Ignore hidden config files when allow_hidden=False (#965)

docs/CHANGELOG.md

@@ -1,6 +1,13 @@
 Jupytext ChangeLog
 ==================
 
+1.13.9 (2022-06-30)
+-------------------
+
+**Changed**
+- Hidden configuration files like `.jupytext.toml` or `.jupytext.py` are now ignored by Jupytext's contents manager when `allow_hidden=False` (that option was introduced in `jupyter_server==2.0.0a1`) ([#964](https://github.com/mwouts/jupytext/issues/964)).
+
+
 1.13.8 (2022-04-04)
 -------------------
 

jupytext/contentsmanager.py

@@ -504,6 +504,11 @@ def get_config_file(self, directory):
             for jupytext_config_file in JUPYTEXT_CONFIG_FILES:
                 path = directory + "/" + jupytext_config_file
                 if self.file_exists(path):
+                    if not self.allow_hidden and jupytext_config_file.startswith("."):
+                        self.log.warning(
+                            f"Ignoring config file {path} (see Jupytext issue #964)"
+                        )
+                        continue
                     return path
 
             pyproject_path = directory + "/" + PYPROJECT_FILE
@@ -529,10 +534,16 @@ def load_config_file(self, config_file, is_os_path=False):
             if config_file.endswith(".py") and not is_os_path:
                 config_file = self._get_os_path(config_file)
                 is_os_path = True
-            if is_os_path:
-                return load_jupytext_configuration_file(config_file)
-            model = self.super.get(config_file, content=True, type="file")
-            return load_jupytext_configuration_file(config_file, model["content"])
+
+            config_content = None
+            if not is_os_path:
+                try:
+                    model = self.super.get(config_file, content=True, type="file")
+                    config_content = model["content"]
+                except HTTPError:
+                    pass
+
+            return load_jupytext_configuration_file(config_file, config_content)
 
         def get_config(self, path, use_cache=False):
             """Return the Jupytext configuration for the given path"""
@@ -548,9 +559,7 @@ def get_config(self, path, use_cache=False):
                         self.cached_config.config = self.load_config_file(config_file)
                     else:
                         config_file = find_global_jupytext_configuration_file()
-                        self.cached_config.config = self.load_config_file(
-                            config_file, True
-                        )
+                        self.cached_config.config = self.load_config_file(config_file)
                     self.cached_config.config_file = config_file
                     self.cached_config.path = parent_dir
                 except JupytextConfigurationError as err:

jupytext/version.py

@@ -1,3 +1,3 @@
 """Jupytext's version number"""
 
-__version__ = "1.13.8"
+__version__ = "1.13.9-dev"

tests/test_cli.py

@@ -1174,6 +1174,11 @@ def no_warning():
             "and will be removed in a future release" in str(record.message)
         ):
             continue  # pragma: no cover
+        if (
+            "unclosed event loop <_UnixSelectorEventLoop running=False closed=False debug=False>"
+            in str(record.message)
+        ):
+            continue  # pragma: no cover
         raise RuntimeError(record)
 
 

tests/test_cm_config.py

@@ -24,7 +24,7 @@ def test_local_config_overrides_cm_config(tmpdir):
     cm.formats = "ipynb,py"
 
     nested = tmpdir.mkdir("nested")
-    with open(str(nested.join(".jupytext.yml")), "w") as fp:
+    with open(str(nested.join("jupytext.yml")), "w") as fp:
         fp.write("formats: ''\n")
 
     cm.save(notebook_model(SAMPLE_NOTEBOOK), "notebook.ipynb")
@@ -61,7 +61,7 @@ def test_pairing_through_config_leaves_ipynb_unmodified(tmpdir):
     cm = jupytext.TextFileContentsManager()
     cm.root_dir = str(tmpdir)
 
-    cfg_file = tmpdir.join(".jupytext.yml")
+    cfg_file = tmpdir.join("jupytext.yml")
     nb_file = tmpdir.join("notebook.ipynb")
     py_file = tmpdir.join("notebook.py")
 
