pychemstation 0.10.3__py3-none-any.whl → 0.10.4__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (29) hide show
  1. pychemstation/__init__.py +1 -1
  2. pychemstation/analysis/__init__.py +1 -6
  3. pychemstation/analysis/base_spectrum.py +7 -7
  4. pychemstation/{utils → analysis}/chromatogram.py +4 -4
  5. pychemstation/analysis/process_report.py +98 -61
  6. pychemstation/control/__init__.py +3 -2
  7. pychemstation/control/controllers/__init__.py +1 -5
  8. pychemstation/control/controllers/comm.py +20 -11
  9. pychemstation/control/controllers/devices/device.py +22 -12
  10. pychemstation/control/controllers/devices/injector.py +20 -9
  11. pychemstation/control/controllers/tables/method.py +233 -100
  12. pychemstation/control/controllers/tables/ms.py +7 -4
  13. pychemstation/control/controllers/tables/sequence.py +133 -53
  14. pychemstation/control/controllers/tables/table.py +151 -91
  15. pychemstation/control/hplc.py +86 -66
  16. pychemstation/generated/__init__.py +0 -2
  17. pychemstation/generated/pump_method.py +15 -19
  18. pychemstation/utils/macro.py +10 -9
  19. pychemstation/utils/method_types.py +1 -0
  20. pychemstation/utils/parsing.py +0 -11
  21. pychemstation/utils/sequence_types.py +2 -3
  22. pychemstation/utils/spec_utils.py +2 -3
  23. pychemstation/utils/table_types.py +10 -9
  24. pychemstation/utils/tray_types.py +45 -36
  25. {pychemstation-0.10.3.dist-info → pychemstation-0.10.4.dist-info}/METADATA +2 -1
  26. pychemstation-0.10.4.dist-info/RECORD +37 -0
  27. pychemstation-0.10.3.dist-info/RECORD +0 -37
  28. {pychemstation-0.10.3.dist-info → pychemstation-0.10.4.dist-info}/WHEEL +0 -0
  29. {pychemstation-0.10.3.dist-info → pychemstation-0.10.4.dist-info}/licenses/LICENSE +0 -0
@@ -313,25 +313,21 @@ class SolventElement:
313
313
  "required": True,
314
314
  },
315
315
  )
316
- channel1_extended_solvent_type: Optional[Channel1ExtendedSolventType] = (
317
- field(
318
- default=None,
319
- metadata={
320
- "name": "Channel1ExtendedSolventType",
321
- "type": "Element",
322
- "required": True,
323
- },
324
- )
325
- )
326
- channel2_extended_solvent_type: Optional[Channel2ExtendedSolventType] = (
327
- field(
328
- default=None,
329
- metadata={
330
- "name": "Channel2ExtendedSolventType",
331
- "type": "Element",
332
- "required": True,
333
- },
334
- )
316
+ channel1_extended_solvent_type: Optional[Channel1ExtendedSolventType] = field(
317
+ default=None,
318
+ metadata={
319
+ "name": "Channel1ExtendedSolventType",
320
+ "type": "Element",
321
+ "required": True,
322
+ },
323
+ )
324
+ channel2_extended_solvent_type: Optional[Channel2ExtendedSolventType] = field(
325
+ default=None,
326
+ metadata={
327
+ "name": "Channel2ExtendedSolventType",
328
+ "type": "Element",
329
+ "required": True,
330
+ },
335
331
  )
336
332
 
337
333
 
@@ -15,7 +15,7 @@ class Response:
15
15
  # See https://www.agilent.com/cs/library/usermanuals/Public/MACROS.PDF
16
16
  class Command(Enum):
17
17
  def __str__(self):
18
- return '%s' % self.value
18
+ return "%s" % self.value
19
19
 
