def test_python_kernel_preserves_R_files(nb_file, tmpdir):
"""Opening a R file with a Jupyter server that has no R kernel should not modify the file"""
tmp_r_file = str(tmpdir.join('script.R'))
with open(nb_file) as fp:
script = fp.read()
with open(tmp_r_file, 'w') as fp:
fp.write(script)
# create contents manager
cm = jupytext.TextFileContentsManager()
cm.root_dir = str(tmpdir)
# open notebook, set Python kernel and save
model = cm.get('script.R')
model['content'].metadata['kernelspec'] = kernelspec_from_language(
'python')
cm.save(model=model, path='script.R')
with open(tmp_r_file) as fp:
script2 = fp.read()
compare(script, script2)
def read(cls, path):
resolved_path, fmt = cls.extract_format(path)
text = _resolved_handler(resolved_path).read(resolved_path)
# Read the document
nb = jupytext.reads(text, fmt=fmt)
# Set a kernel if there was none
if nb.metadata.get('kernelspec', {}).get('name') is None:
language = nb.metadata.get('jupytext', {}).get(
'main_language') or nb.metadata['kernelspec']['language']
if not language:
raise ValueError(
'Cannot infer a kernel as the document language is not defined'
)
kernelspec = kernelspec_from_language(language)
if not kernelspec:
raise ValueError('Found no kernel for {}'.format(language))
nb.metadata['kernelspec'] = kernelspec
# Return the notebook as a JSON string
return nbformat.writes(nb)
reason="isort not found")
requires_flake8 = pytest.mark.skipif(not tool_version("flake8"),
reason="flake8 not found")
requires_autopep8 = pytest.mark.skipif(not tool_version("autopep8"),
reason="autopep8 not found")
requires_nbconvert = pytest.mark.skipif(not tool_version("jupyter nbconvert"),
reason="nbconvert not found")
requires_sphinx_gallery = pytest.mark.skipif(
not rst2md, reason="sphinx_gallery is not available")
requires_pandoc = pytest.mark.skipif(
not is_pandoc_available() or sys.version_info < (3, ),
reason="pandoc>=2.7.2 is not available",
)
requires_no_pandoc = pytest.mark.skipif(is_pandoc_available(),
reason="Pandoc is installed")
requires_ir_kernel = pytest.mark.skipif(kernelspec_from_language("R") is None,
reason="irkernel is not installed")
requires_myst = pytest.mark.skipif(not is_myst_available(),
reason="myst_parser not found")
requires_no_myst = pytest.mark.skipif(is_myst_available(),
reason="myst is available")
skip_on_windows = pytest.mark.skipif(sys.platform.startswith("win"),
reason="Issue 489")
def list_notebooks(path="ipynb", skip="World"):
"""All notebooks in the directory notebooks/path,
or in the package itself"""
if path == "ipynb":
return (list_notebooks("ipynb_julia", skip=skip) +
list_notebooks("ipynb_py", skip=skip) +