pychemstation 0.5.4__tar.gz → 0.5.5__tar.gz

{pychemstation-0.5.4 → pychemstation-0.5.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pychemstation
-Version: 0.5.4
+Version: 0.5.5
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Home-page: https://gitlab.com/heingroup/device-api/pychemstation
 Author: Lucy Hao
@@ -41,7 +41,7 @@ pip install pychemstation
    where you will put your
    MACRO file(s).
 3. Download the [
-   `hplc_talk.mac`](https://github.com/croningp/analyticallabware/blob/master/AnalyticalLabware/devices/Agilent/hplctalk.mac).
+   `hplc_talk.mac`](https://gitlab.com/heingroup/device-api/pychemstation/-/blob/main/tests/hplc_talk.mac).
     - On line 69, change the path name up to `\cmd` and `\reply`. For instance, you should have:
       `MonitorFile "[my path]\cmd", "[my path]\reply"`
     - and then add this file to the folder from the previous step.
@@ -78,13 +78,12 @@ hplc_controller = HPLCController(data_dir=DATA_DIR,
 hplc_controller.preprun()
 hplc_controller.switch_method(method_name=DEFAULT_METHOD)
 hplc_controller.run_method(experiment_name="Run 10")
-data_status_valid, chrom = hplc_controller.get_last_run_method_data()
+chrom = hplc_controller.get_last_run_method_data()
 
-if data_status_valid:
-    # afterwards, save, analyze or plot the data!
-    values = {"x": chrom.x, "y": chrom.y}
-    chromatogram_data = pd.DataFrame.from_dict(values)
-    chromatogram_data.to_csv("Run 10.csv", index=False) 
+# 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.to_csv("Run 10.csv", index=False) 
 ```
 
 ## Adding your own MACROs
@@ -103,3 +102,6 @@ Lucy Hao
 
 - 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),
+  created by members in the Bourne Group.  Copyright © Bourne Group, used under the [MIT](https://opensource.org/license/mit) license.

{pychemstation-0.5.4 → pychemstation-0.5.5}/README.md

@@ -25,7 +25,7 @@ pip install pychemstation
    where you will put your
    MACRO file(s).
 3. Download the [
-   `hplc_talk.mac`](https://github.com/croningp/analyticallabware/blob/master/AnalyticalLabware/devices/Agilent/hplctalk.mac).
+   `hplc_talk.mac`](https://gitlab.com/heingroup/device-api/pychemstation/-/blob/main/tests/hplc_talk.mac).
     - On line 69, change the path name up to `\cmd` and `\reply`. For instance, you should have:
       `MonitorFile "[my path]\cmd", "[my path]\reply"`
     - and then add this file to the folder from the previous step.
@@ -62,13 +62,12 @@ hplc_controller = HPLCController(data_dir=DATA_DIR,
 hplc_controller.preprun()
 hplc_controller.switch_method(method_name=DEFAULT_METHOD)
 hplc_controller.run_method(experiment_name="Run 10")
-data_status_valid, chrom = hplc_controller.get_last_run_method_data()
+chrom = hplc_controller.get_last_run_method_data()
 
-if data_status_valid:
-    # afterwards, save, analyze or plot the data!
-    values = {"x": chrom.x, "y": chrom.y}
-    chromatogram_data = pd.DataFrame.from_dict(values)
-    chromatogram_data.to_csv("Run 10.csv", index=False) 
+# 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.to_csv("Run 10.csv", index=False) 
 ```
 
 ## Adding your own MACROs
@@ -86,4 +85,7 @@ our [GitLab](https://gitlab.com/heingroup/device-api/pychemstation)!
 Lucy Hao
 
 - 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.
+  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),
+  created by members in the Bourne Group.  Copyright © Bourne Group, used under the [MIT](https://opensource.org/license/mit) license.