20
20
  GET_NUM_VAL_CMD = "response_num = {cmd}"
21
21
  GET_TEXT_VAL_CMD = "response$ = {cmd}"
@@ -37,17 +37,17 @@ class Command(Enum):
37
37
  # Method and Sequence Related
38
38
  GET_METHOD_CMD = "response$ = _MethFile$"
39
39
  GET_ROWS_CMD = 'response_num = TabHdrVal({register}, "{table_name}", "{col_name}")'
40
- SWITCH_METHOD_CMD = 'LoadMethod _MethPath$, _MethFile$'
40
+ SWITCH_METHOD_CMD = "LoadMethod _MethPath$, _MethFile$"
41
41
  SWITCH_METHOD_CMD_SPECIFIC = 'LoadMethod "{method_dir}", "{method_name}.M"'
42
42
  START_METHOD_CMD = "StartMethod"
43
43
  RUN_METHOD_CMD = 'RunMethod "{data_dir}",, "{experiment_name}"'
44
44
  STOP_METHOD_CMD = "StopMethod"
45
- UPDATE_METHOD_CMD = 'UpdateMethod'
46
- SWITCH_SEQUENCE_CMD = 'LoadSequence _SeqPath$, _SeqFile$'
47
- SAVE_SEQUENCE_CMD = 'SaveSequence _SeqPath$, _SeqFile$'
45
+ UPDATE_METHOD_CMD = "UpdateMethod"
46
+ SWITCH_SEQUENCE_CMD = "LoadSequence _SeqPath$, _SeqFile$"
47
+ SAVE_SEQUENCE_CMD = "SaveSequence _SeqPath$, _SeqFile$"
48
48
  SAVE_METHOD_CMD = 'SaveMethod _MethPath$, _MethFile$, "{commit_msg}"'
49
- GET_SEQUENCE_CMD = 'response$ = _SeqFile$'
50
- RUN_SEQUENCE_CMD = 'RunSequence'
49
+ GET_SEQUENCE_CMD = "response$ = _SeqFile$"
50
+ RUN_SEQUENCE_CMD = "RunSequence"
51
51
 
52
52
 
53
53
  class HPLCRunningStatus(Enum):
@@ -76,7 +76,6 @@ class HPLCAvailStatus(Enum):
76
76
 
77
77
 
78
78
  class HPLCErrorStatus(Enum):
79
-
80
79
  @classmethod
81
80
  def has_member_key(cls, key):
82
81
  return key in cls.__members__
@@ -87,7 +86,9 @@ class HPLCErrorStatus(Enum):
87
86
  MALFORMED = "MALFORMED"
88
87
 
89
88
 
90
- def str_to_status(status: str) -> Type[HPLCRunningStatus[Any] | HPLCErrorStatus[Any] | HPLCAvailStatus[Any]]:
89
+ def str_to_status(
90
+ status: str,
91
+ ) -> Type[HPLCRunningStatus[Any] | HPLCErrorStatus[Any] | HPLCAvailStatus[Any]]:
91
92
  if HPLCErrorStatus.has_member_key(status):
92
93
  return HPLCErrorStatus[status]
93
94
  if HPLCRunningStatus.has_member_key(status):
@@ -47,6 +47,7 @@ class MethodDetails:
47
47
  :attribute params: the organic modifier (pump B) and flow rate displayed for the method (the time 0 settings)
48
48
  :attribute dad_wavelengthes:
49
49
  """
50
+
50
51
  name: str
51
52
  params: HPLCMethodParams
52
53
  timetable: list[TimeTableEntry]
@@ -27,7 +27,6 @@ UINT32 = ENDIAN + "I"
27
27
 
28
28
 
29
29
  def fread(fid, nelements, dtype):
30
-
31
30
  """Equivalent to Matlab fread function"""
32
31
 
33
32
  if dtype is str:
@@ -42,7 +41,6 @@ def fread(fid, nelements, dtype):
42
41
 
43
42
 
44
43
  def parse_utf16_string(file_, encoding="UTF16"):
45
-
46
44
  """Parse a pascal type UTF16 encoded string from a binary file object"""
47
45
 
