Filter the text_representation metadata in the contents manager (#903)

* Drop the text_information metadata in ipynb files
both in jupytext.write and in the contents manager
* Format suffix may start with '.', '-' or '_'

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018-2021 Marc Wouts
+Copyright (c) 2018-2022 Marc Wouts
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

docs/CHANGELOG.md

@@ -1,6 +1,16 @@
 Jupytext ChangeLog
 ==================
 
+1.13.6 (2022-01-11)
+-------------------
+
+**Fixed**
+- The `text_representation` metadata of text notebooks is filtered from `.ipynb` files both in `jupytext.write` and in the contents manager for Jupyter ([#900](https://github.com/mwouts/jupytext/issues/900))
+
+**Changed**
+- Jupytext will not issue a warning when a format suffix starting with '.', '-' or '_' is passed to the `--to` option ([#901](https://github.com/mwouts/jupytext/issues/901))
+
+
 1.13.5 (2021-12-27)
 -------------------
 

jupytext/cli.py

@@ -452,7 +452,8 @@ def fmt_if_not_ipynb(nb):
         not args.output
         and args.output_format
         and "." in args.output_format
-        and not args.output_format.startswith(".")
+        # a suffix is expected to start with one of these characters #901
+        and not args.output_format.startswith((".", "-", "_"))
         and "//" not in args.output_format
     ):
 
@@ -461,7 +462,7 @@ def single_line(msg, *args, **kwargs):
 
         warnings.formatwarning = single_line
         warnings.warn(
-            "You have passed a file name to the '--to' option, "
+            "You might have passed a file name to the '--to' option, "
             "when a format description was expected. Maybe you want to use the '-o' option instead?"
         )
 

jupytext/contentsmanager.py

@@ -14,8 +14,6 @@
 except ImportError:
     pass
 
-import jupytext
-
 from .config import (
     JUPYTEXT_CONFIG_FILES,
     PYPROJECT_FILE,
@@ -31,6 +29,7 @@
     short_form_multiple_formats,
     short_form_one_format,
 )
+from .jupytext import drop_text_representation_metadata, reads, writes
 from .kernels import set_kernelspec_from_language
 from .paired_paths import (
     InconsistentPath,
@@ -140,7 +139,15 @@ def save_one_file(path, fmt):
 
                     self.create_prefix_dir(path, fmt)
                     if fmt["extension"] == ".ipynb":
-                        return self.super.save(model, path)
+                        return self.super.save(
+                            dict(
+                                type="notebook",
+                                content=drop_text_representation_metadata(
+                                    model["content"]
+                                ),
+                            ),
+                            path,
+                        )
 
                     if (
                         model["content"]["metadata"]
@@ -158,7 +165,7 @@ def save_one_file(path, fmt):
                     text_model = dict(
                         type="file",
                         format="text",
-                        content=jupytext.writes(
+                        content=writes(
                             nbformat.from_dict(model["content"]), fmt=fmt, config=config
                         ),
                     )
@@ -211,7 +218,7 @@ def get(
                     model["format"] = "json"
                     model["mimetype"] = None
                     try:
-                        model["content"] = jupytext.reads(
+                        model["content"] = reads(
                             model["content"], fmt=fmt, config=config
                         )
                     except Exception as err:
@@ -294,7 +301,7 @@ def read_one_file(alt_path, alt_fmt):
                 text = self.super.get(
                     alt_path, content=True, type="file", format=format
                 )["content"]
-                return jupytext.reads(text, fmt=alt_fmt, config=config)
+                return reads(text, fmt=alt_fmt, config=config)
 
             inputs, outputs = latest_inputs_and_outputs(
                 path, fmt, formats, get_timestamp, contents_manager_mode=True

jupytext/jupytext.py

@@ -454,20 +454,9 @@ def writes(notebook, fmt, version=nbformat.NO_CONVERT, config=None, **kwargs):
     ext = fmt["extension"]
     format_name = fmt.get("format_name")
 
-    jupytext_metadata = metadata.get("jupytext", {})
-
     if ext == ".ipynb":
-        # Remove jupytext section if empty
-        jupytext_metadata.pop("text_representation", {})
-        if not jupytext_metadata:
-            metadata.pop("jupytext", {})
         return nbformat.writes(
-            NotebookNode(
-                nbformat=notebook.nbformat,
-                nbformat_minor=notebook.nbformat_minor,
-                metadata=metadata,
-                cells=notebook.cells,
-            ),
+            drop_text_representation_metadata(notebook, metadata),
             version,
             **kwargs,
         )
@@ -483,6 +472,27 @@ def writes(notebook, fmt, version=nbformat.NO_CONVERT, config=None, **kwargs):
     return writer.writes(notebook, metadata)
 
 
+def drop_text_representation_metadata(notebook, metadata=None):
+    """When the notebook is saved to an ipynb file, we drop the text_representation metadata"""
+    if metadata is None:
+        # Make a copy to avoid modification by reference
+        metadata = deepcopy(notebook["metadata"])
+
+    jupytext_metadata = metadata.get("jupytext", {})
+    jupytext_metadata.pop("text_representation", {})
+
+    # Remove the jupytext section if empty
+    if not jupytext_metadata:
+        metadata.pop("jupytext", {})
+
+    return NotebookNode(
+        nbformat=notebook["nbformat"],
+        nbformat_minor=notebook["nbformat_minor"],
+        metadata=metadata,
+        cells=notebook["cells"],
+    )
+
+
 def write(nb, fp, version=nbformat.NO_CONVERT, fmt=None, config=None, **kwargs):
     """Write a notebook to a file name or a file object
 

jupytext/version.py

@@ -1,3 +1,3 @@
 """Jupytext's version number"""
 