@@ -84,8 +84,6 @@ def test_pairing_through_config_leaves_ipynb_unmodified(tmpdir):
         ("jupytext.toml", "not_a_jupytext_option = true"),
         ("pyproject.toml", "[tool.jupytext]\nnot_a_jupytext_option = true"),
         ("jupytext.json", '{"notebook_metadata_filter":"-all",}'),
-        (".jupytext.py", "c.not_a_jupytext_option = True"),
-        (".jupytext.py", "c.hide_notebook_metadata = true"),
     ],
 )
 @pytest.mark.filterwarnings(
@@ -199,7 +197,7 @@ def test_test_no_text_representation_metadata_in_ipynb_900(
     tmpdir,
     python_notebook,
 ):
-    tmpdir.join(".jupytext.toml").write('formats = "ipynb,py:percent"\n')
+    tmpdir.join("jupytext.toml").write('formats = "ipynb,py:percent"\n')
 
     # create a test notebook and save it in Jupyter
     nb = python_notebook

tests/test_pre_commit_1_sync_with_config.py

@@ -34,7 +34,7 @@ def test_pre_commit_hook_sync_with_config(
     tmp_repo.git.add(".pre-commit-config.yaml")
     pre_commit(["install", "--install-hooks", "-f"])
 
-    tmpdir.join(".jupytext.toml").write('formats = "ipynb,py:percent"\n')
+    tmpdir.join("jupytext.toml").write('formats = "ipynb,py:percent"\n')
 
     # create a test notebook and save it in Jupyter
     nb = python_notebook

tests/test_pre_commit_3_sync_black_nbstripout.py

@@ -46,8 +46,8 @@ def test_pre_commit_hook_sync_black_nbstripout(
     tmp_repo.git.add(".pre-commit-config.yaml")
     pre_commit(["install", "--install-hooks", "-f"])
 
-    tmpdir.join(".jupytext.toml").write('formats = "ipynb,py:percent"')
-    tmp_repo.git.add(".jupytext.toml")
+    tmpdir.join("jupytext.toml").write('formats = "ipynb,py:percent"')
+    tmp_repo.git.add("jupytext.toml")
     tmp_repo.index.commit("pair notebooks")
 
     # write a test notebook

tests/test_pre_commit_5_reformat_markdown.py

@@ -55,8 +55,8 @@ def test_pre_commit_hook_sync_reformat_code_and_markdown(
     tmp_repo.git.add(".pre-commit-config.yaml")
     pre_commit(["install", "--install-hooks", "-f"])
 
-    tmpdir.join(".jupytext.toml").write('formats = "ipynb,py:percent"')
-    tmp_repo.git.add(".jupytext.toml")
+    tmpdir.join("jupytext.toml").write('formats = "ipynb,py:percent"')
+    tmp_repo.git.add("jupytext.toml")
     tmp_repo.index.commit("pair notebooks")
 
     # write a test notebook

tests/test_pre_commit_mode.py

@@ -65,7 +65,7 @@ def test_alert_untracked_alerts_when_using_sync(tmpdir, cwd_tmpdir, tmp_repo, ca
     tmpdir.join("test.py").write("print('hello')\n")
     tmp_repo.git.add("test.py")
 
-    tmpdir.join(".jupytext.toml").write('formats = "ipynb,py"')
+    tmpdir.join("jupytext.toml").write('formats = "ipynb,py"')
 
     # Run jupytext
     status = jupytext(["--sync", "--pre-commit-mode", "test.py"])
@@ -133,7 +133,7 @@ def test_alert_inconsistent_versions(tmpdir, cwd_tmpdir, tmp_repo, capsys):
 
 
 def test_pre_commit_local_config(tmpdir, cwd_tmpdir, tmp_repo, python_notebook, capsys):
-    tmpdir.join(".jupytext.toml").write_text(
+    tmpdir.join("jupytext.toml").write_text(
         """notebook_metadata_filter = "-all"
 cell_metadata_filter = "-all"
 formats = "ipynb,py:percent"