From 392899ba9027292d78725782aeb19b7837fe12ea Mon Sep 17 00:00:00 2001
From: Sangjoon Bob Lee <bobleesj@gmail.com>
Date: Mon, 11 Mar 2024 14:11:28 -0400
Subject: [PATCH 1/2] Add linting with black

---
 ...oliynyk_test_atom_mixing_formatted_log.csv |   2 +-
 filter/occupancy.py                           |  46 ++--
 postprocess/bond.py                           |  11 +-
 postprocess/excel.py                          |  53 +++--
 postprocess/histogram.py                      |  32 +--
 postprocess/writer.py                         |  29 ++-
 preprocess/cif_parser.py                      |  67 +++---
 preprocess/cif_parser_handler.py              |  30 ++-
 preprocess/supercell.py                       | 201 +++++++++++-------
 tests/conftest.py                             |   7 +-
 tests/filter/test_occupancy.py                |  92 ++++----
 tests/postprocess/test_bond.py                |   7 +-
 tests/postprocess/test_pair_order.py          |   6 +-
 tests/preprocess/test_cif_parser.py           |  12 +-
 tests/test_single_cif.py                      |   7 +-
 util/folder.py                                |  22 +-
 util/prompt.py                                |  47 ++--
 util/string_parser.py                         |  12 +-
 util/unit.py                                  |   4 +-
 19 files changed, 399 insertions(+), 288 deletions(-)

diff --git a/20240229_oliynyk_test_atom_mixing_formatted/csv/20240229_oliynyk_test_atom_mixing_formatted_log.csv b/20240229_oliynyk_test_atom_mixing_formatted/csv/20240229_oliynyk_test_atom_mixing_formatted_log.csv
index 3ec4892..4cb0089 100644
--- a/20240229_oliynyk_test_atom_mixing_formatted/csv/20240229_oliynyk_test_atom_mixing_formatted_log.csv
+++ b/20240229_oliynyk_test_atom_mixing_formatted/csv/20240229_oliynyk_test_atom_mixing_formatted_log.csv
@@ -1,2 +1,2 @@
 File,Number of atoms in supercell,Processing time (s)
-539016,334,3.585
+539016,334,3.945
diff --git a/filter/occupancy.py b/filter/occupancy.py
index dc5a5a9..6f6c90c 100644
--- a/filter/occupancy.py
+++ b/filter/occupancy.py
@@ -17,9 +17,7 @@ def get_coord_occupancy_sum(cif_loop_values):
     coord_occupancy_sum = {}
 
     for i in range(num_atom_labels):
-        _, occupancy, coordinates = cif_parser.get_atom_info(
-            cif_loop_values, i
-        )
+        _, occupancy, coordinates = cif_parser.get_atom_info(cif_loop_values, i)
         occupancy_num = coord_occupancy_sum.get(coordinates, 0) + occupancy
         coord_occupancy_sum[coordinates] = occupancy_num
 
@@ -69,7 +67,7 @@ def get_all_possible_ordered_label_pairs(cif_loop_values):
     # Get a list of unique pairs from atomic labels
     label_list = cif_parser.get_atom_label_list(cif_loop_values)
     all_possible_label_pairs = list(product(label_list, repeat=2))
-    
+
     # Step 1: Sort each pair to standardize order
     sorted_pairs = pair_order.sort_tuple_in_list(all_possible_label_pairs)
 
@@ -77,17 +75,16 @@ def get_all_possible_ordered_label_pairs(cif_loop_values):
     unique_sorted_pairs = list(set(sorted_pairs))
 
     # Step 3. Order pairs based on Mendeleev ordering
-    unique_sorted_pairs_ordered = (
-        [tuple(pair_order.order_pair_by_mendeleev(pair))
-         for pair in unique_sorted_pairs]
-    )
+    unique_sorted_pairs_ordered = [
+        tuple(pair_order.order_pair_by_mendeleev(pair))
+        for pair in unique_sorted_pairs
+    ]
 
     return unique_sorted_pairs_ordered
 
 
 # Get atom site mixing label for all pairs possible
-def get_atom_site_mixing_dict(
-        atom_site_mixing_file_info, cif_loop_values):
+def get_atom_site_mixing_dict(atom_site_mixing_file_info, cif_loop_values):
     """
     Gets atomic site mixing dictionary for all possible label pairs using cif loop values.
     """
@@ -122,7 +119,7 @@ def get_atom_site_mixing_dict(
             if first_label_occ == 1 and second_label_occ == 1:
                 atom_site_pair_dict[pair] = "4"
                 continue
-    
+
             # Step 4. Check deficiecny at the pair level
             # Check whehter one of the sites is deficient
             is_first_label_site_deficient = None
@@ -136,7 +133,7 @@ def get_atom_site_mixing_dict(
 
                 if occupancy_sum[second_label_coord] < 1:
                     is_second_label_deficient = True
-                    
+
                 else:
                     is_second_label_deficient = False
 
@@ -162,28 +159,29 @@ def get_atom_site_mixing_dict(
             # Assign "3" for "deficiency_no_atomic_mixing"
             # Check 1. One of the labels is deficient
             # Check 2. Both labels are not atomic mixed
-            if ((is_first_label_site_deficient or
-                 is_second_label_deficient) and
-                (not is_first_label_atomic_mixed and
-                 not is_second_label_atomic_mixed)):
+            if (
+                is_first_label_site_deficient or is_second_label_deficient
+            ) and (
+                not is_first_label_atomic_mixed
+                and not is_second_label_atomic_mixed
+            ):
                 atom_site_pair_dict[pair] = "3"
 
             # Assign "2" for "full_occupancy_atomic_mixing"
             # Check 1. Both labels are not deficient
             # Check 2. At least one label is atomic mixed
-            if ((not is_first_label_site_deficient
-                 and not is_second_label_deficient) and
-                (is_first_label_atomic_mixed or
-                 is_second_label_atomic_mixed)):
+            if (
+                not is_first_label_site_deficient
+                and not is_second_label_deficient
+            ) and (is_first_label_atomic_mixed or is_second_label_atomic_mixed):
                 atom_site_pair_dict[pair] = "2"
 
             # Assign "1" for "deficiency"
             # Check 1. At least one label is deficient
             # Check 2. At least one label mixed
-            if ((is_first_label_site_deficient or
-                 is_second_label_deficient) and
-                (is_first_label_atomic_mixed or
-                 is_second_label_atomic_mixed)):
+            if (
+                is_first_label_site_deficient or is_second_label_deficient
+            ) and (is_first_label_atomic_mixed or is_second_label_atomic_mixed):
                 atom_site_pair_dict[pair] = "1"
 
     return atom_site_pair_dict
diff --git a/postprocess/bond.py b/postprocess/bond.py
index 13e1e59..83438e4 100644
--- a/postprocess/bond.py
+++ b/postprocess/bond.py
@@ -86,7 +86,9 @@ def get_sorted_missing_pairs(pair_dict):
     )
 
     # Sort the pairs in the data as well before comparison
-    missing_label_pairs = [pair for pair in all_pairs if pair not in pairs_found]
+    missing_label_pairs = [
+        pair for pair in all_pairs if pair not in pairs_found
+    ]
 
     return missing_label_pairs
 
@@ -118,7 +120,8 @@ def get_unique_pairs_dict(ordered_pairs, filename):
         # if this pair is shorter than the previous pair
         if (
             label_tuple not in unique_pairs_dict[filename]
-            or pair["distance"] < unique_pairs_dict[filename][label_tuple]["distance"]
+            or pair["distance"]
+            < unique_pairs_dict[filename][label_tuple]["distance"]
         ):
             # Add this pair to the dictionary
             unique_pairs_dict[filename][label_tuple] = pair
@@ -126,7 +129,9 @@ def get_unique_pairs_dict(ordered_pairs, filename):
     return unique_pairs_dict
 
