pychemstation 0.5.12__tar.gz → 0.5.13.dev1__tar.gz

{pychemstation-0.5.12 → pychemstation-0.5.13.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pychemstation
-Version: 0.5.12
+Version: 0.5.13.dev1
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Home-page: https://gitlab.com/heingroup/device-api/pychemstation
 Author: Lucy Hao
@@ -14,6 +14,7 @@ Requires-Dist: polling
 Requires-Dist: seabreeze
 Requires-Dist: xsdata
 Requires-Dist: result
+Requires-Dist: rainbow
 
 # Agilent HPLC Macro Control
 
@@ -99,7 +100,7 @@ our [GitLab](https://gitlab.com/heingroup/device-api/pychemstation)!
 
 ## Authors and Acknowledgements
 
-Lucy Hao
+Lucy Hao, Maria Politi
 
 - Adapted from [**AnalyticalLabware**](https://github.com/croningp/analyticallabware), created by members in the Cronin
   Group. Copyright © Cronin Group, used under the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) license.

{pychemstation-0.5.12 → pychemstation-0.5.13.dev1}/README.md

@@ -82,7 +82,7 @@ our [GitLab](https://gitlab.com/heingroup/device-api/pychemstation)!
 
 ## Authors and Acknowledgements
 
-Lucy Hao
+Lucy Hao, Maria Politi
 
 - Adapted from [**AnalyticalLabware**](https://github.com/croningp/analyticallabware), created by members in the Cronin
   Group. Copyright © Cronin Group, used under the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) license.

pychemstation-0.5.13.dev1/pychemstation/control/controllers/__init__.py

@@ -0,0 +1,9 @@
+"""
+.. include:: README.md
+"""
+
+from .comm import CommunicationController
+from .devices.pump import PumpController
+from .devices.column import ColumnController
+from .tables.method import MethodController
+from .tables.sequence import SequenceController

pychemstation-0.5.13.dev1/pychemstation/control/controllers/devices/column.py

@@ -0,0 +1,12 @@
+from ....control.controllers import CommunicationController
+from .device import DeviceController
+from ....utils.table_types import Table
+
+
+class ColumnController(DeviceController):
+
+    def __init__(self, controller: CommunicationController, table: Table):
+        super().__init__(controller, table)
+
+    def get_row(self, row: int):
+        pass

pychemstation-0.5.13.dev1/pychemstation/control/controllers/devices/device.py

@@ -0,0 +1,23 @@
+import abc
+from typing import Union
+
+from ....control.controllers import CommunicationController
+from ....control.controllers.tables.table import TableController
+from ....utils.chromatogram import AgilentChannelChromatogramData
+from ....utils.table_types import Table
+
+
+class DeviceController(TableController, abc.ABC):
+
+    def __init__(self, controller: CommunicationController, table: Table):
+        super().__init__(controller, None, None, table)
+
+    @abc.abstractmethod
+    def get_row(self, row: int):
+        pass
+
+    def retrieve_recent_data_files(self):
+        raise NotImplementedError
+
+    def get_data(self) -> Union[list[AgilentChannelChromatogramData], AgilentChannelChromatogramData]:
+        raise NotImplementedError

pychemstation-0.5.13.dev1/pychemstation/control/controllers/devices/pump.py

@@ -0,0 +1,43 @@
+from ....control.controllers import CommunicationController
+from .device import DeviceController
+from ....utils.pump_types import Pump
+from ....utils.table_types import Table
+
+
+class PumpController(DeviceController):
+
+    def __init__(self, controller: CommunicationController, table: Table):
+        super().__init__(controller, table)
+        self.A1 = Pump(in_use=True, solvent="A1")
+        self.B1 = Pump(in_use=True, solvent="B1")
+        self.A2 = Pump(in_use=False, solvent="A2")
+        self.B2 = Pump(in_use=False, solvent="B2")
+
+    def validate_pumps(self):
+        invalid_A_pump_usage = self.A1.in_use and self.A2.in_use
+        invalid_B_pump_usage = self.B1.in_use and self.B2.in_use
+        if invalid_A_pump_usage or invalid_B_pump_usage:
+            raise AttributeError
+
+    def switch_pump(self, num: int, pump: str):
+        if pump == "A":
+            if num == 1:
+                self.A1.in_use = True
+                self.A2.in_use = False
+            elif num == 2:
+                self.A1.in_use = False
+                self.A2.in_use = True
+        elif pump == "B":
+            if num == 1:
+                self.B1.in_use = True
+                self.B2.in_use = False
+            elif num == 2:
+                self.B1.in_use = False
+                self.B2.in_use = True
+        self.purge()
+
+    def purge(self):
+        pass
+
+    def get_row(self, row: int):
+        pass

