New option --use-source-timestamp (#790)

* New option --use-source-timestamp

* Write the output notebook just once
Adjust 'formats', if required, before writing the notebook

* Destination timestamp might be truncated at the micro-second

docs/CHANGELOG.md

@@ -4,6 +4,9 @@ Jupytext ChangeLog
 1.11.3 (2021-05-??)
 -------------------
 
+**Changed**
+- Jupytext CLI has a new option `--use-source-timestamp` that sets the last modification time of the output file equal to that of the source file (this avoids having to change the timestamp of the source file) ([#784](https://github.com/mwouts/jupytext/issues/784))
+
 **Fixed**
 - Dependencies of the JupyterLab extension have been upgraded to fix a security vulnerability ([#783](https://github.com/mwouts/jupytext/issues/783))
 

jupytext/cli.py

@@ -180,6 +180,13 @@ def parse_jupytext_args(args=None):
         "See also the --opt and --set-formats options for other ways "
         "to operate on the Jupytext metadata.",
     )
+    action.add_argument(
+        "--use-source-timestamp",
+        help="Set the modification timestamp of the output file(s) equal"
+        "to that of the source file, and keep the source file and "
+        "its timestamp unchanged.",
+        action="store_true",
+    )
     action.add_argument(
         "--warn-only",
         "-w",
@@ -771,7 +778,12 @@ def lazy_write(path, fmt=None, action=None, update_timestamp_only=False):
         # Otherwise, we only update the timestamp of the text file to make sure
         # they remain more recent than the ipynb file, for compatibility with the
         # Jupytext contents manager for Jupyter
-        if not modified and not path.endswith(".ipynb"):
+        if args.use_source_timestamp:
+            log(
+                f"[jupytext] Setting the timestamp of {shlex.quote(path)} equal to that of {shlex.quote(nb_file)}"
+            )
+            os.utime(path, (os.stat(path).st_atime, os.stat(nb_file).st_mtime))
+        elif not modified and not path.endswith(".ipynb"):
             log(f"[jupytext] Updating the timestamp of {shlex.quote(path)}")
             os.utime(path, None)
 
@@ -808,27 +820,40 @@ def lazy_write(path, fmt=None, action=None, update_timestamp_only=False):
         else:
             action = ""
 
-        lazy_write(nb_dest, fmt=dest_fmt, action=action)
+        formats = notebook.metadata.get("jupytext", {}).get("formats")
+        formats = long_form_multiple_formats(formats)
+        if formats:
+            try:
+                base_path_out, _ = find_base_path_and_format(nb_dest, formats)
+            except InconsistentPath:
+                # Drop 'formats' if the destination is not part of the paired notebooks
+                formats = {}
+                notebook.metadata.get("jupytext", {}).pop("formats")
 
-    # c. Synchronize paired notebooks
-    if args.sync:
-        write_pair(nb_file, formats, lazy_write)
+        lazy_write(nb_dest, fmt=dest_fmt, action=action)
 
-    elif (
-        os.path.isfile(nb_file)
-        and not nb_file.endswith(".ipynb")
-        and os.path.isfile(nb_dest)
-        and nb_dest.endswith(".ipynb")
-    ):
-        formats = notebook.metadata.get("jupytext", {}).get("formats")
-        if formats is not None and any(
-            os.path.isfile(alt_path) and os.path.samefile(nb_dest, alt_path)
+        nb_dest_in_pair = formats and any(
+            os.path.exists(alt_path) and os.path.samefile(nb_dest, alt_path)
             for alt_path, _ in paired_paths(nb_file, fmt, formats)
+        )
+
+        if (
+            nb_dest_in_pair
+            and os.path.isfile(nb_file)
+            and not nb_file.endswith(".ipynb")
+            and os.path.isfile(nb_dest)
+            and nb_dest.endswith(".ipynb")
         ):
-            # Update the original text file timestamp, as required by our Content Manager
+            # If the destination is an ipynb file and is in the pair, then we
+            # update the original text file timestamp, as required by our Content Manager
             # Otherwise Jupyter will refuse to open the paired notebook #335
+            # NB: An alternative is --use-source-timestamp
             lazy_write(nb_file, update_timestamp_only=True)
 
+    # c. Synchronize paired notebooks
+    elif args.sync:
+        write_pair(nb_file, formats, lazy_write)
+
     return untracked_files
 
 

tests/test_cli.py

@@ -1311,3 +1311,52 @@ def test_jupytext_to_ipynb_does_not_update_timestamp_if_not_paired(
 
     capture = capsys.readouterr()
     assert "Updating the timestamp" not in capture.out
+
+
+@pytest.mark.parametrize("formats", ["ipynb,py", "py:percent", "py", None])
+def test_use_source_timestamp(tmpdir, cwd_tmpdir, python_notebook, capsys, formats):
+    # Write a text notebook
+    nb = python_notebook
+    if formats:
+        nb.metadata["jupytext"] = {"formats": formats}
+
+    test_py = tmpdir.join("test.py")
+    test_ipynb = tmpdir.join("test.ipynb")
+    write(nb, str(test_py))
+    src_timestamp = test_py.stat().mtime
+
+    # Wait...
+    time.sleep(0.1)
+
+    # py -> ipynb
+    jupytext(["--to", "ipynb", "test.py", "--use-source-timestamp"])
+
+    capture = capsys.readouterr()
+    assert "Updating the timestamp" not in capture.out
+
+    dest_timestamp = test_ipynb.stat().mtime
+    # on Mac OS the dest_timestamp is truncated at the microsecond (#790)
+    assert src_timestamp - 1e-6 <= dest_timestamp <= src_timestamp
+
+    # Make sure that we can open the file in Jupyter
+    from jupytext.contentsmanager import TextFileContentsManager
+
+    cm = TextFileContentsManager()
+    cm.outdated_text_notebook_margin = 0.001
+    cm.root_dir = str(tmpdir)
+
+    # No error here
+    cm.get("test.ipynb")
+
+    # But now if we don't use --use-source-timestamp
+    jupytext(["--to", "ipynb", "test.py"])
+    os.utime(test_py, (src_timestamp, src_timestamp))
+
+    # Then we can't open paired notebooks
+    if formats == "ipynb,py":
+        from tornado.web import HTTPError
+
+        with pytest.raises(HTTPError, match="seems more recent than test.py"):
+            cm.get("test.ipynb")
+    else:
+        cm.get("test.ipynb")