Force default indent of flepimop patch to 4

HopkinsIDD · Dec 11, 2024 · d3f89d2 · d3f89d2
1 parent ba22f0b
commit d3f89d2
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Showing 2 changed files with 4 additions and 40 deletions.
diff --git a/flepimop/gempyor_pkg/src/gempyor/cli.py b/flepimop/gempyor_pkg/src/gempyor/cli.py
@@ -21,19 +21,7 @@
 
 
 # add some basic commands to the CLI
-@cli.command(
-    params=[config_files_argument]
-    + list(config_file_options.values())
-    + [
-        click.Option(
-            ["--indent"],
-            type=click.IntRange(min=1),
-            required=False,
-            default=2,
-            help="Indentation level for the output YAML.",
-        )
-    ],
-)
+@cli.command(params=[config_files_argument] + list(config_file_options.values()))
 @click.pass_context
 def patch(ctx: click.Context = mock_context, **kwargs) -> None:
     """Merge configuration files
@@ -64,7 +52,7 @@ def patch(ctx: click.Context = mock_context, **kwargs) -> None:
             gamma:
                 value: 5.6
     EOF
-    $ flepimop patch config1.yml config2.yml --indent 4
+    $ flepimop patch config1.yml config2.yml
     ...: UserWarning: Configuration files contain overlapping keys: {'seir'}.
     warnings.warn(f"Configuration files contain overlapping keys: {intersect}.")
     compartments:
@@ -89,7 +77,7 @@ def patch(ctx: click.Context = mock_context, **kwargs) -> None:
     stoch_traj_flag: false
     write_csv: false
     write_parquet: true
-    $ flepimop patch config2.yml config1.yml --indent 4
+    $ flepimop patch config2.yml config1.yml
     ...: UserWarning: Configuration files contain overlapping keys: {'seir'}.
     warnings.warn(f"Configuration files contain overlapping keys: {intersect}.")
     compartments:
@@ -116,7 +104,7 @@ def patch(ctx: click.Context = mock_context, **kwargs) -> None:
     ```
     """
     parse_config_files(config, ctx, **kwargs)
-    print(yaml.dump(yaml.safe_load(config.dump()), indent=kwargs["indent"]))
+    print(yaml.dump(yaml.safe_load(config.dump()), indent=4))
 
 
 if __name__ == "__main__":

diff --git a/flepimop/gempyor_pkg/tests/cli/test_flepimop_patch_cli.py b/flepimop/gempyor_pkg/tests/cli/test_flepimop_patch_cli.py
@@ -74,27 +74,3 @@ def test_patch_seir_parameters_behavior(
     patched_config = yaml.safe_load(result.output)
     assert "seir" in patched_config
     assert patched_config["seir"]["parameters"] == expected_parameters
-
-
-@pytest.mark.parametrize("indent", (2, 4, 6))
-def test_user_provided_indent_size(
-    tmp_path: Path, monkeypatch: pytest.MonkeyPatch, indent: int
-) -> None:
-    # Setup the test
-    monkeypatch.chdir(tmp_path)
-    config = tmp_path / "config.yml"
-    config.write_text(yaml.dump({"seir": {"parameters": {"beta": {"value": 1.2}}}}))
-
-    # Invoke the command
-    runner = CliRunner()
-    result = runner.invoke(patch, [config.name, "--indent", str(indent)])
-    assert result.exit_code == 0
-
-    # Check the output indentation, manually since `yaml.load` abstracts spacing away
-    for line in result.output.split():
-        stripped_line = line.lstrip()
-        if stripped_line and not stripped_line.startswith("#"):
-            indent_size = len(line) - len(stripped_line)
-            if indent_size > 0:
-                assert indent_size == indent
-                break