{pychemstation-0.5.12/pychemstation/control/controllers → pychemstation-0.5.13.dev1/pychemstation/control/controllers/tables}/method.py

@@ -1,16 +1,15 @@
 import os
 import time
-from typing import Optional, Union
 
 from xsdata.formats.dataclass.parsers import XmlParser
 
-from ...control.controllers.table_controller import TableController
-from ...control.controllers.comm import CommunicationController
-from ...generated import PumpMethod, DadMethod, SolventElement
-from ...utils.chromatogram import TIME_FORMAT, AgilentChannelChromatogramData
-from ...utils.macro import Command
-from ...utils.method_types import PType, TimeTableEntry, Param, MethodDetails, HPLCMethodParams
-from ...utils.table_types import RegisterFlag, TableOperation, Table
+from .table import TableController
+from ....control.controllers import CommunicationController
+from ....generated import PumpMethod, DadMethod, SolventElement
+from ....utils.chromatogram import TIME_FORMAT, AgilentChannelChromatogramData
+from ....utils.macro import *
+from ....utils.method_types import *
+from ....utils.table_types import *
 
 
 class MethodController(TableController):
@@ -46,9 +45,21 @@ class MethodController(TableController):
         )
 
     def get_row(self, row: int) -> TimeTableEntry:
+        flow = None
+        om = None
+
+        try:
+            flow = self.get_num(row, RegisterFlag.TIMETABLE_FLOW)
+        except RuntimeError:
+            pass
+        try:
+            om = self.get_num(row, RegisterFlag.TIMETABLE_SOLVENT_B_COMPOSITION)
+        except RuntimeError:
+            pass
+
         return TimeTableEntry(start_time=self.get_num(row, RegisterFlag.TIME),
-                              organic_modifer=self.get_num(row, RegisterFlag.TIMETABLE_SOLVENT_B_COMPOSITION),
-                              flow=self.get_num(row, RegisterFlag.TIMETABLE_FLOW))
+                              organic_modifer=om,
+                              flow=flow)
 
     def get_timetable(self, rows: int):
         uncoalesced_timetable_rows = [self.get_row(r + 1) for r in range(rows)]
@@ -84,12 +95,11 @@ class MethodController(TableController):
                 cmd=TableOperation.GET_OBJ_HDR_VAL.value.format(
                     register=self.table.register,
                     register_flag=RegisterFlag.POST_TIME))
-            self.table_state = MethodDetails(
-                name=method_name,
-                timetable=timetable_rows,
-                stop_time=stop_time,
-                post_time=post_time,
-                params=params)
+            self.table_state = MethodDetails(name=method_name,
+                                             timetable=timetable_rows,
+                                             stop_time=stop_time,
+                                             post_time=post_time,
+                                             params=params)
             return self.table_state
         else:
             raise RuntimeError(rows.err_value)
@@ -156,17 +166,16 @@ class MethodController(TableController):
                     elif solvent.channel == "Channel_B":
                         organic_modifier = solvent
 
