Arguments to %%R now supported in Rmd and py formats #111

HISTORY.rst

@@ -10,7 +10,7 @@ Release History
 
 - Notebook metadata is filtered - only the most common metadata are stored in the text representation (#105)
 - New config option ``additional_metadata_on_text_files`` on the content manager. Defaults to ``True``. Change its value to ``False`` to avoid creating a YAML header or cell metadata if there was none initially (#110)
-- Language magic arguments are preserved (#111)
+- Language magic arguments are preserved in R Markdown, and also supported in ``light`` and ``percent`` scripts (#111)
 - First markdown cell exported as a docstring when using the Sphinx format (#107)
 
 0.8.3 (2018-10-19)

jupytext/cell_metadata.py

@@ -236,9 +236,6 @@ def rmd_options_to_metadata(options):
         else:
             if update_metadata_from_rmd_options(name, value, metadata):
                 continue
-            if name == 'active':
-                metadata[name] = value.replace('"', '').replace("'", '')
-                continue
             try:
                 metadata[name] = _py_logical_values(value)
                 continue
@@ -251,7 +248,7 @@ def rmd_options_to_metadata(options):
     if ('active' in metadata or metadata.get('run_control', {}).get('frozen') is True) and 'eval' in metadata:
         del metadata['eval']
 
-    return language, metadata
+    return metadata.get('language') or language, metadata
 
 
 def md_options_to_metadata(options):
@@ -282,7 +279,9 @@ def try_eval_metadata(metadata, name):
     value = metadata[name]
     if not isinstance(value, (str, unicode)):
         return
-    if value.startswith('"') or value.startswith("'"):
+    if (value.startswith('"') and value.endswith('"')) or (value.startswith("'") and value.endswith("'")):
+        if name in ['active', 'magic_args', 'language']:
+            metadata[name] = value[1:-1]
         return
     if value.startswith('c(') and value.endswith(')'):
         value = '[' + value[2:-1] + ']'

jupytext/cell_reader.py

@@ -76,7 +76,6 @@ class BaseCellReader(object):
 
     cell_type = None
     language = None
-    default_language = 'python'
     default_comment_magics = None
     metadata = None
     content = []
@@ -95,6 +94,7 @@ class BaseCellReader(object):
     def __init__(self, ext, comment_magics=None):
         """Create a cell reader with empty content"""
         self.ext = ext
+        self.default_language = _SCRIPT_EXTENSIONS.get(ext, {}).get('language', 'python')
         self.comment_magics = comment_magics if comment_magics is not None else self.default_comment_magics
 
     def read(self, lines):
@@ -106,8 +106,7 @@ def read(self, lines):
         self.metadata_and_language_from_option_line(lines[0])
 
         if self.metadata and 'language' in self.metadata:
-            self.language = self.metadata['language']
-            del self.metadata['language']
+            self.language = self.metadata.pop('language')
 
         # Parse cell till its end and set content, lines_to_next_cell
         pos_next_cell = self.find_cell_content(lines)
@@ -202,10 +201,14 @@ def find_cell_content(self, lines):
         # Cell content
         source = lines[cell_start:cell_end_marker]
 
-        self.content = self.uncomment_code_and_magics(source)
+        if not is_active(self.ext, self.metadata) or \
+                ('active' not in self.metadata and self.language and self.language != self.default_language):
+            self.content = uncomment(source, self.comment if self.ext != '.R' else '#')
+        else:
+            self.content = self.uncomment_code_and_magics(source)
 
         # Exactly two empty lines at the end of cell (caused by PEP8)?
-        if (self.ext == '.py' and explicit_eoc and last_two_lines_blank(source)):
+        if self.ext == '.py' and explicit_eoc and last_two_lines_blank(source):
             self.content = source[:-2]
             self.metadata['lines_to_end_of_cell_marker'] = 2
 

jupytext/cell_to_text.py

@@ -31,21 +31,28 @@ def comment_lines(lines, prefix):
 class BaseCellExporter(object):
     """A class that represent a notebook cell as text"""
     default_comment_magics = None
+    parse_cell_language = True
 
