reset index, and add_pheno_to_df index check (#117)

Closes #116

CHANGELOG.rst

@@ -7,6 +7,12 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog <https://keepachangelog.com>`_.
 
 
+main/HEAD
+---------
+- Fixed a `bug <https://github.com/matsengrp/multidms/issues/116>`_ 
+    caused by non-unique indicies in input variant functional score dataframes.
+
+
 0.2.1
 -----
 - Made lineplot_and_heatmap() more private to remove from docs.

multidms/data.py

@@ -205,7 +205,7 @@ def __init__(
         self._conditions = tuple(variants_df["condition"].astype(str).unique())
 
         if str(reference) not in self._conditions:
-            if type(reference) != str:
+            if isinstance(reference, str):
                 raise ValueError(
                     "reference must be a string, note that if your "
                     "condition names are numeric, they are being"
@@ -223,7 +223,7 @@ def __init__(
             raise ValueError("not enough `condition_colors`")
         else:
             self.condition_colors = dict(zip(self._conditions, condition_colors))
-        if not onp.all([type(c) == str for c in self.condition_colors.values()]):
+        if not onp.all([isinstance(c, str) for c in self.condition_colors.values()]):
             raise ValueError("condition_color values must be hexidecimal")
 
         # Check and initialize alphabet & mut parser attributes
@@ -259,7 +259,7 @@ def __init__(
             )
 
         else:
-            df = variants_df.copy()
+            df = variants_df[cols].reset_index(drop=True)
 
         self._split_subs = partial(split_subs, parser=self._mutparser.parse_mut)
         df["wts"], df["sites"], df["muts"] = zip(

multidms/model.py

@@ -280,12 +280,12 @@ def __init__(
                 raise ValueError(
                     "softplus activation requires a lower bound be specified"
                 )
-            elif type(lower_bound) != float:
+            if not isinstance(lower_bound, float):
                 raise ValueError("lower_bound must be a float")
-            else:
-                output_activation = partial(
-                    multidms.biophysical.softplus_activation, lower_bound=lower_bound
-                )
+
+            output_activation = partial(
+                multidms.biophysical.softplus_activation, lower_bound=lower_bound
+            )
 
         for condition in data.conditions:
             self._params[f"gamma_{condition}"] = jnp.zeros(shape=(1,))
@@ -493,7 +493,8 @@ def add_phenotypes_to_df(
         ----------
         df : pandas.DataFrame
             Data frame containing variants. Requirements are the same as
-            those used to initialize the `multidms.Data` object
+            those used to initialize the `multidms.Data` object - except
+            the indices must be unique.
         substitutions_col : str
             Column in `df` giving variants as substitution strings
             with respect to a given variants condition.
@@ -537,6 +538,8 @@ def add_phenotypes_to_df(
             raise ValueError("`df` lacks `substitutions_col` " f"{substitutions_col}")
         if condition_col not in df.columns:
             raise ValueError("`df` lacks `condition_col` " f"{condition_col}")
+        if not df.index.is_unique:
+            raise ValueError("`df` must have unique indices")
 
         # return copy
         ret = df.copy()