Use notebook_extensions from the config file if set #746

docs/CHANGELOG.md

@@ -5,7 +5,8 @@ Jupytext ChangeLog
 -------------------
 
 **Fixed**
-- The `jupytext.toml` can now be used together with the `jupytext` pre-commit hook ([#752](https://github.com/mwouts/jupytext/issues/752))
+- The `jupytext.toml` config file can now be used together with the `jupytext` pre-commit hook ([#752](https://github.com/mwouts/jupytext/issues/752))
+- The `notebook_extensions` option of the `jupytext.toml` file now works ([#746](https://github.com/mwouts/jupytext/issues/746))
 
 **Changed**
 - The options in `jupytext.toml` where renamed to match the `jupytext` metadata in the text notebooks. One should now use `formats` rather than `default_jupytext_formats` and `notebook_metadata_filter` rather than `default_notebook_metadata_filter` ([#753](https://github.com/mwouts/jupytext/issues/753))

jupytext/config.py

@@ -53,11 +53,10 @@ class JupytextConfiguration(Configurable):
         config=True,
     )
     default_jupytext_formats = Unicode(
-        "", help="Deprecated. Use 'formats' instead", config=True
+        help="Deprecated. Use 'formats' instead", config=True
     )
 
     preferred_jupytext_formats_save = Unicode(
-        u"",
         help="Preferred format when saving notebooks as text, per extension. "
         'Use "jl:percent,py:percent,R:percent" if you want to save '
         "Julia, Python and R scripts in the double percent format and "
@@ -66,15 +65,13 @@ class JupytextConfiguration(Configurable):
     )
 
     preferred_jupytext_formats_read = Unicode(
-        u"",
         help="Preferred format when reading notebooks from text, per "
         'extension. Use "py:sphinx" if you want to read all python '
         "scripts as Sphinx gallery scripts.",
         config=True,
     )
 
     notebook_metadata_filter = Unicode(
-        u"",
         help="Notebook metadata that should be save in the text representations. "
         "Examples: 'all', '-all', 'widgets,nteract', 'kernelspec,jupytext-all'",
         config=True,
@@ -100,7 +97,6 @@ class JupytextConfiguration(Configurable):
     )
 
     cell_metadata_filter = Unicode(
-        u"",
         help="Cell metadata that should be saved in the text representations. "
         "Examples: 'all', 'hide_input,hide_output'",
         config=True,
@@ -145,24 +141,22 @@ class JupytextConfiguration(Configurable):
     )
 
     cell_markers = Unicode(
-        u"",
         help='Start and end cell markers for the light format, comma separated. Use "{{{,}}}" to mark cells'
         'as foldable regions in Vim, and "region,endregion" to mark cells as Vscode/PyCharm regions',
         config=True,
     )
 
     default_cell_markers = Unicode(
-        "", help="Deprecated. Use 'cell_markers' instead", config=True
+        help="Deprecated. Use 'cell_markers' instead", config=True
     )
 
-    notebook_extensions = Unicode(
-        u",".join(NOTEBOOK_EXTENSIONS),
-        help="A comma separated list of notebook extensions",
+    notebook_extensions = Union(
+        [List(Unicode(), NOTEBOOK_EXTENSIONS), Unicode()],
+        help="A list of notebook extensions",
         config=True,
     )
 
     custom_cell_magics = Unicode(
-        "",
         help='A comma separated list of cell magics. Use e.g. custom_cell_magics = "configure,local" '
         'if you want code cells starting with the Spark magic cell commands "configure" and "local" '
         "to be commented out when converted to scripts.",
@@ -377,6 +371,8 @@ def load_jupytext_configuration_file(config_file, stream=None):
             for prefix, fmt in config.formats.items()
         ]
     config.formats = short_form_multiple_formats(config.formats)
+    if isinstance(config.notebook_extensions, str):
+        config.notebook_extensions = config.notebook_extensions.split(",")
     return config
 
 

jupytext/contentsmanager.py

@@ -63,11 +63,11 @@ def __init__(self, *args, **kwargs):
             self.super = super(JupytextContentsManager, self)
             self.super.__init__(*args, **kwargs)
 
