first test

.vscode/settings.json

@@ -4,7 +4,7 @@
         "-s",
         "./tests",
         "-p",
-        "*_test.py"
+        "test_*.py"
     ],
     "python.testing.pytestEnabled": false,
     "python.testing.unittestEnabled": true

jws2txt/helpers/helpers.py

@@ -75,25 +75,25 @@ def __init__(self, path: str) -> None:
         fmt = 'f'*self.npoints
 
         try:
-            self.unpack_y_data(y_data, format=fmt, num_chanels=self.numchanels)
+            self.__unpack_y_data(y_data, format=fmt, num_chanels=self.numchanels)
 
-        except:
+        except Exception:
             try:
                 # works in the case of *.jwb file
                 self.numchanels = data_tuple[1]
-                self.unpack_y_data(y_data, format=fmt, num_chanels=self.numchanels)
-            except:
-                print("Incorrect number of channels.")
+                self.__unpack_y_data(y_data, format=fmt, num_chanels=self.numchanels)
+            except Exception as e:
+                print(f"Incorrect number of channels. {e}")
 
         sample_info = file.openstream('SampleInfo').read()[8:].split(b'\x00\x00\x08\x00')
 
         try:
-            self.decode_sample_info(sample_info)
-        except:
+            self.__decode_sample_info(sample_info)
+        except Exception:
             self.sample_name = ''
             self.comment = ''
 
-    def unpack_y_data(self, y_data: bytes, format: str, num_chanels: int) -> None:
+    def __unpack_y_data(self, y_data: bytes, format: str, num_chanels: int) -> None:
         """Unpacks the Y-Data from the JWS file.
         """
         chunk_size = int(len(y_data)/num_chanels)
@@ -107,22 +107,22 @@ def unpack_y_data(self, y_data: bytes, format: str, num_chanels: int) -> None:
         unpacked_data.insert(0, tuple(x_data))
         self.unpacked_data = unpacked_data
 
-    def decode_sample_info(self, sample_info_bytes: list) -> None:
+    def __decode_sample_info(self, sample_info_bytes: list) -> None:
         """Decodes the SampleInfo"""
         if len(sample_info_bytes) == 2:
             sample_name = sample_info_bytes[0].split(b'\x00\x00')[0]
-            self.sample_name = (self.unpack_sample_info(sample_name))
+            self.sample_name = (self.__unpack_sample_info(sample_name))
 
             comment = sample_info_bytes[1].split(b'\x00\x00')[1]
-            self.comment = self.unpack_sample_info(comment)
+            self.comment = self.__unpack_sample_info(comment)
 
         elif len(sample_info_bytes) == 1:
             sample_name = sample_info_bytes[0].split(b'\x00\x00')[0]
-            self.sample_name = self.unpack_sample_info(sample_name)
+            self.sample_name = self.__unpack_sample_info(sample_name)
 
             self.comment = ''
 
-    def unpack_sample_info(self, packed_bytes: bytes) -> str:
+    def __unpack_sample_info(self, packed_bytes: bytes) -> str:
         """Unpacks SampleInfo bytes"""
         if packed_bytes[-1:] not in {b'\x00', b''}:
             packed_bytes += b'\x00'
@@ -140,11 +140,11 @@ def write_data(self, out_file: str,
             with open(out_file, 'x', newline='') as f:
                 writer = csv.writer(f, delimiter=delimiter)
 
-                if write_comments == True:
+                if write_comments is True:
                     writer.writerow([self.sample_name])
                     writer.writerow([self.comment])
 
-                if write_header == True:
+                if write_header is True:
                     if len(self.header_names) == len(self.unpacked_data):
                         writer.writerow(self.header_names)
                     elif len(self.header_names) < len(self.unpacked_data):

jws2txt/jws2txt.py

@@ -16,20 +16,24 @@ def str2bool(v) -> bool:
 
 def main():
 
