Route unmentioned columns to ignore_columns

CHANGELOG.md

@@ -1,3 +1,24 @@
+# 0.17.0 (TBD)
+
+## Breaking Changes
+
+- **CLI: unmentioned columns now go to `ignore_columns` instead of `outcome_columns`**
+  - Previously, when `--outcome_columns` was not explicitly set, all columns that
+    were not the id, weight, or a covariate were automatically classified as
+    outcome columns. Now those columns are placed into `ignore_columns` instead.
+  - Columns that are explicitly mentioned — the id column, weight column,
+    covariate columns, and outcome columns — are **not** ignored.
+
+## Documentation
+
+- **Improved `keep_columns` documentation**
+  - Updated docstrings for `has_keep_columns()`, `keep_columns()`, and the
+    `--keep_columns` argument to clarify that keep columns control which columns
+    appear in the final output CSV. Keep columns that are not id, weight,
+    covariate, or outcome columns will be placed into ``ignore_columns`` during
+    processing but are still retained and available in the output.
+
+
 # 0.16.0 (2026-02-09)
 
 ## New Features

balance/__init__.py

@@ -19,7 +19,7 @@
 from balance.util import TruncationFormatter  # noqa
 
 global __version__
-__version__ = "0.16.0"
+__version__ = "0.16.1"
 
 WELCOME_MESSAGE = f"""
 balance (Version {__version__}) loaded:

balance/cli.py

@@ -280,6 +280,15 @@ def batch_columns(self) -> List[str]:
     def has_keep_columns(self) -> bool:
         """Return True when output keep columns are supplied.
 
+        Keep columns control which columns appear in the final output CSV.
+        After adjustment, the output DataFrame is subsetted to contain
+        **only** these columns (see :meth:`adapt_output`).
+
+        Note that keep columns that are not the id, weight, a covariate,
+        or an explicit outcome column will be placed into
+        ``ignore_columns`` by :meth:`process_batch`.  They are still
+        carried through the ``Sample`` and available in the output.
+
         Returns:
             ``True`` if keep columns are set, otherwise ``False``.
 
@@ -294,6 +303,12 @@ def has_keep_columns(self) -> bool:
     def keep_columns(self) -> List[str] | None:
         """Return the subset of columns to keep in outputs.
 
+        These columns are used to filter the final output DataFrame.
+        Keep columns that are not the id, weight, a covariate, or an
+        explicit outcome column will be placed into ``ignore_columns``
+        during processing but are still retained by the ``Sample`` and
+        included in the output.
+
         Returns:
             List of columns to keep or ``None`` if unspecified.
 
@@ -667,33 +682,22 @@ def process_batch(
                 ),
             }
 
-        # Stuff everything that is not id, weight, or covariate into outcomes
+        # Build the set of explicitly mentioned columns.  Any column not in
+        # this set is placed into ignore_columns so it is carried through
+        # the Sample but does not participate in the adjustment.
         outcome_columns = self.outcome_columns()
-        ignore_columns = None
-        if outcome_columns is None:
-            outcome_columns = [
-                column
-                for column in batch_df.columns
-                if column
-                not in {
-                    self.id_column(),
-                    self.weight_column(),
-                    *self.covariate_columns(),
-                }
-            ]
-        else:
-            ignore_columns = [
-                column
-                for column in batch_df.columns
-                if column
-                not in {
-                    self.id_column(),
-                    self.weight_column(),
-                    *self.covariate_columns(),
-                    *outcome_columns,
-                }
-            ]
-        outcome_columns = tuple(outcome_columns)
+        explicitly_mentioned: set[str] = {
+            self.id_column(),
+            self.weight_column(),
+            *self.covariate_columns(),
+        }
+        if outcome_columns is not None:
+            explicitly_mentioned.update(outcome_columns)
+
+        ignore_columns = [
+            column for column in batch_df.columns if column not in explicitly_mentioned
+        ]
+        outcome_columns = tuple(outcome_columns) if outcome_columns else None
 
