add todo statements to address verbose logging in all script files

src/dialect/__main__.py

@@ -8,12 +8,13 @@
     read_cbase_results_file,
 )
 
+# TODO: Create essential and verbose logging info for all methods
+
 
 def main():
     parser = build_argument_parser()
     args = parser.parse_args()
     configure_logging(args.verbose)
-    # TODO: Add TODO statements to all files requiring logging changes
 
     logging.info("Running DIALECT CLI")
     logging.info(f"Arguments: {args}")

src/dialect/models/gene.py

@@ -3,6 +3,8 @@
 import numpy as np
 from scipy.optimize import minimize
 
+# TODO: Create essential and verbose logging info for all methods
+
 
 class Gene:
     def __init__(self, name, samples, counts, bmr_pmf):

src/dialect/models/interaction.py

@@ -7,6 +7,8 @@
 
 from dialect.models.gene import Gene
 
+# TODO: Create essential and verbose logging info for all methods
+
 
 class Interaction:
     def __init__(self, gene_a, gene_b):

src/dialect/utils/discover.py

@@ -2,6 +2,8 @@
 import pandas as pd
 from discover import DiscoverMatrix, pairwise_discover_test
 
+# TODO: Create essential and verbose logging info for all methods
+
 
 def create_mutation_matrix_from_cnt_df(cnt_df, top_genes):
     """

src/dialect/utils/fishers.py

@@ -1,6 +1,8 @@
 import logging
 from statsmodels.stats.multitest import multipletests
 
+# TODO: Create essential and verbose logging info for all methods
+
 
 def run_fishers_exact_analysis(interactions):
     """

src/dialect/utils/generate.py

@@ -6,6 +6,8 @@
 
 from dialect.utils.helpers import *
 
+# TODO: Create essential and verbose logging info for all methods
+
 # ---------------------------------------------------------------------------- #
 #                               Helper Functions                               #
 # ---------------------------------------------------------------------------- #

src/dialect/utils/helpers.py

@@ -7,6 +7,8 @@
 from dialect.models.gene import Gene
 from dialect.models.interaction import Interaction
 
+# TODO: Create essential and verbose logging info for all methods
+
 
 def check_file_exists(fn):
     """

src/dialect/utils/identify.py

@@ -5,6 +5,8 @@
 from dialect.utils.discover import run_discover_analysis
 from dialect.utils.fishers import run_fishers_exact_analysis
 
+# TODO: Create essential and verbose logging info for all methods
+
 
 # ---------------------------------------------------------------------------- #
 #                               Helper Functions                               #

src/dialect/utils/simulate.py

@@ -6,6 +6,8 @@
 from dialect.models.gene import Gene
 from dialect.models.interaction import Interaction
 
+# TODO: Create essential and verbose logging info for all methods
+
 
 # ---------------------------------------------------------------------------- #
 #                               HELPER FUNCTIONS                               #