def test_read_simple_file(script='''# -*- coding: utf-8 -*-
"""
This is a markdown cell
"""
1 + 2 + 3 + 4
5
6
""
7
#################################
# Another markdown cell
def f(x):
"""Sample docstring"""
return 4
''', ):
nb = jupytext.reads(script, "py:sphinx")
assert nb.cells[0].cell_type == "code"
assert nb.cells[0].source == "%matplotlib inline"
assert nb.cells[1].cell_type == "markdown"
assert nb.cells[1].source == "This is a markdown cell"
assert nb.cells[2].cell_type == "code"
compare(
nb.cells[2].source,
"""1 + 2 + 3 + 4
5
6""",
)
assert nb.cells[3].cell_type == "code"
assert nb.cells[3].source == "7"
assert nb.cells[4].cell_type == "markdown"
assert nb.cells[4].source == "Another markdown cell"
assert nb.cells[5].cell_type == "code"
assert (nb.cells[5].source == '''def f(x):
"""Sample docstring"""
return 4''')
assert len(nb.cells) == 6
script2 = jupytext.writes(nb, "py:sphinx")
compare(script2, script)
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 render(self, name, params):
if name == 'task.ipynb':
p = Path(name)
convert_to = p.suffix[1:]
name = str(p.with_suffix('.py'))
else:
convert_to = None
t = self.get_template(name)
out = t.render(**params)
if convert_to:
nb = jupytext.reads(out, fmt='py:light')
out = jupytext.writes(nb, fmt=convert_to)
return out
def test_notebook_one_blank_line_before_first_markdown_cell(
script="""
# This is a markdown cell
1 + 1
""", ):
notebook = jupytext.reads(script, "py")
script2 = jupytext.writes(notebook, "py")
compare(script2, script)
assert len(notebook.cells) == 3
for cell in notebook.cells:
lines = cell.source.splitlines()
if len(lines):
assert lines[0]
assert lines[-1]
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_markdown_cell_with_code_inside_multiline_string_419(
text='''```python
readme = """
above
```python
x = 2
```
below
"""
```
'''):
nb = jupytext.reads(text, 'md')
compare(jupytext.writes(nb, 'md'), text)
assert len(nb.cells) == 1
def test_read_markdown_cell_with_triple_quote_307(
script="""# This script test that commented triple quotes '''
# do not impede the correct identification of Markdown cells
# Here is Markdown cell number 2 '''
"""):
notebook = jupytext.reads(script, 'py')
assert len(notebook.cells) == 2
assert notebook.cells[0].cell_type == 'markdown'
assert notebook.cells[0].source == """This script test that commented triple quotes '''
do not impede the correct identification of Markdown cells"""
assert notebook.cells[1].cell_type == 'markdown'
assert notebook.cells[1].source == "Here is Markdown cell number 2 '''"
script2 = jupytext.writes(notebook, 'py')
compare(script2, script)
def test_split_on_header(markdown="""A paragraph
# H1 Header
## H2 Header
Another paragraph
"""):
fmt = {'extension': '.md', 'split_at_heading': True}
nb = jupytext.reads(markdown, fmt)
assert nb.cells[0].source == 'A paragraph'
assert nb.cells[1].source == '# H1 Header'
assert nb.cells[2].source == '## H2 Header\n\nAnother paragraph'
assert len(nb.cells) == 3
markdown2 = jupytext.writes(nb, fmt)
compare(markdown, markdown2)
def test_notebook_with_magic_and_bash_cells(script="""# This is a test for issue #181
# %load_ext line_profiler
# !head -4 data/president_heights.csv
"""):
notebook = jupytext.reads(script, 'py')
for cell in notebook.cells:
lines = cell.source.splitlines()
assert lines[0]
assert lines[-1]
assert not cell.metadata, cell.source
script2 = jupytext.writes(notebook, 'py')
compare(script2, script)
def test_read_cell_with_metadata(
script="""# %% a code cell with parameters {"tags": ["parameters"]}
a = 3
""",
):
nb = jupytext.reads(script, "py:percent")
assert len(nb.cells) == 1
assert nb.cells[0].cell_type == "code"
assert nb.cells[0].source == "a = 3"
assert nb.cells[0].metadata == {
"title": "a code cell with parameters",
"tags": ["parameters"],
}
script2 = jupytext.writes(nb, "py:percent")
compare(script2, script)
def saveAsScript(fileName):
if not isJupyterNotebook(): return
fileName = fixPath(fileName)
notebook_path = this_notebook()
if notebook_path is None:
print(
'Can\'t find notebook file. Do you use non standard connection to jupyter server? Save this file as script in main menu'
)
return
with open(notebook_path, 'r', encoding='utf-8') as fp:
