Quote strings in Rmd chunk options

CHANGELOG.md

@@ -35,6 +35,7 @@
 - `jupytext --test textfile.ext` now really compares the text file to its round trip (rather than the corresponding notebook) (#339)
 - Markdown cells that contain code are now preserved in a round trip through the Markdown and R Markdown formats (#361)
 - Code cells with a `%%python3` cell magic are now preserved in a round trip through the Markdown format (#365)
+- Strings in the metadata of code cells are quoted in the Rmd representation. And we escape R code in chunk options with `#R_CODE#` (#383)
 
 
 1.2.4 (2019-09-19)

jupytext/cell_metadata.py

@@ -103,6 +103,13 @@ def metadata_to_rmd_options(language, metadata, use_runtools=False):
             options += ' {}={},'.format(
                 opt_name, 'c({})'.format(
                     ', '.join(['"{}"'.format(str(v)) for v in opt_value])))
+        elif isinstance(opt_value, (str, unicode)):
+            if opt_value.startswith('#R_CODE#'):
+                options += ' {}={},'.format(opt_name, opt_value[8:])
+            elif '"' not in opt_value:
+                options += ' {}="{}",'.format(opt_name, opt_value)
+            else:
+                options += " {}='{}',".format(opt_name, opt_value)
         else:
             options += ' {}={},'.format(opt_name, str(opt_value))
     if not language:
@@ -267,13 +274,12 @@ def metadata_to_md_options(metadata):
 
 
 def try_eval_metadata(metadata, name):
-    """Evaluate given metadata to a python object, if possible"""
+    """Evaluate the metadata to a python object, if possible"""
     value = metadata[name]
     if not isinstance(value, (str, unicode)):
         return
     if (value.startswith('"') and value.endswith('"')) or (value.startswith("'") and value.endswith("'")):
-        if name in ['active', 'magic_args', 'language']:
-            metadata[name] = value[1:-1]
+        metadata[name] = value[1:-1]
         return
     if value.startswith('c(') and value.endswith(')'):
         value = '[' + value[2:-1] + ']'
@@ -282,6 +288,8 @@ def try_eval_metadata(metadata, name):
     try:
         metadata[name] = ast.literal_eval(value)
     except (SyntaxError, ValueError):
+        if name != 'name':
+            metadata[name] = '#R_CODE#' + value
         return
 
 

jupytext/cell_to_text.py

@@ -41,9 +41,6 @@ def __init__(self, cell, default_language, fmt=None):
 
         if self.language:
             if magic_args:
-                if self.ext.endswith('.Rmd'):
-                    quote = '"' if "'" in magic_args else "'"
-                    magic_args = quote + magic_args + quote
                 self.metadata['magic_args'] = magic_args
 
             if not self.ext.endswith('.Rmd'):

tests/notebooks/mirror/ipynb_to_Rmd/Notebook with metadata and long cells.Rmd

@@ -49,6 +49,6 @@ This is a markdown cell with cell metadata `{"key": "value"}`
 """This is a code cell with metadata `{"tags":["parameters"], ".class":null}`"""
 ```
 
-```{python key=value, active="", eval=FALSE}
+```{python key="value", active="", eval=FALSE}
 This is a raw cell with cell metadata `{"key": "value"}`
 ```

tests/notebooks/mirror/ipynb_to_Rmd/Notebook_with_R_magic.Rmd

@@ -24,6 +24,6 @@ ggplot(iris, aes(x = Sepal.Length, y = Petal.Length, color=Species)) + geom_poin
 
 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'}
+```{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_Rmd/Notebook_with_more_R_magic_111.Rmd

@@ -20,7 +20,7 @@ df = pd.DataFrame(
 )
 ```
 
-```{r magic_args='-i df'}
+```{r magic_args="-i df"}
 library("ggplot2")
 ggplot(data = df) + geom_point(aes(x = X, y = Y, color = Letter, size = Z))
 ```

tests/notebooks/mirror/ipynb_to_Rmd/The flavors of raw cells.Rmd

@@ -6,23 +6,23 @@ jupyter:
     name: python3
 ---
 
-```{python raw_mimetype=text/latex, active="", eval=FALSE}
+```{python raw_mimetype="text/latex", active="", eval=FALSE}
 $1+1$
 ```
 
-```{python raw_mimetype=text/restructuredtext, active="", eval=FALSE}
+```{python raw_mimetype="text/restructuredtext", active="", eval=FALSE}
 :math:`1+1`
 ```
 
