fix set-kernel when extension is implicit

Closes #326

HISTORY.rst

@@ -14,6 +14,8 @@ Release History
 **BugFixes**
 
 - Flag `--warn-only` catches every possible error (#263)
+- Treat `.md` and `.markdown` files identically (#325)
+- Make sure `--set-kernel` can be used with pipes (#326)
 
 1.2.3 (2019-09-02)
 ++++++++++++++++++++++

jupytext/cli.py

@@ -311,8 +311,7 @@ def jupytext_single_file(nb_file, args, log):
     if args.update_metadata:
         log("[jupytext] Updating notebook metadata with '{}'".format(json.dumps(args.update_metadata)))
         # Are we updating a text file that has a metadata filter? #212
-        if fmt['extension'] != '.ipynb' and \
-                notebook.metadata.get('jupytext', {}).get('notebook_metadata_filter') == '-all':
+        if notebook.metadata.get('jupytext', {}).get('notebook_metadata_filter') == '-all':
             notebook.metadata.get('jupytext', {}).pop('notebook_metadata_filter')
         recursive_update(notebook.metadata, args.update_metadata)
 

tests/test_cli.py

@@ -2,6 +2,7 @@
 import sys
 import time
 import stat
+from io import StringIO
 
 try:
     import unittest.mock as mock
@@ -16,7 +17,7 @@
 from nbformat.v4.nbbase import new_notebook, new_markdown_cell, new_code_cell
 from jupyter_client.kernelspec import find_kernel_specs, get_kernel_spec
 from jupytext import __version__
-from jupytext import read, write, writes
+from jupytext import read, reads, write, writes
 from jupytext.cli import parse_jupytext_args, jupytext, system, str2bool
 from jupytext.compare import compare_notebooks
 from jupytext.paired_paths import paired_paths, InconsistentPath
@@ -753,6 +754,20 @@ def test_cli_can_infer_jupytext_format_from_stdin(nb_file, tmpdir):
     compare_notebooks(nb, nb2, 'Rmd')
 
 
+def test_set_kernel_works_with_pipes_326(capsys):
+    md = u"""```python
+1 + 1
+```"""
+
+    with mock.patch('sys.stdin', StringIO(md)):
+        jupytext(['--to', 'ipynb', '--set-kernel', '-', '-'])
+
+    out, err = capsys.readouterr()
+    assert err == ''
+    nb = reads(out, 'ipynb')
+    assert 'kernelspec' in nb.metadata
+
+
 @requires_jupytext_installed
 def test_cli_expect_errors(tmp_ipynb):
     with pytest.raises(ValueError):