     def __init__(self, cell, default_language, ext, comment_magics=None, cell_metadata_filter=None):
         self.ext = ext
         self.cell_type = cell.cell_type
         self.source = cell_source(cell)
         self.unfiltered_metadata = cell.metadata
         self.metadata = filter_metadata(copy(cell.metadata), cell_metadata_filter, _IGNORE_CELL_METADATA)
-        self.language, magic_args = cell_language(self.source)
-        if magic_args:
-            if ext.endswith('.Rmd'):
-                if "'" in magic_args:
-                    magic_args = '"' + magic_args + '"'
-                else:
-                    magic_args = "'" + magic_args + "'"
-            self.metadata['magic_args'] = magic_args
+        self.language, magic_args = cell_language(self.source) if self.parse_cell_language else (None, None)
+
+        if self.language:
+            if magic_args:
+                if ext.endswith('.Rmd'):
+                    if "'" in magic_args:
+                        magic_args = '"' + magic_args + '"'
+                    else:
+                        magic_args = "'" + magic_args + "'"
+                self.metadata['magic_args'] = magic_args
+
+            if not ext.endswith('.Rmd'):
+                self.metadata['language'] = self.language
+
         self.language = self.language or default_language
         self.default_language = default_language
         self.comment = _SCRIPT_EXTENSIONS.get(ext, {}).get('comment', '#')
@@ -184,10 +191,8 @@ def is_code(self):
     def code_to_text(self):
         """Return the text representation of a code cell"""
         active = is_active(self.ext, self.metadata)
-        if active and self.language != self.default_language:
+        if self.language != self.default_language and 'active' not in self.metadata:
             active = False
-            self.metadata['active'] = 'ipynb'
-            self.metadata['language'] = self.language
 
         source = copy(self.source)
         escape_code_start(source, self.ext, self.language)
@@ -282,6 +287,7 @@ class DoublePercentCellExporter(BaseCellExporter):
     """A class that can represent a notebook cell as an
     Hydrogen/Spyder/VScode script (#59)"""
     default_comment_magics = False
+    parse_cell_language = False
 
     def code_to_text(self):
         """Not used"""

jupytext/languages.py

@@ -47,9 +47,6 @@ def set_main_and_cell_language(metadata, cells, ext):
             if language != main_language and language in _JUPYTER_LANGUAGES:
                 if 'magic_args' in cell['metadata']:
                     magic_args = cell['metadata'].pop('magic_args')
-                    if (magic_args.startswith('"') and magic_args.endswith('"')) or \
-                            (magic_args.startswith("'") and magic_args.endswith("'")):
-                        magic_args = magic_args[1:-1]
                     cell['source'] = u'%%{} {}\n'.format(language, magic_args) + cell['source']
                 else:
                     cell['source'] = u'%%{}\n'.format(language) + cell['source']

tests/notebooks/mirror/ipynb_to_Rmd/Notebook_with_R_magic.Rmd

@@ -0,0 +1,39 @@
+---
+jupyter:
+  kernelspec:
+    display_name: Python 2
+    language: python
+    name: python2
+  language_info:
+    codemirror_mode:
+      name: ipython
+      version: 2
+    file_extension: .py
+    mimetype: text/x-python
+    name: python
+    nbconvert_exporter: python
+    pygments_lexer: ipython2
+    version: 2.7.11
+---
+
+# A notebook with R cells
+
+This notebook shows the use of R cells to generate plots
+
+```{python}
+# %load_ext rpy2.ipython
+```
+
+```{r}
+suppressMessages(require(tidyverse))
+```
+
+```{r}
+ggplot(iris, aes(x = Sepal.Length, y = Petal.Length, color=Species)) + geom_point()
+```
+
+The default plot dimensions are not good for us, so we use the -w and -h parameters in %%R magic to set the plot size
+
+```{r magic_args='-w 400 -h 240'}
+ggplot(iris, aes(x = Sepal.Length, y = Petal.Length, color=Species)) + geom_point()
+```

tests/notebooks/mirror/ipynb_to_percent/Notebook_with_R_magic.py

@@ -0,0 +1,40 @@
+# ---
+# jupyter:
+#   kernelspec:
+#     display_name: Python 2
+#     language: python
+#     name: python2
+#   language_info:
+#     codemirror_mode:
+#       name: ipython
+#       version: 2
+#     file_extension: .py
+#     mimetype: text/x-python
+#     name: python
+#     nbconvert_exporter: python
+#     pygments_lexer: ipython2
+#     version: 2.7.11
+# ---
+
+# %% [markdown]
+# # A notebook with R cells
+#
+# This notebook shows the use of R cells to generate plots
+
+# %%
+%load_ext rpy2.ipython
+
+# %%
+%%R
+suppressMessages(require(tidyverse))
+
+# %%
+%%R
+ggplot(iris, aes(x = Sepal.Length, y = Petal.Length, color=Species)) + geom_point()
+
+# %% [markdown]
+# The default plot dimensions are not good for us, so we use the -w and -h parameters in %%R magic to set the plot size
+
+# %%
+%%R -w 400 -h 240
+ggplot(iris, aes(x = Sepal.Length, y = Petal.Length, color=Species)) + geom_point()