-            self.table_state = MethodDetails(
-                name=method_name,
-                params=HPLCMethodParams(organic_modifier=organic_modifier.percentage,
-                                        flow=method.flow),
-                stop_time=method.stop_time.stop_time_value,
-                post_time=method.post_time.post_time_value,
-                timetable=[TimeTableEntry(start_time=tte.time,
-                                          organic_modifer=tte.percent_b,
-                                          flow=method.flow
-                                          ) for tte in method.timetable.timetable_entry],
-                dad_wavelengthes=dad.signals.signal)
+            self.table_state = MethodDetails(name=method_name,
+                                             params=HPLCMethodParams(organic_modifier=organic_modifier.percentage,
+                                                                     flow=method.flow),
+                                             stop_time=method.stop_time.stop_time_value,
+                                             post_time=method.post_time.post_time_value,
+                                             timetable=[TimeTableEntry(start_time=tte.time,
+                                                                       organic_modifer=tte.percent_b,
+                                                                       flow=method.flow
+                                                                       ) for tte in method.timetable.timetable_entry],
+                                             dad_wavelengthes=dad.signals.signal)
             return self.table_state
         else:
             raise FileNotFoundError
@@ -186,7 +195,7 @@ class MethodController(TableController):
                                 ptype=PType.NUM)
         post_time: Param = Param(val=updated_method.post_time,
                                  chemstation_key=RegisterFlag.POST_TIME,
-                                 ptype=PType.NUM)  # TODO check postime works
+                                 ptype=PType.NUM)
         flow: Param = Param(val=updated_method.params.flow,
                             chemstation_key=RegisterFlag.FLOW,
                             ptype=PType.NUM)
@@ -205,19 +214,15 @@ class MethodController(TableController):
         self._update_param(initial_organic_modifier)
         self._update_param(flow)
         if self.table_state.stop_time:
-            self._update_param(Param(val="Set",
-                                     chemstation_key=RegisterFlag.STOPTIME_MODE,
-                                     ptype=PType.STR))
+            self._update_param(Param(val="Set", chemstation_key=RegisterFlag.STOPTIME_MODE, ptype=PType.STR))
             self._update_param(max_time)
         else:
-            self._update_param(Param(val="Off",
-                                     chemstation_key=RegisterFlag.STOPTIME_MODE,
-                                     ptype=PType.STR))
+            self._update_param(Param(val="Off", chemstation_key=RegisterFlag.STOPTIME_MODE, ptype=PType.STR))
         if self.table_state.post_time:
-            self._update_param(Param(val="Set",
-                                     chemstation_key=RegisterFlag.POSTIME_MODE,
-                                     ptype=PType.STR))
+            self._update_param(Param(val="Set", chemstation_key=RegisterFlag.POSTIME_MODE, ptype=PType.STR))
             self._update_param(post_time)
+        else:
+            self._update_param(Param(val="Off", chemstation_key=RegisterFlag.POSTIME_MODE, ptype=PType.STR))
         self.download()
 
     def _update_param(self, method_param: Param):
@@ -246,34 +251,33 @@ class MethodController(TableController):
 
