pychemstation 0.10.1__tar.gz → 0.10.3__tar.gz

{pychemstation-0.10.1 → pychemstation-0.10.3}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.10.1
-Summary: Library to interact with Chemstation software, primarily used in Hein lagit branch -mb
+Version: 0.10.3
+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
 Author-email: lucyhao <hao.lucyy@gmail.com>
@@ -79,29 +79,55 @@ HPLCTalk_Run
 
 ```python
 from pychemstation.control import HPLCController
+from pychemstation.utils.method_types import *
 import pandas as pd
 
-# these paths will be unique to your Chemstation setup
-DEFAULT_METHOD = "GENERAL-POROSHELL"
-DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\"
 DEFAULT_METHOD_DIR = "C:\\ChemStation\\1\\Methods\\"
-DATA_DIR_2 = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data\\"
-DATA_DIR_3 = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data\\"
-SEQUENCE_DIR = "C:\\USERS\\PUBLIC\\DOCUMENTS\\CHEMSTATION\\2\\Sequence\\"
+SEQUENCE_DIR = "C:\\USERS\\PUBLIC\\DOCUMENTS\\CHEMSTATION\\3\\Sequence"
+DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\"
+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],
                                  comm_dir=DEFAULT_COMMAND_PATH,
-                                 sequence_dir=SEQUENCE_DIR,
-                                 method_dir=DEFAULT_METHOD_DIR)
-
-hplc_controller.preprun()
-hplc_controller.switch_method(method_name=DEFAULT_METHOD)
-hplc_controller.run_method(experiment_name="Run 10")
+                                 method_dir=DEFAULT_METHOD_DIR,
+                                 sequence_dir=SEQUENCE_DIR)
+
+# Switching a method
+hplc_controller.switch_method("General-Poroshell")
+
+# Editing a method
+new_method = MethodDetails(
+    name="General-Poroshell",
+    params=HPLCMethodParams(
+        organic_modifier=7,
+        flow=0.44),
+    timetable=[
+        TimeTableEntry(
+            start_time=0.10,
+            organic_modifer=7,
+            flow=0.34
+        ),
+        TimeTableEntry(
+            start_time=4,
+            organic_modifer=99,
+            flow=0.55
+        )
+    ],
+    stop_time=5,
+    post_time=2
+)
+hplc_controller.edit_method(new_method)
+
+# Run a method and get a report or data from last run method
+hplc_controller.run_method(experiment_name="test_experiment")
+report = hplc_controller.get_last_run_method_report()
+vial_location = report.vial_location
+
+# Save, analyze or plot the data!
 chrom = hplc_controller.get_last_run_method_data()
-
-# afterwards, save, analyze or plot the data!
-values = {"x": chrom.A.x, "y": chrom.A.y}
-chromatogram_data = pd.DataFrame.from_dict(values)
+chromatogram_data = pd.DataFrame.from_dict({"x": chrom.A.x, "y": chrom.A.y})
 chromatogram_data.to_csv("Run 10.csv", index=False) 
 ```
 
@@ -122,7 +148,6 @@ 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.
 - Adapted from the [MACROS](https://github.com/Bourne-Group/HPLCMethodOptimisationGUI) used in [**Operator-free HPLC
-  automated method development guided by Bayesian optimization
-  **](https://pubs.rsc.org/en/content/articlelanding/2024/dd/d4dd00062e),
+  automated method development guided by Bayesian optimization**](https://pubs.rsc.org/en/content/articlelanding/2024/dd/d4dd00062e),
   created by members in the Bourne Group. Copyright © Bourne Group, used under
   the [MIT](https://opensource.org/license/mit) license.