 
-def get_dist_mix_pair_dict(dist_pair_dict, unique_pairs_dict, label_pair_mixing_dict):
+def get_dist_mix_pair_dict(
+    dist_pair_dict, unique_pairs_dict, label_pair_mixing_dict
+):
     """
     Returns dict containing files and dist per pair.
     """
diff --git a/postprocess/excel.py b/postprocess/excel.py
index 732cf71..a1748fa 100644
--- a/postprocess/excel.py
+++ b/postprocess/excel.py
@@ -17,10 +17,12 @@ def write_label_pair_dict_to_excel_json(input_dict, pair_tpye, dir_path):
         os.makedirs(output_dir)
 
     folder_name = os.path.basename(os.path.normpath(dir_path))
-    excel_file_path = os.path.join(output_dir,
-                                   f"{folder_name}_{pair_tpye}_pairs.xlsx")
-    json_file_path = os.path.join(output_dir,
-                                  f"{folder_name}_{pair_tpye}_pairs.json")
+    excel_file_path = os.path.join(
+        output_dir, f"{folder_name}_{pair_tpye}_pairs.xlsx"
+    )
+    json_file_path = os.path.join(
+        output_dir, f"{folder_name}_{pair_tpye}_pairs.json"
+    )
 
     category_mapping = {
         1: "deficiency",
@@ -43,14 +45,17 @@ def write_label_pair_dict_to_excel_json(input_dict, pair_tpye, dir_path):
                 inplace=True,
             )
 
-            df["Distance"] = pd.to_numeric(df["Distance"],
-                                           errors="coerce").astype(float)
+            df["Distance"] = pd.to_numeric(
+                df["Distance"], errors="coerce"
+            ).astype(float)
 
             # Convert 'Atomic Mixing' column to numeric, coerce errors
-            df["Atomic Mixing"] = df["Atomic Mixing"].apply(pd.to_numeric,
-                                                            errors="coerce")
+            df["Atomic Mixing"] = df["Atomic Mixing"].apply(
+                pd.to_numeric, errors="coerce"
+            )
             df["Atomic Mixing"] = (
-                df["Atomic Mixing"].map(category_mapping).fillna("Unknown"))
+                df["Atomic Mixing"].map(category_mapping).fillna("Unknown")
+            )
             df["File"] = df["File"].apply(lambda x: f"{x}.cif")
             df.sort_values(by="Distance", inplace=True)
 
@@ -76,10 +81,12 @@ def write_element_pair_dict_to_excel_json(input_dict, pair_type, dir_path):
     os.makedirs(output_dir, exist_ok=True)
 
     folder_name = os.path.basename(os.path.normpath(dir_path))
-    excel_file_path = os.path.join(output_dir,
-                                   f"{folder_name}_{pair_type}_pairs.xlsx")
-    json_file_path = os.path.join(output_dir,
-                                  f"{folder_name}_{pair_type}_pairs.json")
+    excel_file_path = os.path.join(
+        output_dir, f"{folder_name}_{pair_type}_pairs.xlsx"
+    )
+    json_file_path = os.path.join(
+        output_dir, f"{folder_name}_{pair_type}_pairs.json"
+    )
 
     category_mapping = {
         "1": "deficiency",
@@ -96,23 +103,27 @@ def write_element_pair_dict_to_excel_json(input_dict, pair_type, dir_path):
                 for info in infos:  # Here infos is a list of dictionaries
                     info_copy = info.copy()
                     info_copy[
-                        "File"] = f"{file_id}.cif"  # Add the file ID as 'File'
+                        "File"
+                    ] = f"{file_id}.cif"  # Add the file ID as 'File'
                     aggregated_info.append(info_copy)
 
             # Create a DataFrame from the aggregated information
             df = pd.DataFrame(aggregated_info)
 
             # Rename columns to match the expected format
-            df.rename(columns={
-                "dist": "Distance",
-                "mixing": "Atomic Mixing"
-            },
-                      inplace=True)
+            df.rename(
+                columns={"dist": "Distance", "mixing": "Atomic Mixing"},
+                inplace=True,
+            )
 
             # Apply numeric transformation and category mapping
             df["Distance"] = pd.to_numeric(df["Distance"], errors="coerce")
-            df["Atomic Mixing"] = (df["Atomic Mixing"].astype(str).map(
-                category_mapping).fillna("Unknown"))
+            df["Atomic Mixing"] = (
+                df["Atomic Mixing"]
+                .astype(str)
+                .map(category_mapping)
+                .fillna("Unknown")
+            )
             df.sort_values(by="Distance", inplace=True)
 
             # Specify the desired column order
diff --git a/postprocess/histogram.py b/postprocess/histogram.py
index 15f1463..2b883da 100644
--- a/postprocess/histogram.py
+++ b/postprocess/histogram.py
@@ -54,8 +54,9 @@ def plot_histograms_from_label_dict(data, directory_path):
         labels = []
         for cat, _ in categories_colors.items():
             category_distances = [
-                float(pair_info["dist"]) for sub_key, 
-                pair_info in pair_info.items() if pair_info["mixing"] == cat
+                float(pair_info["dist"])
+                for sub_key, pair_info in pair_info.items()
+                if pair_info["mixing"] == cat
             ]
             if category_distances:
                 stacked_data.append(category_distances)
@@ -69,18 +70,19 @@ def plot_histograms_from_label_dict(data, directory_path):
                 color=[categories_colors[cat] for cat in labels],
                 label=[categories_mapping[cat] for cat in labels],
                 stacked=True,
-                edgecolor='black'
+                edgecolor="black",
             )
 
         ax.set_title(atomic_pair)
         ax.set_xlabel("Distance (Å)")
         ax.set_ylabel("Count")
-        ax.legend(loc='upper right')
+        ax.legend(loc="upper right")
 
     plt.tight_layout()
-    plt.savefig(os.path.join(
-        directory_path,
-        "output", "histograms_label_pair.png"), dpi=150)
+    plt.savefig(
+        os.path.join(directory_path, "output", "histograms_label_pair.png"),
+        dpi=150,
+    )
 
     plt.close()
 
@@ -114,7 +116,7 @@ def plot_histograms_from_element_dict(data, directory_path):
     for atomic_pair, records in data.items():
         for infos in records.values():
             for info in infos:
-                distances.append(float(info['dist']))
+                distances.append(float(info["dist"]))
 
     all_distances = sorted(distances)
     bins = np.linspace(min(all_distances), max(all_distances), 21)
@@ -129,8 +131,10 @@ def plot_histograms_from_element_dict(data, directory_path):
         labels = []
         for cat, color in categories_colors.items():
             category_distances = [
-                float(info['dist']) for infos in records.values()
-                for info in infos if info['mixing'] == cat
+                float(info["dist"])
+                for infos in records.values()
+                for info in infos
+                if info["mixing"] == cat
             ]
             if category_distances:
                 stacked_data.append(category_distances)
@@ -144,15 +148,17 @@ def plot_histograms_from_element_dict(data, directory_path):
                 color=[categories_colors[cat] for cat in labels],
                 label=[categories_mapping[cat] for cat in labels],
                 stacked=True,
-                edgecolor='black'
+                edgecolor="black",
             )
 
         ax.set_xlabel("Distance (Å)")
         ax.set_ylabel("Count")
-        ax.legend(loc='upper right')
+        ax.legend(loc="upper right")
 
     plt.tight_layout()
     output_dir = os.path.join(directory_path, "output")
     os.makedirs(output_dir, exist_ok=True)  # Ensure output directory exists
-    plt.savefig(os.path.join(output_dir, "histograms_element_pair.png"), dpi=150)
+    plt.savefig(
+        os.path.join(output_dir, "histograms_element_pair.png"), dpi=150
+    )
     plt.close()
diff --git a/postprocess/writer.py b/postprocess/writer.py
index 6cca398..8a62c8e 100644
--- a/postprocess/writer.py
+++ b/postprocess/writer.py
@@ -3,10 +3,8 @@
 
 
 def write_summary_and_missing_pairs(
-        dist_mix_pair_dict,
-        missing_pairs,
-        text_filename,
-        dir_path):
+    dist_mix_pair_dict, missing_pairs, text_filename, dir_path
+):
     """
     Writes a summary of unique atomic pairs, including counts and distances,
     and a list of missing pairs to a file.
@@ -22,16 +20,16 @@ def write_summary_and_missing_pairs(
     # Step 1: Collect data
     data = []
     for pair, files in dist_mix_pair_dict.items():
-        distances = sorted(float(info['dist']) for info in files.values())
+        distances = sorted(float(info["dist"]) for info in files.values())
         count = len(distances)
-        dists = ', '.join(f"{distance:.3f}" for distance in distances)
+        dists = ", ".join(f"{distance:.3f}" for distance in distances)
         data.append((pair, count, dists))
 
