fix linting

Author: Laurenz0908

.gitattributes

@@ -1,3 +1,5 @@
 *.fna filter=lfs diff=lfs merge=lfs -text
 *.k2d filter=lfs diff=lfs merge=lfs -text
 *.bz2 filter=lfs diff=lfs merge=lfs -text
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

.gitignore

@@ -4,3 +4,10 @@ dist/
 guacamole_bio.egg-info/
 __pycache__/
 tests/test_out_pytest/
+.ruffcache
+# pixi environments
+.pixi/*
+pixi.lock
+pixi.toml
+.venv/
+uv.lock

guacamole/create_reference_dist.py

@@ -1,4 +1,5 @@
-import os, sys
+import os
+import sys
 from datetime import datetime
 from time import localtime, strftime
 import pandas as pd

guacamole/guacamole.py

@@ -1,20 +1,17 @@
 # %%
-import os, sys, argparse
-from time import gmtime, localtime
+import os
+import sys
+import argparse
+from time import localtime
 from time import strftime
 from datetime import datetime
 import pandas as pd
 import numpy as np
 import Bio.SeqIO as SeqIO
 import guacamole.library as lib
 import matplotlib.pyplot as plt
-import seaborn as sns
 from math import floor
 from numpy.random import uniform
-from shutil import copyfile
-import subprocess
-import contextlib
-import argparse
 
 
 np.seterr(divide='ignore', invalid='ignore')
@@ -293,10 +290,6 @@ def main():
     time_start = strftime("%m-%d-%Y %H:%M:%S", localtime())
     sys.stdout.write("PROGRAM START TIME: " + time_start + '\n')
 
-    lvl_dict = {'D': 'domains', 'P': 'phylums', 'O': 'orders', 'C': 'classes', 'F': 'families', 'G': 'genuses',
-                'S': 'species'}
-    if level in lvl_dict:
-        abundance_lvl = lvl_dict[level]
     branch = 0
     if len(level) > 1:
         branch = int(level[1:])
@@ -312,7 +305,6 @@ def main():
     n_lvl_total = 0
     n_lvl_est = 0
     n_lvl_del = 0
-    lvl_nodes = []
     leaf_nodes = []
 
     all_nodes = {}
@@ -334,10 +326,6 @@ def main():
         [name, taxid, level_num, level_id, all_reads, level_reads] = report_vals
         total_reads += level_reads
         # Skip unclassified
-        if level_id == 'U':
-            unclassified_line = line
-            u_reads = level_reads
-            continue
         # Tree Root
         if taxid == '1':
             root_node = Tree(name, taxid, level_num, 'R', all_reads, level_reads)