pychemstation 0.5.13.dev2__tar.gz → 0.5.13.dev3__tar.gz

{pychemstation-0.5.13.dev2 → pychemstation-0.5.13.dev3}/PKG-INFO

@@ -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 → pychemstation-0.5.13.dev3}/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-0.5.13.dev2 → pychemstation-0.5.13.dev3}/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-0.5.13.dev2 → pychemstation-0.5.13.dev3}/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 → pychemstation-0.5.13.dev3}/pychemstation.egg-info/PKG-INFO

@@ -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 → pychemstation-0.5.13.dev3}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="pychemstation",
-    version="0.5.13.dev2",
+    version="0.5.13.dev3",
     author="Lucy Hao",
     author_email="lhao03@student.ubc.ca",
     description="Library to interact with Chemstation software, primarily used in Hein lab",