pychemstation 0.8.4__py3-none-any.whl → 0.9.1__py3-none-any.whl

pychemstation/utils/table_types.py

@@ -7,28 +7,30 @@ from typing import TypeVar
 
 class TableOperation(Enum):
     def __str__(self):
-        return '%s' % self.value
+        return "%s" % self.value
 
     DELETE_TABLE = 'DelTab {register}, "{table_name}"'
     CREATE_TABLE = 'NewTab {register}, "{table_name}"'
     NEW_ROW = 'InsTabRow {register}, "{table_name}"'
     DELETE_ROW = 'DelTabRow {register}, "{table_name}", {row}'
     EDIT_ROW_VAL = 'SetTabVal "{register}", "{table_name}", {row}, "{col_name}", {val}'
-    EDIT_ROW_TEXT = 'SetTabText "{register}", "{table_name}", {row}, "{col_name}", "{val}"'
+    EDIT_ROW_TEXT = (
+        'SetTabText "{register}", "{table_name}", {row}, "{col_name}", "{val}"'
+    )
     GET_ROW_VAL = 'TabVal("{register}", "{table_name}", {row}, "{col_name}")'
     GET_ROW_TEXT = 'TabText$("{register}", "{table_name}", {row}, "{col_name}")'
     GET_NUM_ROWS = 'Rows = TabHdrVal({register}, "{table_name}", "{col_name}")'
     GET_OBJ_HDR_VAL = 'ObjHdrVal("{register}", "{register_flag}")'
     GET_OBJ_HDR_TEXT = 'ObjHdrText$("{register}", "{register_flag}")'
-    UPDATE_OBJ_HDR_VAL = 'SetObjHdrVal {register}, {register_flag}, {val}'
-    UPDATE_OBJ_HDR_TEXT = 'SetObjHdrText {register}, {register_flag}, {val}'
+    UPDATE_OBJ_HDR_VAL = "SetObjHdrVal {register}, {register_flag}, {val}"
+    UPDATE_OBJ_HDR_TEXT = "SetObjHdrText {register}, {register_flag}, {val}"
     NEW_COL_TEXT = 'NewColText {register}, "{table_name}", "{col_name}", "{val}"'
     NEW_COL_VAL = 'NewColVal {register}, "{table_name}", "{col_name}", {val}'
 
 
 class RegisterFlag(Enum):
     def __str__(self):
-        return '%s' % self.value
+        return "%s" % self.value
 
     # for table
     NUM_ROWS = "NumberOfRows"
@@ -40,7 +42,7 @@ class RegisterFlag(Enum):
     SOLVENT_D_COMPOSITION = "PumpChannel4_CompositionPercentage"
     FLOW = "Flow"
     MAX_TIME = "StopTime_Time"
-    POST_TIME = "PostTime_Time" #TODO: check
+    POST_TIME = "PostTime_Time"  # TODO: check
     COLUMN_OVEN_TEMP1 = "TemperatureControl_Temperature"
     COLUMN_OVEN_TEMP2 = "TemperatureControl2_Temperature"
     STOPTIME_MODE = "StopTime_Mode"
@@ -55,7 +57,6 @@ class RegisterFlag(Enum):
     EXTERNAL_CONTACT = "ExternalContact"
     FUNCTION = "Function"
 
-
     # for Sequence
     VIAL_LOCATION = "Vial"
     NAME = "SampleName"
@@ -86,10 +87,10 @@ class RegisterFlag(Enum):
     REMOTE_DUR = "RemoteDuration"
 
 
-
 @dataclass
 class Table:
     register: str
     name: str
 
-T = TypeVar('T')
+
+T = TypeVar("T")

pychemstation/utils/tray_types.py

@@ -19,16 +19,16 @@ class Num(Enum):
     @classmethod
     def from_num(cls, num: int):
         num_mapping = {
-        1: Num.ONE,
-        2: Num.TWO,
-        3: Num.THREE,
-        4: Num.FOUR,
-        5: Num.FIVE,
-        6: Num.SIX,
-        7: Num.SEVEN,
-        8: Num.EIGHT,
-        9: Num.NINE
-    }
+            1: Num.ONE,
+            2: Num.TWO,
+            3: Num.THREE,
+            4: Num.FOUR,
+            5: Num.FIVE,
+            6: Num.SIX,
+            7: Num.SEVEN,
+            8: Num.EIGHT,
+            9: Num.NINE,
+        }
 