     # Step 2: Sort the data first by count (descending) then by pair name
     sorted_data = sorted(data, key=lambda x: (-x[1], x[0]))
 
     # Step 3: Write sorted data to file
-    with open(file_path, 'w', encoding="utf-8") as file:
+    with open(file_path, "w", encoding="utf-8") as file:
         file.write("Summary:\n")
         for pair, count, dists in sorted_data:
             file.write(f"Pair: {pair}, Count: {count} Distances: {dists}\n")
@@ -54,10 +52,8 @@ def write_summary_and_missing_pairs(
 
 
 def write_summary_and_missing_pairs_with_element_dict(
-        dist_mix_pair_dict,
-        missing_pairs,
-        text_filename,
-        dir_path):
+    dist_mix_pair_dict, missing_pairs, text_filename, dir_path
+):
     """
     Writes a summary of unique atomic pairs, including counts and distances,
     and a list of missing pairs to a file.
@@ -76,25 +72,26 @@ def write_summary_and_missing_pairs_with_element_dict(
         distances = []
         for file_infos in files.values():
             for info in file_infos:  # Access each list in the dictionary
-                distances.append(float(info['dist']))
+                distances.append(float(info["dist"]))
         distances = sorted(distances)
         count = len(distances)
-        dists = ', '.join(f"{distance:.3f}" for distance in distances)
+        dists = ", ".join(f"{distance:.3f}" for distance in distances)
         data.append((pair, count, dists))
 
     # Step 2: Sort the data first by count (descending) then by pair name
     sorted_data = sorted(data, key=lambda x: (-x[1], x[0]))
 
     # Step 3: Write sorted data to file
-    with open(file_path, 'w', encoding="utf-8") as file:
-
+    with open(file_path, "w", encoding="utf-8") as file:
         print("\nMissing pairs:")
         file.write("Summary:\n")
         for pair, count, dists in sorted_data:
             file.write(f"Pair: {pair}, Count: {count}, Distances: {dists}\n")
 
         file.write("\nMissing pairs:\n")
-        missing_pairs_sorted = sorted(missing_pairs, key=lambda x: (x[0][0], x[0], x[1]))
+        missing_pairs_sorted = sorted(
+            missing_pairs, key=lambda x: (x[0][0], x[0], x[1])
+        )
         for pair in missing_pairs_sorted:
             atom_1, atom_2 = pair
             file.write(f"{atom_1}-{atom_2}\n")
diff --git a/preprocess/cif_parser.py b/preprocess/cif_parser.py
index 5e6dc50..07662f5 100755
--- a/preprocess/cif_parser.py
+++ b/preprocess/cif_parser.py
@@ -8,10 +8,10 @@ def get_atom_type(label):
     """
     Returns the element from the given label
     """
-    parts = re.split(r'[()]', label)
+    parts = re.split(r"[()]", label)
     for part in parts:
         # Attempt to extract the atom type
-        match = re.search(r'([A-Z][a-z]*)', part)
+        match = re.search(r"([A-Z][a-z]*)", part)
         if match:
             return match.group(1)
     return None
@@ -21,14 +21,16 @@ def get_loop_tags():
     """
     Returns tags commonly used for atomic description.
     """
-    loop_tags = ["_atom_site_label",
-                 "_atom_site_type_symbol",
-                 "_atom_site_symmetry_multiplicity", 
-                 "_atom_site_Wyckoff_symbol",
-                 "_atom_site_fract_x",
-                 "_atom_site_fract_y",
-                 "_atom_site_fract_z",
-                 "_atom_site_occupancy"]
+    loop_tags = [
+        "_atom_site_label",
+        "_atom_site_type_symbol",
+        "_atom_site_symmetry_multiplicity",
+        "_atom_site_Wyckoff_symbol",
+        "_atom_site_fract_x",
+        "_atom_site_fract_y",
+        "_atom_site_fract_z",
+        "_atom_site_occupancy",
+    ]
 
     return loop_tags
 
@@ -37,22 +39,16 @@ def get_unit_cell_lengths_angles(block):
     """
     Returns the unit cell lengths and angles from a given block.
     """
-    keys_lengths = [
-        '_cell_length_a',
-        '_cell_length_b',
-        '_cell_length_c'
+    keys_lengths = ["_cell_length_a", "_cell_length_b", "_cell_length_c"]
+    keys_angles = ["_cell_angle_alpha", "_cell_angle_beta", "_cell_angle_gamma"]
+
+    lengths = [
+        remove_string_braket(block.find_value(key)) for key in keys_lengths
     ]
-    keys_angles = [
-        '_cell_angle_alpha',
-        '_cell_angle_beta',
-        '_cell_angle_gamma'
+    angles = [
+        remove_string_braket(block.find_value(key)) for key in keys_angles
     ]
 
-    lengths = [remove_string_braket(block.find_value(key))
-               for key in keys_lengths]
-    angles = [remove_string_braket(block.find_value(key))
-              for key in keys_angles]
-
     return tuple(lengths + angles)
 
 
@@ -74,9 +70,11 @@ def get_loop_values(block, loop_tags):
     loop_values = [block.find_loop(tag) for tag in loop_tags]
 
     # Check for zero or missing coordinates
-    if (len(loop_values[4]) == 0 or
-        len(loop_values[5]) == 0 or
-        len(loop_values[6]) == 0):
+    if (
+        len(loop_values[4]) == 0
+        or len(loop_values[5]) == 0
+        or len(loop_values[6]) == 0
+    ):
         raise RuntimeError("Missing atomic coordinates")
 
     return loop_values
@@ -88,7 +86,14 @@ def get_cell_lenghts_angles_rad(CIF_block):
     """
     # Extract cell dimensions and angles from CIF block
     cell_lengths_angles = get_unit_cell_lengths_angles(CIF_block)
-    cell_len_a, cell_len_b, cell_len_c, alpha_deg, beta_deg, gamma_deg = cell_lengths_angles
+    (
+        cell_len_a,
+        cell_len_b,
+        cell_len_c,
+        alpha_deg,
+        beta_deg,
+        gamma_deg,
+    ) = cell_lengths_angles
 
     # Convert angles from degrees to radians
     alpha_rad, beta_rad, gamma_rad = get_radians_from_degrees(
@@ -140,9 +145,11 @@ def get_atom_info(cif_loop_values, i):
     """
     label = cif_loop_values[0][i]
     occupancy = float(remove_string_braket(cif_loop_values[7][i]))
-    coordinates = (remove_string_braket(cif_loop_values[4][i]),
-                   remove_string_braket(cif_loop_values[5][i]),
-                   remove_string_braket(cif_loop_values[6][i]))
+    coordinates = (
+        remove_string_braket(cif_loop_values[4][i]),
+        remove_string_braket(cif_loop_values[5][i]),
+        remove_string_braket(cif_loop_values[6][i]),
+    )
 
     return label, occupancy, coordinates
 
diff --git a/preprocess/cif_parser_handler.py b/preprocess/cif_parser_handler.py
index af0f3ee..34f0d15 100644
--- a/preprocess/cif_parser_handler.py
+++ b/preprocess/cif_parser_handler.py
@@ -9,17 +9,24 @@ def get_cif_info(file_path, loop_tags, supercell_generation_method=3):
     Parse CIF data from file path.
     """
     cif_block = cif_parser.get_cif_block(file_path)
-    cell_lengths, cell_angles_rad = cif_parser.get_cell_lenghts_angles_rad(cif_block)
+    cell_lengths, cell_angles_rad = cif_parser.get_cell_lenghts_angles_rad(
+        cif_block
+    )
     cif_loop_values = cif_parser.get_loop_values(cif_block, loop_tags)
     all_coords_list = supercell.get_coords_list(cif_block, cif_loop_values)
     all_points, unique_labels, atom_site_list = supercell.get_points_and_labels(
-        all_coords_list,
-        cif_loop_values,
-        supercell_generation_method
+        all_coords_list, cif_loop_values, supercell_generation_method
     )
 
