pychemstation 0.10.2__py3-none-any.whl → 0.10.4__py3-none-any.whl

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-0.10.2.dist-info → pychemstation-0.10.4.dist-info}/METADATA

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.10.2
-Summary: Library to interact with Chemstation software, primarily used in Hein lagit branch -mb
+Version: 0.10.4
+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>
@@ -18,6 +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: pytest>=7.3.5
 Requires-Dist: rainbow-api>=1.0.10
 Requires-Dist: result>=0.17.0
@@ -79,29 +80,55 @@ 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 +149,6 @@ 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-0.10.4.dist-info/RECORD

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pychemstation-0.10.2.dist-info/RECORD

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