48
46
  # First read the expected number of CHARACTERS
@@ -53,7 +51,6 @@ def parse_utf16_string(file_, encoding="UTF16"):
53
51
 
54
52
 
55
53
  class cached_property(object):
56
-
57
54
  """A property that is only computed once per instance and then replaces
58
55
  itself with an ordinary attribute. Deleting the attribute resets the
59
56
  property.
@@ -73,7 +70,6 @@ class cached_property(object):
73
70
 
74
71
 
75
72
  class CHFile(object):
76
-
77
73
  """Class that implementats the Agilent .ch file format version
78
74
  130. Warning: Not all aspects of the file header is understood,
79
75
  so there may and probably is information that is not parsed. See
@@ -122,7 +118,6 @@ class CHFile(object):
122
118
  supported_versions = {130}
123
119
 
124
120
  def __init__(self, filepath):
125
-
126
121
  self.filepath = filepath
127
122
  self.metadata = {}
128
123
  with open(self.filepath, "rb") as file_:
@@ -130,7 +125,6 @@ class CHFile(object):
130
125
  self.values = self._parse_data(file_)
131
126
 
132
127
  def _parse_header(self, file_):
133
-
134
128
  """Parse the header"""
135
129
 
136
130
  # Parse and check version
@@ -154,7 +148,6 @@ class CHFile(object):
154
148
  ]
155
149
 
156
150
  def _parse_header_status(self):
157
-
158
151
  """Print known and unknown parts of the header"""
159
152
 
160
153
  file_ = open(self.filepath, "rb")
@@ -234,7 +227,6 @@ class CHFile(object):
234
227
  file_.close()
235
228
 
236
229
  def _parse_data(self, file_):
237
-
238
230
  """Parse the data. Decompress the delta-encoded data, and scale them
239
231
  with y-scaling"""
240
232
 
@@ -252,7 +244,6 @@ class CHFile(object):
252
244
  buff = [0, 0, 0, 0]
253
245
 
254
246
  while file_.tell() < stop:
255
-
256
247
  buff[0] = fread(file_, 1, INT16)[0][0]
257
248
  buff[1] = buff[3]
258
249
 
@@ -260,7 +251,6 @@ class CHFile(object):
260
251
  break
261
252
 
262
253
  for i in range(buff[0] & 4095):
263
-
264
254
  buff[2] = fread(file_, 1, INT16)[0][0]
265
255
 
266
256
  if buff[2] != -32768:
@@ -279,7 +269,6 @@ class CHFile(object):
279
269
 
280
270
  @cached_property
281
271
  def times(self):
282
-
283
272
  """The time values (x-value) for the data set in minutes"""
284
273
 
285
274
  return np.linspace(
@@ -1,9 +1,8 @@
1
1
  from __future__ import annotations
2
2
 
3
- from dataclasses import dataclass
4
3
  from enum import Enum
5
4
  from typing import Optional, List
6
-
5
+ from dataclasses import dataclass, field
7
6
  from pychemstation.utils.tray_types import Tray
8
7
 
9
8
 
@@ -11,7 +10,7 @@ from pychemstation.utils.tray_types import Tray
11
10
  class SequenceDataFiles:
12
11
  sequence_name: str
13
12
  dir: str
14
- child_dirs: Optional[List[str]] = None
13
+ child_dirs: List[str] = field(default_factory=list)
15
14
 
16
15
 
17
16
  class SampleType(Enum):
@@ -28,7 +28,6 @@ def create_binary_peak_map(data):
28
28
  peak_map = np.full_like(data_c, False, dtype=bool)
29
29
 