     def edit_row(self, row: TimeTableEntry, first_row: bool = False):
         if first_row:
-            self.add_row()
-            self.add_new_col_text(col_name=RegisterFlag.FUNCTION,
-                                  val=RegisterFlag.SOLVENT_COMPOSITION.value)
-            self.add_new_col_num(col_name=RegisterFlag.TIME, val=row.start_time)
-            self.add_new_col_num(col_name=RegisterFlag.TIMETABLE_SOLVENT_B_COMPOSITION,
-                                 val=row.organic_modifer)
-            self.add_row()
-            self.get_num_rows()
-            self.edit_row_text(col_name=RegisterFlag.FUNCTION, val=RegisterFlag.FLOW.value)
-            self.add_new_col_num(col_name=RegisterFlag.TIMETABLE_FLOW, val=row.flow)
-            self.edit_row_num(col_name=RegisterFlag.TIMETABLE_FLOW, val=row.flow)
+            if row.organic_modifer:
+                self.add_row()
+                self.add_new_col_text(col_name=RegisterFlag.FUNCTION, val=RegisterFlag.SOLVENT_COMPOSITION.value)
+                self.add_new_col_num(col_name=RegisterFlag.TIME, val=row.start_time)
+                self.add_new_col_num(col_name=RegisterFlag.TIMETABLE_SOLVENT_B_COMPOSITION, val=row.organic_modifer)
+            if row.flow:
+                self.add_row()
+                self.get_num_rows()
+                self.edit_row_text(col_name=RegisterFlag.FUNCTION, val=RegisterFlag.FLOW.value)
+                self.add_new_col_num(col_name=RegisterFlag.TIMETABLE_FLOW, val=row.flow)
+                self.edit_row_num(col_name=RegisterFlag.TIMETABLE_FLOW, val=row.flow)
             self.download()
         else:
-            self.add_row()
-            self.get_num_rows()
-            self.edit_row_text(col_name=RegisterFlag.FUNCTION,
-                               val=RegisterFlag.SOLVENT_COMPOSITION.value)
-            self.edit_row_num(col_name=RegisterFlag.TIME, val=row.start_time)
-            self.edit_row_num(col_name=RegisterFlag.TIMETABLE_SOLVENT_B_COMPOSITION,
-                              val=row.organic_modifer)
-            self.download()
-
-            self.add_row()
-            self.get_num_rows()
-            self.edit_row_text(col_name=RegisterFlag.FUNCTION, val=RegisterFlag.FLOW.value)
-            self.edit_row_num(col_name=RegisterFlag.TIMETABLE_FLOW, val=row.flow)
-            self.edit_row_num(col_name=RegisterFlag.TIME, val=row.start_time)
-            self.download()
+            if row.organic_modifer:
+                self.add_row()
+                self.get_num_rows()
+                self.edit_row_text(col_name=RegisterFlag.FUNCTION, val=RegisterFlag.SOLVENT_COMPOSITION.value)
+                self.edit_row_num(col_name=RegisterFlag.TIME, val=row.start_time)
+                self.edit_row_num(col_name=RegisterFlag.TIMETABLE_SOLVENT_B_COMPOSITION, val=row.organic_modifer)
+                self.download()
+            if row.flow:
+                self.add_row()
+                self.get_num_rows()
+                self.edit_row_text(col_name=RegisterFlag.FUNCTION, val=RegisterFlag.FLOW.value)
+                self.edit_row_num(col_name=RegisterFlag.TIMETABLE_FLOW, val=row.flow)
+                self.edit_row_num(col_name=RegisterFlag.TIME, val=row.start_time)
+                self.download()
 
     def _update_method_timetable(self, timetable_rows: list[TimeTableEntry]):
         self.get_num_rows()
@@ -309,30 +313,34 @@ class MethodController(TableController):
         if not self.table_state:
             self.table_state = self.load()
 
-        timestamp = time.strftime(TIME_FORMAT)
-        self.send(Command.RUN_METHOD_CMD.value.format(data_dir=self.data_dir,
-                                                      experiment_name=experiment_name,
-                                                      timestamp=timestamp))
-
-        if self.check_hplc_is_running():
+        folder_name = ""
+        hplc_is_running = self.check_hplc_is_running()
+        while not hplc_is_running:
+            timestamp = time.strftime(TIME_FORMAT)
+            self.send(Command.RUN_METHOD_CMD.value.format(data_dir=self.data_dir,
+                                                          experiment_name=experiment_name,
+                                                          timestamp=timestamp))
             folder_name = f"{experiment_name}_{timestamp}.D"
-            self.data_files.append(os.path.join(self.data_dir, folder_name))
-
-            if stall_while_running:
-                run_completed = self.check_hplc_done_running(method=self.table_state)
-                if run_completed.is_ok():
-                    self.data_files[-1] = run_completed.value
-                else:
-                    raise RuntimeError("Run error has occurred.")
+            hplc_is_running = self.check_hplc_is_running()
+
+        self.data_files.append(os.path.join(self.data_dir, folder_name))
+
+        if stall_while_running:
+            run_completed = self.check_hplc_done_running(method=self.table_state)
+            if run_completed.is_ok():
+                self.data_files[-1] = run_completed.ok_value
             else:
-                self.data_files[-1].dir = self.fuzzy_match_most_recent_folder(folder_name).ok_value
+                raise RuntimeError("Run error has occurred.")
+        else:
+            self.data_files[-1].dir = self.fuzzy_match_most_recent_folder(folder_name).ok_value
 
     def retrieve_recent_data_files(self) -> str:
         return self.data_files[-1]
 