notebook = nbformat.read(fp, as_version=4)
script = jupytext.writes(notebook, ext='.py', fmt='py')
script_path = fileName
if script_path[-3:] != '.py': script_path += '.py'
with open(script_path, 'w', encoding='utf-8') as fp:
fp.write(script)
def test_round_trip_python_with_js_cell_no_cell_metadata():
notebook = new_notebook(cells=[
new_code_cell('''import notebook.nbextensions
notebook.nbextensions.install_nbextension('jupytext.js', user=True)'''),
new_code_cell('''%%javascript
Jupyter.utils.load_extensions('jupytext')''')
],
metadata={
'jupytext': {
'notebook_metadata_filter': '-all',
'cell_metadata_filter': '-all'
}
})
text = jupytext.writes(notebook, 'py')
notebook2 = jupytext.reads(text, 'py')
compare_notebooks(notebook, notebook2)
def test_docstring_with_quadruple_quote(nb=new_notebook(cells=[
new_code_cell('''def fun_1(df):
""""
docstring starting with 4 double quotes and ending with 3
"""
return df'''),
new_code_cell('''def fun_2(df):
"""
docstring
"""
return df'''),
])):
"""Reproduces https://github.com/mwouts/jupytext/issues/460"""
py = jupytext.writes(nb, "py:percent")
nb2 = jupytext.reads(py, "py")
compare_notebooks(nb2, nb)
def test_split_on_header(markdown="""A paragraph
# H1 Header
## H2 Header
Another paragraph
""", ):
fmt = {"extension": ".md", "split_at_heading": True}
nb = jupytext.reads(markdown, fmt)
assert nb.cells[0].source == "A paragraph"
assert nb.cells[1].source == "# H1 Header"
assert nb.cells[2].source == "## H2 Header\n\nAnother paragraph"
assert len(nb.cells) == 3
markdown2 = jupytext.writes(nb, fmt)
compare(markdown2, markdown)
def test_markdown_cell_with_metadata_json(
markdown="""<!-- #region {"key": "value"} -->
A long
markdown cell
<!-- #endregion -->
""", ):
nb = jupytext.reads(markdown, "md")
compare(
nb.cells[0],
new_markdown_cell(source="A long\n\n\nmarkdown cell",
metadata={"key": "value"}),
)
markdown2 = jupytext.writes(nb, "md")
compare(markdown2, markdown)
def test_cell_metadata_filter_is_updated():
text = """---
jupyter:
jupytext:
cell_metadata_filter: -all
---
```{r cache=FALSE}
1+1
```
"""
nb = reads(text, "Rmd")
assert nb.metadata["jupytext"]["cell_metadata_filter"] == "cache,-all"
text2 = writes(nb, "Rmd")
assert text.splitlines()[-3:] == text2.splitlines()[-3:]
def test_multiple_empty_cells():
nb = new_notebook(
cells=[new_code_cell(), new_code_cell(), new_code_cell()],
metadata={"jupytext": {"notebook_metadata_filter": "-all"}},
)
text = jupytext.writes(nb, "py:percent")
expected = """# %%
# %%
# %%
"""
compare(text, expected)
nb2 = jupytext.reads(text, "py:percent")
nb2.metadata = nb.metadata
compare_notebooks(nb2, nb)
def test_hide_code_tag(
no_jupytext_version_number,
nb=new_notebook(
metadata={"jupytext": {
"main_language": "matlab"
}},
cells=[new_code_cell("1 + 1", metadata={"tags": ["hide_code"]})],
),
text="""% + tags=["hide_code"]
1 + 1
""",
):
text2 = jupytext.writes(nb, "m")
compare(text2, text)
nb2 = jupytext.reads(text, "m")
compare_notebooks(nb2, nb)
def test_cell_metadata_filter_is_updated():
text = """---
jupyter:
jupytext:
cell_metadata_filter: -all
---
```{r cache=FALSE}
1+1
```
"""
nb = reads(text, 'Rmd')
assert nb.metadata['jupytext']['cell_metadata_filter'] == 'cache,-all'
text2 = writes(nb, 'Rmd')
assert text.splitlines()[-3:] == text2.splitlines()[-3:]
def test_multiline_comments_format_option():
text = '''# %% [markdown]
"""
a
long
cell
"""
'''
nb = new_notebook(
cells=[new_markdown_cell("a\nlong\ncell")],
metadata={
"jupytext": {"cell_markers": '"""', "notebook_metadata_filter": "-all"}
},
)
py = jupytext.writes(nb, "py:percent")
compare(py, text)
def test_notebook_blank_lines(script="""# +
# This is a comment
# followed by two variables
a = 3
b = 4
# -
# New cell is a variable
c = 5
# +
# Now we have two functions
def f(x):
return x + x
def g(x):
return x + x + x
# -
# A commented block that is two lines away
# from previous cell
# A function again
def h(x):
return x + 1
# variable
d = 6
""", ):
notebook = jupytext.reads(script, "py")
assert len(notebook.cells) >= 6
for cell in notebook.cells:
lines = cell.source.splitlines()
if len(lines) != 1:
assert lines[0], cell.source
assert lines[-1], cell.source
script2 = jupytext.writes(notebook, "py")
compare(script2, script)