30
30
  for _ in range(100500): # shouldn't take more iterations
31
-
32
31
  # looking for peaks
33
32
  peaks_found = np.logical_or(
34
33
  data_c > np.mean(data_c) + np.std(data_c) * 3,
@@ -156,14 +155,14 @@ def filter_noisy_regions(y_data, peaks_regions):
156
155
  # compute the actual regions data points
157
156
  y_data_regions = []
158
157
  for region in peaks_regions:
159
- y_data_regions.append(y_data[region[0]: region[-1]])
158
+ y_data_regions.append(y_data[region[0] : region[-1]])
160
159
 
161
160
  # compute noise data regions, i.e. in between peak regions
162
161
  noise_data_regions = []
163
162
  for row, _ in enumerate(peaks_regions):
164
163
  try:
165
164
  noise_data_regions.append(
166
- y_data[peaks_regions[row][1]: peaks_regions[row + 1][0]]
165
+ y_data[peaks_regions[row][1] : peaks_regions[row + 1][0]]
167
166
  )
168
167
  except IndexError:
169
168
  # exception for the last row -> discard
@@ -7,28 +7,30 @@ from typing import TypeVar
7
7
 
8
8
  class TableOperation(Enum):
9
9
  def __str__(self):
10
- return '%s' % self.value
10
+ return "%s" % self.value
11
11
 
12
12
  DELETE_TABLE = 'DelTab {register}, "{table_name}"'
13
13
  CREATE_TABLE = 'NewTab {register}, "{table_name}"'
14
14
  NEW_ROW = 'InsTabRow {register}, "{table_name}"'
15
15
  DELETE_ROW = 'DelTabRow {register}, "{table_name}", {row}'
16
16
  EDIT_ROW_VAL = 'SetTabVal "{register}", "{table_name}", {row}, "{col_name}", {val}'
17
- EDIT_ROW_TEXT = 'SetTabText "{register}", "{table_name}", {row}, "{col_name}", "{val}"'
17
+ EDIT_ROW_TEXT = (
18
+ 'SetTabText "{register}", "{table_name}", {row}, "{col_name}", "{val}"'
19
+ )
18
20
  GET_ROW_VAL = 'TabVal("{register}", "{table_name}", {row}, "{col_name}")'
19
21
  GET_ROW_TEXT = 'TabText$("{register}", "{table_name}", {row}, "{col_name}")'
20
22
  GET_NUM_ROWS = 'Rows = TabHdrVal({register}, "{table_name}", "{col_name}")'
21
23
  GET_OBJ_HDR_VAL = 'ObjHdrVal("{register}", "{register_flag}")'
22
24
  GET_OBJ_HDR_TEXT = 'ObjHdrText$("{register}", "{register_flag}")'
23
- UPDATE_OBJ_HDR_VAL = 'SetObjHdrVal {register}, {register_flag}, {val}'
24
- UPDATE_OBJ_HDR_TEXT = 'SetObjHdrText {register}, {register_flag}, {val}'
25
+ UPDATE_OBJ_HDR_VAL = "SetObjHdrVal {register}, {register_flag}, {val}"
26
+ UPDATE_OBJ_HDR_TEXT = "SetObjHdrText {register}, {register_flag}, {val}"
25
27
  NEW_COL_TEXT = 'NewColText {register}, "{table_name}", "{col_name}", "{val}"'
26
28
  NEW_COL_VAL = 'NewColVal {register}, "{table_name}", "{col_name}", {val}'
27
29
 
28
30
 
29
31
  class RegisterFlag(Enum):
30
32
  def __str__(self):
31
- return '%s' % self.value
33
+ return "%s" % self.value
32
34
 
33
35
  # for table
34
36
  NUM_ROWS = "NumberOfRows"
@@ -40,7 +42,7 @@ class RegisterFlag(Enum):
40
42
  SOLVENT_D_COMPOSITION = "PumpChannel4_CompositionPercentage"
41
43
  FLOW = "Flow"
42
44
  MAX_TIME = "StopTime_Time"
43
- POST_TIME = "PostTime_Time" #TODO: check
45
+ POST_TIME = "PostTime_Time" # TODO: check
44
46
  COLUMN_OVEN_TEMP1 = "TemperatureControl_Temperature"
45
47
  COLUMN_OVEN_TEMP2 = "TemperatureControl2_Temperature"
46
48
  STOPTIME_MODE = "StopTime_Mode"
@@ -55,7 +57,6 @@ class RegisterFlag(Enum):
55
57
  EXTERNAL_CONTACT = "ExternalContact"
56
58
  FUNCTION = "Function"
57
59
 