{pychemstation-0.5.4 → pychemstation-0.5.5}/pychemstation/control/__init__.py

@@ -1,5 +1,4 @@
 """
 .. include:: README.md
 """
-from .comm import CommunicationController
 from .hplc import HPLCController

{pychemstation-0.5.4/pychemstation/control/table → pychemstation-0.5.5/pychemstation/control/controllers}/__init__.py

@@ -1,3 +1,4 @@
 from .method import MethodController
 from .sequence import SequenceController
 from .table_controller import TableController
+from .comm import CommunicationController

{pychemstation-0.5.4/pychemstation/control → pychemstation-0.5.5/pychemstation/control/controllers}/comm.py

@@ -14,8 +14,8 @@ import os
 import time
 
 from result import Result, Ok, Err
-from ..utils.macro import *
-from ..utils.method_types import *
+
+from ...utils.macro import *
 
 
 class CommunicationController:

{pychemstation-0.5.4/pychemstation/control/table → pychemstation-0.5.5/pychemstation/control/controllers}/method.py

@@ -1,13 +1,13 @@
 import os
 import time
-from typing import Optional, Any
+from typing import Optional
 
 from xsdata.formats.dataclass.parsers import XmlParser
 
-from .. import CommunicationController
-from ...control.table.table_controller import TableController
+from ...control.controllers.table_controller import TableController
+from ...control.controllers.comm import CommunicationController
 from ...generated import PumpMethod, DadMethod, SolventElement
-from ...utils.chromatogram import TIME_FORMAT, AgilentHPLCChromatogram
+from ...utils.chromatogram import TIME_FORMAT, AgilentChannelChromatogramData
 from ...utils.macro import Command
 from ...utils.method_types import PType, TimeTableEntry, Param, MethodTimetable, HPLCMethodParams
 from ...utils.table_types import RegisterFlag, TableOperation, Table
@@ -269,6 +269,6 @@ class MethodController(TableController):
     def retrieve_recent_data_files(self) -> str:
         return self.data_files[-1]
 
-    def get_data(self) -> dict[str, AgilentHPLCChromatogram]:
+    def get_data(self) -> AgilentChannelChromatogramData:
         self.get_spectrum(self.data_files[-1])
-        return self.spectra
+        return AgilentChannelChromatogramData(**self.spectra)

{pychemstation-0.5.4/pychemstation/control/table → pychemstation-0.5.5/pychemstation/control/controllers}/sequence.py

@@ -1,17 +1,12 @@
-from typing import Any
-
-from copy import deepcopy
-
 import os
 import time
 
-from .table_controller import TableController
-from ...control import CommunicationController
-from ...utils.chromatogram import SEQUENCE_TIME_FORMAT, AgilentHPLCChromatogram
+from ...control.controllers.table_controller import TableController
+from ...control.controllers.comm import CommunicationController
+from ...utils.chromatogram import SEQUENCE_TIME_FORMAT, AgilentChannelChromatogramData
 from ...utils.macro import Command
 from ...utils.sequence_types import SequenceTable, SequenceEntry, SequenceDataFiles, InjectionSource, SampleType
 from ...utils.table_types import TableOperation, RegisterFlag, Table
-from ...utils.tray_types import TenColumn
 
 
 class SequenceController(TableController):
@@ -197,14 +192,20 @@ class SequenceController(TableController):
         sequence_data_files: SequenceDataFiles = self.data_files[-1]
         return sequence_data_files.dir
 
-    def get_data(self) -> list[dict[str, AgilentHPLCChromatogram]]:
+    def get_data(self) -> list[AgilentChannelChromatogramData]:
         parent_dir = self.data_files[-1].dir
         subdirs = [x[0] for x in os.walk(self.data_dir)]
         potential_folders = sorted(list(filter(lambda d: parent_dir in d, subdirs)))
-        self.data_files[-1].child_dirs = [f for f in potential_folders if parent_dir in f and ".M" not in f and ".D" in f]
+        self.data_files[-1].child_dirs = [f for f in potential_folders if
+                                          parent_dir in f and ".M" not in f and ".D" in f]
 
-        spectra: list[dict[str, AgilentHPLCChromatogram]] = []
+        spectra: list[AgilentChannelChromatogramData] = []
         for row in self.data_files[-1].child_dirs:
             self.get_spectrum(row)
-            spectra.append(deepcopy(self.spectra))
+            spectra.append(
+                AgilentChannelChromatogramData(
+                    A=self.spectra["A"],
+                    B=self.spectra["B"],
+                    C=self.spectra["C"],
+                    D=self.spectra["D"]))
         return spectra