tests/notebooks/mirror/ipynb_to_script/Notebook_with_R_magic.py

@@ -0,0 +1,35 @@
+# ---
+# jupyter:
+#   kernelspec:
+#     display_name: Python 2
+#     language: python
+#     name: python2
+#   language_info:
+#     codemirror_mode:
+#       name: ipython
+#       version: 2
+#     file_extension: .py
+#     mimetype: text/x-python
+#     name: python
+#     nbconvert_exporter: python
+#     pygments_lexer: ipython2
+#     version: 2.7.11
+# ---
+
+# # A notebook with R cells
+#
+# This notebook shows the use of R cells to generate plots
+
+# %load_ext rpy2.ipython
+
+# + {"language": "R"}
+# suppressMessages(require(tidyverse))
+
+# + {"language": "R"}
+# ggplot(iris, aes(x = Sepal.Length, y = Petal.Length, color=Species)) + geom_point()
+# -
+
+# The default plot dimensions are not good for us, so we use the -w and -h parameters in %%R magic to set the plot size
+
+# + {"magic_args": "-w 400 -h 240", "language": "R"}
+# ggplot(iris, aes(x = Sepal.Length, y = Petal.Length, color=Species)) + geom_point()

tests/test_contentsmanager.py

@@ -545,25 +545,28 @@ def test_metadata_filter_is_effective(nb_file, tmpdir):
     cm.root_dir = str(tmpdir)
 
     # save notebook to tmpdir
-    cm.save(model=dict(type='notebook', content=nb), path=tmp_ipynb)
+    with mock.patch('jupytext.header.INSERT_AND_CHECK_VERSION_NUMBER', True):
+        cm.save(model=dict(type='notebook', content=nb), path=tmp_ipynb)
 
     # set config
     cm.default_jupytext_formats = 'ipynb, py'
-    cm.default_notebook_metadata_filter = 'jupytext,-all'
+    cm.default_notebook_metadata_filter = 'language_info,jupytext,-all'
     cm.default_cell_metadata_filter = '-all'
 
     # load notebook
-    nb = cm.get(tmp_ipynb)['content']
+    with mock.patch('jupytext.header.INSERT_AND_CHECK_VERSION_NUMBER', True):
+        nb = cm.get(tmp_ipynb)['content']
 
     # save notebook again
     with mock.patch('jupytext.header.INSERT_AND_CHECK_VERSION_NUMBER', True):
         cm.save(model=dict(type='notebook', content=nb), path=tmp_ipynb)
 
     # read text version
-    nb2 = jupytext.readf(str(tmpdir.join(tmp_script)))
+    with mock.patch('jupytext.header.INSERT_AND_CHECK_VERSION_NUMBER', True):
+        nb2 = jupytext.readf(str(tmpdir.join(tmp_script)))
 
     # test no metadata
-    assert set(nb2.metadata.keys()) == {'jupytext'}
+    assert set(nb2.metadata.keys()) <= {'language_info', 'jupytext'}
     for cell in nb2.cells:
         assert not cell.metadata
 

tests/test_mirror.py

@@ -138,7 +138,7 @@ def test_percent_to_ipynb(nb_file):
     assert_conversion_same_as_mirror(nb_file, '.ipynb', 'script_to_ipynb', format_name='percent')
 
 
-@pytest.mark.parametrize('nb_file', list_notebooks('ipynb_py', skip='(raw|hash|frozen)'))
+@pytest.mark.parametrize('nb_file', list_notebooks('ipynb_py', skip='(raw|hash|frozen|magic)'))
 def test_ipynb_to_python_sphinx(nb_file):
     assert_conversion_same_as_mirror(nb_file, '.py', 'ipynb_to_sphinx', format_name='sphinx')
 
@@ -164,6 +164,6 @@ def test_ipynb_to_Rmd(nb_file):
     assert_conversion_same_as_mirror(nb_file, '.Rmd', 'ipynb_to_Rmd')
 
 
-@pytest.mark.parametrize('nb_file', list_notebooks('ipynb', skip='(66|frozen)'))
+@pytest.mark.parametrize('nb_file', list_notebooks('ipynb', skip='(66|frozen|magic)'))
 def test_ipynb_to_md(nb_file):
     assert_conversion_same_as_mirror(nb_file, '.md', 'ipynb_to_md')