Make dotenv run forward flags to given command

Changes for users:

- (BREAKING) Forward flags passed after `dotenv run` to the given
  command instead of interpreting them.
    - This means that an invocation such as `dotenv run ls --help` will
      show the help page of `ls` instead of that of `dotenv run`.
    - To pass flags to `dotenv run` itself, pass them right after `run`:
      `dotenv run --help` or `dotenv run --override ls`.
    - As usual, generic options should be passed right after `dotenv`:
      `dotenv --file path/to/env run ls`

Author: bbc2

src/dotenv/cli.py

@@ -156,15 +156,21 @@ def unset(ctx: click.Context, key: Any) -> None:
         sys.exit(1)
 
 
-@cli.command(context_settings={"ignore_unknown_options": True})
+@cli.command(
+    context_settings={
+        "allow_extra_args": True,
+        "allow_interspersed_args": False,
+        "ignore_unknown_options": True,
+    }
+)
 @click.pass_context
 @click.option(
     "--override/--no-override",
     default=True,
     help="Override variables from the environment file with those from the .env file.",
 )
 @click.argument("commandline", nargs=-1, type=click.UNPROCESSED)
-def run(ctx: click.Context, override: bool, commandline: List[str]) -> None:
+def run(ctx: click.Context, override: bool, commandline: tuple[str, ...]) -> None:
     """Run command with environment variables present."""
     file = ctx.obj["FILE"]
     if not os.path.isfile(file):
@@ -180,7 +186,8 @@ def run(ctx: click.Context, override: bool, commandline: List[str]) -> None:
     if not commandline:
         click.echo("No command given.")
         sys.exit(1)
-    run_command(commandline, dotenv_as_dict)
+
+    run_command([*commandline, *ctx.args], dotenv_as_dict)
 
 
 def run_command(command: List[str], env: Dict[str, str]) -> None:

tests/test_cli.py

@@ -1,6 +1,7 @@
 import os
+import subprocess
 from pathlib import Path
-from typing import Optional
+from typing import Optional, Sequence
 
 import pytest
 import sh
@@ -10,6 +11,21 @@
 from dotenv.version import __version__
 
 
+def invoke_sub(args: Sequence[str]) -> subprocess.CompletedProcess:
+    """
+    Invoke the `dotenv` CLI in a subprocess.
+
+    This is necessary to test subcommands like `dotenv run` that replace the
+    current process.
+    """
+
+    return subprocess.run(
+        ["dotenv", *args],
+        capture_output=True,
+        text=True,
+    )
+
+
 @pytest.mark.parametrize(
     "output_format,content,expected",
     (
@@ -249,3 +265,29 @@ def test_run_with_version(cli):
 
     assert result.exit_code == 0
     assert result.output.strip().endswith(__version__)
+
+
+def test_run_with_command_flags(dotenv_path):
+    """
+    Check that command flags passed after `dotenv run` are not interpreted.
+
+    Here, we want to run `printenv --version`, not `dotenv --version`.
+    """
+
+    result = invoke_sub(["--file", dotenv_path, "run", "printenv", "--version"])
+
+    assert result.returncode == 0
+    assert result.stdout.strip().startswith("printenv ")
+
+
+def test_run_with_dotenv_and_command_flags(cli, dotenv_path):
+    """
+    Check that dotenv flags supersede command flags.
+    """
+
+    result = invoke_sub(
+        ["--version", "--file", dotenv_path, "run", "printenv", "--version"]
+    )
+
+    assert result.returncode == 0
+    assert result.stdout.strip().startswith("dotenv, version")