chore: remove unused imports and variables

barcodeforge/cli.py

@@ -318,7 +318,6 @@ def extract_auspice_data(
     Inspired by Dr. John Huddleston's Gist on processing Auspice JSON files.
     Source: https://gist.github.com/huddlej/5d7bd023d3807c698bd18c706974f2db
     """
-    is_debug = ctx.obj.get("DEBUG", False)  # More robust way to get debug status
     print_info(f"Processing Auspice JSON file:\t{auspice_json_path}", bold=True)
     process_auspice_json(
         tree_json_path=auspice_json_path,

barcodeforge/generate_barcodes.py

@@ -4,7 +4,7 @@
 
 import pandas as pd
 import rich_click as click
-from .utils import sortFun, print_error, print_success, print_info, print_debug
+from .utils import sortFun, print_error, print_success, print_info
 
 
 def parse_tree_paths(df: pd.DataFrame) -> pd.DataFrame:

barcodeforge/plot_barcode.py

@@ -1,7 +1,7 @@
 """Plot barcode from CSV file."""
 
 import pandas as pd
-from .utils import sortFun, print_info, print_debug
+from .utils import print_info, print_debug
 import seaborn as sns
 import matplotlib.pyplot as plt
 from matplotlib.colors import ListedColormap
@@ -46,7 +46,6 @@ def create_barcode_visualization(
     # Prepare chunks
     chunks = []
     dims = []
-    cat_dtype = pd.CategoricalDtype(categories=base_list, ordered=True)
     for i in range(num_chunks):
         ps = all_pos[i * CHUNK : (i + 1) * CHUNK]
         sub = plot_df[plot_df.pos.isin(ps)]

barcodeforge/ref_muts.py

@@ -2,7 +2,7 @@
 from Bio import SeqIO
 from collections import OrderedDict
 import re
-from .utils import print_error, print_warning, print_success, print_info, print_debug
+from .utils import print_warning, print_success, print_info, print_debug
 
 
 def _load_sample_mutations(path):

tests/test_cli.py

@@ -90,9 +90,7 @@ def test_barcode_command_default_options(runner, temp_files, mocker):
         "barcodeforge.cli.create_barcodes_from_lineage_paths"
     )
     mock_create_plot = mocker.patch("barcodeforge.cli.create_barcode_plot")
-    mock_cli_console = mocker.patch.object(
-        barcodeforge.utils, "console", MagicMock(spec=Console)
-    )
+    mocker.patch.object(barcodeforge.utils, "console", MagicMock(spec=Console))
 
     args = [
         "barcode",
@@ -225,9 +223,7 @@ def test_barcode_command_custom_options(runner, temp_files, mocker):
         "barcodeforge.cli.create_barcodes_from_lineage_paths"
     )
     mock_create_plot = mocker.patch("barcodeforge.cli.create_barcode_plot")
-    mock_cli_console = mocker.patch.object(
-        barcodeforge.utils, "console", MagicMock(spec=Console)
-    )
+    mocker.patch.object(barcodeforge.utils, "console", MagicMock(spec=Console))
 
     prefix = "MYPREFIX"
     custom_usher_args = "-U -l"
@@ -376,9 +372,7 @@ def test_barcode_command_nexus_tree(runner, temp_files, mocker):
     mocker.patch("barcodeforge.cli.process_and_reroot_lineages")
     mocker.patch("barcodeforge.cli.create_barcodes_from_lineage_paths")
     mocker.patch("barcodeforge.cli.create_barcode_plot")
-    mock_cli_console = mocker.patch.object(
-        barcodeforge.utils, "console", MagicMock(spec=Console)
-    )
+    mocker.patch.object(barcodeforge.utils, "console", MagicMock(spec=Console))
 
     args = [
         "barcode",
@@ -432,9 +426,7 @@ def test_barcode_command_newick_tree_reformat(runner, temp_files, mocker):
     mocker.patch("barcodeforge.cli.process_and_reroot_lineages")
     mocker.patch("barcodeforge.cli.create_barcodes_from_lineage_paths")
     mocker.patch("barcodeforge.cli.create_barcode_plot")
-    mock_cli_console = mocker.patch.object(
-        barcodeforge.utils, "console", MagicMock(spec=Console)
-    )
+    mocker.patch.object(barcodeforge.utils, "console", MagicMock(spec=Console))
 
     args = [
         "barcode",

tests/test_format_tree.py

@@ -2,7 +2,6 @@
 from pathlib import Path
 from barcodeforge.format_tree import convert_nexus_to_newick, _remove_quotes_from_file
 import tempfile
-import os
 
 # Sample Nexus content
 SAMPLE_NEXUS_CONTENT = """

tests/test_generate_barcodes.py

@@ -12,7 +12,6 @@
     create_barcodes_from_lineage_paths,
     check_allele_consistency,
 )
-from barcodeforge.utils import sortFun  # Assuming sortFun is in utils
 
 
 # Sample data for testing

tests/test_plot_barcode.py

@@ -1,10 +1,7 @@
 import pytest
 import pandas as pd
 from pathlib import Path
-from barcodeforge.plot_barcode import create_barcode_visualization, create_barcode_plot
-import matplotlib.pyplot as plt
-import seaborn as sns
-from matplotlib.colors import ListedColormap
+from barcodeforge.plot_barcode import create_barcode_visualization
 
 
 @pytest.fixture

tests/test_ref_muts.py

@@ -3,11 +3,9 @@
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 from collections import OrderedDict
-from pathlib import Path
 import copy  # Ensure copy is imported
-from unittest.mock import MagicMock, call  # For console mocking
+from unittest.mock import MagicMock  # For console mocking
 from rich.console import Console  # For console spec
-import barcodeforge.utils
 from barcodeforge.ref_muts import (
     _load_sample_mutations,
     _extract_mutations,
@@ -74,11 +72,6 @@ def test_load_sample_mutations(sample_muts_file):
 
 
 def test_extract_mutations():
-    sample_with_muts = {"mutations": "gene1:A123T,C456G>gene2:X1Y"}
-    extracted = _extract_mutations(sample_with_muts)
-    expected = OrderedDict(
-        [("gene2:X1Y", ["gene2:X1Y"]), ("gene1:A123T,C456G", ["gene1:A123T", "C456G"])]
-    )
     # The original code's MUT_PATTERN and splitting logic might be different.
     # This test is based on a common interpretation. Adjust if your MUT_PATTERN is more complex.
     # Based on the provided code: MUT_PATTERN = re.compile(r"([^:]+):([A-Za-z0-9,]+)")