-    parser = argparse.ArgumentParser(description='Converts *.jws or *jwb files to human-readable text files.')
+    parser = argparse.ArgumentParser(description='Converts *.jws or *jwb files to human\
+                                     -readable text files.')
     parser.add_argument('--in-path', type=str, required=True,
                         help="Path to file or folder containing files for conversion.")
     parser.add_argument('--out-dir', type=str,  help='Output folder')
-    parser.add_argument('--delimiter', type=str, default='\t', help='Delimiter used in saved text files.')
-    parser.add_argument('--comments', type=str2bool, choices=[True, False], default=True, help='Write sample information.')
-    parser.add_argument('--header', type=str2bool, choices=[True, False], default=True, help='Write header.')
+    parser.add_argument('--delimiter', type=str, default='\t', help='Delimiter used in\
+                         saved text files.')
+    parser.add_argument('--comments', type=str2bool, choices=[True, False], default=True,  # noqa: E501
+                         help='Write sample information.')
+    parser.add_argument('--header', type=str2bool, choices=[True, False], default=True,
+                         help='Write header.')
 
     args = parser.parse_args()
 
     if not os.path.exists(args.in_path):
         raise FileNotFoundError(f"{args.in_path} does not exist.")
 
-    if args.out_dir == None:
+    if args.out_dir is None:
         args.out_dir = args.in_path
 
     if not os.path.exists(args.out_dir):
@@ -40,7 +44,8 @@ def main():
 
         for file in gen:
 
-            out_file_path = os.path.join(args.out_dir, ''.join((os.path.splitext(file)[0], '.txt')))
+            out_file_path = os.path.join(args.out_dir, ''.join((os.path.splitext(file)[0],  # noqa: E501
+                                                                 '.txt')))
             jws_file_path = os.path.join(root, file)
 
             JWSFile(path=jws_file_path).write_data(out_file=out_file_path,

temp/test.py

@@ -2,12 +2,12 @@
 import jws2txt
 import matplotlib.pyplot as plt
 
-test_file = jws2txt.JWSFile(r'sample_CD_HT_Abs.jws')
+test_file = jws2txt.JWSFile(r'001Hg.jws')
 
 
 x, cd, ht, abs = test_file.unpacked_data
 
-
+#%%
 # %%
 
 # %%
@@ -19,3 +19,10 @@
 plt.show()
 # %%
 
+
+test_file.decode_sample_info()
+# %%
+test_file.unpacked_data[0][2]
+test_file.unpacked_data[1][2]
+test_file.unpacked_data[2][2]
+test_file.unpacked_data[3][2]

tests/test_helpers.py

@@ -1 +1,47 @@
-from unittest import TestCase
+import unittest
+import jws2txt
+
+class JWSFileTest(unittest.TestCase):
+
+    def setUp(self) -> None:
+        self.three_channels = jws2txt.JWSFile(r'tests/files/001Hg.jws')
+
+
+    def test_three_channels_creation(self):
+        # Test file creation and initialization
+
+        self.assertEqual(self.three_channels.numchanels, 3)
+        self.assertEqual(self.three_channels.npoints, 1201)
+        self.assertEqual(self.three_channels.x_for_first_point, 320.0)
+        self.assertEqual(self.three_channels.x_for_last_point, 200.0)
+        self.assertEqual(self.three_channels.x_increment, -0.1)
+        self.assertEqual(self.three_channels.header_codes, (268435715, 4097, 8193, 3))
+        self.assertEqual(self.three_channels.header_names, ['WAVELENGTH', 'CD', 'HT VOLTAGE', 'ABSORBANCE'])
+        self.assertEqual(self.three_channels.data_list, [3,
+                                                        1,
+                                                        0,
+                                                        3,
+                                                        1,
+                                                        1201,
+                                                        320.0,
+                                                        200.0,
+                                                        -0.1,
+                                                        268435715,
+                                                        4097,
+                                                        8193,
+                                                        3,
+                                                        8.6939493804496e-311,
+                                                        200.0,
+                                                        1.0,
+                                                        320.0])
+        self.assertEqual(self.three_channels.sample_name, 'HK14_CN')
+        self.assertEqual(self.three_channels.comment, '1mm')
+        #test x-axis and 3 channels
+        self.assertEqual(self.three_channels.unpacked_data[0][2], 319.8)
+        self.assertEqual(self.three_channels.unpacked_data[1][2], 0.1975005567073822)
+        self.assertEqual(self.three_channels.unpacked_data[2][2], 206.2129669189453)
+        self.assertEqual(self.three_channels.unpacked_data[3][2], 0.11851496249437332)
+
+
+if __name__=='__main__':
+	unittest.main()