From bb5b4a9fce3e789b015db40972b77ef811f5f08a Mon Sep 17 00:00:00 2001
From: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: Tue, 24 Oct 2023 12:21:43 -0700
Subject: [PATCH] Added all the tests and stuff.

---
 src/biocframe/BiocFrame.py   | 10 +++-------
 src/biocframe/_validators.py |  5 -----
 tests/test_combine.py        | 27 +++++++++++++++++++++++++++
 tests/test_initialize.py     | 25 +++++++++++++++++++++++++
 tests/test_methods.py        | 25 +++++++++++++++++++++++++
 5 files changed, 80 insertions(+), 12 deletions(-)

diff --git a/src/biocframe/BiocFrame.py b/src/biocframe/BiocFrame.py
index d91e1e1..077c873 100644
--- a/src/biocframe/BiocFrame.py
+++ b/src/biocframe/BiocFrame.py
@@ -191,7 +191,7 @@ def _validate(self):
             self._data, self._number_of_rows, self._row_names
         )
         self._column_names, self._data, self._mcols = validate_cols(
-            self._column_names, self._data
+            self._column_names, self._data, self._mcols
         )
 
         if self._number_of_rows is None:
@@ -370,17 +370,13 @@ def mcols(self) -> Union[None, "BiocFrame"]:
         # TODO: need to attach row names.
         return self._mcols
 
+    @mcols.setter
     def mcols(self, mcols: Union[None, "BiocFrame"]):
         if mcols is not None:
             if mcols.shape[0] != self.shape[1]:
                 raise ValueError(
                     "Number of rows in `mcols` should be equal to the number of columns."
                 )
-            if mcols.row_names is not None:
-                if mcols.row_names != column_names:
-                    raise ValueError(
-                        "Row names of `mcols` should be equal to the column names."
-                    )
         self._mcols = mcols
 
     @property
@@ -544,7 +540,7 @@ def _slice(
         mcols = self._mcols
         if mcols is not None:
             if column_indices_or_names is not None:
-                mcols = mcols._slice(new_column_indices)
+                mcols = mcols._slice(new_column_indices, None)
 
         current_class_const = type(self)
         return current_class_const(
diff --git a/src/biocframe/_validators.py b/src/biocframe/_validators.py
index 8708aaa..e43753a 100644
--- a/src/biocframe/_validators.py
+++ b/src/biocframe/_validators.py
@@ -121,11 +121,6 @@ def validate_cols(
             raise ValueError(
                 "Number of rows in `mcols` should be equal to the number of columns."
             )
-        if mcols.row_names is not None:
-            if mcols.row_names != column_names:
-                raise ValueError(
-                    "Row names of `mcols` should be equal to the column names."
-                )
 
     return column_names, data, mcols
 
diff --git a/tests/test_combine.py b/tests/test_combine.py
index 1691c8e..518c0e7 100644
--- a/tests/test_combine.py
+++ b/tests/test_combine.py
@@ -93,3 +93,30 @@ def test_combine_generic_preserve_types():
     assert isinstance(merged, BiocFrame)
     assert isinstance(merged.column("odd"), np.ndarray)
     assert isinstance(merged.column("even"), list)
+
+
+def test_combine_with_extras():
+    obj1 = BiocFrame(
+        {
+            "column1": [1, 2, 3],
+            "column2": [4, 5, 6],
+        },
+        mcols = BiocFrame(
+            { 
+                "foo": [ -1, -2 ], 
+                "bar": [ "A", "B" ]
+            }
+        ),
+        metadata = { "YAY": 2 }
+    )
+
+    obj2 = BiocFrame(
+        {
+            "column1": [1, 2, 3],
+            "column2": [4, 5, 6],
+        },
+    )
+
+    merged = combine(obj1, obj2)
+    assert merged.metadata == obj1.metadata
+    assert merged.mcols.shape == obj1.mcols.shape
diff --git a/tests/test_initialize.py b/tests/test_initialize.py
index c4a30bc..af83537 100644
--- a/tests/test_initialize.py
+++ b/tests/test_initialize.py
@@ -115,3 +115,28 @@ def test_nested_biocFrame():
     assert isinstance(nested_col, BiocFrame)
     assert nested_col.row_names is None
     assert len(nested_col.column_names) == 3
+
+
+def test_extra_bits():
+    bframe = BiocFrame(
+        {
+            "column1": [1, 2, 3],
+        },
+        mcols = BiocFrame(
+            { 
+                "foo": [ 1 ], 
+                "bar": [ "A" ]
+            }
+        ),
+        metadata = { "YAY": 2 }
+    )
+
+    assert isinstance(bframe.mcols, BiocFrame)
+    assert bframe.metadata["YAY"] == 2
+
+    # Setters work correctly.
+    bframe.mcols = BiocFrame({ "STUFF": [ 2.5 ] })
+    assert bframe.mcols.column_names == ["STUFF"]
+
+    bframe.metadata = { "FOO": "A" }
+    assert bframe.metadata["FOO"] == "A"
diff --git a/tests/test_methods.py b/tests/test_methods.py
index f1df1e7..bcf90f5 100644
--- a/tests/test_methods.py
+++ b/tests/test_methods.py
@@ -217,6 +217,31 @@ def test_bframe_slice():
     assert sliced_list.dims == (2, 2)
 
 
+def test_bframe_slice_with_extras():
+    bframe = BiocFrame(
+        {
+            "column1": [1, 2, 3],
+            "column2": [4, 5, 6],
+        },
+        mcols = BiocFrame(
+            { 
+                "foo": [ -1, -2 ], 
+                "bar": [ "A", "B" ]
+            }
+        ),
+        metadata = { "YAY": 2 }
+    )
+
+    subframe = bframe[0:2,:]
+    assert subframe.mcols.shape[0] == bframe.mcols.shape[1]
+    assert subframe.metadata == bframe.metadata
+
+    subframe = bframe[:,[1]]
+    assert subframe.mcols.shape[0] == 1
+    assert subframe.mcols.column("foo") == [-2]
+    assert subframe.metadata == bframe.metadata
+
+
 def test_bframe_unary_slice():
     obj = {
         "column1": [1, 2, 3],