-        def all_nb_extensions(self):
+        def all_nb_extensions(self, config):
             """All extensions that should be classified as notebooks"""
             return [
                 ext if ext.startswith(".") else "." + ext
-                for ext in self.notebook_extensions.split(",")
+                for ext in config.notebook_extensions
             ]
 
         def drop_paired_notebook(self, path):
@@ -192,11 +192,14 @@ def get(
             if (
                 not self.file_exists(path)
                 or self.dir_exists(path)
-                or (type != "notebook" if type else ext not in self.all_nb_extensions())
+                or (type is not None and type != "notebook")
             ):
                 return self.super.get(path, content, type, format)
 
             config = self.get_config(path, use_cache=content is False)
+            if ext not in self.all_nb_extensions(config):
+                return self.super.get(path, content, type, format)
+
             fmt = preferred_format(ext, config.preferred_jupytext_formats_read)
             if ext == ".ipynb":
                 model = self.super.get(path, content, type="notebook", format=format)
@@ -371,7 +374,8 @@ def new_untitled(self, path="", type="", ext=""):
                 raise HTTPError(404, "No such directory: %s" % path)
 
             untitled = self.untitled_notebook
-            name = self.increment_notebook_filename(untitled + ext, path)
+            config = self.get_config(path)
+            name = self.increment_notebook_filename(config, untitled + ext, path)
             path = u"{0}/{1}".format(path, name)
 
             model = {"type": "notebook"}
@@ -383,7 +387,7 @@ def new_untitled(self, path="", type="", ext=""):
 
             return self.new(model, path)
 
-        def increment_notebook_filename(self, filename, path=""):
+        def increment_notebook_filename(self, config, filename, path=""):
             """Increment a notebook filename until it is unique, regardless of extension"""
             # Extract the full suffix from the filename (e.g. .tar.gz)
             path = path.strip("/")
@@ -399,7 +403,7 @@ def increment_notebook_filename(self, filename, path=""):
                 name = basename_i + ext
                 if not any(
                     self.exists(u"{}/{}{}".format(path, basename_i, nb_ext))
-                    for nb_ext in self.notebook_extensions.split(",")
+                    for nb_ext in config.notebook_extensions
                 ):
                     break
             return name
@@ -533,6 +537,8 @@ def get_config(self, path, use_cache=False):
                     self.cached_config.config_file,
                 )
                 return self.cached_config.config
+            if isinstance(self.notebook_extensions, str):
+                self.notebook_extensions = self.notebook_extensions.split(",")
             return self
 
     return JupytextContentsManager

tests/test_contentsmanager.py

@@ -1562,20 +1562,36 @@ def test_save_file_with_cell_markers(tmpdir):
     assert nb2.metadata["jupytext"]["cell_markers"] == "region,endregion"
 
 
-def test_notebook_extensions(tmpdir):
-    tmp_py = str(tmpdir.join("script.py"))
-    tmp_rmd = str(tmpdir.join("notebook.Rmd"))
-    tmp_ipynb = str(tmpdir.join("notebook.ipynb"))
+def test_notebook_extensions(tmpdir, cwd_tmpdir):
+    nb = new_notebook()
+    write(nb, "script.py")
+    write(nb, "notebook.Rmd")
+    write(nb, "notebook.ipynb")
+
+    cm = jupytext.TextFileContentsManager()
+    cm.root_dir = str(tmpdir)
+    cm.notebook_extensions = "ipynb,Rmd"
 
+    model = cm.get("notebook.ipynb")
+    assert model["type"] == "notebook"
+
+    model = cm.get("notebook.Rmd")
+    assert model["type"] == "notebook"
+
+    model = cm.get("script.py")
+    assert model["type"] == "file"
+
+
+def test_notebook_extensions_in_config(tmpdir, cwd_tmpdir):
     nb = new_notebook()
-    write(nb, tmp_py)
-    write(nb, tmp_rmd)
-    write(nb, tmp_ipynb)
+    write(nb, "script.py")
+    write(nb, "notebook.Rmd")
+    write(nb, "notebook.ipynb")
+    tmpdir.join("jupytext.toml").write("""notebook_extensions = ["ipynb", "Rmd"]""")
 
     cm = jupytext.TextFileContentsManager()
     cm.root_dir = str(tmpdir)
 
-    cm.notebook_extensions = "ipynb,Rmd"
     model = cm.get("notebook.ipynb")
     assert model["type"] == "notebook"