pychemstation 0.10.4__py3-none-any.whl → 0.10.5__py3-none-any.whl

pychemstation/control/controllers/tables/table.py

@@ -31,7 +31,7 @@ from pychemstation.analysis.chromatogram import (
 from ....utils.macro import Command, HPLCRunningStatus, Response
 from ....utils.method_types import MethodDetails
 from ....utils.sequence_types import SequenceTable
-from ....utils.table_types import RegisterFlag, T, Table, TableOperation
+from ....utils.table_types import RegisterFlag, Table, TableOperation, T
 
 TableType = Union[MethodDetails, SequenceTable]
 
@@ -39,9 +39,9 @@ TableType = Union[MethodDetails, SequenceTable]
 class TableController(abc.ABC):
     def __init__(
         self,
-        controller: CommunicationController,
-        src: Optional[str],
-        data_dirs: Optional[List[str]],
+        controller: Optional[CommunicationController],
+        src: str,
+        data_dirs: List[str],
         table: Table,
         offline: bool = False,
     ):
@@ -63,7 +63,7 @@ class TableController(abc.ABC):
             self.src: str = src
             self.data_dirs: List[str] = data_dirs
 
-        self.spectra: dict[str, Optional[AgilentHPLCChromatogram]] = {
+        self.spectra: dict[str, AgilentHPLCChromatogram] = {
             "A": AgilentHPLCChromatogram(),
             "B": AgilentHPLCChromatogram(),
             "C": AgilentHPLCChromatogram(),
@@ -73,17 +73,19 @@ class TableController(abc.ABC):
             "G": AgilentHPLCChromatogram(),
             "H": AgilentHPLCChromatogram(),
         }
-        self.report: Optional[AgilentReport] = None
         self.uv: Dict[int, AgilentHPLCChromatogram] = {}
         self.data_files: List = []
 
     def receive(self) -> Result[Response, str]:
-        for _ in range(10):
-            try:
-                return self.controller.receive()
-            except IndexError:
-                continue
-        return Err("Could not parse response")
+        if self.controller:
+            for _ in range(10):
+                try:
+                    return self.controller.receive()
+                except IndexError:
+                    continue
+            return Err("Could not parse response")
+        else:
+            raise ValueError("Controller is offline!")
 
     def send(self, cmd: Union[Command, str]):
         if not self.controller:
@@ -93,7 +95,10 @@ class TableController(abc.ABC):
         self.controller.send(cmd)
 
     def sleepy_send(self, cmd: Union[Command, str]):
-        self.controller.sleepy_send(cmd)
+        if self.controller:
+            self.controller.sleepy_send(cmd)
+        else:
+            raise ValueError("Controller is offline")
 
     def sleep(self, seconds: int):
         """
@@ -104,24 +109,30 @@ class TableController(abc.ABC):
         self.send(Command.SLEEP_CMD.value.format(seconds=seconds))
 
     def get_num(self, row: int, col_name: RegisterFlag) -> Union[int, float]:
-        return self.controller.get_num_val(
-            TableOperation.GET_ROW_VAL.value.format(
-                register=self.table_locator.register,
-                table_name=self.table_locator.name,
-                row=row,
-                col_name=col_name.value,
+        if self.controller:
+            return self.controller.get_num_val(
+                TableOperation.GET_ROW_VAL.value.format(
+                    register=self.table_locator.register,
+                    table_name=self.table_locator.name,
+                    row=row,
+                    col_name=col_name.value,
+                )
             )
-        )
+        else:
+            raise ValueError("Controller is offline")
 
     def get_text(self, row: int, col_name: RegisterFlag) -> str:
-        return self.controller.get_text_val(
-            TableOperation.GET_ROW_TEXT.value.format(
-                register=self.table_locator.register,
-                table_name=self.table_locator.name,
-                row=row,
-                col_name=col_name.value,
+        if self.controller:
+            return self.controller.get_text_val(
+                TableOperation.GET_ROW_TEXT.value.format(
+                    register=self.table_locator.register,
+                    table_name=self.table_locator.name,
+                    row=row,
+                    col_name=col_name.value,
+                )
             )
-        )
+        else:
+            raise ValueError("Controller is offline")
 
