pychemstation 0.5.13.dev2__py3-none-any.whl → 0.5.13.dev3__py3-none-any.whl

pychemstation/control/controllers/tables/method.py

@@ -314,14 +314,19 @@ class MethodController(TableController):
             self.table_state = self.load()
 
         folder_name = ""
-        hplc_is_running = self.check_hplc_is_running()
-        while not hplc_is_running:
+        hplc_is_running = False
+        tries = 0
+        while not hplc_is_running and tries < 10:
             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"
             hplc_is_running = self.check_hplc_is_running()
+            tries += 1
+
+        if hplc_is_running:
+            raise RuntimeError
 
         self.data_files.append(os.path.join(self.data_dir, folder_name))
 

pychemstation/control/controllers/tables/table.py

@@ -11,6 +11,7 @@ from typing import Union, Optional
 
 import numpy as np
 import polling
+from polling import MaxCallException
 from rainbow import DataFile
 from result import Result, Ok, Err
 import pandas as pd
@@ -34,20 +35,25 @@ class ChromData:
 
 class TableController(abc.ABC):
 
-    def __init__(self, controller: CommunicationController, src: str, data_dir: str, table: Table):
+    def __init__(self, controller: CommunicationController,
+                 src: str,
+                 data_dir: str,
+                 table: Table,
+                 offline: bool = False):
         self.controller = controller
         self.table = table
         self.table_state: Optional[TableType] = None
 
-        if os.path.isdir(src):
-            self.src: str = src
-        else:
-            raise FileNotFoundError(f"dir: {src} not found.")
+        if not offline:
+            if os.path.isdir(src):
+                self.src: str = src
+            else:
+                raise FileNotFoundError(f"dir: {src} not found.")
 
-        if os.path.isdir(data_dir):
-            self.data_dir: str = data_dir
-        else:
-            raise FileNotFoundError(f"dir: {data_dir} not found.")
+            if os.path.isdir(data_dir):
+                self.data_dir: str = data_dir
+            else:
+                raise FileNotFoundError(f"dir: {data_dir} not found.")
 
         self.spectra: dict[str, Optional[AgilentHPLCChromatogram]] = {
             "A": AgilentHPLCChromatogram(self.data_dir),
@@ -202,10 +208,11 @@ class TableController(abc.ABC):
             return Err("No rows could be read.")
 
     def check_hplc_is_running(self) -> bool:
-        started_running = polling.poll(
-            lambda: isinstance(self.controller.get_status(), HPLCRunningStatus),
-            step=5,
-            max_tries=40)
+        try:
+            started_running = polling.poll(lambda: isinstance(self.controller.get_status(), HPLCRunningStatus),
+                                           step=3, max_tries=10)
+        except MaxCallException:
+            return False
         return started_running
 
     def check_hplc_done_running(self,

pychemstation/control/hplc.py

@@ -41,18 +41,20 @@ class HPLCController:
         `comm_dir` must match the file path in the macro file.
 
         :param comm_dir: Name of directory for communication, where ChemStation will read and write from. Can be any existing directory.
-        :raises FileNotFoundError: If either `data_dir`, `method_dir` or `comm_dir` is not a valid directory.
+        :raises FileNotFoundError: If either `data_dir`, `method_dir`, `sequence_dir`, or `comm_dir` is not a valid directory.
         """
         self.comm = CommunicationController(comm_dir=comm_dir) if not offline else None
         self.method_controller = MethodController(controller=self.comm,
                                                   src=method_dir,
                                                   data_dir=data_dir,
-                                                  table=self.METHOD_TIMETABLE)
+                                                  table=self.METHOD_TIMETABLE,
+                                                  offline=offline)
         self.sequence_controller = SequenceController(controller=self.comm,
                                                       src=sequence_dir,
                                                       data_dir=data_dir,
                                                       table=self.SEQUENCE_TABLE,
-                                                      method_dir=method_dir)
+                                                      method_dir=method_dir,
+                                                      offline=offline)
 
     def send(self, cmd: Union[Command, str]):
         if not self.comm:
@@ -142,21 +144,25 @@ class HPLCController:
         """
         self.sequence_controller.edit_row(row, num)
 
-    def get_last_run_method_data(self, data: Optional[str] = None) -> AgilentChannelChromatogramData:
+    def get_last_run_method_data(self, read_uv: bool = False,
+                                 data: Optional[str] = None) -> AgilentChannelChromatogramData:
         """
         Returns the last run method data.
 
         :param data: If you want to just load method data but from a file path. This file path must be the complete file path.
+        :param read_uv: whether to also read the UV file
         """
-        return self.method_controller.get_data(custom_path=data)
+        return self.method_controller.get_data(custom_path=data, read_uv=read_uv)
 
-    def get_last_run_sequence_data(self, data: Optional[str] = None) -> list[AgilentChannelChromatogramData]:
+    def get_last_run_sequence_data(self, read_uv: bool = False,
+                                   data: Optional[str] = None) -> list[AgilentChannelChromatogramData]:
         """
         Returns data for all rows in the last run sequence data.
 