-    return cif_block, cell_lengths, cell_angles_rad, \
-           all_coords_list, all_points, unique_labels, atom_site_list
+    return (
+        cif_block,
+        cell_lengths,
+        cell_angles_rad,
+        all_coords_list,
+        all_points,
+        unique_labels,
+        atom_site_list,
+    )
 
 
 def get_cif_loop_values(file_path: str) -> list:
@@ -33,9 +40,7 @@ def get_cif_loop_values(file_path: str) -> list:
     return cif_loop_values
 
 
-def get_folder_and_files_info(
-        script_directory: str,
-        is_interactive_mode: bool):
+def get_folder_and_files_info(script_directory: str, is_interactive_mode: bool):
     """
     Get info about folders and files.
     """
@@ -51,8 +56,11 @@ def get_folder_and_files_info(
 
     filtered_folder_name = f"{folder_name}_filter_dist_min"
     filtered_folder = os.path.join(folder_info, filtered_folder_name)
-    files_lst = [os.path.join(folder_info, file)
-                 for file in os.listdir(folder_info) if file.endswith('.cif')]
+    files_lst = [
+        os.path.join(folder_info, file)
+        for file in os.listdir(folder_info)
+        if file.endswith(".cif")
+    ]
     num_of_files = len(files_lst)
     loop_tags = cif_parser.get_loop_tags()
 
diff --git a/preprocess/supercell.py b/preprocess/supercell.py
index 7a14254..65e1c46 100755
--- a/preprocess/supercell.py
+++ b/preprocess/supercell.py
@@ -22,9 +22,30 @@ def calculate_distance(point1, point2, cell_lengths, angles):
     dz_sq = (cell_lengths[2] * delta_z) ** 2
 
     # Calculate cross terms
-    cross_x = 2 * cell_lengths[1] * cell_lengths[2] * np.cos(angles[0]) * delta_y * delta_z
-    cross_y = 2 * cell_lengths[2] * cell_lengths[0] * np.cos(angles[1]) * delta_z * delta_x
-    cross_z = 2 * cell_lengths[0] * cell_lengths[1] * np.cos(angles[2]) * delta_x * delta_y
+    cross_x = (
+        2
+        * cell_lengths[1]
+        * cell_lengths[2]
+        * np.cos(angles[0])
+        * delta_y
+        * delta_z
+    )
+    cross_y = (
+        2
+        * cell_lengths[2]
+        * cell_lengths[0]
+        * np.cos(angles[1])
+        * delta_z
+        * delta_x
+    )
+    cross_z = (
+        2
+        * cell_lengths[0]
+        * cell_lengths[1]
+        * np.cos(angles[2])
+        * delta_x
+        * delta_y
+    )
 
     # Calculate squared distance
     result = dx_sq + dy_sq + dz_sq + cross_x + cross_y + cross_z
@@ -35,10 +56,9 @@ def calculate_distance(point1, point2, cell_lengths, angles):
     return distance, label1, label2
 
 
-
-def shift_and_append_points(points, atom_site_label,
-                            num_unitcell_atom,
-                            supercell_generation_method):
+def shift_and_append_points(
+    points, atom_site_label, num_unitcell_atom, supercell_generation_method
+):
     """
     Shift and duplicate points to create supercell.
     """
@@ -55,52 +75,83 @@ def shift_and_append_points(points, atom_site_label,
             all_points = []
             for point_group in shifted_points:
                 for point in point_group:
-                    new_point = (*np.round(point,5), atom_site_label)
+                    new_point = (*np.round(point, 5), atom_site_label)
                     all_points.append(new_point)
 
             return all_points
 
-        if supercell_generation_method == 2:        
-            shifts = np.array([
-                [0, 0, 0], [1, 0, 0], [0, 1, 0],
-                [1, 1, 0], [0, 0, 1], [1, 0, 1],
-                [0, 1, 1], [1, 1, 1]
-            ])
+        if supercell_generation_method == 2:
+            shifts = np.array(
+                [
+                    [0, 0, 0],
+                    [1, 0, 0],
+                    [0, 1, 0],
+                    [1, 1, 0],
+                    [0, 0, 1],
+                    [1, 0, 1],
+                    [0, 1, 1],
+                    [1, 1, 1],
+                ]
+            )
             shifted_points = points[:, None, :] + shifts[None, :, :]
             all_points = []
             for point_group in shifted_points:
                 for point in point_group:
-                    new_point = (*np.round(point,5), atom_site_label)
+                    new_point = (*np.round(point, 5), atom_site_label)
                     all_points.append(new_point)
 
             return all_points
 
-        if supercell_generation_method == 3:        
-            shifts = np.array([
-                [0, 0, 0],[1, 0, 0], [0, 1, 0],
-                [1, 1, 0], [0, 0, 1], [1, 0, 1],
-                [0, 1, 1], [1, 1, 1], [-1, 0, 0],
-                [0, -1, 0], [-1, -1, 0], [0, 0, -1],
-                [1, 0, -1], [0, -1, -1], [-1, -1, -1]
-            ])
-            
+        if supercell_generation_method == 3:
+            shifts = np.array(
+                [
+                    [0, 0, 0],
+                    [1, 0, 0],
+                    [0, 1, 0],
+                    [1, 1, 0],
+                    [0, 0, 1],
+                    [1, 0, 1],
+                    [0, 1, 1],
+                    [1, 1, 1],
+                    [-1, 0, 0],
+                    [0, -1, 0],
+                    [-1, -1, 0],
+                    [0, 0, -1],
+                    [1, 0, -1],
+                    [0, -1, -1],
+                    [-1, -1, -1],
+                ]
+            )
+
             shifted_points = points[:, None, :] + shifts[None, :, :]
             all_points = []
             for point_group in shifted_points:
                 for point in point_group:
-                    new_point = (*np.round(point,5), atom_site_label)
+                    new_point = (*np.round(point, 5), atom_site_label)
                     all_points.append(new_point)
 
             return all_points
 
     # General method for files below 200 atoms in the unit cell
-    shifts = np.array([
-        [0, 0, 0], [1, 0, 0], [0, 1, 0],
-        [1, 1, 0], [0, 0, 1], [1, 0, 1],
-        [0, 1, 1], [1, 1, 1], [-1, 0, 0],
-        [0, -1, 0], [-1, -1, 0], [0, 0, -1],
-        [1, 0, -1], [0, -1, -1], [-1, -1, -1]
-    ])
+    shifts = np.array(
+        [
+            [0, 0, 0],
+            [1, 0, 0],
+            [0, 1, 0],
+            [1, 1, 0],
+            [0, 0, 1],
+            [1, 0, 1],
+            [0, 1, 1],
+            [1, 1, 1],
+            [-1, 0, 0],
+            [0, -1, 0],
+            [-1, -1, 0],
+            [0, 0, -1],
+            [1, 0, -1],
+            [0, -1, -1],
+            [-1, -1, -1],
+        ]
+    )
 
     shifted_points = points[:, None, :] + shifts[None, :, :]
     all_points = []
@@ -114,7 +165,7 @@ def shift_and_append_points(points, atom_site_label,
 
 def get_coords_list(block, loop_values):
     """
-    Computes the new coordinates after applying 
+    Computes the new coordinates after applying
     symmetry operations to the initial coordinates.
     """
 