     def add_new_col_num(self, col_name: RegisterFlag, val: Union[int, float]):
         self.sleepy_send(
@@ -227,7 +238,10 @@ class TableController(abc.ABC):
                 col_name=RegisterFlag.NUM_ROWS,
             )
         )
-        res = self.controller.receive()
+        if self.controller:
+            res = self.controller.receive()
+        else:
+            raise ValueError("Controller is offline")
 
         if res.is_ok():
             self.send("Sleep 0.1")
@@ -237,33 +251,38 @@ class TableController(abc.ABC):
             return Err("No rows could be read.")
 
     def check_hplc_is_running(self) -> bool:
-        try:
-            started_running = polling.poll(
-                lambda: isinstance(self.controller.get_status(), HPLCRunningStatus),
-                step=1,
-                max_tries=20,
-            )
-        except Exception as e:
-            print(e)
-            return False
-        if started_running:
-            self.curr_run_starting_time = time.time()
-        return started_running
+        if self.controller:
+            try:
+                started_running = polling.poll(
+                    lambda: isinstance(self.controller.get_status(), HPLCRunningStatus),
+                    step=1,
+                    max_tries=20,
+                )
+            except Exception as e:
+                print(e)
+                return False
+            if started_running:
+                self.curr_run_starting_time = time.time()
+            return started_running
+        else:
+            raise ValueError("Controller is offline")
 
     def check_hplc_run_finished(self) -> Tuple[float, bool]:
-        done_running = self.controller.check_if_not_running()
-        if self.curr_run_starting_time and self.timeout:
-            time_passed = time.time() - self.curr_run_starting_time
-            if time_passed > self.timeout:
-                enough_time_passed = time_passed >= self.timeout
-                run_finished = enough_time_passed and done_running
-                if run_finished:
-                    self._reset_time()
-                    return 0, run_finished
-            else:
-                time_left = self.timeout - time_passed
-                return time_left, self.controller.check_if_not_running()
-        return 0, self.controller.check_if_not_running()
+        if self.controller:
+            done_running = self.controller.check_if_not_running()
+            if self.curr_run_starting_time and self.timeout:
+                time_passed = time.time() - self.curr_run_starting_time
+                if time_passed > self.timeout:
+                    enough_time_passed = time_passed >= self.timeout
+                    run_finished = enough_time_passed and done_running
+                    if run_finished:
+                        self._reset_time()
+                        return 0, run_finished
+                else:
+                    time_left = self.timeout - time_passed
+                    return time_left, self.controller.check_if_not_running()
+            return 0, self.controller.check_if_not_running()
+        raise ValueError("Controller is offline!")
 
     def check_hplc_done_running(self) -> Ok[T] | Err[str]:
         """
@@ -271,31 +290,34 @@ class TableController(abc.ABC):
 
         :return: Data file object containing most recent run file information.
         """
-        finished_run = False
-        minutes = math.ceil(self.timeout / 60)
-        try:
-            finished_run = not polling.poll(
-                lambda: self.check_hplc_run_finished()[1],
-                max_tries=minutes - 1,
-                step=50,
-            )
-        except (
-            polling.TimeoutException,
-            polling.PollingException,
-            polling.MaxCallException,
-        ):
+        if self.timeout is not None:
+            finished_run = False
+            minutes = math.ceil(self.timeout / 60)
             try:
-                finished_run = polling.poll(
+                finished_run = not polling.poll(
                     lambda: self.check_hplc_run_finished()[1],
-                    timeout=self.timeout / 2,
-                    step=1,
+                    max_tries=minutes - 1,
+                    step=50,
                 )
             except (
                 polling.TimeoutException,
                 polling.PollingException,
                 polling.MaxCallException,
             ):
-                pass
+                try:
+                    finished_run = polling.poll(
+                        lambda: self.check_hplc_run_finished()[1],
+                        timeout=self.timeout / 2,
+                        step=1,
+                    )
+                except (
+                    polling.TimeoutException,
+                    polling.PollingException,
+                    polling.MaxCallException,
+                ):
+                    pass
+        else:
+            raise ValueError("Timeout value is None, no comparison can be made.")
 