{pychemstation-0.10.1 → pychemstation-0.10.3}/README.md

@@ -49,29 +49,55 @@ HPLCTalk_Run
 
 ```python
 from pychemstation.control import HPLCController
+from pychemstation.utils.method_types import *
 import pandas as pd
 
-# these paths will be unique to your Chemstation setup
-DEFAULT_METHOD = "GENERAL-POROSHELL"
-DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\"
 DEFAULT_METHOD_DIR = "C:\\ChemStation\\1\\Methods\\"
-DATA_DIR_2 = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data\\"
-DATA_DIR_3 = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data\\"
-SEQUENCE_DIR = "C:\\USERS\\PUBLIC\\DOCUMENTS\\CHEMSTATION\\2\\Sequence\\"
+SEQUENCE_DIR = "C:\\USERS\\PUBLIC\\DOCUMENTS\\CHEMSTATION\\3\\Sequence"
+DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\"
+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],
                                  comm_dir=DEFAULT_COMMAND_PATH,
-                                 sequence_dir=SEQUENCE_DIR,
-                                 method_dir=DEFAULT_METHOD_DIR)
-
-hplc_controller.preprun()
-hplc_controller.switch_method(method_name=DEFAULT_METHOD)
-hplc_controller.run_method(experiment_name="Run 10")
+                                 method_dir=DEFAULT_METHOD_DIR,
+                                 sequence_dir=SEQUENCE_DIR)
+
+# Switching a method
+hplc_controller.switch_method("General-Poroshell")
+
+# Editing a method
+new_method = MethodDetails(
+    name="General-Poroshell",
+    params=HPLCMethodParams(
+        organic_modifier=7,
+        flow=0.44),
+    timetable=[
+        TimeTableEntry(
+            start_time=0.10,
+            organic_modifer=7,
+            flow=0.34
+        ),
+        TimeTableEntry(
+            start_time=4,
+            organic_modifer=99,
+            flow=0.55
+        )
+    ],
+    stop_time=5,
+    post_time=2
+)
+hplc_controller.edit_method(new_method)
+
+# Run a method and get a report or data from last run method
+hplc_controller.run_method(experiment_name="test_experiment")
+report = hplc_controller.get_last_run_method_report()
+vial_location = report.vial_location
+
+# Save, analyze or plot the data!
 chrom = hplc_controller.get_last_run_method_data()
-
-# afterwards, save, analyze or plot the data!
-values = {"x": chrom.A.x, "y": chrom.A.y}
-chromatogram_data = pd.DataFrame.from_dict(values)
+chromatogram_data = pd.DataFrame.from_dict({"x": chrom.A.x, "y": chrom.A.y})
 chromatogram_data.to_csv("Run 10.csv", index=False) 
 ```
 
@@ -92,7 +118,6 @@ 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.
 - Adapted from the [MACROS](https://github.com/Bourne-Group/HPLCMethodOptimisationGUI) used in [**Operator-free HPLC
-  automated method development guided by Bayesian optimization
-  **](https://pubs.rsc.org/en/content/articlelanding/2024/dd/d4dd00062e),
+  automated method development guided by Bayesian optimization**](https://pubs.rsc.org/en/content/articlelanding/2024/dd/d4dd00062e),
   created by members in the Bourne Group. Copyright © Bourne Group, used under
   the [MIT](https://opensource.org/license/mit) license.

pychemstation-0.10.3/pychemstation/analysis/__init__.py

@@ -0,0 +1,9 @@
+from .base_spectrum import AbstractSpectrum
+from .process_report import CSVProcessor
+from .process_report import TXTProcessor
+
+__all__ = [
+    'AbstractSpectrum',
+    'CSVProcessor',
+    'TXTProcessor'
+]

{pychemstation-0.10.1 → pychemstation-0.10.3}/pychemstation/analysis/process_report.py

@@ -23,13 +23,13 @@ from pychemstation.utils.tray_types import FiftyFourVialPlate, Tray
 
 @dataclass
 class AgilentPeak:
+    peak_number: Optional[int]
     retention_time: float
+    peak_type: Optional[str]
     width: float
     area: float
     height: float
-    peak_number: Optional[int]
-    peak_type: Optional[str]
-    height_percent: Optional[float]
+    area_percent: Optional[float]
 
 
 @dataclass
@@ -73,7 +73,7 @@ class CSVProcessor(ReportProcessor):
         """
         Method to parse details from CSV report.
 
