tidy, types

countess/core/parameters.py

@@ -455,7 +455,7 @@ def get_column(self, df):
 
 
 class ColumnOrStringParam(ColumnChoiceParam):
-    DEFAULT_VALUE = ""
+    DEFAULT_VALUE : Any = ""
     PREFIX = "— "
 
     def set_column_choices(self, choices):
@@ -475,7 +475,7 @@ def get_value(self, data: dict):
     def get_column_or_value(self, df: pd.DataFrame, numeric: bool):
         if self.value.startswith(self.PREFIX):
             col = df[self.value[len(self.PREFIX) :]]
-            return col.astype('f' if numeric else 'string')
+            return col.astype("f" if numeric else "string")
         else:
             return float(self.value) if numeric else str(self.value)
 
@@ -493,7 +493,16 @@ def set_choices(self, choices: Iterable[str]):
 
 
 class ColumnOrIntegerParam(ColumnOrStringParam):
-    DEFAULT_VALUE = 0
+    DEFAULT_VALUE : int = 0
+
+    def __init__(
+        self,
+        label: str,
+        value: Optional[int] = 0,
+        choices: Optional[Iterable[str]] = None,
+    ):
+        super().__init__(label, choices=choices)
+        self.value = value
 
     def clean_value(self, value):
         if type(value) is str and value.startswith(self.PREFIX):

countess/plugins/variant.py

@@ -4,7 +4,14 @@
 
 from countess import VERSION
 from countess.core.logger import Logger
-from countess.core.parameters import BooleanParam, ColumnChoiceParam, ColumnOrIntegerParam, ColumnOrStringParam, IntegerParam, StringParam
+from countess.core.parameters import (
+    BooleanParam,
+    ColumnChoiceParam,
+    ColumnOrIntegerParam,
+    ColumnOrStringParam,
+    IntegerParam,
+    StringParam,
+)
 from countess.core.plugins import PandasTransformDictToDictPlugin
 from countess.utils.variant import find_variant_string
 
@@ -31,6 +38,8 @@ class VariantPlugin(PandasTransformDictToDictPlugin):
 
     def process_dict(self, data, logger: Logger) -> dict:
         assert isinstance(self.parameters["reference"], ColumnOrStringParam)
+        assert isinstance(self.parameters["offset"], ColumnOrIntegerParam)
+
         sequence = data[self.parameters["column"].value]
         if not sequence:
             return {}

tests/plugins/test_python.py

@@ -1,5 +1,5 @@
-import pandas as pd
 import numpy as np
+import pandas as pd
 import pytest
 
 from countess.core.logger import ConsoleLogger
@@ -8,16 +8,23 @@
 logger = ConsoleLogger()
 
 
-dfi = pd.DataFrame([[1,1,2,7,11],[2,2,3,8,1],[3,3,4,9,3],[4,4,5,10,4],[5,5,6,12,7]], columns=['a','b','c','d','e'])
+dfi = pd.DataFrame(
+    [[1, 1, 2, 7, 11], [2, 2, 3, 8, 1], [3, 3, 4, 9, 3], [4, 4, 5, 10, 4], [5, 5, 6, 12, 7]],
+    columns=["a", "b", "c", "d", "e"],
+)
+
 
 def test_python_builtins():
     plugin = PythonPlugin()
-    plugin.set_parameter("code", """
+    plugin.set_parameter(
+        "code",
+        """
 x = mean(a,b,c,d,e)
 y = std(a,b,c,d,e)
 z = sqrt(pow(a,2) + pow(b,2))
 v = var(a,b,c,d,e)
-    """)
+    """,
+    )
 
     plugin.prepare(["test"], None)
     dfo = plugin.process_dataframe(dfi, logger)
@@ -31,11 +38,14 @@ def test_python_builtins():
 
 def test_python_dropna():
     plugin = PythonPlugin()
-    plugin.set_parameter("code", """
+    plugin.set_parameter(
+        "code",
+        """
 a = None
 n = None
 if d >= 10: d = None
-    """)
+    """,
+    )
     plugin.set_parameter("dropna", True)
 
     plugin.prepare(["test"], None)
@@ -45,5 +55,5 @@ def test_python_dropna():
     assert "n" not in dfo.columns
     assert "d" in dfo.columns
 
-    assert any(np.isnan(dfo['d']))
-    assert not any(np.isnan(dfo['b']))
+    assert any(np.isnan(dfo["d"]))
+    assert not any(np.isnan(dfo["b"]))

tests/plugins/test_variant.py

@@ -47,7 +47,11 @@ def test_variant_ref_column():
 
 def test_variant_ref_offset():
     input_df = pd.DataFrame(
-        [{"seq": "TGAAGTAGAGG", "offs": "0"}, {"seq": "AGAAGTTGTGG", "offs": "10"}, {"seq": "ATAAGAAGAGG", "offs": "100"}]
+        [
+            {"seq": "TGAAGTAGAGG", "offs": "0"},
+            {"seq": "AGAAGTTGTGG", "offs": "10"},
+            {"seq": "ATAAGAAGAGG", "offs": "100"},
+        ]
     )
 
     plugin = VariantPlugin()