         check_folder = self.fuzzy_match_most_recent_folder(self.data_files[-1])
         if check_folder.is_ok() and finished_run:
@@ -324,15 +346,13 @@ class TableController(abc.ABC):
 
     @abc.abstractmethod
     def get_data_uv(
-        self,
-    ) -> Union[
-        List[Dict[str, AgilentHPLCChromatogram]], Dict[str, AgilentHPLCChromatogram]
-    ]:
+        self, custom_path: str | None = None
+    ) -> Dict[int, AgilentHPLCChromatogram]:
         pass
 
     @abc.abstractmethod
     def get_report(
-        self, report_type: ReportType = ReportType.TXT
+        self, custom_path: str, report_type: ReportType = ReportType.TXT
     ) -> List[AgilentReport]:
         pass
 
@@ -351,12 +371,16 @@ class TableController(abc.ABC):
         if report_type is ReportType.TXT:
             txt_report = TXTProcessor(path).process_report()
             if txt_report.is_ok():
-                self.report = txt_report.ok_value
+                return txt_report.ok_value
+            elif txt_report.is_err():
+                raise ValueError(txt_report.err_value)
         if report_type is ReportType.CSV:
             csv_report = CSVProcessor(path).process_report()
             if csv_report.is_ok():
-                self.report = csv_report.ok_value
-        return self.report
+                return csv_report.ok_value
+            elif csv_report.is_err():
+                raise ValueError(csv_report.err_value)
+        raise ValueError("Expected one of ReportType.TXT or ReportType.CSV")
 
     def get_spectrum_at_channels(self, data_path: str):
         """

pychemstation/control/hplc.py

@@ -8,22 +8,18 @@ from __future__ import annotations
 
 from typing import Dict, List, Optional, Tuple, Union
 
+from pychemstation.analysis.chromatogram import AgilentChannelChromatogramData
 from pychemstation.analysis.chromatogram import (
     AgilentHPLCChromatogram,
 )
-
+from .controllers.devices.injector import InjectorController
+from .controllers.tables.sequence import SequenceController, MethodController
 from ..analysis.process_report import AgilentReport, ReportType
-from ..control.controllers import (
-    CommunicationController,
-    MethodController,
-    SequenceController,
-)
-from pychemstation.analysis.chromatogram import AgilentChannelChromatogramData
+from ..control.controllers import CommunicationController
 from ..utils.macro import Command, Response, Status
 from ..utils.method_types import MethodDetails
 from ..utils.sequence_types import SequenceTable
 from ..utils.table_types import Table
-from .controllers.devices.injector import InjectorController
 
 
 class HPLCController:
@@ -56,12 +52,10 @@ class HPLCController:
         :param sequence_dir: Name of directory where sequence files are stored.
         :raises FileNotFoundError: If either `data_dir`, `method_dir`, `sequence_dir`, `sequence_data_dir`or `comm_dir` is not a valid directory.
         """
-        self.comm = (
-            CommunicationController(comm_dir=comm_dir, debug=debug)
-            if not offline
-            else None
+        self.comm: CommunicationController = CommunicationController(
+            comm_dir=comm_dir, debug=debug
         )
-        self.method_controller = MethodController(
+        self.method_controller: MethodController = MethodController(
             controller=self.comm,
             src=method_dir,
             data_dirs=data_dirs,
@@ -71,7 +65,7 @@ class HPLCController:
                 controller=self.comm, table=self.INJECTOR_TABLE, offline=offline
             ),
         )
-        self.sequence_controller = SequenceController(
+        self.sequence_controller: SequenceController = SequenceController(
             controller=self.comm,
             src=sequence_dir,
             data_dirs=data_dirs,
@@ -92,7 +86,7 @@ class HPLCController:
             )
         self.comm.send(cmd)
 
-    def receive(self) -> Response:
+    def receive(self) -> None | Response | str:
         """
         Get the most recent response from Chemstation.
 