@@ -127,22 +178,24 @@ def get_coords_list(block, loop_values):
         atom_site_label = loop_values[0][i]
 
         coords_after_symmetry_operations = get_coords_after_sym_operations(
-            block, 
+            block,
             float(atom_site_x),
             float(atom_site_y),
             float(atom_site_z),
-            atom_site_label
+            atom_site_label,
         )
         coords_list.append(coords_after_symmetry_operations)
 
     return coords_list
 
 
-def get_coords_after_sym_operations(block,
-                                    atom_site_fract_x,
-                                    atom_site_fract_y,
-                                    atom_site_fract_z,
-                                    atom_site_label):
+def get_coords_after_sym_operations(
+    block,
+    atom_site_fract_x,
+    atom_site_fract_y,
+    atom_site_fract_z,
+    atom_site_label,
+):
     """
     Generates a list of coordinates for each atom site
     """
@@ -151,11 +204,9 @@ def get_coords_after_sym_operations(block,
         operation = operation.replace("'", "")
         try:
             op = gemmi.Op(operation)
-            new_x, new_y, new_z = op.apply_to_xyz([
-                atom_site_fract_x,
-                atom_site_fract_y,
-                atom_site_fract_z
-            ])
+            new_x, new_y, new_z = op.apply_to_xyz(
+                [atom_site_fract_x, atom_site_fract_y, atom_site_fract_z]
+            )
             new_x = round(new_x, 5)
             new_y = round(new_y, 5)
             new_z = round(new_z, 5)
@@ -164,14 +215,16 @@ def get_coords_after_sym_operations(block,
 
         except RuntimeError as e:
             print(f"Skipping operation '{operation}': {str(e)}")
-            raise RuntimeError("An error occurred while processing symmetry operation") from e
+            raise RuntimeError(
+                "An error occurred while processing symmetry operation"
+            ) from e
 
     return list(all_coords)
 
 
-def get_points_and_labels(all_coords_list,
-                          loop_values,
-                          supercell_generation_method):
+def get_points_and_labels(
+    all_coords_list, loop_values, supercell_generation_method
+):
     """
     Process coordinates and loop values to extract points, labels, and atom types.
     """
@@ -183,30 +236,37 @@ def get_points_and_labels(all_coords_list,
     num_unitcell_atom = 0
 
     for i, all_coords in enumerate(all_coords_list):
-        points = np.array([list(map(float, coord[:-1])) for coord in all_coords])
+        points = np.array(
+            [list(map(float, coord[:-1])) for coord in all_coords]
+        )
         num_unitcell_atom += len(points)
 
-
     for i, all_coords in enumerate(all_coords_list):
-        points = np.array([list(map(float, coord[:-1])) for coord in all_coords])
+        points = np.array(
+            [list(map(float, coord[:-1])) for coord in all_coords]
+        )
         atom_site_label = loop_values[0][i]
         atom_site_type = loop_values[1][i]
 
         unique_labels.append(atom_site_label)
         unique_atoms_tuple.append(atom_site_type)
 
-        all_points.extend(shift_and_append_points(
-            points, 
-            atom_site_label,
-            num_unitcell_atom,
-            supercell_generation_method
-        ))
+        all_points.extend(
+            shift_and_append_points(
+                points,
+                atom_site_label,
+                num_unitcell_atom,
+                supercell_generation_method,
+            )
+        )
 
         if atom_site_type in atom_site_label:
             continue
 
         if cif_parser.get_atom_type(atom_site_label) != atom_site_type:
-            raise RuntimeError("Different elements found in atom site and label")
+            raise RuntimeError(
+                "Different elements found in atom site and label"
+            )
 
     return list(set(all_points)), unique_labels, unique_atoms_tuple
 
@@ -224,23 +284,22 @@ def get_atomic_pair_list(flattened_points, cell_lengths, angles):
         for j, point2 in enumerate(flattened_points):
             if i != j:
                 pair = tuple(sorted([i, j]))
-                if pair not in pairs_set:  
+                if pair not in pairs_set:
                     distance, atom_label1, atom_label2 = calculate_distance(
-                        point1,
-                        point2,
-                        cell_lengths,
-                        angles
+                        point1, point2, cell_lengths, angles
                     )
                     if abs(distance) > 1e-3:
-                        distances_from_point_i.append({
-                            'point_pair': (i + 1, j + 1),
-                            'labels': (atom_label1, atom_label2),
-                            'coordinates': (point1[:3], point2[:3]),
-                            'distance': np.round(distance, 5)
-                        })
+                        distances_from_point_i.append(
+                            {
+                                "point_pair": (i + 1, j + 1),
+                                "labels": (atom_label1, atom_label2),
+                                "coordinates": (point1[:3], point2[:3]),
+                                "distance": np.round(distance, 5),
+                            }
+                        )
                         pairs_set.add(pair)
 
-        distances_from_point_i.sort(key=lambda x: x['distance'])
+        distances_from_point_i.sort(key=lambda x: x["distance"])
         atomic_info_list.extend(distances_from_point_i)
 
     return atomic_info_list
diff --git a/tests/conftest.py b/tests/conftest.py
index cbe41d2..f1f620f 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,7 +1,8 @@
-#conftest.py
+# conftest.py
 import pytest
 import preprocess.cif_parser_handler as cif_parser_handler
 
+
 @pytest.fixture
 def get_cif_527000_loop_values():
     CIF_loop_values = cif_parser_handler.get_cif_loop_values(
@@ -26,7 +27,7 @@ def get_cif_300160_loop_values():
     return CIF_loop_values
 
 
-@pytest.fixture 
+@pytest.fixture
 def get_cif_1831432_loop_values():
     CIF_loop_values = cif_parser_handler.get_cif_loop_values(
         "tests/filter/cifs/1831432.cif"
@@ -56,5 +57,3 @@ def get_cif_URhIn_loop_values():
         "tests/filter/cifs/URhIn.cif"
     )
     return CIF_loop_values
-
-
diff --git a/tests/filter/test_occupancy.py b/tests/filter/test_occupancy.py
index 94aa840..be67be4 100644
--- a/tests/filter/test_occupancy.py
+++ b/tests/filter/test_occupancy.py
@@ -10,6 +10,7 @@ def test_get_atom_site_mixing_info(get_cif_527000_loop_values):
     )
     assert atom_mixing_type == "3"
 
+
 @pytest.mark.fast
 def test_get_atom_site_mixing_info(get_cif_1803318_loop_values):
     atom_mixing_type = occupancy.get_atom_site_mixing_info(
@@ -20,25 +21,28 @@ def test_get_atom_site_mixing_info(get_cif_1803318_loop_values):
 
 @pytest.mark.fast
 def test_get_all_possible_ordered_label_pair_tuples_300160(
-        get_cif_300160_loop_values):
-
+    get_cif_300160_loop_values,
+):
     ordered_label_pairs = occupancy.get_all_possible_ordered_label_pairs(
         get_cif_300160_loop_values
     )
     assert len(ordered_label_pairs) == 6
-    assert sorted(ordered_label_pairs) == sorted([
-        ("Rh1", "Rh1"),
-        ("Ge1", "Ge1"),
-        ("Sm1", "Sm1"),
-        ("Sm1", "Rh1"),
-        ("Sm1", "Ge1"),
-        ("Rh1", "Ge1")
-        ])
+    assert sorted(ordered_label_pairs) == sorted(
+        [
+            ("Rh1", "Rh1"),
+            ("Ge1", "Ge1"),
+            ("Sm1", "Sm1"),
+            ("Sm1", "Rh1"),
+            ("Sm1", "Ge1"),
+            ("Rh1", "Ge1"),
+        ]
+    )
+
 
 @pytest.mark.fast
 def test_get_all_possible_ordered_label_pair_tuples_URhIn(
-        get_cif_URhIn_loop_values):
-
+    get_cif_URhIn_loop_values,
+):
     ordered_label_pairs = occupancy.get_all_possible_ordered_label_pairs(
         get_cif_URhIn_loop_values
     )
@@ -47,18 +51,21 @@ def test_get_all_possible_ordered_label_pair_tuples_URhIn(
     # In1, U1, Rh1, Rh2
 
     assert len(ordered_label_pairs) == 10
-    assert sorted(ordered_label_pairs) == sorted([
-        ("In1", "In1"),
-        ("U1", "U1"),
-        ("Rh2", "Rh2"),
-        ("Rh1", "Rh1"),  # 4 same pairs
-        ("U1", "In1"),
-        ("Rh1", "In1"),
-        ("Rh2", "In1"),  # 3 pairs below In1
-        ("Rh1", "Rh2"),
-        ("U1", "Rh2"),   # 2 pairs below Rh2
-        ("U1", "Rh1")    # 1 pair below Rh1
-        ])
+    assert sorted(ordered_label_pairs) == sorted(
+        [
+            ("In1", "In1"),
+            ("U1", "U1"),
+            ("Rh2", "Rh2"),
+            ("Rh1", "Rh1"),  # 4 same pairs
+            ("U1", "In1"),
+            ("Rh1", "In1"),
+            ("Rh2", "In1"),  # 3 pairs below In1
+            ("Rh1", "Rh2"),
+            ("U1", "Rh2"),  # 2 pairs below Rh2
+            ("U1", "Rh1"),  # 1 pair below Rh1
+        ]
+    )
+
 