-    def get_data(self, custom_path: Optional[str] = None) -> AgilentChannelChromatogramData:
+    def get_data(self, custom_path: Optional[str] = None,
+                 read_uv: bool = False) -> AgilentChannelChromatogramData:
         if not custom_path:
-            self.get_spectrum(self.data_files[-1])
+            self.get_spectrum(self.data_files[-1], read_uv)
         else:
-            self.get_spectrum(custom_path)
-        return AgilentChannelChromatogramData(**self.spectra)
+            self.get_spectrum(custom_path, read_uv)
+        return AgilentChannelChromatogramData(**self.spectra) if not read_uv else self.uv

{pychemstation-0.5.12/pychemstation/control/controllers → pychemstation-0.5.13.dev1/pychemstation/control/controllers/tables}/sequence.py

@@ -1,14 +1,14 @@
 import os
 import time
-from typing import Optional
+from typing import Optional, Union
 
-from ...control.controllers.comm import CommunicationController
-from ...control.controllers.table_controller import TableController
-from ...utils.chromatogram import SEQUENCE_TIME_FORMAT, AgilentChannelChromatogramData
-from ...utils.macro import Command
-from ...utils.sequence_types import SequenceTable, SequenceEntry, SequenceDataFiles, InjectionSource, SampleType
-from ...utils.table_types import RegisterFlag, Table
-from ...utils.tray_types import TenVialColumn
+from .table import TableController, ChromData
+from ....control.controllers.comm import CommunicationController
+from ....utils.chromatogram import SEQUENCE_TIME_FORMAT, AgilentChannelChromatogramData
+from ....utils.macro import Command
+from ....utils.sequence_types import SequenceTable, SequenceEntry, SequenceDataFiles, InjectionSource, SampleType
+from ....utils.table_types import RegisterFlag, Table
+from ....utils.tray_types import TenVialColumn, FiftyFourVialPlate
 
 
 class SequenceController(TableController):
@@ -117,8 +117,10 @@ class SequenceController(TableController):
 
         if row.vial_location:
             loc = row.vial_location
-            if isinstance(row.vial_location, TenVialColumn):
+            if isinstance(loc, TenVialColumn):
                 loc = row.vial_location.value
+            elif isinstance(loc, FiftyFourVialPlate):
+                loc = row.vial_location.value()
             self.edit_row_num(row=row_num, col_name=RegisterFlag.VIAL_LOCATION, val=loc)
 
         if row.method:
@@ -139,7 +141,10 @@ class SequenceController(TableController):
 
         if row.sample_name:
             self.edit_row_text(row=row_num, col_name=RegisterFlag.NAME, val=row.sample_name)
-            self.edit_row_text(row=row_num, col_name=RegisterFlag.DATA_FILE, val=row.sample_name)
+            if row.data_file:
+                self.edit_row_text(row=row_num, col_name=RegisterFlag.DATA_FILE, val=row.data_file)
+            else:
+                self.edit_row_text(row=row_num, col_name=RegisterFlag.DATA_FILE, val=row.sample_name)
 
         if row.sample_type:
             self.edit_row_num(row=row_num, col_name=RegisterFlag.SAMPLE_TYPE, val=row.sample_type.value)
@@ -176,15 +181,19 @@ class SequenceController(TableController):
         sequence_data_files: SequenceDataFiles = self.data_files[-1]
         return sequence_data_files.dir
 
-    def get_data(self, custom_path: Optional[str] = None) -> list[AgilentChannelChromatogramData]:
+    def get_data(self, custom_path: Optional[str] = None,
+                 read_uv: bool = False) -> list[AgilentChannelChromatogramData]:
         parent_dir = self.data_files[-1].dir if not custom_path else custom_path
         subdirs = [x[0] for x in os.walk(self.data_dir)]
         potential_folders = sorted(list(filter(lambda d: parent_dir in d, subdirs)))
         self.data_files[-1].child_dirs = [f for f in potential_folders if
                                           parent_dir in f and ".M" not in f and ".D" in f]
 