         if num in num_mapping:
             return num_mapping[num]
@@ -58,13 +58,13 @@ class Letter(Enum):
     @classmethod
     def from_str(cls, let: str) -> Letter:
         letter_mapping = {
-        "A": Letter.A,
-        "B": Letter.B,
-        "C": Letter.C,
-        "D": Letter.D,
-        "E": Letter.E,
-        "F": Letter.F
-    }
+            "A": Letter.A,
+            "B": Letter.B,
+            "C": Letter.C,
+            "D": Letter.D,
+            "E": Letter.E,
+            "F": Letter.F,
+        }
 
         if let in letter_mapping:
             return letter_mapping[let]
@@ -83,6 +83,7 @@ class FiftyFourVialPlate:
     valid vial locations: P1-A2, P2-F9
     invalid vial locations: P3-A1, P1-Z3, P2-B10
     """
+
     plate: Plate
     letter: Letter
     num: Num
@@ -94,21 +95,28 @@ 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:
-            raise ValueError("Plate locations must be PX-LY, where X is either 1 or 2 and Y is 1 to 9")
+            raise ValueError(
+                "Plate locations must be PX-LY, where X is either 1 or 2 and Y is 1 to 9"
+            )
         try:
             plate = int(loc[1])
             letter = loc[3]
             num = int(loc[4])
-            return FiftyFourVialPlate(plate=Plate.from_num(plate),
-                                      letter=Letter.from_str(letter),
-                                      num=Num.from_num(num))
-        except Exception as e:
-            raise ValueError("Plate locations must be PX-LY, where X is either 1 or 2 and Y is 1 to 9")
+            return FiftyFourVialPlate(
+                plate=Plate.from_num(plate),
+                letter=Letter.from_str(letter),
+                num=Num.from_num(num),
+            )
+        except Exception:
+            raise ValueError(
+                "Plate locations must be PX-LY, where X is either 1 or 2 and Y is 1 to 9"
+            )
 
     @classmethod
     def from_int(cls, num: int) -> Tray:
@@ -116,7 +124,7 @@ 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):
@@ -124,19 +132,19 @@ class FiftyFourVialPlate:
 
         row_starts = [
             # plate 1
-            FiftyFourVialPlate.from_str('P1-F1'),
-            FiftyFourVialPlate.from_str('P1-E1'),
-            FiftyFourVialPlate.from_str('P1-D1'),
-            FiftyFourVialPlate.from_str('P1-C1'),
-            FiftyFourVialPlate.from_str('P1-B1'),
-            FiftyFourVialPlate.from_str('P1-A1'),
+            FiftyFourVialPlate.from_str("P1-F1"),
+            FiftyFourVialPlate.from_str("P1-E1"),
+            FiftyFourVialPlate.from_str("P1-D1"),
+            FiftyFourVialPlate.from_str("P1-C1"),
+            FiftyFourVialPlate.from_str("P1-B1"),
+            FiftyFourVialPlate.from_str("P1-A1"),
             # plate 2
-            FiftyFourVialPlate.from_str('P2-F1'),
-            FiftyFourVialPlate.from_str('P2-E1'),
-            FiftyFourVialPlate.from_str('P2-D1'),
-            FiftyFourVialPlate.from_str('P2-C1'),
-            FiftyFourVialPlate.from_str('P2-B1'),
-            FiftyFourVialPlate.from_str('P2-A1'),
+            FiftyFourVialPlate.from_str("P2-F1"),
+            FiftyFourVialPlate.from_str("P2-E1"),
+            FiftyFourVialPlate.from_str("P2-D1"),
+            FiftyFourVialPlate.from_str("P2-C1"),
+            FiftyFourVialPlate.from_str("P2-B1"),
+            FiftyFourVialPlate.from_str("P2-A1"),
         ]
 
