'git add' is also required if the output file is modified

jupytext/cli.py

@@ -738,18 +738,17 @@ def write_function(path, fmt):
             if args.pre_commit:
                 system("git", "add", path)
             if args.alert_untracked and is_untracked(path):
+                log(
+                    "[jupytext] Output file {nb_dest} is not up-to-date in the git index. "
+                    "Please run 'git add {nb_dest}' to fix this".format(nb_dest=path)
+                )
+
                 nonlocal untracked_paths
                 untracked_paths.append(path)
 
         formats = prepare_notebook_for_save(notebook, config, nb_file)
         write_pair(nb_file, formats, write_function)
         if untracked_paths:
-            log(
-                "[jupytext] Output file {nb_dest} is not tracked in the git index, "
-                "add it to the index using 'git add' to fix this.".format(
-                    nb_dest=", ".join(untracked_paths)
-                )
-            )
             return 1
 
     elif (
@@ -765,8 +764,8 @@ def write_function(path, fmt):
 
     if args.alert_untracked and is_untracked(nb_dest):
         log(
-            "[jupytext] Output file {nb_dest} is not tracked in the git index, "
-            "add it to the index using 'git add' to fix this.".format(nb_dest=nb_dest)
+            "[jupytext] Output file {nb_dest} is not up-to-date in the git index. "
+            "Please run 'git add {nb_dest}' to fix this".format(nb_dest=nb_dest)
         )
         return 1
     else:
@@ -791,11 +790,19 @@ def notebooks_in_git_index(fmt):
 
 
 def is_untracked(filepath):
-    """Check whether a file is untracked by the git index"""
+    """Check whether a file was created or modified and needs to be added to the git index"""
     if not filepath:
         return False
+
     output = system("git", "ls-files", filepath).strip()
-    return output == ""
+    if output == "":
+        return True
+
+    output = system("git", "diff", filepath).strip()
+    if output != "":
+        return True
+
+    return False
 
 
 def print_paired_paths(nb_file, fmt):

tests/test_alert_untracked.py

@@ -19,6 +19,14 @@ def test_is_untracked(tmpdir, cwd_tmpdir, tmp_repo):
     tmp_repo.index.commit("test")
     assert not is_untracked(file)
 
+    # changed
+    tmpdir.join(file).write("modified file\n")
+    assert is_untracked(file)
+
+    # added, not committed
+    tmp_repo.git.add(file)
+    assert not is_untracked(file)
+
 
 def test_ignore_unmatched_ignores(tmpdir, cwd_tmpdir):
     # Unmatched file
@@ -45,7 +53,7 @@ def test_alert_untracked_alerts(tmpdir, cwd_tmpdir, tmp_repo, capsys):
     assert tmpdir.join("test.ipynb").exists()
 
     out = capsys.readouterr()
-    assert "Output file test.ipynb is not tracked in the git index" in out.out
+    assert "Please run 'git add test.ipynb'" in out.out
 
 
 def test_alert_untracked_alerts_when_using_sync(tmpdir, cwd_tmpdir, tmp_repo, capsys):
@@ -61,10 +69,10 @@ def test_alert_untracked_alerts_when_using_sync(tmpdir, cwd_tmpdir, tmp_repo, ca
     assert tmpdir.join("test.ipynb").exists()
 
     out = capsys.readouterr()
-    assert "Output file test.ipynb is not tracked in the git index" in out.out
+    assert "Please run 'git add test.ipynb'" in out.out
 
 
-def test_alert_untracked_not_alerts_for_tracked(tmpdir, cwd_tmpdir, tmp_repo):
+def test_alert_untracked_alerts_for_modified(tmpdir, cwd_tmpdir, tmp_repo, capsys):
     # write test notebook
     nb = new_notebook(cells=[new_markdown_cell("A short notebook")])
     write(nb, "test.ipynb")
@@ -80,4 +88,6 @@ def test_alert_untracked_not_alerts_for_tracked(tmpdir, cwd_tmpdir, tmp_repo):
         ["--from", "ipynb", "--to", "py:light", "--alert-untracked", "test.ipynb"]
     )
 
-    assert status == 0
+    assert status == 1
+    out = capsys.readouterr()
+    assert "Please run 'git add test.py'" in out.out

tests/test_pre_commit.py

@@ -52,7 +52,8 @@ def test_pre_commit_hook_for_new_file(
 
     # try again, it will still fail because the output hasn't been added
     with pytest.raises(
-        HookExecutionError, match="Output file test.py is not tracked in the git index"
+        HookExecutionError,
+        match="Please run 'git add test.py'",
     ):
         tmp_repo.index.commit("still failing")
 
@@ -99,8 +100,10 @@ def test_pre_commit_hook_for_existing_changed_file(
     with pytest.raises(HookExecutionError, match="files were modified by this hook"):
         tmp_repo.index.commit("fails")
 
-    # TODO: Not sure this is the expected message?
-    with pytest.raises(HookExecutionError, match="files were modified by this hook"):
+    with pytest.raises(
+        HookExecutionError,
+        match="Please run 'git add test.py'",
+    ):
         tmp_repo.index.commit("fails again")
 
     # once we add the changes, it will pass