         # definitions for diagnostics
         covariate_columns_for_diagnostics = self.covariate_columns_for_diagnostics()
@@ -1218,8 +1222,9 @@ def add_arguments_to_parser(parser: ArgumentParser) -> ArgumentParser:
         required=False,
         default=None,
         help=(
-            "Set of columns used as outcomes. If not supplied, all columns that are "
-            "not in id, weight, or covariate columns are treated as outcomes."
+            "Comma-separated columns used as outcomes. If not supplied, "
+            "columns that are not id, weight, or covariates are placed into "
+            "ignore_columns (carried through but not used in adjustment)."
         ),
     )
     parser.add_argument(
@@ -1255,7 +1260,10 @@ def add_arguments_to_parser(parser: ArgumentParser) -> ArgumentParser:
         "--keep_columns",
         type=str,
         required=False,
-        help="Set of columns we include in the output csv file",
+        help=(
+            "Comma-separated columns to include in the output csv file. "
+            "The output will be subsetted to only these columns."
+        ),
     )
     parser.add_argument(
         "--keep_row_column",

tests/test_cli.py

@@ -147,7 +147,7 @@ def _make_batch_df(self) -> pd.DataFrame:
     # pyre-ignore[3]: Intentionally returning a dynamically created class
     def _recording_sample_cls(self):
         class RecordingSample:
-            calls: list[tuple[str, ...]] = []
+            calls: list[tuple[str, ...] | None] = []
             ignore_calls: list[list[str] | None] = []
 
             def __init__(self, df: pd.DataFrame) -> None:
@@ -164,8 +164,6 @@ def from_frame(
                 ignore_columns: list[str] | None = None,
                 **kwargs: object,
             ) -> "RecordingSample":
-                if outcome_columns is None:
-                    raise AssertionError("Expected outcome_columns to be provided.")
                 cls.calls.append(outcome_columns)
                 cls.ignore_calls.append(ignore_columns)
                 return cls(df)
@@ -190,7 +188,7 @@ def diagnostics(
 
         return RecordingSample
 
-    def test_cli_outcome_columns_default_inference_preserves_order(self) -> None:
+    def test_cli_unmentioned_columns_go_to_ignore(self) -> None:
         RecordingSample = self._recording_sample_cls()
         cli = self._make_cli()
         cli.process_batch(
@@ -200,12 +198,15 @@ def test_cli_outcome_columns_default_inference_preserves_order(self) -> None:
         )
         self.assertEqual(
             RecordingSample.calls,
+            [None, None],
+        )
+        self.assertEqual(
+            RecordingSample.ignore_calls,
             [
-                ("is_respondent", "outcome_b", "outcome_a", "extra"),
-                ("is_respondent", "outcome_b", "outcome_a", "extra"),
+                ["is_respondent", "outcome_b", "outcome_a", "extra"],
+                ["is_respondent", "outcome_b", "outcome_a", "extra"],
             ],
         )
-        self.assertEqual(RecordingSample.ignore_calls, [None, None])
 
     def test_cli_outcome_columns_explicit_selection(self) -> None:
         RecordingSample = self._recording_sample_cls()
@@ -1324,6 +1325,52 @@ def test_check_input_columns_raises_when_keep_column_missing(self) -> None:
         with self.assertRaises(AssertionError):
             cli.check_input_columns(columns)
 
+    def test_keep_columns_preserved_in_adjusted_output(self) -> None:
+        """Test that --keep_columns columns survive adjustment via ignore_columns.
+
+        A keep column that is not id, weight, covariate, or outcome should be
+        routed to ignore_columns by process_batch, carried through the Sample,
+        and available for adapt_output to subset without KeyError.
+        """
+        with (
+            tempfile.TemporaryDirectory() as temp_dir,
+            tempfile.NamedTemporaryFile("w", suffix=".csv", delete=False) as in_file,
+        ):
+            in_contents = (
+                "x,y,is_respondent,id,weight,extra_col\n"
+                + ("1.0,50,1,1,1,abc\n" * 100)
+                + ("2.0,60,0,1,1,def\n" * 100)
+            )
+            in_file.write(in_contents)
+            in_file.close()
+            out_file = os.path.join(temp_dir, "out.csv")
+
+            parser = make_parser()
+            args = parser.parse_args(
+                [
+                    "--input_file",
+                    in_file.name,
+                    "--output_file",
+                    out_file,
+                    "--covariate_columns",
+                    "x,y",
+                    "--keep_columns",
+                    "id,weight,extra_col",
+                ]
+            )
+            cli = BalanceCLI(args)
+            cli.update_attributes_for_main_used_by_adjust()
+            cli.main()
+
+            self.assertTrue(os.path.isfile(out_file))
+            pd_out = pd.read_csv(out_file)
+            # adapt_output should have subsetted to exactly these columns
+            self.assertEqual(
+                sorted(pd_out.columns.tolist()), ["extra_col", "id", "weight"]
+            )
+            # extra_col values should be preserved from the sample rows
+            self.assertTrue((pd_out["extra_col"] == "abc").all())
+
 
 class TestBalanceCLI_num_lambdas(balance.testutil.BalanceTestCase):
     """Test cases for num_lambdas method (line 401)."""