{pychemstation-0.5.4/pychemstation/control/table → pychemstation-0.5.5/pychemstation/control/controllers}/table_controller.py

@@ -12,8 +12,8 @@ from typing import Union, Optional
 import polling
 from result import Result, Ok, Err
 
-from ...control import CommunicationController
-from ...utils.chromatogram import AgilentHPLCChromatogram
+from ...control.controllers.comm import CommunicationController
+from ...utils.chromatogram import AgilentHPLCChromatogram, AgilentChannelChromatogramData
 from ...utils.macro import Command, HPLCRunningStatus, Response
 from ...utils.method_types import MethodTimetable
 from ...utils.sequence_types import SequenceDataFiles, SequenceTable
@@ -187,7 +187,7 @@ class TableController(abc.ABC):
         pass
 
     @abc.abstractmethod
-    def get_data(self) -> tuple[bool,]:
+    def get_data(self) -> Union[list[AgilentChannelChromatogramData], AgilentChannelChromatogramData]:
         pass
 
     def get_spectrum(self, data_file: str):

{pychemstation-0.5.4 → pychemstation-0.5.5}/pychemstation/control/hplc.py

@@ -6,9 +6,8 @@ Authors: Lucy Hao
 
 from typing import Union, Optional
 
-from ..control import CommunicationController
-from ..control.table import MethodController, SequenceController
-from ..utils.chromatogram import AgilentHPLCChromatogram
+from ..control.controllers import MethodController, SequenceController, CommunicationController
+from ..utils.chromatogram import AgilentHPLCChromatogram, AgilentChannelChromatogramData
 from ..utils.macro import Command, HPLCRunningStatus, HPLCAvailStatus, HPLCErrorStatus, Response
 from ..utils.method_types import MethodTimetable
 from ..utils.sequence_types import SequenceTable, SequenceEntry
@@ -65,8 +64,8 @@ class HPLCController:
         only 'General-Poroshell' is needed.
 
         :param method_name: any available method in Chemstation method directory
-        :raise IndexError: Response did not have expected format. Try again.
-        :raise AssertionError: The desired method is not selected. Try again.
+        :raises  IndexError: Response did not have expected format. Try again.
+        :raises  AssertionError: The desired method is not selected. Try again.
         """
         self.method_controller.switch(method_name)
 
@@ -127,13 +126,13 @@ class HPLCController:
         """
         self.sequence_controller.edit_row(row, num)
 
-    def get_last_run_method_data(self) -> dict[str, AgilentHPLCChromatogram]:
+    def get_last_run_method_data(self) -> AgilentChannelChromatogramData:
         """
         Returns the last run method data.
         """
         return self.method_controller.get_data()
 
-    def get_last_run_sequence_data(self) -> list[dict[str, AgilentHPLCChromatogram]]:
+    def get_last_run_sequence_data(self) -> list[AgilentChannelChromatogramData]:
         """
         Returns data for all rows in the last run sequence data.
         """

{pychemstation-0.5.4 → pychemstation-0.5.5}/pychemstation/utils/chromatogram.py

@@ -1,17 +1,14 @@
 """Module for HPLC chromatogram data loading and manipulating"""
 
 import os
-import logging
 import time
+from dataclasses import dataclass
 
 import numpy as np
 
 from .parsing import CHFile
 from ..analysis import AbstractSpectrum
 
-# Chemstation data path
-DATA_DIR = r"C:\Chem32\1\Data"
-
 # standard filenames for spectral data
 CHANNELS = {"A": "01", "B": "02", "C": "03", "D": "04"}
 
@@ -105,26 +102,10 @@ class AgilentHPLCChromatogram(AbstractSpectrum):
             np.savez_compressed(npz_file, times=data.times, values=data.values)
             return np.array(data.times), np.array(data.values)
 
-    def extract_peakarea(self, experiment_dir: str):
-        """
-        Reads processed data from Chemstation report files.
 