         :param data: If you want to just load sequence data but from a file path. This file path must be the complete file path.
+        :param read_uv: whether to also read the UV file
         """
-        return self.sequence_controller.get_data(custom_path=data)
+        return self.sequence_controller.get_data(custom_path=data, read_uv=read_uv)
 
     def check_loaded_sequence(self) -> str:
         """

{pychemstation-0.5.13.dev2.dist-info → pychemstation-0.5.13.dev3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pychemstation
-Version: 0.5.13.dev2
+Version: 0.5.13.dev3
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Home-page: https://gitlab.com/heingroup/device-api/pychemstation
 Author: Lucy Hao

{pychemstation-0.5.13.dev2.dist-info → pychemstation-0.5.13.dev3.dist-info}/RECORD

@@ -5,7 +5,7 @@ pychemstation/analysis/spec_utils.py,sha256=UOo9hJR3evJfmaohEEsyb7aq6X996ofuUfu-
 pychemstation/analysis/utils.py,sha256=ISupAOb_yqA4_DZRK9v18UL-XjUQccAicIJKb1VMnGg,2055
 pychemstation/control/__init__.py,sha256=4xTy8X-mkn_PPZKr7w9rnj1wZhtmTesbQptPhpYmKXs,64
 pychemstation/control/comm.py,sha256=u44g1hTluQ0yUG93Un-QAshScoDpgYRrZfFTgweP5tY,7386
-pychemstation/control/hplc.py,sha256=5xC5q-hrAn5hKdz-ZwT_Dlas9LWLV27jZvhCKj7Lzg4,8761
+pychemstation/control/hplc.py,sha256=UlafodQoFFow2UVo-INK1ZjxyJ5vrVvv1TjB5VyAsHo,9178
 pychemstation/control/controllers/__init__.py,sha256=EM6LBNSTJqYVatmnvPq0P-S3q0POA88c-y64zL79I_I,252
 pychemstation/control/controllers/comm.py,sha256=IU4I_Q42VNCNUlVi93MxCmw2EBY9hiBDkU9FxubKg3c,7441
 pychemstation/control/controllers/method.py,sha256=XUclB7lQ_SIkquR58MBmmi9drHIPEq9AR8VprTLenvI,15503
@@ -16,9 +16,9 @@ pychemstation/control/controllers/devices/column.py,sha256=SCpCnVFZFUM9LM51MbWkV
 pychemstation/control/controllers/devices/device.py,sha256=SF1JK93FjmACnYrlKvldX3gEeA21qnXZegeNhc9QJGQ,738
 pychemstation/control/controllers/devices/pump.py,sha256=DJQh4lNXEraeC1CWrsKmsITOjuYlRI3tih_XRB3F1hg,1404
 pychemstation/control/controllers/tables/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pychemstation/control/controllers/tables/method.py,sha256=TlP7FwEmN-QGwewoxXNuzLBAzDipRms9TMTgdAaKJmM,16033
+pychemstation/control/controllers/tables/method.py,sha256=pZO0Z5JAXaiYHyo6OCdKEEDS6LwrVEgoGUZZUASU-eg,16126
 pychemstation/control/controllers/tables/sequence.py,sha256=Yq31YhcIhmu1A3iVEFV_d_N68QHABGVOkqn1QrvyKu0,8766
-pychemstation/control/controllers/tables/table.py,sha256=LAxDNKY2sEypikYR6v6o8SiuP70Ay-FYcvuCfVSFhsQ,11621
+pychemstation/control/controllers/tables/table.py,sha256=56kvNb_U8ka_m1r4sk-6yzRiXTT3CuszP7aoX6-TIlE,11886
 pychemstation/control/table/__init__.py,sha256=RgMN4uIWHdNUHpGRBWdzmzAbk7XEKl6Y-qtqWCxzSZU,124
 pychemstation/control/table/method.py,sha256=THVoGomSXff_CTU3eAYme0BYwkPzab5UgZKsiZ29QSk,12196
 pychemstation/control/table/sequence.py,sha256=Eri52AnbE3BGthfrRSvYKYciquUzvHKo0lYUTySYYE8,10542
@@ -43,8 +43,8 @@ tests/test_comm.py,sha256=EYOpVXzEMQLGhhKYDPO-KaLcJdPSMPTD9Y4jSI0yVQY,2516
 tests/test_inj.py,sha256=yaPGZoHiOC3ZSgsmrtiqp8QtSo2bMxB9FJhaFlOpad0,1412
 tests/test_method.py,sha256=r1Q1irqiVzs31QuTYLX3u_A0FpX8rIAQ1L4WOk9tLbk,2473
 tests/test_sequence.py,sha256=Nz2iqp1cJgw6kcQvnwSkfBmhxpOH62PoEu6o_5rO-PY,4929
-pychemstation-0.5.13.dev2.dist-info/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
-pychemstation-0.5.13.dev2.dist-info/METADATA,sha256=KRy25kSutKC7MXyLmp6YYcIkiIRh9s0GzglAVa1rudg,4372
-pychemstation-0.5.13.dev2.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-pychemstation-0.5.13.dev2.dist-info/top_level.txt,sha256=zXfKu_4nYWwPHo3OsuhshMNC3SPkcoTGCyODjURaghY,20
-pychemstation-0.5.13.dev2.dist-info/RECORD,,
+pychemstation-0.5.13.dev3.dist-info/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
+pychemstation-0.5.13.dev3.dist-info/METADATA,sha256=2av4WWulIZZUNvF5vg-WDRPUAVBE7YQthe2toAg6YIs,4372
+pychemstation-0.5.13.dev3.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+pychemstation-0.5.13.dev3.dist-info/top_level.txt,sha256=zXfKu_4nYWwPHo3OsuhshMNC3SPkcoTGCyODjURaghY,20
+pychemstation-0.5.13.dev3.dist-info/RECORD,,