-        :returns: subset of complete report details, specifically the sample location, solvents in pumps,
+        :return: subset of complete report details, specifically the sample location, solvents in pumps,
          and list of peaks at each wavelength channel.
         """
         labels = os.path.join(self.path, 'REPORT00.CSV')
@@ -95,11 +95,11 @@ class CSVProcessor(ReportProcessor):
                                          encoding="utf-16", header=None)
                         peaks = df.apply(lambda row: AgilentPeak(*row), axis=1)
                         wavelength = df_labels[1][pos + s].partition(",4 Ref=off")[0][-3:]
-                        signals[wavelength] = peaks
+                        signals[wavelength] = list(peaks)
                     break
 
             return Ok(AgilentReport(
-                signals=[Signals(wavelength=w, peaks=s, data=None) for w, s in signals.items()],
+                signals=[Signals(wavelength=int(w), peaks=s, data=None) for w, s in signals.items()],
                 vial_location=FiftyFourVialPlate.from_int(int(vial_location)),
                 solvents=solvents
             ))
@@ -155,13 +155,12 @@ class TXTProcessor(ReportProcessor):
     def process_report(self) -> Result[AgilentReport, AnyStr]:
         """
         Method to parse details from CSV report.
-
-        :returns: subset of complete report details, specifically the sample location, solvents in pumps,
-         and list of peaks at each wavelength channel.
-
         If you want more functionality, use `aghplctools`.
         `from aghplctools.ingestion.text import pull_hplc_area_from_txt`
         `signals = pull_hplc_area_from_txt(file_path)`
+
+        :return: subset of complete report details, specifically the sample location, solvents in pumps,
+         and list of peaks at each wavelength channel.
         """
 
         with open(os.path.join(self.path, "REPORT.TXT"), 'r', encoding='utf-16') as openfile:
@@ -176,7 +175,7 @@ class TXTProcessor(ReportProcessor):
 
         parsed_signals = []
         for wavelength, wavelength_dict in signals.items():
-            current_wavelength_signals = Signals(wavelength=wavelength, peaks=[], data=None)
+            current_wavelength_signals = Signals(wavelength=int(wavelength), peaks=[], data=None)
             for ret_time, ret_time_dict in wavelength_dict.items():
                 if self.min_ret_time <= ret_time <= self.max_ret_time:
                     current_wavelength_signals.peaks.append(AgilentPeak(retention_time=ret_time,
@@ -185,7 +184,7 @@ class TXTProcessor(ReportProcessor):
                                                                         height=ret_time_dict['Height'],
                                                                         peak_number=None,
                                                                         peak_type=ret_time_dict['Type'],
-                                                                        height_percent=None))
+                                                                        area_percent=None))
             parsed_signals.append(current_wavelength_signals)
 
