.writes(nb, "py")
compare(py, text)
def test_read_raw_cell_markdown_version_1_1(markdown="""---
jupyter:
jupytext:
text_representation:
extension: .md
format_name: markdown
format_version: '1.1'
jupytext_version: 1.1.0
---
```key="value"
raw content
```
"""):
nb = jupytext.reads(markdown, 'md')
compare(nb.cells[0], new_raw_cell(source='raw content', metadata={'key': 'value'}))
md2 = jupytext.writes(nb, 'md')
assert "format_version: '1.1'" not in md2
def translatenb_v4(cells):
from nbformat.v4 import (new_code_cell, new_markdown_cell, new_notebook)
from nbformat.v4.nbbase import new_raw_cell
nb_cells = []
for cell_type, language, block in cells:
block = '\n'.join(block)
if cell_type == 'markdown':
if block != "":
nb_cells.append(new_markdown_cell(source=block))
elif cell_type == 'code':
nb_cells.append(new_code_cell(source=block))
elif cell_type == 'raw':
nb_cells.append(new_raw_cell(source=block))
else:
raise ValueError(
'Wrong cell_type was given [{}]'.format(cell_type))
nb = new_notebook(cells=nb_cells)
from nbformat import writes
return writes(nb, version=4)
def create_cells(rdfgraph, cell, cell_index, **kwargs):
provenance_metadata = create_provenance(rdfgraph, cell, cell_index)
cell_type = str(kwargs['cell_type'])
source = get_cell_source(rdfgraph, cell_index)
if source:
kwargs['source'] = source
kwargs['metadata'] = provenance_metadata
if cell_type == 'code':
output = get_cell_output(rdfgraph, cell_index)
if output:
output = create_cell_output(**output)
if output:
kwargs['outputs'] = [output]
else:
kwargs['outputs'] = []
notebook_cell = nbbase.new_code_cell(**kwargs)
elif cell_type == 'markdown':
notebook_cell = nbbase.new_markdown_cell(**kwargs)
elif cell_type == 'raw':
notebook_cell = nbbase.new_raw_cell(**kwargs)
return notebook_cell
offset = -1
else:
cells_new.append(new_code_cell(
source=cell.source,
metadata=cell.metadata,
outputs=[],
# print cell.execution_count
execution_count=cell.execution_count+offset))
# print cell.execution_count+offset
elif cell["cell_type"] == "markdown":
cells_new.append(new_markdown_cell(
source=cell.source,
metadata=cell.metadata))
else:
cells_new.append(new_raw_cell(
source=cell.source,
metadata=cell.metadata))
# print cell.cell_type
nb_new = new_notebook(cells=cells_new,
metadata=nb.metadata,
nbformat=nb.nbformat,
nbformat_minor=nb.nbformat_minor
)
with codecs.open(outfilename, encoding='utf-8', mode='w') as out:
nbformat.write(nb_new, out)
# nbformat.write(nb, fp, version=nbformat.NO_CONVERT, **kwargs)
#################################################################