58
-
59
60
  # for Sequence
60
61
  VIAL_LOCATION = "Vial"
61
62
  NAME = "SampleName"
@@ -86,10 +87,10 @@ class RegisterFlag(Enum):
86
87
  REMOTE_DUR = "RemoteDuration"
87
88
 
88
89
 
89
-
90
90
  @dataclass
91
91
  class Table:
92
92
  register: str
93
93
  name: str
94
94
 
95
- T = TypeVar('T')
95
+
96
+ T = TypeVar("T")
@@ -19,16 +19,16 @@ class Num(Enum):
19
19
  @classmethod
20
20
  def from_num(cls, num: int):
21
21
  num_mapping = {
22
- 1: Num.ONE,
23
- 2: Num.TWO,
24
- 3: Num.THREE,
25
- 4: Num.FOUR,
26
- 5: Num.FIVE,
27
- 6: Num.SIX,
28
- 7: Num.SEVEN,
29
- 8: Num.EIGHT,
30
- 9: Num.NINE
31
- }
22
+ 1: Num.ONE,
23
+ 2: Num.TWO,
24
+ 3: Num.THREE,
25
+ 4: Num.FOUR,
26
+ 5: Num.FIVE,
27
+ 6: Num.SIX,
28
+ 7: Num.SEVEN,
29
+ 8: Num.EIGHT,
30
+ 9: Num.NINE,
31
+ }
32
32
 
33
33
  if num in num_mapping:
34
34
  return num_mapping[num]
@@ -58,13 +58,13 @@ class Letter(Enum):
58
58
  @classmethod
59
59
  def from_str(cls, let: str) -> Letter:
60
60
  letter_mapping = {
61
- "A": Letter.A,
62
- "B": Letter.B,
63
- "C": Letter.C,
64
- "D": Letter.D,
65
- "E": Letter.E,
66
- "F": Letter.F
67
- }
61
+ "A": Letter.A,
62
+ "B": Letter.B,
63
+ "C": Letter.C,
64
+ "D": Letter.D,
65
+ "E": Letter.E,
66
+ "F": Letter.F,
67
+ }
68
68
 
69
69
  if let in letter_mapping:
70
70
  return letter_mapping[let]
@@ -83,6 +83,7 @@ class FiftyFourVialPlate:
83
83
  valid vial locations: P1-A2, P2-F9
84
84
  invalid vial locations: P3-A1, P1-Z3, P2-B10
85
85
  """
86
+
86
87
  plate: Plate
87
88
  letter: Letter
88
89
  num: Num
@@ -100,16 +101,22 @@ class FiftyFourVialPlate:
100
101
  :raises: ValueError if string is invalid tray location
101
102
  """
102
103
  if len(loc) != 5:
103
- raise ValueError("Plate locations must be PX-LY, where X is either 1 or 2 and Y is 1 to 9")
104
+ raise ValueError(
105
+ "Plate locations must be PX-LY, where X is either 1 or 2 and Y is 1 to 9"
106
+ )
104
107
  try:
105
108
  plate = int(loc[1])
106
109
  letter = loc[3]
107
110
  num = int(loc[4])
108
- return FiftyFourVialPlate(plate=Plate.from_num(plate),
109
- letter=Letter.from_str(letter),
110
- num=Num.from_num(num))
111
- except Exception as e:
112
- raise ValueError("Plate locations must be PX-LY, where X is either 1 or 2 and Y is 1 to 9")
111
+ return FiftyFourVialPlate(
112
+ plate=Plate.from_num(plate),
113
+ letter=Letter.from_str(letter),
114
+ num=Num.from_num(num),
115
+ )
116
+ except Exception:
117
+ raise ValueError(
118
+ "Plate locations must be PX-LY, where X is either 1 or 2 and Y is 1 to 9"
119
+ )
113
120
 