@@ -224,7 +218,7 @@ class HPLCController:
 
     def get_last_run_method_data(
         self, read_uv: bool = False, custom_path: Optional[str] = None
-    ) -> Dict[str, AgilentHPLCChromatogram] | AgilentChannelChromatogramData:
+    ) -> Dict[int, AgilentHPLCChromatogram] | AgilentChannelChromatogramData:
         """
         Returns the last run method data.
 
@@ -264,7 +258,7 @@ class HPLCController:
         :param read_uv: whether to also read the UV file
         """
         if read_uv:
-            return self.sequence_controller.get_data_uv(custom_path=custom_path)
+            return self.sequence_controller.get_data_mult_uv(custom_path=custom_path)
         else:
             return self.sequence_controller.get_data(custom_path=custom_path)
 

pychemstation/utils/injector_types.py

@@ -25,7 +25,7 @@ class Draw:
 
 @dataclass
 class Wait:
-    duration: int
+    duration: Union[int, float]
 
 
 @dataclass

pychemstation/utils/macro.py

@@ -2,7 +2,7 @@ from __future__ import annotations
 
 from dataclasses import dataclass
 from enum import Enum
-from typing import Union, Any, Type
+from typing import Union
 
 
 @dataclass
@@ -88,7 +88,7 @@ class HPLCErrorStatus(Enum):
 
 def str_to_status(
     status: str,
-) -> Type[HPLCRunningStatus[Any] | HPLCErrorStatus[Any] | HPLCAvailStatus[Any]]:
+):
     if HPLCErrorStatus.has_member_key(status):
         return HPLCErrorStatus[status]
     if HPLCRunningStatus.has_member_key(status):

pychemstation/utils/method_types.py

@@ -31,7 +31,7 @@ class HPLCMethodParams:
 @dataclass
 class TimeTableEntry:
     start_time: float
-    organic_modifer: float
+    organic_modifer: Optional[float]
     flow: Optional[float] = None
 
 

{pychemstation-0.10.4.dist-info → pychemstation-0.10.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.10.4
+Version: 0.10.5
 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
@@ -12,7 +12,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.10
-Requires-Dist: aghplctools>=4.8.8
+Requires-Dist: aghplctools==4.8.6
 Requires-Dist: coverage>=7.6.1
 Requires-Dist: matplotlib>=3.7.5
 Requires-Dist: pandas>=2.0.3
@@ -35,8 +35,8 @@ Description-Content-Type: text/markdown
 
 [![PyPI Latest Release](https://img.shields.io/pypi/v/pychemstation.svg)](https://pypi.org/project/pychemstation/)
 
-> **_NOTE:_** If you are running Python **3.8**, use versions 0.**8**.x. If you are running Python **>=3.10**, use
-> version 0.**10**.x. You are welcome to use newer pychemstation versions with older Python versions, but functionality
+> **_NOTE:_** If you are running Python **3.8**, use versions 0.**8**.x. If you are running Python **3.9** use versions 0.**9**.x.
+> If you are running Python **>=3.10**, use version 0.**10**.x. You are welcome to use newer pychemstation versions with older Python versions, but functionality
 > is not guaranteed!
 
