pychemstation 0.10.5__tar.gz → 0.10.7__tar.gz

{pychemstation-0.10.5 → pychemstation-0.10.7}/.gitignore

@@ -6,4 +6,4 @@
 target
 .DS_Store
 env
-venv
+venv

{pychemstation-0.10.5 → pychemstation-0.10.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.10.5
+Version: 0.10.7
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Project-URL: Documentation, https://pychemstation-e5a086.gitlab.io/pychemstation.html
 Project-URL: Repository, https://gitlab.com/heingroup/device-api/pychemstation
@@ -18,7 +18,7 @@ Requires-Dist: matplotlib>=3.7.5
 Requires-Dist: pandas>=2.0.3
 Requires-Dist: pdoc>=14.7.0
 Requires-Dist: polling>=0.3.2
-Requires-Dist: pre-commit>=4.2.0
+Requires-Dist: pre-commit>=3.5.0
 Requires-Dist: pytest>=7.3.5
 Requires-Dist: rainbow-api>=1.0.10
 Requires-Dist: result>=0.17.0
@@ -90,7 +90,7 @@ DATA_DIR_2 = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data"
 DATA_DIR_3 = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data"
 
 # Initialize HPLC Controller
-hplc_controller = HPLCController(data_dirs=[DATA_DIR_2, DATA_DIR_3],
+hplc_controller = HPLCController(extra_data_dirs=[DATA_DIR_2, DATA_DIR_3],
                                  comm_dir=DEFAULT_COMMAND_PATH,
                                  method_dir=DEFAULT_METHOD_DIR,
                                  sequence_dir=SEQUENCE_DIR)

{pychemstation-0.10.5 → pychemstation-0.10.7}/README.md

@@ -59,7 +59,7 @@ DATA_DIR_2 = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data"
 DATA_DIR_3 = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data"
 
 # Initialize HPLC Controller
-hplc_controller = HPLCController(data_dirs=[DATA_DIR_2, DATA_DIR_3],
+hplc_controller = HPLCController(extra_data_dirs=[DATA_DIR_2, DATA_DIR_3],
                                  comm_dir=DEFAULT_COMMAND_PATH,
                                  method_dir=DEFAULT_METHOD_DIR,
                                  sequence_dir=SEQUENCE_DIR)

{pychemstation-0.10.5 → pychemstation-0.10.7}/out.txt

@@ -375,3 +375,137 @@ LoadMethod "D:\Chemstation\1\Methods\", "GENERAL-POROSHELL-OPT.M"
 response$ = _MethFile$
 Rows = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
 response_num = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
+response$ = AcqStatus$
+Local Rows
+SaveMethod _MethPath$, _MethFile$, "method saved by pychemstation"
+SaveSequence _SeqPath$, _SeqFile$
+LIDoOperation "TURN_ON"
+PrepRun
+_SeqFile$ = "hplc_testing.S"
+_SeqPath$ = "C:\1\Sequence\"
+LoadSequence _SeqPath$, _SeqFile$
+response$ = _SeqFile$
+Rows = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+response_num = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+Sleep 0.1
+Print Rows
+response$ = _SeqFile$
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "SampleName")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "Vial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "Method")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "InjVial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjVolume")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjectionSource")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "SampleType")
+Rows = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+response_num = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+Sleep 0.1
+Print Rows
+response$ = _SeqFile$
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "SampleName")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "Vial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "Method")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "InjVial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjVolume")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjectionSource")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "SampleType")
+response$ = AcqStatus$
+Local Rows
+SaveMethod _MethPath$, _MethFile$, "method saved by pychemstation"
+SaveSequence _SeqPath$, _SeqFile$
+LIDoOperation "TURN_ON"
+PrepRun
+_SeqFile$ = "hplc_testing.S"
+_SeqPath$ = "C:\1\Sequence\"
+LoadSequence _SeqPath$, _SeqFile$
+response$ = _SeqFile$
+Rows = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+response_num = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+Sleep 0.1
+Print Rows
+response$ = _SeqFile$
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "SampleName")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "Vial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "Method")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "InjVial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjVolume")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjectionSource")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "SampleType")
+PrepRun
+SaveMethod _MethPath$, _MethFile$, "{commit_msg}"
+SaveSequence _SeqPath$, _SeqFile$
+response_num = ObjHdrVal("RCPMP1Method[1]", "PostTime_Time")
+response_num = ObjHdrVal("RCPMP1Method[1]", "StopTime_Time")
+response$ = _MethFile$
+RunSequence
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+Local Rows
+SaveMethod _MethPath$, _MethFile$, "method saved by pychemstation"
+SaveSequence _SeqPath$, _SeqFile$
+LIDoOperation "TURN_ON"
+PrepRun
+_SeqFile$ = "hplc_testing.S"
+_SeqPath$ = "C:\1\Sequence\"
+LoadSequence _SeqPath$, _SeqFile$
+response$ = _SeqFile$
+Rows = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+response_num = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+Sleep 0.1
+Print Rows
+response$ = _SeqFile$
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "SampleName")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "Vial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "Method")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "InjVial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjVolume")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjectionSource")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "SampleType")
+PrepRun
+SaveMethod _MethPath$, _MethFile$, "{commit_msg}"
+SaveSequence _SeqPath$, _SeqFile$
+response_num = ObjHdrVal("RCPMP1Method[1]", "PostTime_Time")
+response_num = ObjHdrVal("RCPMP1Method[1]", "StopTime_Time")
+response$ = _MethFile$
+RunSequence
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$