         # find which row
@@ -160,7 +168,8 @@ class FiftyFourVialPlate:
                     return FiftyFourVialPlate(
                         plate=starting_loc.plate,
                         letter=starting_loc.letter,
-                        num=Num.from_num(i))
+                        num=Num.from_num(i),
+                    )
         raise ValueError("Number didn't match any location. " + str(num))
 
 
@@ -168,6 +177,7 @@ class TenVialColumn(Enum):
     """
     Class to represent the 10 vial locations.
     """
+
     ONE = 1
     TWO = 2
     THREE = 3

{pychemstation-0.8.4.dist-info → pychemstation-0.9.1.dist-info}/METADATA

@@ -1,16 +1,25 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.8.4
-Summary: Library to interact with Chemstation software, primarily used in Hein lab.
+Version: 0.9.1
+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>
 License-File: LICENSE
-Requires-Python: >=3.8
-Requires-Dist: aghplctools>=4.8.8
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: ~=3.9
+Requires-Dist: aghplctools==4.8.6
 Requires-Dist: coverage>=7.6.1
 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: pytest>=7.3.5
 Requires-Dist: rainbow-api>=1.0.10
 Requires-Dist: result>=0.17.0
@@ -27,8 +36,12 @@ 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 **3.9** 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
+> is not guaranteed!
+
 Unofficial Python package to control Agilent Chemstation; we are not affiliated with Agilent.
-Check out the [docs](https://hein-analytical-control-5e6e85.gitlab.io/) for usage instructions. This project is under
+Check out the [docs](https://pychemstation-e5a086.gitlab.io/pychemstation.html) for usage instructions. This project is under
 active development, and breaking changes may occur at any moment.
 
 ## Getting started
@@ -68,29 +81,55 @@ 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) 
 ```
 
@@ -110,6 +149,7 @@ 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),
-  created by members in the Bourne Group.  Copyright © Bourne Group, used under the [MIT](https://opensource.org/license/mit) 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-0.9.1.dist-info/RECORD

@@ -0,0 +1,37 @@
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+pychemstation/analysis/process_report.py,sha256=uW5sqAIw_YR3-MHaid1dDEF8qdys-ZEZfa-1vqV-nms,13363
+pychemstation/control/README.md,sha256=_7ITj4hD17YIwci6UY6xBebC9gPCBpzBFTB_Gx0eJBc,3124
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+pychemstation/control/hplc.py,sha256=mV-IO-6wdzB7MuV5LcZYwb4yZibBgEKX2LtbJ9WiKNw,12304
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+pychemstation/generated/pump_method.py,sha256=s3MckKDw2-nZUC5lHrJVvXYdneWP8-9UvblNuGryPHY,12092
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+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
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+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-0.9.1.dist-info/METADATA,sha256=ypplz0GWS-erPPVfmLxVQXR6vm7__Mo8UIoSs1VD24o,5981
+pychemstation-0.9.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+pychemstation-0.9.1.dist-info/licenses/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
+pychemstation-0.9.1.dist-info/RECORD,,

pychemstation-0.8.4.dist-info/RECORD

@@ -1,37 +0,0 @@
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-pychemstation/analysis/__init__.py,sha256=EWoU47iyn9xGS-b44zK9eq50bSjOV4AC5dvt420YMI4,44
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-pychemstation/control/README.md,sha256=7Q0rY014y7Qq8wfL7GSQG0l2P1PXfmgB0qZ2YkkE7n0,3350
-pychemstation/control/__init__.py,sha256=4xTy8X-mkn_PPZKr7w9rnj1wZhtmTesbQptPhpYmKXs,64
-pychemstation/control/hplc.py,sha256=E_QFMOqUabiqCO6Pu4lZYTsiWhdQULw4AqyKPwiQx90,12628
-pychemstation/control/controllers/README.md,sha256=S5cd4NJmPjs6TUH98BtPJJhiS1Lu-mxLCNS786ogOrQ,32
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-pychemstation/control/controllers/comm.py,sha256=fRCFh3Ye-HnoGaur69NRdkLHNtdlMoJjIOTqeJe1tAk,7720
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-pychemstation/control/controllers/tables/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pychemstation/control/controllers/tables/method.py,sha256=sX83sHlnaAm8Wop_d28RDAk4DBPvQWduH3Atodtmw4A,17714
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