         return Ok(AgilentReport(vial_location=None,

{pychemstation-0.10.1 → pychemstation-0.10.3}/pychemstation/control/README.md

@@ -1,30 +1,24 @@
 # Examples of usecases
 
-## Initialization
-
 ```python
 from pychemstation.control import HPLCController
 
 DEFAULT_METHOD_DIR = "C:\\ChemStation\\1\\Methods\\"
-DATA_DIR = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data"
 SEQUENCE_DIR = "C:\\USERS\\PUBLIC\\DOCUMENTS\\CHEMSTATION\\3\\Sequence"
 DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\"
+DATA_DIR_2 = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data"
+DATA_DIR_3 = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data"
 
-hplc_controller = HPLCController(data_dir=DATA_DIR,
+# Initialize HPLC Controller
+hplc_controller = HPLCController(data_dirs=[DATA_DIR_2, DATA_DIR_3],
                                  comm_dir=DEFAULT_COMMAND_PATH,
                                  method_dir=DEFAULT_METHOD_DIR,
                                  sequence_dir=SEQUENCE_DIR)
-```
-
-## Switching a method
 
-```python
+# Switching a method
 hplc_controller.switch_method("General-Poroshell")
-```
 
-## Editing a method
-
-```python
+# Editing a method
 from pychemstation.utils.method_types import *
 
 new_method = MethodDetails(
@@ -47,52 +41,27 @@ new_method = MethodDetails(
     stop_time=5,
     post_time=2
 )
-
 hplc_controller.edit_method(new_method)
-```
-
-## Running a method and get data from last run method
 
-```python
+# Run a method and get a report or data from last run method
 hplc_controller.run_method(experiment_name="test_experiment")
 chrom = hplc_controller.get_last_run_method_data()
 channel_a_time = chrom.A.x
-```
+report = hplc_controller.get_last_run_method_report()
+vial_location = report.vial_location
 
-## Switching a sequence
-
-```python
+# switch the currently loaded sequence
 hplc_controller.switch_sequence(sequence_name="hplc_testing")
-```
 
-## Editing a Sequence Row
-
-```python
-from pychemstation.utils.sequence_types import *
-from pychemstation.utils.tray_types import *
-
-hplc_controller.edit_sequence_row(SequenceEntry(
-    vial_location=FiftyFourVialPlate(plate=Plate.TWO, letter=Letter.A, num=Num.SEVEN).value(),
-    method="General-Poroshell",
-    num_inj=3,
-    inj_vol=4,
-    sample_name="Blank",
-    sample_type=SampleType.BLANK,
-    inj_source=InjectionSource.HIP_ALS
-), 1)
-```
-
-## Editing entire Sequence Table
-
-```python
+# edit the sequence table
 from pychemstation.utils.tray_types import *
 from pychemstation.utils.sequence_types import *
 
 seq_table = SequenceTable(
-    name=DEFAULT_SEQUENCE,
+    name="hplc_testing",
     rows=[
         SequenceEntry(
-            vial_location=FiftyFourVialPlate(plate=Plate.TWO, letter=Letter.A, num=Num.SEVEN).value(),
+            vial_location=FiftyFourVialPlate.from_str("P1-A1"),
             method="General-Poroshell",
             num_inj=3,
             inj_vol=4,
@@ -101,7 +70,7 @@ seq_table = SequenceTable(
             inj_source=InjectionSource.MANUAL
         ),
         SequenceEntry(
-            vial_location=TenVialColumn.ONE.value,
+            vial_location=TenVialColumn.ONE,
             method="General-Poroshell",
             num_inj=1,
             inj_vol=1,
@@ -110,7 +79,7 @@ seq_table = SequenceTable(
             inj_source=InjectionSource.AS_METHOD
         ),
         SequenceEntry(
-            vial_location=10,
+            vial_location=FiftyFourVialPlate.from_str("P2-B4"),
             method="General-Poroshell",
             num_inj=3,
             inj_vol=4,
@@ -121,12 +90,11 @@ seq_table = SequenceTable(
     ]
 )
 hplc_controller.edit_sequence(seq_table)
-```
 
-## Running a sequence and get data from last run sequence
-
-```python
-hplc_controller.run_sequence(seq_table)
-chroms = hplc_controller.get_last_run_sequence_data()
-channel_A_time = chroms[0].A.x
+# Run a sequence and get data or report from last run sequence
+hplc_controller.run_sequence()
+chroms = hplc_controller.get_last_run_sequence_data(read_uv=True)
+row_1_channel_A_abs = chroms[0][210].y
+report = hplc_controller.get_last_run_sequence_reports()
+vial_location_row_1 = report[0].vial_location
 ```

{pychemstation-0.10.1 → pychemstation-0.10.3}/pychemstation/control/controllers/devices/injector.py

@@ -1,10 +1,9 @@
-from __future__ import annotations
 
-from .device import DeviceController
 from ....control.controllers import CommunicationController
 from ....utils.injector_types import (
     Draw,
     Inject,
+    InjectorFunction,
     InjectorTable,
     Mode,
     Remote,
@@ -14,6 +13,7 @@ from ....utils.injector_types import (
 )
 from ....utils.table_types import RegisterFlag, Table
 from ....utils.tray_types import Tray
+from .device import DeviceController
 
 
 class InjectorController(DeviceController):
@@ -21,7 +21,7 @@ class InjectorController(DeviceController):
     def __init__(self, controller: CommunicationController, table: Table, offline: bool):
         super().__init__(controller, table, offline)
 
-    def get_row(self, row: int) -> None | Remote | Draw | Wait | Inject:
+    def get_row(self, row: int) -> InjectorFunction:
         def return_tray_loc() -> Tray:
             pass
 
@@ -43,9 +43,8 @@ class InjectorController(DeviceController):
             return Remote(command=RemoteCommand(self.get_text(row, RegisterFlag.REMOTE)),
                           duration=self.get_num(row, RegisterFlag.REMOTE_DUR))
 
-    def load(self) -> InjectorTable | None:
+    def load(self) -> InjectorTable:
         rows = self.get_num_rows()
         if rows.is_ok():
             return InjectorTable(functions=[self.get_row(i) for i in range(int(rows.ok_value.num_response))])
 
-   

{pychemstation-0.10.1 → pychemstation-0.10.3}/pychemstation/control/controllers/tables/sequence.py

@@ -249,11 +249,11 @@ class SequenceController(TableController):
         except Exception:
             return Err("Failed to get sequence folder")
 