pychemstation-0.10.7/pychemstation/analysis/__init__.py

@@ -0,0 +1,11 @@
+from .process_report import CSVProcessor
+from .process_report import TXTProcessor
+from .chromatogram import AgilentChannelChromatogramData
+from .chromatogram import AgilentHPLCChromatogram
+
+__all__ = [
+    "CSVProcessor",
+    "TXTProcessor",
+    "AgilentChannelChromatogramData",
+    "AgilentHPLCChromatogram",
+]

{pychemstation-0.10.5 → pychemstation-0.10.7}/pychemstation/control/README.md

@@ -10,7 +10,7 @@ DATA_DIR_2 = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data"
 DATA_DIR_3 = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data"
 
 # Initialize HPLC Controller
-hplc_controller = HPLCController(data_dirs=[DATA_DIR_2, DATA_DIR_3],
+hplc_controller = HPLCController(extra_data_dirs=[DATA_DIR_2, DATA_DIR_3],
                                  comm_dir=DEFAULT_COMMAND_PATH,
                                  method_dir=DEFAULT_METHOD_DIR,
                                  sequence_dir=SEQUENCE_DIR)

{pychemstation-0.10.5 → pychemstation-0.10.7}/pychemstation/control/controllers/__init__.py

@@ -3,6 +3,6 @@
 """
 
 from .comm import CommunicationController
-from . import tables
+from . import data_aq
 
-__all__ = ["CommunicationController", "tables"]
+__all__ = ["CommunicationController", "data_aq"]

pychemstation-0.10.5/pychemstation/control/controllers/comm.py → pychemstation-0.10.7/pychemstation/control/controllers/abc_tables/abc_comm.py

@@ -10,25 +10,20 @@ been processed.
 Authors: Alexander Hammer, Hessam Mehr, Lucy Hao
 """
 
+import abc
 import os
 import time
-from typing import Optional, Union
+from abc import abstractmethod
+from typing import Union
 
 from result import Err, Ok, Result
 
-from ...utils.macro import (
-    str_to_status,
-    HPLCAvailStatus,
-    HPLCErrorStatus,
-    Command,
-    Status,
-    Response,
-)
+from ....utils.macro import Status, HPLCAvailStatus, Command, Response
 
 
-class CommunicationController:
+class ABCCommunicationController(abc.ABC):
     """
-    Class that communicates with Agilent using Macros
+    Abstract class representing the communication controller.
     """
 
     # maximum command number
@@ -62,51 +57,28 @@ class CommunicationController:
             open(self.reply_file, "a").close()
 
             self.reset_cmd_counter()
-
-            # Initialize row counter for table operations
             self._most_recent_hplc_status: Status = self.get_status()
             self.send("Local Rows")
 
+    @abstractmethod
     def get_num_val(self, cmd: str) -> Union[int, float]:
-        tries = 10
-        for _ in range(tries):
-            self.send(Command.GET_NUM_VAL_CMD.value.format(cmd=cmd))
-            res = self.receive()
-            if res.is_ok():
-                return res.ok_value.num_response
-        raise RuntimeError("Failed to get number.")
+        pass
 
