From 80de97dc40bed5e0bd6c3c9168e44063d1633dd5 Mon Sep 17 00:00:00 2001
From: Matthew Colpus <mpcolpus@gmail.com>
Date: Fri, 15 Mar 2024 14:12:26 +0000
Subject: [PATCH] style: formatting

---
 gumpy/difference.py                  |  1 +
 gumpy/gene.py                        | 18 +++++++++++-------
 gumpy/genome.py                      |  2 +-
 gumpy/variantfile.py                 |  5 ++++-
 tests/unit/test_minor_populations.py |  1 +
 5 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/gumpy/difference.py b/gumpy/difference.py
index 79f584b..a57e40e 100644
--- a/gumpy/difference.py
+++ b/gumpy/difference.py
@@ -17,6 +17,7 @@
         nucleotides to an array of codons.
     setup_codon_aa_dict() -> dict: Returns a dictionary mapping codon->amino_acid
 """
+
 import warnings
 from abc import ABC  # Python library for abstract classes
 from typing import Dict, List, Tuple
diff --git a/gumpy/gene.py b/gumpy/gene.py
index 9e8d16a..fc9613f 100644
--- a/gumpy/gene.py
+++ b/gumpy/gene.py
@@ -1,6 +1,7 @@
 """
 Gene object
 """
+
 import copy
 import re
 
@@ -13,7 +14,6 @@
 
 # FIXME: problems with rrs, mfpB
 class Gene(object):
-
     """Gene object that uses underlying numpy arrays"""
 
     def __init__(
@@ -363,9 +363,11 @@ def minority_populations_GARC(
                 #   and mixed for mixed indels and SNPs
                 c = Counter(
                     [
-                        (nc_idx, "indel")
-                        if type_ in ["ins", "del"]
-                        else (nc_idx, type_)
+                        (
+                            (nc_idx, "indel")
+                            if type_ in ["ins", "del"]
+                            else (nc_idx, type_)
+                        )
                         for nc_idx, type_, bases, cov, frs in gene_pos_map[gene_pos]
                     ]
                 )
@@ -519,9 +521,11 @@ def __duplicate(self, index: int):
         # Check for promoters before the codons
         first_half = [self.nucleotide_number[i] for i in range(index)]
         second_half = [
-            self.nucleotide_number[i] + 1
-            if self.nucleotide_number[i] > 0
-            else self.nucleotide_number[i]
+            (
+                self.nucleotide_number[i] + 1
+                if self.nucleotide_number[i] > 0
+                else self.nucleotide_number[i]
+            )
             for i in range(index, len(self.nucleotide_number))
         ]
         self.nucleotide_number = numpy.array(
diff --git a/gumpy/genome.py b/gumpy/genome.py
index cf5ba0b..c5a1313 100644
--- a/gumpy/genome.py
+++ b/gumpy/genome.py
@@ -1,6 +1,7 @@
 """
 Genome object
 """
+
 import copy
 import gzip
 import pathlib
@@ -16,7 +17,6 @@
 
 
 class Genome(object):
-
     """Genome object"""
 
     def __init__(
diff --git a/gumpy/variantfile.py b/gumpy/variantfile.py
index 2ed74c0..1be2cbc 100644
--- a/gumpy/variantfile.py
+++ b/gumpy/variantfile.py
@@ -1,6 +1,7 @@
 """
 Classes used to parse and store VCF data
 """
+
 import copy
 import pathlib
 import warnings
@@ -523,7 +524,9 @@ def __find_calls(self):
                 variant_type = "ref"
 
             if index in record_positions:
-                raise ValueError("Multiple calls at position " + str(index) + " in VCF file")
+                raise ValueError(
+                    "Multiple calls at position " + str(index) + " in VCF file"
+                )
             record_positions.add(index)
 
             # if the REF, ALT pair are the same length, check if we can decompose
diff --git a/tests/unit/test_minor_populations.py b/tests/unit/test_minor_populations.py
index 6df3b3f..2cc4487 100644
--- a/tests/unit/test_minor_populations.py
+++ b/tests/unit/test_minor_populations.py
@@ -1,5 +1,6 @@
 """Tests relating to minor populations
 """
+
 import pytest
 
 import gumpy