 @pytest.mark.fast
 def test_get_atom_site_mixing_dict_1(get_cif_300160_loop_values):
@@ -67,8 +74,7 @@ def test_get_atom_site_mixing_dict_1(get_cif_300160_loop_values):
     )
 
     atom_site_pair_dict = occupancy.get_atom_site_mixing_dict(
-        atom_site_mixing_file_info,
-        get_cif_300160_loop_values
+        atom_site_mixing_file_info, get_cif_300160_loop_values
     )
 
     # Mendeleev # - Ge 79, Rh 59, Sm 23
@@ -83,17 +89,16 @@ def test_get_atom_site_mixing_dict_1(get_cif_300160_loop_values):
 
 @pytest.mark.fast
 def test_get_atom_site_mixing_dict_2(get_cif_527000_loop_values):
-    '''
+    """
     Pair: Rh2-Si 2.28 Å - deficiency_no_atomic_mixing
     Pair: Rh1-Rh1 2.524 Å - full_occupancy
-    '''
+    """
     atom_site_mixing_file_info = occupancy.get_atom_site_mixing_info(
         get_cif_527000_loop_values
     )
 
     atom_site_pair_dict = occupancy.get_atom_site_mixing_dict(
-        atom_site_mixing_file_info,
-        get_cif_527000_loop_values
+        atom_site_mixing_file_info, get_cif_527000_loop_values
     )
 
     # Mendeleev # - Rh 59, Si 78
@@ -108,32 +113,31 @@ def test_get_atom_site_mixing_dict_2(get_cif_527000_loop_values):
 
 @pytest.mark.fast
 def test_get_atom_site_mixing_dict_3(get_cif_1831432_loop_values):
-    '''
+    """
     Mendeleev # - Fe 55, Ge 79
     1831432.cif
     Fe Fe 8 b 0.375 0.375 0.375 0.01
     Ge1 Ge 8 a 0.125 0.125 0.125 0.944
     Fe2 Fe 8 a 0.125 0.125 0.125 0.056
-    
+
     Result:
     Fe-Fe 2.448 deficiency,
     Fe-Ge 2.448 mixing-deficiency,
     Fe-Fe 2.448 mixing-deficiency
-    '''
+    """
 
     atom_site_mixing_file_info = occupancy.get_atom_site_mixing_info(
         get_cif_1831432_loop_values
     )
 
     atom_site_pair_dict = occupancy.get_atom_site_mixing_dict(
-        atom_site_mixing_file_info,
-        get_cif_1831432_loop_values
+        atom_site_mixing_file_info, get_cif_1831432_loop_values
     )
 
     assert len(atom_site_pair_dict) == 6
     assert atom_site_pair_dict[("Fe", "Fe")] == "3"
     assert atom_site_pair_dict[("Fe", "Fe2")] == "1"
-    assert atom_site_pair_dict[("Fe", "Ge1")] == "1" 
+    assert atom_site_pair_dict[("Fe", "Ge1")] == "1"
     assert atom_site_pair_dict[("Fe2", "Ge1")] == "2"
     assert atom_site_pair_dict[("Fe2", "Fe2")] == "2"
     assert atom_site_pair_dict[("Ge1", "Ge1")] == "2"
@@ -141,7 +145,7 @@ def test_get_atom_site_mixing_dict_3(get_cif_1831432_loop_values):
 
 @pytest.mark.fast
 def test_get_atom_site_mixing_dict_4(get_cif_529848_loop_values):
-    '''
+    """
     Mendeleev # - Ni 61, Sb 85
     529848.cif
     Ni1 Ni 4 a 0 0 0 0.92
@@ -149,14 +153,13 @@ def test_get_atom_site_mixing_dict_4(get_cif_529848_loop_values):
 
     Result:
     529848: Ni-Sb 2.531 mixing
-    '''
+    """
     atom_site_mixing_file_info = occupancy.get_atom_site_mixing_info(
         get_cif_529848_loop_values
     )
 
     atom_site_pair_dict = occupancy.get_atom_site_mixing_dict(
-        atom_site_mixing_file_info,
-        get_cif_529848_loop_values
+        atom_site_mixing_file_info, get_cif_529848_loop_values
     )
 
     assert len(atom_site_pair_dict) == 3
@@ -167,23 +170,22 @@ def test_get_atom_site_mixing_dict_4(get_cif_529848_loop_values):
 
 @pytest.mark.fast
 def test_get_atom_site_mixing_dict_5(get_cif_1617211_loop_values):
-    '''
+    """
     Mendeleev # - Fe 55, Si 78
     1617211.cif
     Si1 Si 2 h 0.5 0.5 0.2700 1
     Fe1A Fe 1 a 0 0 0 0.85008
     Si1B Si 1 a 0 0 0 0.06992
-    
+
     Result:
     529848: Ni-Sb 2.531 mixing
-    '''
+    """
     atom_site_mixing_file_info = occupancy.get_atom_site_mixing_info(
         get_cif_1617211_loop_values
     )
 
     atom_site_pair_dict = occupancy.get_atom_site_mixing_dict(
-        atom_site_mixing_file_info,
-        get_cif_1617211_loop_values
+        atom_site_mixing_file_info, get_cif_1617211_loop_values
     )
 
     assert len(atom_site_pair_dict) == 6
diff --git a/tests/postprocess/test_bond.py b/tests/postprocess/test_bond.py
index fb625ec..0d94aa0 100644
--- a/tests/postprocess/test_bond.py
+++ b/tests/postprocess/test_bond.py
@@ -3,7 +3,7 @@
 
 @pytest.mark.fast
 def test_remove_duplicate_pairs():
-    '''
+    """
     unique_pairs_distances_test = {
         ('Ga1A', 'Ga1'): ['2.601'],
         ('Ga1', 'La1'): ['3.291'],
@@ -11,7 +11,7 @@ def test_remove_duplicate_pairs():
         ('Ga1', 'Ga1A'): ['2.601'],
         ('Ga1', 'Ga1'): ['2.358']}
 
-    to 
+    to
 
     adjusted_pairs_test == {
         ('Ga1', 'Ga1A'): ['2.601'],
@@ -19,8 +19,7 @@ def test_remove_duplicate_pairs():
         ('Co1B', 'Ga1'): ['2.601'],
         ('Ga1', 'Ga1A'): ['2.601'],
         ('Ga1', 'Ga1'): ['2.358']}
-    '''
-
+    """
 
 
 #     # 560709.cif
diff --git a/tests/postprocess/test_pair_order.py b/tests/postprocess/test_pair_order.py
index a5ef643..3edf707 100644
--- a/tests/postprocess/test_pair_order.py
+++ b/tests/postprocess/test_pair_order.py
@@ -27,7 +27,7 @@ def test_order_pair_by_mendeleev_and_label():
 
     expected = pair_order.order_pair_by_mendeleev(("In", "Rh"))
     assert expected == ("Rh", "In")
-    
+
     expected = pair_order.order_pair_by_mendeleev(("Rh4", "Rh2"))
     assert expected == ("Rh2", "Rh4")
 
@@ -51,7 +51,3 @@ def test_sort_tuple_in_list():
     tuple_pairs = [("Co2A", "Co1A")]
     sorted_tuple_pairs = pair_order.sort_tuple_in_list(tuple_pairs)
     assert sorted_tuple_pairs == [("Co1A", "Co2A")]
-
-
-
-
diff --git a/tests/preprocess/test_cif_parser.py b/tests/preprocess/test_cif_parser.py
index a5cf5e8..69c01c3 100644
--- a/tests/preprocess/test_cif_parser.py
+++ b/tests/preprocess/test_cif_parser.py
@@ -6,9 +6,7 @@
 def test_get_unique_element_list(get_cif_527000_loop_values):
     CIF_loop_values = get_cif_527000_loop_values
 