-        spectra: list[AgilentChannelChromatogramData] = []
+        spectra: list[Union[AgilentChannelChromatogramData, ChromData]] = []
+        all_w_spectra: list[Union[AgilentChannelChromatogramData, ChromData]] = []
         for row in self.data_files[-1].child_dirs:
-            self.get_spectrum(row)
+            self.get_spectrum(row, read_uv)
             spectra.append(AgilentChannelChromatogramData(**self.spectra))
-        return spectra
+            all_w_spectra.append(self.uv)
+
+        return spectra if not read_uv else all_w_spectra

pychemstation-0.5.12/pychemstation/control/controllers/table_controller.py → pychemstation-0.5.13.dev1/pychemstation/control/controllers/tables/table.py

@@ -6,21 +6,32 @@ Authors: Lucy Hao
 
 import abc
 import os
+from dataclasses import dataclass
 from typing import Union, Optional
 
+import numpy as np
 import polling
+from rainbow import DataFile
 from result import Result, Ok, Err
+import pandas as pd
+import rainbow as rb
 
-from ...control.controllers.comm import CommunicationController
-from ...utils.chromatogram import AgilentHPLCChromatogram, AgilentChannelChromatogramData
-from ...utils.macro import Command, HPLCRunningStatus, Response
-from ...utils.method_types import MethodDetails
-from ...utils.sequence_types import SequenceDataFiles, SequenceTable
-from ...utils.table_types import Table, TableOperation, RegisterFlag
+from ....control.controllers.comm import CommunicationController
+from ....utils.chromatogram import AgilentHPLCChromatogram, AgilentChannelChromatogramData
+from ....utils.macro import Command, HPLCRunningStatus, Response
+from ....utils.method_types import MethodDetails
+from ....utils.sequence_types import SequenceDataFiles, SequenceTable
+from ....utils.table_types import Table, TableOperation, RegisterFlag
 
 TableType = Union[MethodDetails, SequenceTable]
 
 
+@dataclass
+class ChromData:
+    x: np.array
+    y: np.array
+
+
 class TableController(abc.ABC):
 
     def __init__(self, controller: CommunicationController, src: str, data_dir: str, table: Table):
@@ -51,6 +62,8 @@ class TableController(abc.ABC):
 
         self.data_files: Union[list[SequenceDataFiles], list[str]] = []
 
+        self.uv = None
+
         # Initialize row counter for table operations
         self.send('Local Rows')
 
@@ -191,8 +204,8 @@ class TableController(abc.ABC):
     def check_hplc_is_running(self) -> bool:
         started_running = polling.poll(
             lambda: isinstance(self.controller.get_status(), HPLCRunningStatus),
-            step=5,
-            max_tries=100)
+            step=2,
+            max_tries=10)
         return started_running
 
     def check_hplc_done_running(self,
@@ -254,13 +267,21 @@ class TableController(abc.ABC):
     def get_data(self) -> Union[list[AgilentChannelChromatogramData], AgilentChannelChromatogramData]:
         pass
 
-    def get_spectrum(self, data_file: str):
+    def get_uv_spectrum(self, path: str):
+        data_uv: DataFile = rb.agilent.chemstation.parse_file(os.path.join(path, "DAD1.UV"))
+        zipped_data = zip(data_uv.ylabels, data_uv.data)
+        self.uv = {str(w_a[0]): ChromData(x=data_uv.xlabels, y=w_a[1]) for w_a in zipped_data}
+
+    def get_spectrum(self, data_path: str, read_uv: bool = False):
         """
         Load chromatogram for any channel in spectra dictionary.
         """
+        if read_uv:
+            self.get_uv_spectrum(data_path)
+
         for channel, spec in self.spectra.items():
             try:
-                spec.load_spectrum(data_path=data_file, channel=channel)
+                spec.load_spectrum(data_path=data_path, channel=channel)
             except FileNotFoundError:
                 self.spectra[channel] = None
                 print(f"No data at channel: {channel}")

pychemstation-0.5.13.dev1/pychemstation/utils/injector_types.py

@@ -0,0 +1,30 @@
+from dataclasses import dataclass
+from typing import Any
+
+from pychemstation.utils.tray_types import Tray
+
+
+@dataclass
+class Draw:
+    amount: float
+    source: Tray
+    speed: Any
+    offset: Any
+
+
+@dataclass
+class Wait:
+    time: int
+
+
+@dataclass
+class Inject:
+    pass
+
+
+InjectorFunction = [Draw, Wait, Inject]
+
+
+@dataclass
+class InjectorTable:
+    functions: list[InjectorFunction]