-        Args:
-            experiment_dir: .D directory with the report files
-        """
-        # filename = os.path.join(experiment_dir, f"REPORT{CHANNELS[channel]}.csv")
-        # TODO parse file properly
-        # data = np.genfromtxt(filename, delimiter=',')
-        # return data
-        pass
-
-    def default_processing(self):
-        """
-        Processes the chromatogram in place.
-        """
-        # trim first 5 min and last 3 min of run
-        self.trim(5, 25)
-        # parameters found to work best for chromatogram data
-        self.correct_baseline(lmbd=1e5, p=0.0001, n_iter=10)
-        # get all peaks in processed chromatogram
-        self.find_peaks()
+@dataclass
+class AgilentChannelChromatogramData:
+    A: AgilentHPLCChromatogram
+    B: AgilentHPLCChromatogram
+    C: AgilentHPLCChromatogram
+    D: AgilentHPLCChromatogram

{pychemstation-0.5.4 → pychemstation-0.5.5}/pychemstation.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pychemstation
-Version: 0.5.4
+Version: 0.5.5
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Home-page: https://gitlab.com/heingroup/device-api/pychemstation
 Author: Lucy Hao
@@ -41,7 +41,7 @@ pip install pychemstation
    where you will put your
    MACRO file(s).
 3. Download the [
-   `hplc_talk.mac`](https://github.com/croningp/analyticallabware/blob/master/AnalyticalLabware/devices/Agilent/hplctalk.mac).
+   `hplc_talk.mac`](https://gitlab.com/heingroup/device-api/pychemstation/-/blob/main/tests/hplc_talk.mac).
     - On line 69, change the path name up to `\cmd` and `\reply`. For instance, you should have:
       `MonitorFile "[my path]\cmd", "[my path]\reply"`
     - and then add this file to the folder from the previous step.
@@ -78,13 +78,12 @@ hplc_controller = HPLCController(data_dir=DATA_DIR,
 hplc_controller.preprun()
 hplc_controller.switch_method(method_name=DEFAULT_METHOD)
 hplc_controller.run_method(experiment_name="Run 10")
-data_status_valid, chrom = hplc_controller.get_last_run_method_data()
+chrom = hplc_controller.get_last_run_method_data()
 
-if data_status_valid:
-    # afterwards, save, analyze or plot the data!
-    values = {"x": chrom.x, "y": chrom.y}
-    chromatogram_data = pd.DataFrame.from_dict(values)
-    chromatogram_data.to_csv("Run 10.csv", index=False) 
+# 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.to_csv("Run 10.csv", index=False) 
 ```
 
 ## Adding your own MACROs
@@ -103,3 +102,6 @@ Lucy Hao
 
 - 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),
+  created by members in the Bourne Group.  Copyright © Bourne Group, used under the [MIT](https://opensource.org/license/mit) license.

{pychemstation-0.5.4 → pychemstation-0.5.5}/pychemstation.egg-info/SOURCES.txt

@@ -13,12 +13,12 @@ pychemstation/analysis/base_spectrum.py
 pychemstation/analysis/spec_utils.py
 pychemstation/analysis/utils.py
 pychemstation/control/__init__.py
-pychemstation/control/comm.py
 pychemstation/control/hplc.py
-pychemstation/control/table/__init__.py
-pychemstation/control/table/method.py
-pychemstation/control/table/sequence.py
-pychemstation/control/table/table_controller.py
+pychemstation/control/controllers/__init__.py
+pychemstation/control/controllers/comm.py
+pychemstation/control/controllers/method.py
+pychemstation/control/controllers/sequence.py
+pychemstation/control/controllers/table_controller.py
 pychemstation/generated/__init__.py
 pychemstation/generated/dad_method.py
 pychemstation/generated/pump_method.py

{pychemstation-0.5.4 → pychemstation-0.5.5}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="pychemstation",
-    version="0.5.4",
+    version="0.5.5",
     author="Lucy Hao",
     author_email="lhao03@student.ubc.ca",
     description="Library to interact with Chemstation software, primarily used in Hein lab",