-    unique_element_list = cif_parser.get_unique_element_list(
-      CIF_loop_values
-    )
+    unique_element_list = cif_parser.get_unique_element_list(CIF_loop_values)
     assert set(unique_element_list) == set(["Rh", "Si"])
 
 
@@ -16,9 +14,7 @@ def test_get_unique_element_list(get_cif_527000_loop_values):
 def test_get_atom_label_list(get_cif_527000_loop_values):
     CIF_loop_values = get_cif_527000_loop_values
 
-    label_list = cif_parser.get_atom_label_list(
-      CIF_loop_values
-    )
+    label_list = cif_parser.get_atom_label_list(CIF_loop_values)
     assert label_list == ["Rh2", "Si", "Rh1"]
 
 
@@ -26,7 +22,5 @@ def test_get_atom_label_list(get_cif_527000_loop_values):
 def test_get_num_of_atom_labels(get_cif_527000_loop_values):
     CIF_loop_values = get_cif_527000_loop_values
 
-    num_of_atom_labels = cif_parser.get_num_of_atom_labels(
-      CIF_loop_values
-    )
+    num_of_atom_labels = cif_parser.get_num_of_atom_labels(CIF_loop_values)
     assert num_of_atom_labels == 3
diff --git a/tests/test_single_cif.py b/tests/test_single_cif.py
index 9b9f546..f58207a 100644
--- a/tests/test_single_cif.py
+++ b/tests/test_single_cif.py
@@ -1,4 +1,6 @@
-from main import main  # Assuming main.py and this test file are in the same directory
+from main import (
+    main,
+)  # Assuming main.py and this test file are in the same directory
 import os
 import json
 import util.folder as folder
@@ -10,6 +12,7 @@ def cleanup(dir_path):
     output_dir_path = os.path.join(dir_path, "output")
     folder.remove_directories([csv_dir_path, output_dir_path])
 
+
 # def run_test(dir_path, expected_json):
 #     cif_folder_name = os.path.basename(dir_path)
 #     output_dir_path = os.path.join(dir_path, "output")
@@ -17,7 +20,7 @@ def cleanup(dir_path):
 
 #     # Run
 #     main(False, dir_path)
-    
+
 #     # Load output
 #     with open(json_output_path, 'r') as file:
 #         actual_output = json.load(file)
diff --git a/util/folder.py b/util/folder.py
index db56401..4963945 100644
--- a/util/folder.py
+++ b/util/folder.py
@@ -8,10 +8,16 @@ def choose_CIF_directory(script_directory):
     """
     Allows the user to select a directory from the given path.
     """
-    directories = [d for d in os.listdir(script_directory) 
-                   if os.path.isdir(join(script_directory, d)) 
-                   and any(file.endswith('.cif') for file in os.listdir(join(script_directory, d)))]
-    
+    directories = [
+        d
+        for d in os.listdir(script_directory)
+        if os.path.isdir(join(script_directory, d))
+        and any(
+            file.endswith(".cif")
+            for file in os.listdir(join(script_directory, d))
+        )
+    ]
+
     if not directories:
         print("No directories found in the current path containing .cif files!")
         return None
@@ -23,9 +29,11 @@ def choose_CIF_directory(script_directory):
         try:
             choice = int(input("\nEnter folder # having .cif files: "))
             if 1 <= choice <= len(directories):
-                return join(script_directory, directories[choice-1])
+                return join(script_directory, directories[choice - 1])
             else:
-                print(f"Please enter a number between 1 and {len(directories)}.")
+                print(
+                    f"Please enter a number between 1 and {len(directories)}."
+                )
         except ValueError:
             print("Invalid input. Please enter a number.")
 
@@ -35,7 +43,7 @@ def save_to_csv_directory(folder_info, df, base_filename):
     Saves the dataframe as a CSV inside a 'csv' sub-directory.
     """
     # Create the sub-directory for CSVs if it doesn't exist
-    
+
     csv_directory = join(folder_info, "csv")
     if not os.path.exists(csv_directory):
         os.mkdir(csv_directory)
diff --git a/util/prompt.py b/util/prompt.py
index 0d2b708..ab9f5a1 100644
--- a/util/prompt.py
+++ b/util/prompt.py
@@ -3,9 +3,11 @@
 from click import style, echo
 import json
 
+
 def print_intro_prompt():
     """Filters and moves CIF files based on the shortest atomic distance."""
-    intro_prompt = textwrap.dedent("""\
+    intro_prompt = textwrap.dedent(
+        """\
     ===
     Welcome to the CIF Bond Analyzer!
                                    
@@ -19,28 +21,41 @@ def print_intro_prompt():
                                     
     Let's get started!
     ===
-    """)
+    """
+    )
     print(intro_prompt)
 
 
 def get_user_input_on_supercell_method():
-    click.echo("\nDo you want to modify the supercell generation method for CIF files with more than 100 atoms in the unit cell?")
-    is_supercell_generation_method_modified = click.confirm('(Default: N)', default=False)
+    click.echo(
+        "\nDo you want to modify the supercell generation method for CIF files with more than 100 atoms in the unit cell?"
+    )
+    is_supercell_generation_method_modified = click.confirm(
+        "(Default: N)", default=False
+    )
 
     if is_supercell_generation_method_modified:
         click.echo("\nChoose a supercell generation method:")
         click.echo("1. No shift (fastest)")
         click.echo("2. +1 +1 +1 shifts in x, y, z directions")
-        click.echo("3. +-1, +-1, +-1 shifts (2x2x2 supercell generation, requires heavy computation, slowest)")
-        
-        method = click.prompt("Choose your option by entering a number", type=int)
-        
+        click.echo(
+            "3. +-1, +-1, +-1 shifts (2x2x2 supercell generation, requires heavy computation, slowest)"
+        )
+
+        method = click.prompt(
+            "Choose your option by entering a number", type=int
+        )
+
         if method == 1:
             click.echo("You've selected: No shift (fastest)\n")
         elif method == 2:
-            click.echo("You've selected: +1 +1 +1 shifts in x, y, z directions\n")
+            click.echo(
+                "You've selected: +1 +1 +1 shifts in x, y, z directions\n"
+            )
         elif method == 3:
-            click.echo("You've selected: +-1, +-1, +-1 shifts (2x2x2 supercell generation, slowest)\n")
+            click.echo(
+                "You've selected: +-1, +-1, +-1 shifts (2x2x2 supercell generation, slowest)\n"
+            )
         else:
             click.echo("Invalid option. Defaulting to No shift (fastest)\n")
             method = 1
@@ -52,11 +67,13 @@ def get_user_input_on_supercell_method():
 
 def print_progress(filename_with_ext, num_of_atoms, elapsed_time, is_finished):
     if is_finished:
-        echo(style(
-            f"Processed {filename_with_ext} with {num_of_atoms} atoms in "
-            f"{round(elapsed_time, 2)} s\n",
-            fg="blue"
-        ))
+        echo(
+            style(
+                f"Processed {filename_with_ext} with {num_of_atoms} atoms in "
+                f"{round(elapsed_time, 2)} s\n",
+                fg="blue",
+            )
+        )
 
 
 def print_dict_in_json(data):
diff --git a/util/string_parser.py b/util/string_parser.py
index 36e4e66..fe1b988 100755
--- a/util/string_parser.py
+++ b/util/string_parser.py
@@ -2,7 +2,11 @@
 
 
 def remove_string_braket(value_string):
-        """
-        Removes parentheses from a value string and convert to float if possible.
-        """
-        return float(value_string.split('(')[0]) if '(' in value_string else float(value_string)
+    """
+    Removes parentheses from a value string and convert to float if possible.
+    """
+    return (
+        float(value_string.split("(")[0])
+        if "(" in value_string
+        else float(value_string)
+    )
diff --git a/util/unit.py b/util/unit.py
index e26adfb..f26eba4 100755
--- a/util/unit.py
+++ b/util/unit.py
@@ -14,7 +14,5 @@ def rounded_distance(distance, precision=2):
     """
     Round a distance value to a specified precision.
     """
-    
-    return round(distance, precision)
-
 