{pychemstation-0.5.12 → pychemstation-0.5.13.dev1}/pychemstation/utils/macro.py

@@ -34,6 +34,7 @@ class Command(Enum):
     INSTRUMENT_OFF = 'macro "SHUTDOWN.MAC" ,go'
     INSTRUMENT_ON = 'LIDoOperation "TURN_ON"'
 
+    # Method and Sequence Related
     GET_METHOD_CMD = "response$ = _MethFile$"
     GET_ROWS_CMD = 'response_num = TabHdrVal({register}, "{table_name}", "{col_name}")'
     SWITCH_METHOD_CMD = 'LoadMethod "{method_dir}", "{method_name}.M"'

pychemstation-0.5.13.dev1/pychemstation/utils/pump_types.py

@@ -0,0 +1,7 @@
+from dataclasses import dataclass
+
+
+@dataclass
+class Pump:
+    solvent: str
+    in_use: bool

{pychemstation-0.5.12 → pychemstation-0.5.13.dev1}/pychemstation/utils/sequence_types.py

@@ -4,7 +4,7 @@ from dataclasses import dataclass
 from enum import Enum
 from typing import Optional, Union
 
-from pychemstation.utils.tray_types import TenVialColumn
+from pychemstation.utils.tray_types import TenVialColumn, Tray
 
 
 @dataclass
@@ -39,7 +39,8 @@ class InjectionSource(Enum):
 @dataclass
 class SequenceEntry:
     sample_name: str
-    vial_location: Union[TenVialColumn, int]
+    vial_location: Tray
+    data_file: Optional[str] = None
     method: Optional[str] = None
     num_inj: Optional[int] = 1
     inj_vol: Optional[int] = 2

{pychemstation-0.5.12 → pychemstation-0.5.13.dev1}/pychemstation/utils/tray_types.py

@@ -2,6 +2,7 @@ from __future__ import annotations
 
 from dataclasses import dataclass
 from enum import Enum
+from typing import Union
 
 
 class Num(Enum):
@@ -50,3 +51,6 @@ class TenVialColumn(Enum):
     EIGHT = 8
     NINE = 9
     TEN = 10
+
+
+Tray = Union[FiftyFourVialPlate, TenVialColumn]

{pychemstation-0.5.12 → pychemstation-0.5.13.dev1}/pychemstation.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pychemstation
-Version: 0.5.12
+Version: 0.5.13.dev1
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Home-page: https://gitlab.com/heingroup/device-api/pychemstation
 Author: Lucy Hao
@@ -14,6 +14,7 @@ Requires-Dist: polling
 Requires-Dist: seabreeze
 Requires-Dist: xsdata
 Requires-Dist: result
+Requires-Dist: rainbow
 
 # Agilent HPLC Macro Control
 
@@ -99,7 +100,7 @@ our [GitLab](https://gitlab.com/heingroup/device-api/pychemstation)!
 
 ## Authors and Acknowledgements
 
-Lucy Hao
+Lucy Hao, Maria Politi
 
 - Adapted from [**AnalyticalLabware**](https://github.com/croningp/analyticallabware), created by members in the Cronin
   Group. Copyright © Cronin Group, used under the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) license.

