Small changes to variant formatter

src/genophenocorr/view/_formatter.py

@@ -13,8 +13,7 @@ def format_as_string(self, item: T) -> str:
         to more easily read the item in tables or other visualizers.
 
         Args:
-            item (T): a genophenocorr class
-            tx_id (typing.Optional[str]): The desired transcript ID, if not the MANE transcript
+            item (T): an element to be formatted
 
         Returns:
             str: a human readable string 
@@ -32,7 +31,6 @@ def format_as_string(self, item: Variant) -> str:
         """ 
         Args:
             item (Variant): An object of class `Variant` representing a variant.
-            tx_id (typing.Optional[str]): The transcript ID, needed if using a transcript other than the MANE transcript.
 
         Returns:
             str: A human readable string for the variant.
@@ -48,4 +46,5 @@ def format_as_string(self, item: Variant) -> str:
         elif item.variant_coordinates.variant_key is not None:
             return item.variant_coordinates.variant_key
         else:
+            # To be reevaluated
             return f"Variant {item} has no string format."

tests/model/test_variant.py

@@ -3,17 +3,8 @@
 import typing
 
 from genophenocorr.model import Variant, Cohort
-from genophenocorr.view import VariantFormatter
-
 
 class TestVariant:
-
-    @pytest.fixture
-    def test_cohort(
-        self, 
-        suox_cohort: Cohort
-    ) -> Cohort:
-        return suox_cohort
 
     @pytest.fixture
     def some_variant(
@@ -36,20 +27,4 @@ def test_get_hgvs_cdna_by_tx(
     ):
         hgvs = some_variant.get_hgvs_cdna_by_tx_id(transcript_id=tx_id)
 
-        assert hgvs == expected
-
-    @pytest.mark.parametrize(
-        "variant, expected",
-        [
-            ('12_56004525_56004525_A_G', "NM_001032386.2:c.1136A>G"),
-        ]
-    )
-    def test_variant_formatter(
-        self, 
-        variant: str,
-        expected: str,
-        test_cohort: Cohort
-    ):
-        var = test_cohort.get_variant_by_key(variant)
-        formatter = VariantFormatter()
-        assert formatter.format_as_string(var) == expected
+        assert hgvs == expected

tests/view/test_formatter.py

@@ -0,0 +1,24 @@
+import pytest
+
+import typing
+
+from genophenocorr.model import Cohort
+from genophenocorr.view import VariantFormatter
+
+class TestFormatter:
+
+    @pytest.mark.parametrize(
+        "variant, expected",
+        [
+            ('12_56004525_56004525_A_G', "NM_001032386.2:c.1136A>G"),
+        ]
+    )
+    def test_variant_formatter(
+        self, 
+        variant: str,
+        expected: str,
+        suox_cohort: Cohort
+    ):
+        var = suox_cohort.get_variant_by_key(variant)
+        formatter = VariantFormatter()
+        assert formatter.format_as_string(var) == expected