def test_markdown_cell_with_code_inside_multiline_string_419(
text='''```python
readme = """
above
```python
x = 2
```
below
"""
```
''', ):
"""A code cell containing triple backticks is converted to a code cell encapsulated with four backticks"""
nb = jupytext.reads(text, "md")
compare(jupytext.writes(nb, "md"), "`" + text[:-1] + "`\n")
assert len(nb.cells) == 1
def test_read_prev_function(
pynb="""def test_read_cell_explicit_start_end(pynb='''
import pandas as pd
# +
def data():
return pd.DataFrame({'A': [0, 1]})
data()
'''):
nb = jupytext.reads(pynb, 'py')
pynb2 = jupytext.writes(nb, 'py')
compare(pynb2, pynb)
""", ):
nb = jupytext.reads(pynb, "py")
pynb2 = jupytext.writes(nb, "py")
compare(pynb2, pynb)
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_multiline_comments_format_option():
text = '''# %% [markdown]
"""
a
long
cell
"""
'''
nb = new_notebook(cells=[new_markdown_cell("a\nlong\ncell")],
metadata={
'jupytext': {
'cell_markers': '"""',
'notebook_metadata_filter': '-all'
}
})
py = jupytext.writes(nb, 'py:percent')
compare(py, text)
def test_read_simple_file(script="""# -*- coding: utf-8 -*-
'''
This is a markdown cell
'''
1 + 2 + 3 + 4
5
6
''
7
#################################
# Another markdown cell
def f(x):
'''Sample docstring'''
return 4
"""):
nb = jupytext.reads(script, ext='.py', format_name='sphinx')
assert nb.cells[0].cell_type == 'code'
assert nb.cells[0].source == '%matplotlib inline'
assert nb.cells[1].cell_type == 'markdown'
assert nb.cells[1].source == 'This is a markdown cell'
assert nb.cells[2].cell_type == 'code'
compare(nb.cells[2].source, '''1 + 2 + 3 + 4
5
6''')
assert nb.cells[3].cell_type == 'markdown'
assert nb.cells[3].source == ''
assert nb.cells[4].cell_type == 'code'
assert nb.cells[4].source == '7'
assert nb.cells[5].cell_type == 'markdown'
assert nb.cells[5].source == 'Another markdown cell'
assert nb.cells[6].cell_type == 'code'
assert nb.cells[6].source == """def f(x):
'''Sample docstring'''
return 4"""
assert len(nb.cells) == 7
script2 = jupytext.writes(nb, ext='.py', format_name='sphinx')
compare(script, script2)
def test_questions_in_unmarked_cells_are_not_uncommented_297(
text="""# This cell has no explicit marker
# question?
1 + 2
""",
nb=new_notebook(cells=[
new_code_cell(
"# This cell has no explicit marker\n# question?\n1 + 2",
metadata={"comment_questions": False},
)
]),
):
nb2 = jupytext.reads(text, "py")
compare_notebooks(nb2, nb)
text2 = jupytext.writes(nb2, "py")
compare(text2, text)
def test_pep8_bis():
text = """# This is a markdown cell
# a code cell
def f(x):
return x + 1
# And another markdown cell
# Separated from f by just one line
# As there is no code here
"""
nb = reads(text, "py")
for cell in nb.cells:
assert not cell.metadata
text2 = writes(nb, "py")
compare(text2, text)
def convert_notebook_files(nb_files,
nb_dest,
test_round_trip=False,
preserve_outputs=True):
"""
Export R markdown notebooks, python or R scripts, or Jupyter notebooks,
to the opposite format
:param nb_files: one or more notebooks files
:param nb_dest: destination file, extension ('.py') or format ('py')
:param test_round_trip: should round trip conversion be tested?
:param preserve_outputs: preserve the current outputs of .ipynb file
when possible
:return:
"""
if len(nb_files) > 1 and nb_dest not in NOTEBOOK_EXTENSIONS:
raise ValueError("Converting multiple files requires "
"that destination be one of '{}'".format(
"', '".join(NOTEBOOK_EXTENSIONS)))
for nb_file in nb_files:
file, current_ext = os.path.splitext(nb_file)
if current_ext not in NOTEBOOK_EXTENSIONS:
raise TypeError('File {} is not a notebook'.format(nb_file))
notebook = readf(nb_file)
dest, dest_ext = os.path.splitext(nb_dest)
if not dest_ext:
dest = file
if nb_dest in NOTEBOOK_EXTENSIONS:
dest_ext = nb_dest
else:
dest_ext = '.' + nb_dest
if dest_ext not in NOTEBOOK_EXTENSIONS:
raise TypeError(
'Destination extension {} is not a notebook'.format(dest_ext))
if test_round_trip:
test_round_trip_conversion(notebook, dest_ext, preserve_outputs)
if '.' in nb_dest:
save_notebook_as(notebook, nb_file, dest + dest_ext,
preserve_outputs)
elif not test_round_trip:
print(writes(notebook, ext=dest_ext))
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)