{pychemstation-0.5.12 → pychemstation-0.5.13.dev1}/pychemstation.egg-info/SOURCES.txt

@@ -16,17 +16,24 @@ pychemstation/control/__init__.py
 pychemstation/control/hplc.py
 pychemstation/control/controllers/__init__.py
 pychemstation/control/controllers/comm.py
-pychemstation/control/controllers/method.py
-pychemstation/control/controllers/sequence.py
-pychemstation/control/controllers/table_controller.py
+pychemstation/control/controllers/devices/__init__.py
+pychemstation/control/controllers/devices/column.py
+pychemstation/control/controllers/devices/device.py
+pychemstation/control/controllers/devices/pump.py
+pychemstation/control/controllers/tables/__init__.py
+pychemstation/control/controllers/tables/method.py
+pychemstation/control/controllers/tables/sequence.py
+pychemstation/control/controllers/tables/table.py
 pychemstation/generated/__init__.py
 pychemstation/generated/dad_method.py
 pychemstation/generated/pump_method.py
 pychemstation/utils/__init__.py
 pychemstation/utils/chromatogram.py
+pychemstation/utils/injector_types.py
 pychemstation/utils/macro.py
 pychemstation/utils/method_types.py
 pychemstation/utils/parsing.py
+pychemstation/utils/pump_types.py
 pychemstation/utils/sequence_types.py
 pychemstation/utils/table_types.py
 pychemstation/utils/tray_types.py
@@ -34,5 +41,6 @@ tests/__init__.py
 tests/constants.py
 tests/test_comb.py
 tests/test_comm.py
+tests/test_inj.py
 tests/test_method.py
 tests/test_sequence.py

{pychemstation-0.5.12 → pychemstation-0.5.13.dev1}/pychemstation.egg-info/requires.txt

@@ -2,3 +2,4 @@ polling
 seabreeze
 xsdata
 result
+rainbow

{pychemstation-0.5.12 → pychemstation-0.5.13.dev1}/pyproject.toml

@@ -18,7 +18,9 @@ pdoc = "^15.0.1"
 xsdata = "^24.12"
 scipy = "^1.15.1"
 result = "^0.17.0"
-
+rainbow-api = "^1.0.10"
+rainbow = "^2.8.0"
+pandas = "^2.2.3"
 
 [tool.poetry.group.dev.dependencies]
 mypy = "^1.14.1"

{pychemstation-0.5.12 → pychemstation-0.5.13.dev1}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="pychemstation",
-    version="0.5.12",
+    version="0.5.13.dev1",
     author="Lucy Hao",
     author_email="lhao03@student.ubc.ca",
     description="Library to interact with Chemstation software, primarily used in Hein lab",
@@ -17,7 +17,8 @@ setuptools.setup(
         'polling',
         'seabreeze',
         'xsdata',
-        'result'
+        'result',
+        'rainbow'
     ],
     classifiers=[
         "Programming Language :: Python :: 3",

pychemstation-0.5.13.dev1/tests/test_inj.py

@@ -0,0 +1,38 @@
+import os
+import unittest
+
+from pychemstation.control import HPLCController
+from tests.constants import *
+
+
+class TestInj(unittest.TestCase):
+    def setUp(self):
+        path_constants = room(254)
+        for path in path_constants:
+            if not os.path.exists(path):
+                self.fail(
+                    f"{path} does not exist on your system. If you would like to run tests, please change this path.")
+
+        self.hplc_controller = HPLCController(comm_dir=path_constants[0],
+                                              method_dir=path_constants[1],
+                                              data_dir=path_constants[2],
+                                              sequence_dir=path_constants[3])
+
+    def test_load_inj(self):
+        self.hplc_controller.switch_method(DEFAULT_METHOD)
+        try:
+            gp_mtd = self.hplc_controller.method_controller.load_from_disk(DEFAULT_METHOD)
+            self.assertTrue(gp_mtd.first_row.organic_modifier == 5)
+        except Exception as e:
+            self.fail(f"Should have not failed, {e}")
+
+    def test_edit_inj(self):
+        self.hplc_controller.method_controller.switch(DEFAULT_METHOD)
+        new_method = gen_rand_method()
+        try:
+            self.hplc_controller.edit_method(new_method)
+        except Exception as e:
+            self.fail(f"Should have not failed: {e}")
+
+if __name__ == '__main__':
+    unittest.main()

pychemstation-0.5.12/pychemstation/control/controllers/__init__.py

@@ -1,4 +0,0 @@
-from .method import MethodController
-from .sequence import SequenceController
-from .table_controller import TableController
-from .comm import CommunicationController