+    @abstractmethod
     def get_text_val(self, cmd: str) -> str:
-        tries = 10
-        for _ in range(tries):
-            self.send(Command.GET_TEXT_VAL_CMD.value.format(cmd=cmd))
-            res = self.receive()
-            if res.is_ok():
-                return res.ok_value.string_response
-        raise RuntimeError("Failed to get string")
+        pass
 
+    @abstractmethod
     def get_status(self) -> Status:
-        """Get device status(es).
+        pass
 
-        :return: list of ChemStation's current status
-        """
-        self.send(Command.GET_STATUS_CMD)
-        time.sleep(1)
-
-        try:
-            res = self.receive()
-            if res.is_err():
-                return HPLCErrorStatus.NORESPONSE
-            if res.is_ok():
-                parsed_response = self.receive().value.string_response
-                self._most_recent_hplc_status = str_to_status(parsed_response)
-                return self._most_recent_hplc_status
-            else:
-                raise RuntimeError("Failed to get status")
-        except IOError:
-            return HPLCErrorStatus.NORESPONSE
-        except IndexError:
-            return HPLCErrorStatus.MALFORMED
+    @abstractmethod
+    def _send(self, cmd: str, cmd_no: int, num_attempts=5) -> None:
+        pass
+
+    @abstractmethod
+    def _receive(self, cmd_no: int, num_attempts=100) -> Result[str, str]:
+        pass
 
     def set_status(self):
         """Updates current status of HPLC machine"""
@@ -123,69 +95,6 @@ class CommunicationController:
         hplc_actually_avail = isinstance(self._most_recent_hplc_status, HPLCAvailStatus)
         return hplc_avail and hplc_actually_avail
 
-    def _send(self, cmd: str, cmd_no: int, num_attempts=5) -> None:
-        """Low-level execution primitive. Sends a command string to HPLC.
-
-        :param cmd: string to be sent to HPLC
-        :param cmd_no: Command number
-        :param num_attempts: Number of attempts to send the command before raising exception.
-        :raises IOError: Could not write to command file.
-        """
-        err = None
-        for _ in range(num_attempts):
-            time.sleep(1)
-            try:
-                with open(self.cmd_file, "w", encoding="utf8") as cmd_file:
-                    cmd_file.write(f"{cmd_no} {cmd}")
-            except IOError as e:
-                err = e
-                continue
-            else:
-                return
-        else:
-            raise IOError(f"Failed to send command #{cmd_no}: {cmd}.") from err
-
-    def _receive(self, cmd_no: int, num_attempts=100) -> Result[str, str]:
-        """Low-level execution primitive. Recives a response from HPLC.
-
-        :param cmd_no: Command number
-        :param num_attempts: Number of retries to open reply file
-        :raises IOError: Could not read reply file.
-        :return: Potential ChemStation response
-        """
-        err: Optional[Union[OSError, IndexError, ValueError]] = None
-        err_msg = ""
-        for _ in range(num_attempts):
-            time.sleep(1)
-
-            try:
-                with open(self.reply_file, "r", encoding="utf_16") as reply_file:
-                    response = reply_file.read()
-            except OSError as e:
-                err = e
-                continue
-
-            try:
-                first_line = response.splitlines()[0]
-                try:
-                    response_no = int(first_line.split()[0])
-                except ValueError as e:
-                    err = e
-                    err_msg = f"Caused by {first_line}"
-            except IndexError as e:
-                err = e
-                continue
-
-            # check that response corresponds to sent command
-            if response_no == cmd_no:
-                return Ok(response)
-            else:
-                continue
-        else:
-            return Err(
-                f"Failed to receive reply to command #{cmd_no} due to {err} caused by {err_msg}."
-            )
-
     def sleepy_send(self, cmd: Union[Command, str]):
         self.send("Sleep 0.1")
         self.send(cmd)

pychemstation-0.10.7/pychemstation/control/controllers/abc_tables/device.py

@@ -0,0 +1,20 @@
+from __future__ import annotations
+
+from abc import ABC
+
+from ....control.controllers import CommunicationController
+from ....utils.table_types import Table
+from .table import ABCTableController
+
+
+class DeviceController(ABCTableController, ABC):
+    def __init__(
+        self, controller: CommunicationController, table: Table, offline: bool
+    ):
+        super().__init__(controller=controller, table=table)
+        self.offline = offline
+
+    def __new__(cls, *args, **kwargs):
+        if cls is ABCTableController:
+            raise TypeError(f"only children of '{cls.__name__}' may be instantiated")
+        return object.__new__(cls)