-    def get_data_uv(self,custom_path: Optional[str] = None) -> List[Dict[str, AgilentHPLCChromatogram]]:
+    def get_data_uv(self,custom_path: Optional[str] = None) -> List[Dict[int, AgilentHPLCChromatogram]]:
         custom_path = SequenceDataFiles(dir=custom_path, child_dirs=[], sequence_name="") if custom_path else self.data_files[-1]
         if len(custom_path.child_dirs) == 0:
             self.data_files[-1] = self.fuzzy_match_most_recent_folder(custom_path).ok_value
-        all_w_spectra: List[Dict[str, AgilentHPLCChromatogram]] = []
+        all_w_spectra: List[Dict[int, AgilentHPLCChromatogram]] = []
         for row in self.data_files[-1].child_dirs:
             self.get_uv_spectrum(row)
             all_w_spectra.append(self.uv)

{pychemstation-0.10.1 → pychemstation-0.10.3}/pychemstation/control/controllers/tables/table.py

@@ -71,7 +71,7 @@ class TableController(abc.ABC):
             "H": AgilentHPLCChromatogram(),
         }
         self.report: Optional[AgilentReport] = None
-        self.uv: Dict[str, AgilentHPLCChromatogram] = {}
+        self.uv: Dict[int, AgilentHPLCChromatogram] = {}
         self.data_files: List = []
 
     def receive(self) -> Result[Response, str]:

{pychemstation-0.10.1 → pychemstation-0.10.3}/pychemstation/control/hplc.py

@@ -10,7 +10,7 @@ from typing import Dict, List, Optional, Tuple, Union
 from pychemstation.utils.chromatogram import (
     AgilentHPLCChromatogram,
 )
-from .controllers.devices.injector import InjectorController
+
 from ..analysis.process_report import AgilentReport, ReportType
 from ..control.controllers import (
     CommunicationController,
@@ -18,11 +18,11 @@ from ..control.controllers import (
     SequenceController,
 )
 from ..utils.chromatogram import AgilentChannelChromatogramData
-from ..utils.injector_types import InjectorTable
 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:
@@ -96,7 +96,7 @@ class HPLCController:
         """
         Get the most recent response from Chemstation.
 
-        :returns: most recent response from a macro that returned a response.
+        :return: most recent response from a macro that returned a response.
         """
         if not self.comm:
             raise RuntimeError(
@@ -107,7 +107,7 @@ class HPLCController:
         """
         Get the current status of the HPLC machine.
 
-        :returns: current status of the HPLC machine; Status types can be found in `pychemstation.utils.macro`
+        :return: current status of the HPLC machine; Status types can be found in `pychemstation.utils.macro`
         """
         if not self.comm:
             raise RuntimeError(
@@ -168,7 +168,7 @@ class HPLCController:
         """
         Check if the currently running method (if any) is done.
 
-        :returns: the percent of the method run completed, and whether the run is complete.
+        :returns the percent of the method run completed, and whether the run is complete.
         """
         return self.method_controller.check_hplc_run_finished()
 
@@ -176,7 +176,7 @@ class HPLCController:
         """
         Check if the currently running sequence (if any) is done.
 
-        :returns: the percent of the sequence run completed, and whether the run is complete.
+        :return: the percent of the sequence run completed, and whether the run is complete.
         """
         return self.sequence_controller.check_hplc_run_finished()
 
@@ -202,9 +202,10 @@ class HPLCController:
                                    report_type: ReportType = ReportType.CSV) -> AgilentReport:
         """
         Return data contained in the REPORT files. Use `aghplctools` if you want more report processing utility.
+
         :param custom_path: path to sequence folder
         :param report_type: read either the TXT or CSV version
-        :returns: report data for method
+        :return: report data for method
         """
         return self.method_controller.get_report(custom_path=custom_path, report_type=report_type)[0]
 