 Unofficial Python package to control Agilent Chemstation; we are not affiliated with Agilent.

pychemstation-0.10.5.dist-info/RECORD

@@ -0,0 +1,36 @@
+pychemstation/__init__.py,sha256=Sc4z8LRVFMwJUoc_DPVUriSXTZ6PO9MaJ80PhRbKyB8,34
+pychemstation/analysis/__init__.py,sha256=dcX7OeHoKdyrECHRCSXgKZN81nOXSAmZRxXzRT0jpDc,126
+pychemstation/analysis/base_spectrum.py,sha256=t_VoxAtBph1V7S4fOsziERHiOBkYP0_nH7LTwbTEvcE,16529
+pychemstation/analysis/chromatogram.py,sha256=cHxPd5-miA6L3FjwN5cSFyq4xEeZoHWFFk8gU6tCgg4,3946
+pychemstation/analysis/process_report.py,sha256=xckcpqnYfzFTIo1nhgwP5A4GPJsW3PQ_qzuy5Z1KOuI,14714
+pychemstation/control/README.md,sha256=_7ITj4hD17YIwci6UY6xBebC9gPCBpzBFTB_Gx0eJBc,3124
+pychemstation/control/__init__.py,sha256=7lSkY7Qa7Ikdz82-2FESc_oqktv7JndsjltCkiMqnMI,147
+pychemstation/control/hplc.py,sha256=H6ilH0e3vhk0B6ZFi8ecomKSi144Qw-TLRwyL7XFB-o,12356
+pychemstation/control/controllers/README.md,sha256=S5cd4NJmPjs6TUH98BtPJJhiS1Lu-mxLCNS786ogOrQ,32
+pychemstation/control/controllers/__init__.py,sha256=GFVjjLxPL-FoRHxijdIkHggYvBqIQrnXaoGZgjuArdo,144
+pychemstation/control/controllers/comm.py,sha256=XgEECwlrUMHaZoHSqbYqaA5Kkoy5RRRnyoI6Mv64DWM,8571
+pychemstation/control/controllers/devices/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pychemstation/control/controllers/devices/device.py,sha256=ObcPeHFu4siRtt-XHllDgLruR1o8zWv1Gy0ar5bYgO4,2375
+pychemstation/control/controllers/devices/injector.py,sha256=97xzayu0doxwtdfCgq-VI9rIHkZuGw65X1-JjIGQeFg,2798
+pychemstation/control/controllers/tables/__init__.py,sha256=w-Zgbit10niOQfz780ZmRHjUFxV1hMkdui7fOMPqeLA,132
+pychemstation/control/controllers/tables/method.py,sha256=8fwGcm8QRpayLnQ5q3Iyg2aaWWBY4SFT7_ZfJIxigZs,18208
+pychemstation/control/controllers/tables/sequence.py,sha256=_u3YY2OrYub7jGvqRds5dmjqCB9pnWqTOI71MuGSMB0,15759
+pychemstation/control/controllers/tables/table.py,sha256=qWjkh1S42FdUoN4PKgYg0yvar86QPDze9QRX_iHE6rk,13853
+pychemstation/generated/__init__.py,sha256=xnEs0QTjeuGYO3tVUIy8GDo95GqTV1peEjosGckpOu0,977
+pychemstation/generated/dad_method.py,sha256=xTUiSCvkXcxBUhjVm1YZKu-tHs16k23pF-0xYrQSwWA,8408
+pychemstation/generated/pump_method.py,sha256=s3MckKDw2-nZUC5lHrJVvXYdneWP8-9UvblNuGryPHY,12092
+pychemstation/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pychemstation/utils/injector_types.py,sha256=lGgBZhWdh93hwYT4N9LLQuZXu4Xcuc3j0RDBzOWg8P8,836
+pychemstation/utils/macro.py,sha256=Y_0CwTHcDQKoxYrNHqdF14-ciwtx56Y65SzNtOFPhNk,2848
+pychemstation/utils/method_types.py,sha256=_2djFz_uWFc9aoZcyPMIjC5KYBs003WPoQGx7ZhMiOg,1649
+pychemstation/utils/num_utils.py,sha256=dDs8sLZ_SdtvDKhyhF3IkljiVf16IYqpMTO5tEk9vMk,2079
+pychemstation/utils/parsing.py,sha256=mzdpxrH5ux4-_i4CwZvnIYnIwAnRnOptKb3fZyYJcx0,9307
+pychemstation/utils/pump_types.py,sha256=HWQHxscGn19NTrfYBwQRCO2VcYfwyko7YfBO5uDhEm4,93
+pychemstation/utils/sequence_types.py,sha256=T0IP2iMqorUrdzH4at9Vsmmb3SCAEmN4z1cUlFaeTXw,1089
+pychemstation/utils/spec_utils.py,sha256=lS27Xi4mFNDWBfmBqOoxTcVchPAkLK2mSdoaWDOfaPI,10211
+pychemstation/utils/table_types.py,sha256=inOVpwSsic31VdVdJkfuq35QfKd7PoNoXY1QnOxZ6Sw,3235
+pychemstation/utils/tray_types.py,sha256=9yLRIBn3IPVMbhrFqJQJ5gCQJI7H9DD2cdIFQDp2-8k,5184
+pychemstation-0.10.5.dist-info/METADATA,sha256=RfxUkxoudjZSf-bxO4eSHpsqTxML-JQJYnAmBTr0wFQ,5933
+pychemstation-0.10.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+pychemstation-0.10.5.dist-info/licenses/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
+pychemstation-0.10.5.dist-info/RECORD,,

