Fix pylint issues

1 files changed, 36 insertions, 28 deletions

diff --git a/gn3/csvcmp.py b/gn3/csvcmp.py
index ac09cc3..82d74d0 100644
--- a/gn3/csvcmp.py
+++ b/gn3/csvcmp.py
@@ -1,50 +1,59 @@
+"""This module contains functions for manipulating and working with csv
+texts"""
 import json
 import os
 import uuid
 from gn3.commands import run_cmd
 
 
-def extract_strain_name(csv_header, data, seek="Strain Name"):
+def extract_strain_name(csv_header, data, seek="Strain Name") -> str:
+    """Extract a strain's name given a csv header"""
     for column, value in zip(csv_header.split(","), data.split(",")):
         if seek in column:
             return value
     return ""
 
 
-def create_dirs_if_not_exists(dirs: list):
+def create_dirs_if_not_exists(dirs: list) -> None:
+    """Create directories from a list"""
     for dir_ in dirs:
         if not os.path.exists(dir_):
             os.makedirs(dir_)
 
 
 def remove_insignificant_edits(diff_data, epsilon=0.001):
-    _mod = []
+    """Remove or ignore edits that are not within ε"""
+    __mod = []
     for mod in diff_data.get("Modifications"):
         original = mod.get("Original").split(",")
         current = mod.get("Current").split(",")
-        for i, (x, y) in enumerate(zip(original, current)):
-            if (x.replace('.', '').isdigit() and
-                y.replace('.', '').isdigit() and
-                    abs(float(x) - float(y)) < epsilon):
-                current[i] = x
+        for i, (_x, _y) in enumerate(zip(original, current)):
+            if (
+                _x.replace(".", "").isdigit()
+                and _y.replace(".", "").isdigit()
+                and abs(float(_x) - float(_y)) < epsilon
+            ):
+                current[i] = _x
         if not (__o := ",".join(original)) == (__c := ",".join(current)):
-            _mod.append({
-                "Original": __o,
-                "Current": __c,
-            })
-    diff_data['Modifications'] = _mod
+            __mod.append(
+                {
+                    "Original": __o,
+                    "Current": __c,
+                }
+            )
+    diff_data["Modifications"] = __mod
     return diff_data
 
 
-def csv_diff(base_csv, delta_csv, tmp_dir="/tmp"):
+def csv_diff(base_csv, delta_csv, tmp_dir="/tmp") -> dict:
+    """Diff 2 csv strings"""
     base_csv_list = base_csv.strip().split("\n")
     delta_csv_list = delta_csv.strip().split("\n")
 
-    base_csv_header, delta_csv_header, header = "", "", ""
+    base_csv_header, delta_csv_header = "", ""
     for i, line in enumerate(base_csv_list):
         if line.startswith("Strain Name,Value,SE,Count"):
-            header = line
-            base_csv_header, delta_csv_header= line, delta_csv_list[i]
+            base_csv_header, delta_csv_header = line, delta_csv_list[i]
             break
     longest_header = max(base_csv_header, delta_csv_header)
 
@@ -53,22 +62,21 @@ def csv_diff(base_csv, delta_csv, tmp_dir="/tmp"):
             base_csv = base_csv.replace("Strain Name,Value,SE,Count",
                                         longest_header, 1)
         else:
-            delta_csv = delta_csv.replace("Strain Name,Value,SE,Count",
-                                          longest_header, 1)
+            delta_csv = delta_csv.replace(
+                "Strain Name,Value,SE,Count", longest_header, 1
+            )
     file_name1 = os.path.join(tmp_dir, str(uuid.uuid4()))
     file_name2 = os.path.join(tmp_dir, str(uuid.uuid4()))
 
-    with open(file_name1, "w") as f_:
+    with open(file_name1, "w", encoding="utf-8") as _f:
         _l = len(longest_header.split(","))
-        f_.write(fill_csv(csv_text=base_csv,
-                          width=_l))
-    with open(file_name2, "w") as f_:
-        f_.write(fill_csv(delta_csv,
-                          width=_l))
+        _f.write(fill_csv(csv_text=base_csv, width=_l))
+    with open(file_name2, "w", encoding="utf-8") as _f:
+        _f.write(fill_csv(delta_csv, width=_l))
 
     # Now we can run the diff!
     _r = run_cmd(cmd=('"csvdiff '
-                      f'{file_name1} {file_name2} '
+                      f"{file_name1} {file_name2} "
                       '--format json"'))
     if _r.get("code") == 0:
         _r = json.loads(_r.get("output"))
@@ -86,6 +94,7 @@ def csv_diff(base_csv, delta_csv, tmp_dir="/tmp"):
 
 
 def fill_csv(csv_text, width, value="x"):
+    """Fill a csv text with 'value' if it's length is less than width"""
     data = []
     for line in csv_text.strip().split("\n"):
         if line.startswith("Strain") or line.startswith("#"):
@@ -95,6 +104,5 @@ def fill_csv(csv_text, width, value="x"):
             for i, val in enumerate(_n):
                 if not val.strip():
                     _n[i] = value
-            data.append(
-                ",".join(_n + [value] * (width - len(_n))))
+            data.append(",".join(_n + [value] * (width - len(_n))))
     return "\n".join(data)