@@ -226,14 +227,15 @@ class HPLCController:
                                       report_type: ReportType = ReportType.CSV) -> List[AgilentReport]:
         """
         Return data contained in the REPORT files. Use `aghplctools` if you want more report processing utility.
+
         :param custom_path: path to sequence folder
         :param report_type: read either the TXT or CSV version
-        :returns: list of reports for each row
+        :return: list of reports for each row
         """
         return self.sequence_controller.get_report(custom_path=custom_path, report_type=report_type)
 
     def get_last_run_sequence_data(self, read_uv: bool = False,
-                                   custom_path: Optional[str] = None) -> List[Dict[str, AgilentHPLCChromatogram]] | \
+                                   custom_path: Optional[str] = None) -> List[Dict[int, AgilentHPLCChromatogram]] | \
                                                                          List[AgilentChannelChromatogramData]:
         """
         Returns data for all rows in the last run sequence data.
@@ -254,10 +256,6 @@ class HPLCController:
         """Returns the name of the currently loaded method."""
         return self.method_controller.check()
 
-    def load_injector_program(self) -> InjectorTable:
-        """Returns all details of the injector program for the currently loaded method."""
-        return self.method_controller.injector_controller.load()
-
     def load_method(self) -> MethodDetails:
         """Returns details of the currently loaded method, such as its starting modifier conditions and timetable."""
         return self.method_controller.load()

{pychemstation-0.10.1 → pychemstation-0.10.3}/pychemstation/utils/num_utils.py

@@ -11,7 +11,7 @@ def find_nearest_value_index(array, value) -> Tuple[float, int]:
     :param value: Target value.
     :type value: float
 
-    :returns: Nearest value in array and its index.
+    :return: Nearest value in array and its index.
     """
 
     index_ = np.argmin(np.abs(array - value))
@@ -34,7 +34,7 @@ def interpolate_to_index(array, ids, precision: int = 100) -> np.array:
     :type ids: np.array[float]
     :param precision: Desired presion.
 
-    :returns: New array with interpolated values according to provided indexes "ids".
+    :return: New array with interpolated values according to provided indexes "ids".
 
     Example:
         >>> interpolate_to_index(np.array([1.5]), np.array([1,2,3], 100))

{pychemstation-0.10.1 → pychemstation-0.10.3}/pychemstation/utils/tray_types.py

@@ -94,8 +94,9 @@ class FiftyFourVialPlate:
     def from_str(cls, loc: str):
         """
         Converts a string representing the vial location into numerical representation for Chemstation.
+
         :param loc: vial location
-        :returns: `FiftyFourVialPlate` object representing the vial location
+        :return: `FiftyFourVialPlate` object representing the vial location
         :raises: ValueError if string is invalid tray location
         """
         if len(loc) != 5:
@@ -116,7 +117,7 @@ class FiftyFourVialPlate:
         Converts an integer representation of a vial location to a `FiftyFourVialPlate` or `TenVialColumn` object
 
         :param num: numerical representation of a vial location
-        :returns: the proper vial location object
+        :return: the proper vial location object
         :raises: ValueError no matching can be made
         """
         if num in range(1, 11):

{pychemstation-0.10.1 → pychemstation-0.10.3}/pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "hatchling.build"
 
 [project]
 name = "pychemstation"
-version = "0.10.1"
-description = "Library to interact with Chemstation software, primarily used in Hein lagit branch -mb"
+version = "0.10.3"
+description = "Library to interact with Chemstation software, primarily used in Hein lab"
 authors = [{ name = "lucyhao", email = "hao.lucyy@gmail.com" }]
 requires-python = ">=3.10"
 readme = "README.md"

{pychemstation-0.10.1 → pychemstation-0.10.3}/update-lib.sh

@@ -1,7 +1,6 @@
 rm -rf dist
 uv build
-python -m build
-twine upload dist/*
+uv publish
 git add .
 git commit -m "$1"
 git push

pychemstation-0.10.1/pychemstation/analysis/__init__.py

@@ -1,5 +0,0 @@
-from .base_spectrum import AbstractSpectrum
-
-__all__ = [
-    'AbstractSpectrum',
-]

pychemstation-0.10.1/setup.py

@@ -1,24 +0,0 @@
-import setuptools
-
-with open("README.md", "r") as fh:
-    long_description = fh.read()
-
-setuptools.setup(
-    name="pychemstation",
-    version="0.10.0",
-    author="Lucy Hao",
-    author_email="lhao03@student.ubc.ca",
-    description="Library to interact with Chemstation software, primarily used in Hein lab",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    url="https://gitlab.com/heingroup/device-api/pychemstation",
-    packages=setuptools.find_packages(),
-    install_requires=[
-        'polling',
-        'seabreeze',
-        'xsdata',
-        'result',
-        'rainbow-api',
-        'aghplctools'
-    ],
-)