pychemstation/control/controllers/tables/ms.py

@@ -1,24 +0,0 @@
-from typing import Union
-
-from ....control.controllers import CommunicationController
-from ....control.controllers.tables.table import TableController
-from pychemstation.analysis.chromatogram import AgilentChannelChromatogramData
-from ....utils.table_types import Table
-
-
-class MassSpecController(TableController):
-    def __init__(
-        self, controller: CommunicationController, src: str, data_dir: str, table: Table
-    ):
-        super().__init__(controller, src, data_dir, table)
-
-    def get_row(self, row: int):
-        pass
-
-    def retrieve_recent_data_files(self):
-        pass
-
-    def get_data(
-        self,
-    ) -> Union[list[AgilentChannelChromatogramData], AgilentChannelChromatogramData]:
-        pass

pychemstation-0.10.4.dist-info/RECORD

@@ -1,37 +0,0 @@
-pychemstation/__init__.py,sha256=Sc4z8LRVFMwJUoc_DPVUriSXTZ6PO9MaJ80PhRbKyB8,34
-pychemstation/analysis/__init__.py,sha256=dcX7OeHoKdyrECHRCSXgKZN81nOXSAmZRxXzRT0jpDc,126
-pychemstation/analysis/base_spectrum.py,sha256=t_VoxAtBph1V7S4fOsziERHiOBkYP0_nH7LTwbTEvcE,16529
-pychemstation/analysis/chromatogram.py,sha256=cBfLh58PrBZMg9-u5o_Q-FCuu3MlB0q0ZFm9_2uaciU,3270
-pychemstation/analysis/process_report.py,sha256=mUBuMHFNNUa-dP0-OZse9XcDahMNX84cCz705Eg6T3A,12250
-pychemstation/control/README.md,sha256=_7ITj4hD17YIwci6UY6xBebC9gPCBpzBFTB_Gx0eJBc,3124
-pychemstation/control/__init__.py,sha256=uzfsVAGDhMP6SyV10KAH264ytDLMsMRZXRK5XhWS-rc,102
-pychemstation/control/hplc.py,sha256=mV-IO-6wdzB7MuV5LcZYwb4yZibBgEKX2LtbJ9WiKNw,12304
-pychemstation/control/controllers/README.md,sha256=S5cd4NJmPjs6TUH98BtPJJhiS1Lu-mxLCNS786ogOrQ,32
-pychemstation/control/controllers/__init__.py,sha256=XXTKee3bQpDJ2EO0k-ekJoZuq1h6WeO_DsOafxkBgTo,247
-pychemstation/control/controllers/comm.py,sha256=64VXS0C3BHTKCjuYCadmmxKWiVvMqtZebzyCOJifyUA,7994
-pychemstation/control/controllers/devices/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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