+    return round(distance, precision)

From 54ed34684365dc074b867ecbd0e3aaea791465a4 Mon Sep 17 00:00:00 2001
From: Sangjoon Bob Lee <bobleesj@gmail.com>
Date: Mon, 11 Mar 2024 14:16:25 -0400
Subject: [PATCH 2/2] Added linting

---
 main.py               | 86 +++++++++++++++----------------------------
 util/prompt.py        |  4 +-
 util/string_parser.py |  3 --
 3 files changed, 31 insertions(+), 62 deletions(-)

diff --git a/main.py b/main.py
index 6970fcf..3a032e3 100644
--- a/main.py
+++ b/main.py
@@ -41,8 +41,10 @@ def main(is_iteractive_mode=True, dir_path=None):
 
         # If the user chooses no option, then it's simply 3
         if not supercell_method:
-            print("\nYour default option is generating a 2-2-2 supercell for",
-                "files more than 100 atoms in the unit cell.")
+            print(
+                "\nYour default option is generating a 2-2-2 supercell for",
+                "files more than 100 atoms in the unit cell.",
+            )
             supercell_method = 1
 
     if not is_iteractive_mode:
@@ -52,7 +54,7 @@ def main(is_iteractive_mode=True, dir_path=None):
     file_path_list = folder.get_cif_file_path_list(dir_path)
 
     # PART 2: PREPROCESS
-    
+
     dist_mix_pair_dict = {}
 
     overall_start_time = time.perf_counter()
@@ -62,17 +64,13 @@ def main(is_iteractive_mode=True, dir_path=None):
         filename_with_ext = os.path.basename(file_path)
         filename, ext = os.path.splitext(filename_with_ext)
         num_of_atoms = None
-    
+
         # Process CIF files and return a list of coordinates
         result = cif_parser_handler.get_cif_info(
-            file_path,
-            cif_parser.get_loop_tags(),
-            supercell_method
+            file_path, cif_parser.get_loop_tags(), supercell_method
         )
 
-        CIF_loop_values = cif_parser_handler.get_cif_loop_values(
-            file_path
-        )
+        CIF_loop_values = cif_parser_handler.get_cif_loop_values(file_path)
 
         _, lenghts, angles_rad, _, all_points, _, atom_site_list = result
 
@@ -82,14 +80,13 @@ def main(is_iteractive_mode=True, dir_path=None):
         echo(
             style(
                 f"Processing {filename_with_ext} with "
-                f"{num_of_atoms} atoms {index}", fg="yellow"
+                f"{num_of_atoms} atoms {index}",
+                fg="yellow",
             )
         )
 
         atomic_pair_list = supercell.get_atomic_pair_list(
-            all_points,
-            lenghts,
-            angles_rad
+            all_points, lenghts, angles_rad
         )
 
         # Get atomic site mixing info -> String
@@ -104,35 +101,26 @@ def main(is_iteractive_mode=True, dir_path=None):
 
         # Find the shortest pair from each reference atom
         ordered_pairs = bond.process_and_order_pairs(
-            all_points,
-            atomic_pair_list
+            all_points, atomic_pair_list
         )
 
         # Determine unique pairs and get the shortest dist for each pair
-        unique_pairs_dict = bond.get_unique_pairs_dict(
-            ordered_pairs,
-            filename
-        )
+        unique_pairs_dict = bond.get_unique_pairs_dict(ordered_pairs, filename)
 
         dist_mix_pair_dict = bond.get_dist_mix_pair_dict(
-            dist_mix_pair_dict,
-            unique_pairs_dict,
-            label_pair_mixing_dict
+            dist_mix_pair_dict, unique_pairs_dict, label_pair_mixing_dict
         )
 
         elapsed_time = time.perf_counter() - start_time
 
         prompt.print_progress(
-            filename_with_ext,
-            num_of_atoms,
-            elapsed_time,
-            is_finished=True
+            filename_with_ext, num_of_atoms, elapsed_time, is_finished=True
         )
 
         data = {
-            'File': filename,
+            "File": filename,
             "Number of atoms in supercell": num_of_atoms,
-            "Processing time (s)": round(elapsed_time, 3)
+            "Processing time (s)": round(elapsed_time, 3),
         }
         log_list.append(data)
 
@@ -147,10 +135,8 @@ def main(is_iteractive_mode=True, dir_path=None):
 
     prompt.print_dict_in_json(dist_mix_element_pair_dict)
 
-    missing_label_pairs = bond.get_sorted_missing_pairs(
-        dist_mix_pair_dict
-    )
-    
+    missing_label_pairs = bond.get_sorted_missing_pairs(dist_mix_pair_dict)
+
     missing_element_pairs = bond.get_sorted_missing_pairs(
         dist_mix_element_pair_dict
     )
@@ -170,54 +156,40 @@ def main(is_iteractive_mode=True, dir_path=None):
             dist_mix_pair_dict,
             missing_label_pairs,
             "summary_label.txt",
-            dir_path
+            dir_path,
         )
-        
+
         # Save Excel file with label pair
         excel.write_label_pair_dict_to_excel_json(
-            dist_mix_pair_dict,
-            "label",
-            dir_path
+            dist_mix_pair_dict, "label", dir_path
         )
 
         # Draw histograms with label pari
-        histogram.plot_histograms_from_label_dict(
-            dist_mix_pair_dict,
-            dir_path
-        )
-        
+        histogram.plot_histograms_from_label_dict(dist_mix_pair_dict, dir_path)
+
         # Write elesummary-element.txt
         writer.write_summary_and_missing_pairs_with_element_dict(
             dist_mix_element_pair_dict,
             missing_element_pairs,
             "summary_element.txt",
-            dir_path
-        ) 
+            dir_path,
+        )
 
         # Save Excel file with element pair
         excel.write_element_pair_dict_to_excel_json(
-            dist_mix_element_pair_dict,
-            "element",
-            dir_path
+            dist_mix_element_pair_dict, "element", dir_path
         )
 
         # Draw histograms with element pair
         histogram.plot_histograms_from_element_dict(
-            dist_mix_element_pair_dict,
-            dir_path
+            dist_mix_element_pair_dict, dir_path
         )
-        
-
 
         total_elapsed_time = time.perf_counter() - overall_start_time
         print(f"Total processing time: {total_elapsed_time:.2f}s")
 
         # Save log csv
-        folder.save_to_csv_directory(
-            dir_path,
-            pd.DataFrame(log_list),
-            "log"
-        )
+        folder.save_to_csv_directory(dir_path, pd.DataFrame(log_list), "log")
 
     # print("\nAll files successfully processed.")
 
diff --git a/util/prompt.py b/util/prompt.py
index ab9f5a1..727b350 100644
--- a/util/prompt.py
+++ b/util/prompt.py
@@ -39,7 +39,7 @@ def get_user_input_on_supercell_method():
         click.echo("1. No shift (fastest)")
         click.echo("2. +1 +1 +1 shifts in x, y, z directions")
         click.echo(
-            "3. +-1, +-1, +-1 shifts (2x2x2 supercell generation, requires heavy computation, slowest)"
+            "3. +-1, +-1, +-1 shifts (2x2x2 supercell generation, slowest)"
         )
 
         method = click.prompt(
@@ -54,7 +54,7 @@ def get_user_input_on_supercell_method():
             )
         elif method == 3:
             click.echo(
-                "You've selected: +-1, +-1, +-1 shifts (2x2x2 supercell generation, slowest)\n"
+                "You've selected: +-1, +-1, +-1 shifts (2x2x2 supercell, slowest)\n"
             )
         else:
             click.echo("Invalid option. Defaulting to No shift (fastest)\n")
diff --git a/util/string_parser.py b/util/string_parser.py
index fe1b988..64064dc 100755
--- a/util/string_parser.py
+++ b/util/string_parser.py
@@ -1,6 +1,3 @@
-import re
-
-
 def remove_string_braket(value_string):
     """
     Removes parentheses from a value string and convert to float if possible.