-__version__ = "1.13.5"
+__version__ = "1.13.6"

tests/test_cm_config.py

@@ -8,6 +8,7 @@
 from tornado.web import HTTPError
 
 import jupytext
+from jupytext import TextFileContentsManager
 from jupytext.compare import compare_cells
 
 from .utils import notebook_model
@@ -192,3 +193,32 @@ def test_metadata_filter_from_config_has_precedence_over_notebook_metadata(
 
     py = tmpdir.join("test.py").read()
     assert "notebook_metadata_filter: all" in py
+
+
+def test_test_no_text_representation_metadata_in_ipynb_900(
+    tmpdir,
+    python_notebook,
+):
+    tmpdir.join(".jupytext.toml").write('formats = "ipynb,py:percent"\n')
+
+    # create a test notebook and save it in Jupyter
+    nb = python_notebook
+    cm = TextFileContentsManager()
+    cm.root_dir = str(tmpdir)
+    cm.save(dict(type="notebook", content=nb), "test.ipynb")
+
+    # Assert that "text_representation" is in the Jupytext metadata #900
+    assert "text_representation" in tmpdir.join("test.py").read()
+    # But not in the ipynb notebook
+    assert "text_representation" not in tmpdir.join("test.ipynb").read()
+
+    # modify the ipynb file in Jupyter
+    # Reload the notebook
+    nb = cm.get("test.ipynb")["content"]
+    nb.cells.append(new_markdown_cell("A new cell"))
+    cm.save(dict(type="notebook", content=nb), "test.ipynb")
+
+    # The text representation metadata is in the py file
+    assert "text_representation" in tmpdir.join("test.py").read()
+    # But not in the ipynb notebook
+    assert "text_representation" not in tmpdir.join("test.ipynb").read()

tests/test_pre_commit_1_sync_with_config.py

@@ -0,0 +1,88 @@
+import pytest
+from git.exc import HookExecutionError
+from nbformat.v4.nbbase import new_markdown_cell
+from pre_commit.main import main as pre_commit
+
+from jupytext import TextFileContentsManager, read
+
+from .utils import (
+    skip_pre_commit_tests_on_windows,
+    skip_pre_commit_tests_when_jupytext_folder_is_not_a_git_repo,
+)
+
+
+@skip_pre_commit_tests_on_windows
+@skip_pre_commit_tests_when_jupytext_folder_is_not_a_git_repo
+def test_pre_commit_hook_sync_with_config(
+    tmpdir,
+    cwd_tmpdir,
+    tmp_repo,
+    jupytext_repo_root,
+    jupytext_repo_rev,
+    python_notebook,
+):
+    pre_commit_config_yaml = f"""
+repos:
+- repo: {jupytext_repo_root}
+  rev: {jupytext_repo_rev}
+  hooks:
+  - id: jupytext
+    args: [--sync]
+"""
+    tmpdir.join(".pre-commit-config.yaml").write(pre_commit_config_yaml)
+
+    tmp_repo.git.add(".pre-commit-config.yaml")
+    pre_commit(["install", "--install-hooks", "-f"])
+
+    tmpdir.join(".jupytext.toml").write('formats = "ipynb,py:percent"\n')
+
+    # create a test notebook and save it in Jupyter
+    nb = python_notebook
+    cm = TextFileContentsManager()
+    cm.root_dir = str(tmpdir)
+    cm.save(dict(type="notebook", content=nb), "test.ipynb")
+
+    # Assert that "text_representation" is in the Jupytext metadata #900
+    assert "text_representation" in tmpdir.join("test.py").read()
+    # But not in the ipynb notebook
+    assert "text_representation" not in tmpdir.join("test.ipynb").read()
+
+    # try to commit it, should fail as the py version hasn't been added
+    tmp_repo.git.add("test.ipynb")
+    with pytest.raises(
+        HookExecutionError,
+        match="git add test.py",
+    ):
+        tmp_repo.index.commit("failing")
+
+    # add the py file, now the commit will succeed
+    tmp_repo.git.add("test.py")
+    tmp_repo.index.commit("passing")
+    assert "test.ipynb" in tmp_repo.tree()
+    assert "test.py" in tmp_repo.tree()
+
+    # The text representation metadata is still in the py file
+    assert "text_representation" in tmpdir.join("test.py").read()
+    # But not in the ipynb notebook
+    assert "text_representation" not in tmpdir.join("test.ipynb").read()
+
+    # modify the ipynb file in Jupyter
+    # Reload the notebook
+    nb = cm.get("test.ipynb")["content"]
+    nb.cells.append(new_markdown_cell("A new cell"))
+    cm.save(dict(type="notebook", content=nb), "test.ipynb")
+
+    # The text representation metadata is in the py file
+    assert "text_representation" in tmpdir.join("test.py").read()
+    # But not in the ipynb notebook
+    assert "text_representation" not in tmpdir.join("test.ipynb").read()
+
+    # the text file has been updated (and the ipynb file as well)
+    assert "A new cell" in tmpdir.join("test.py").read()
+    nb = read("test.ipynb")
+    assert len(nb.cells) == 2
+
+    # add both files, the commit will succeed
+    tmp_repo.git.add("test.ipynb")
+    tmp_repo.git.add("test.py")
+    tmp_repo.index.commit("passing")