-```{python raw_mimetype=text/html, active="", eval=FALSE}
+```{python raw_mimetype="text/html", active="", eval=FALSE}
 <b>Bold text<b>
 ```
 
-```{python raw_mimetype=text/markdown, active="", eval=FALSE}
+```{python raw_mimetype="text/markdown", active="", eval=FALSE}
 **Bold text**
 ```
 
-```{python raw_mimetype=text/x-python, active="", eval=FALSE}
+```{python raw_mimetype="text/x-python", active="", eval=FALSE}
 1 + 1
 ```
 

tests/test_cell_metadata.py

@@ -8,19 +8,19 @@
 
 SAMPLES = [('r', ('R', {})),
            ('r plot_1, dpi=72, fig.path="fig_path/"',
-            ('R', {'name': 'plot_1', 'dpi': 72, 'fig.path': '"fig_path/"'})),
-           ("r plot_1, bool=TRUE, fig.path='fig_path/'",
+            ('R', {'name': 'plot_1', 'dpi': 72, 'fig.path': 'fig_path/'})),
+           ('r plot_1, bool=TRUE, fig.path="fig_path/"',
             ('R', {'name': 'plot_1', 'bool': True,
-                   'fig.path': "'fig_path/'"})),
+                   'fig.path': 'fig_path/'})),
            ('r echo=FALSE',
             ('R', {'tags': ['remove_input']})),
            ('r plot_1, echo=TRUE',
             ('R', {'name': 'plot_1', 'echo': True})),
            ('python echo=if a==5 then TRUE else FALSE',
-            ('python', {'echo': 'if a==5 then TRUE else FALSE'})),
+            ('python', {'echo': '#R_CODE#if a==5 then TRUE else FALSE'})),
            ('python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}',
             ('python', {'name': 'noname', 'tags': ['a', 'b', 'c'],
-                        'echo': '{sum(a+c(1,2))>1}'})),
+                        'echo': '#R_CODE#{sum(a+c(1,2))>1}'})),
            ('python active="ipynb,py"',
             ('python', {'active': 'ipynb,py'})),
            ('python include=FALSE, active="Rmd"',

tests/test_read_simple_rmd.py

@@ -24,7 +24,7 @@ def test_read_mostly_py_rmd_file(rmd="""---
 ls()
 ```
 
-```{r, results='asis', magic_args='-i x'}
+```{r, results="asis", magic_args="-i x"}
 cat(stringi::stri_rand_lipsum(3), sep='\n\n')
 ```
 """):
@@ -49,7 +49,7 @@ def test_read_mostly_py_rmd_file(rmd="""---
                         'source': '%%R\nls()',
                         'outputs': []},
                        {'cell_type': 'code',
-                        'metadata': {'results': "'asis'"},
+                        'metadata': {'results': 'asis'},
                         'execution_count': None,
                         'source': "%%R -i x\ncat(stringi::"
                                   "stri_rand_lipsum(3), sep='\n\n')",
@@ -99,3 +99,23 @@ def test_tags_in_rmd(rmd='''---
 ''', nb=new_notebook(cells=[new_code_cell('p = 1', metadata={'tags': ['parameters']})])):
     nb2 = jupytext.reads(rmd, 'Rmd')
     compare_notebooks(nb2, nb)
+
+
+def round_trip_cell_metadata(cell_metadata):
+    nb = new_notebook(metadata={'jupytext': {'main_language': 'python'}},
+                      cells=[new_code_cell('1 + 1', metadata=cell_metadata)])
+    text = jupytext.writes(nb, 'Rmd')
+    nb2 = jupytext.reads(text, 'Rmd')
+    compare_notebooks(nb2, nb)
+
+
+def test_comma_in_metadata(cell_metadata={'a': 'b, c'}):
+    round_trip_cell_metadata(cell_metadata)
+
+
+def test_dict_in_metadata(cell_metadata={'a': {'b': 'c'}}):
+    round_trip_cell_metadata(cell_metadata)
+
+
+def test_list_in_metadata(cell_metadata={'d': ['e']}):
+    round_trip_cell_metadata(cell_metadata)