114
121
  @classmethod
115
122
  def from_int(cls, num: int) -> Tray:
@@ -125,19 +132,19 @@ class FiftyFourVialPlate:
125
132
 
126
133
  row_starts = [
127
134
  # plate 1
128
- FiftyFourVialPlate.from_str('P1-F1'),
129
- FiftyFourVialPlate.from_str('P1-E1'),
130
- FiftyFourVialPlate.from_str('P1-D1'),
131
- FiftyFourVialPlate.from_str('P1-C1'),
132
- FiftyFourVialPlate.from_str('P1-B1'),
133
- FiftyFourVialPlate.from_str('P1-A1'),
135
+ FiftyFourVialPlate.from_str("P1-F1"),
136
+ FiftyFourVialPlate.from_str("P1-E1"),
137
+ FiftyFourVialPlate.from_str("P1-D1"),
138
+ FiftyFourVialPlate.from_str("P1-C1"),
139
+ FiftyFourVialPlate.from_str("P1-B1"),
140
+ FiftyFourVialPlate.from_str("P1-A1"),
134
141
  # plate 2
135
- FiftyFourVialPlate.from_str('P2-F1'),
136
- FiftyFourVialPlate.from_str('P2-E1'),
137
- FiftyFourVialPlate.from_str('P2-D1'),
138
- FiftyFourVialPlate.from_str('P2-C1'),
139
- FiftyFourVialPlate.from_str('P2-B1'),
140
- FiftyFourVialPlate.from_str('P2-A1'),
142
+ FiftyFourVialPlate.from_str("P2-F1"),
143
+ FiftyFourVialPlate.from_str("P2-E1"),
144
+ FiftyFourVialPlate.from_str("P2-D1"),
145
+ FiftyFourVialPlate.from_str("P2-C1"),
146
+ FiftyFourVialPlate.from_str("P2-B1"),
147
+ FiftyFourVialPlate.from_str("P2-A1"),
141
148
  ]
142
149
 
143
150
  # find which row
@@ -161,7 +168,8 @@ class FiftyFourVialPlate:
161
168
  return FiftyFourVialPlate(
162
169
  plate=starting_loc.plate,
163
170
  letter=starting_loc.letter,
164
- num=Num.from_num(i))
171
+ num=Num.from_num(i),
172
+ )
165
173
  raise ValueError("Number didn't match any location. " + str(num))
166
174
 
167
175
 
@@ -169,6 +177,7 @@ class TenVialColumn(Enum):
169
177
  """
170
178
  Class to represent the 10 vial locations.
171
179
  """
180
+
172
181
  ONE = 1
173
182
  TWO = 2
174
183
  THREE = 3
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: pychemstation
3
- Version: 0.10.3
3
+ Version: 0.10.4
4
4
  Summary: Library to interact with Chemstation software, primarily used in Hein lab
5
5
  Project-URL: Documentation, https://pychemstation-e5a086.gitlab.io/pychemstation.html
6
6
  Project-URL: Repository, https://gitlab.com/heingroup/device-api/pychemstation
@@ -18,6 +18,7 @@ Requires-Dist: matplotlib>=3.7.5
18
18
  Requires-Dist: pandas>=2.0.3
19
19
  Requires-Dist: pdoc>=14.7.0
20
20
  Requires-Dist: polling>=0.3.2
21
+ Requires-Dist: pre-commit>=4.2.0
21
22
  Requires-Dist: pytest>=7.3.5
22
23
  Requires-Dist: rainbow-api>=1.0.10
23
24
  Requires-Dist: result>=0.17.0
@@ -0,0 +1,37 @@
1
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