Fix the handling of bibliography sections (mwouts#1180)

in R Markdown notebooks

src/jupytext/cell_reader.py

@@ -443,9 +443,12 @@ def find_cell_end(self, lines):
                         return i - 1, i, False
                     return i, i, False
 
-                if self.start_code_re.match(line) and not line.startswith(
-                    "```{bibliography}"
-                ):
+                if self.start_code_re.match(line):
+                    if line.startswith("```{bibliography}"):
+                        in_explicit_code_block = True
+                        prev_blank = 0
+                        continue
+
                     # Cells with a .noeval attribute are markdown cells #347
                     _, metadata = self.options_to_metadata(
                         self.start_code_re.findall(line)[0]

tests/functional/simple_notebooks/test_read_simple_rmd.py

@@ -274,10 +274,16 @@ def test_bibliography_in_rmd(
 
 ```{bibliography}
 ```
+
+```{r}
+6
+```
 """,
 ):
     nb = jupytext.reads(rmd, fmt="Rmd")
-    assert len(nb.cells) == 1, nb.cells
+    assert len(nb.cells) == 2, nb.cells
     assert nb.cells[0].cell_type == "markdown"
+    assert nb.cells[1].cell_type == "code"
+    assert nb.cells[1].source == "6"
     rmd2 = jupytext.writes(nb, fmt="Rmd")
     compare(rmd2, rmd)