pychemstation 0.10.5__py3-none-any.whl → 0.10.7__py3-none-any.whl

pychemstation/utils/injector_types.py

@@ -19,10 +19,25 @@ class Mode(Enum):
 @dataclass
 class Draw:
     amount: Optional[float] = None
-    location: Optional[str] = None
+    location: Optional[Tray] = None
     source: Optional[Tray] = None
 
 
+@dataclass
+class DrawDefaultVolume:
+    location: Optional[Tray] = None
+
+
+@dataclass
+class DrawDefaultLocation:
+    amount: Optional[float] = None
+
+
+@dataclass
+class DrawDefault:
+    pass
+
+
 @dataclass
 class Wait:
     duration: Union[int, float]
@@ -35,6 +50,9 @@ class Inject:
 
 class RemoteCommand(Enum):
     START = "START"
+    NOT_READY = "NOT_READY"
+    STOP = "STOP"
+    READY = "READY"
     PREPARE = "PREPARE"
 
 
@@ -44,7 +62,9 @@ class Remote:
     duration: int
 
 
-InjectorFunction = Union[Draw, Wait, Inject, Remote]
+InjectorFunction = Union[
+    Draw, DrawDefault, DrawDefaultVolume, DrawDefaultLocation, Wait, Inject, Remote
+]
 
 
 @dataclass

pychemstation/utils/macro.py

@@ -48,6 +48,17 @@ class Command(Enum):
     SAVE_METHOD_CMD = 'SaveMethod _MethPath$, _MethFile$, "{commit_msg}"'
     GET_SEQUENCE_CMD = "response$ = _SeqFile$"
     RUN_SEQUENCE_CMD = "RunSequence"
+    CURRENT_RUNNING_SEQ_LINE = "response_num = _SEQCURRLINE1"
+
+    # Get directories
+    GET_METHOD_DIR = "response$ = _METHPATH$"
+    GET_SEQUENCE_DIR = "response$ = _SEQUENCEPATHS$"
+    GET_DATA_DIRS = "response$ = _DATAPATHS$"
+    GET_CURRENT_RUN_DATA_DIR = "response$ = _DATAPath$"
+    GET_CURRENT_RUN_DATA_FILE = "response$ = _DATAFILE1$"
+
+    # Debuggng
+    ERROR = "response$ = _ERROR$"
 
 
 class HPLCRunningStatus(Enum):

pychemstation/utils/mocking/mock_comm.py

@@ -0,0 +1,5 @@
+from ...control.controllers.abc_tables.abc_comm import ABCCommunicationController
+
+
+class MockCommunicationController(ABCCommunicationController):
+    pass

pychemstation/utils/mocking/mock_hplc.py

@@ -0,0 +1,2 @@
+class MockHPLC:
+    pass

pychemstation/utils/sequence_types.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import os.path
 from enum import Enum
 from typing import Optional, List
 from dataclasses import dataclass, field
@@ -10,6 +11,7 @@ from pychemstation.utils.tray_types import Tray
 class SequenceDataFiles:
     sequence_name: str
     dir: str
+    _data_files: List[str] = field(default_factory=list)
     child_dirs: List[str] = field(default_factory=list)
 
 
@@ -37,9 +39,9 @@ class InjectionSource(Enum):
 
 @dataclass
 class SequenceEntry:
-    sample_name: str
+    data_file: str
     vial_location: Tray
-    data_file: Optional[str] = None
+    sample_name: Optional[str] = None
     method: Optional[str] = None
     num_inj: Optional[int] = 1
     inj_vol: Optional[float] = 2
@@ -51,3 +53,21 @@ class SequenceEntry:
 class SequenceTable:
     name: str
     rows: list[SequenceEntry]
+
+    def __eq__(self, other):
+        equal = False
+        if not isinstance(other, SequenceTable):
+            return False
+
+        for self_row, other_row in zip(self.rows, other.rows):
+            equal |= self_row.vial_location == other_row.vial_location
+            equal |= self_row.data_file == other_row.data_file
+            equal |= (
+                os.path.split(os.path.normpath(self_row.method))[-1]
+                == os.path.split(os.path.normpath(other_row.method))[-1]
+            )
+            equal |= self_row.num_inj == other_row.num_inj
+            equal |= self_row.inj_vol == other_row.inj_vol
+            equal |= self_row.inj_source == other_row.inj_source
+            equal |= self_row.sample_name == other_row.sample_name
+            equal |= self_row.sample_type == other_row.sample_type

pychemstation/utils/table_types.py

@@ -43,6 +43,12 @@ class RegisterFlag(Enum):
     FLOW = "Flow"
     MAX_TIME = "StopTime_Time"
     POST_TIME = "PostTime_Time"  # TODO: check
+    SIGNAL_A = "Signal_Wavelength"
+    SIGNAL_B = "Signal2_Wavelength"
+    SIGNAL_C = "Signal3_Wavelength"
+    SIGNAL_D = "Signal4_Wavelength"
+    SIGNAL_E = "Signal5_Wavelength"
+    SIGNAL_A_USED = "Signal1_IsUsed"
     COLUMN_OVEN_TEMP1 = "TemperatureControl_Temperature"
     COLUMN_OVEN_TEMP2 = "TemperatureControl2_Temperature"
     STOPTIME_MODE = "StopTime_Mode"

pychemstation/utils/tray_types.py

@@ -71,6 +71,22 @@ class Letter(Enum):
         else:
             raise ValueError("Letter must be one of A to F")
 
+    @classmethod
+    def from_int(cls, num: int) -> Letter:
+        letter_mapping = {
+            "A": Letter.A,
+            "B": Letter.B,
+            "C": Letter.C,
+            "D": Letter.D,
+            "E": Letter.E,
+            "F": Letter.F,
+        }
+
+        if num <= len(letter_mapping):
+            return list(letter_mapping.values())[num]
+        else:
+            raise ValueError("Letter must be one of A to F")
+
 
 @dataclass
 class FiftyFourVialPlate:
@@ -91,6 +107,17 @@ class FiftyFourVialPlate:
     def value(self) -> int:
         return self.plate.value + self.letter.value + self.num.value
 
+    @classmethod
+    def from_tray_row_col(cls, tray: int, row: int, col: int):
+        try:
+            return FiftyFourVialPlate(
+                plate=Plate.from_num(tray),
+                letter=Letter.from_int(row),
+                num=Num.from_num(col),
+            )
+        except Exception:
+            raise ValueError("Could not parse tray location.")
+
     @classmethod
     def from_str(cls, loc: str):
         """
@@ -190,4 +217,12 @@ class TenVialColumn(Enum):
     TEN = 10
 
 
-Tray = Union[FiftyFourVialPlate, TenVialColumn]
+@dataclass
+class LocationPlus:
+    unit: int
+    tray: int
+    row: int
+    col: int
+
+
+Tray = Union[FiftyFourVialPlate, TenVialColumn, LocationPlus]

{pychemstation-0.10.5.dist-info → pychemstation-0.10.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.10.5
+Version: 0.10.7
 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
@@ -18,7 +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: pre-commit>=3.5.0
 Requires-Dist: pytest>=7.3.5
 Requires-Dist: rainbow-api>=1.0.10
 Requires-Dist: result>=0.17.0
@@ -90,7 +90,7 @@ 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],
+hplc_controller = HPLCController(extra_data_dirs=[DATA_DIR_2, DATA_DIR_3],
                                  comm_dir=DEFAULT_COMMAND_PATH,
                                  method_dir=DEFAULT_METHOD_DIR,
                                  sequence_dir=SEQUENCE_DIR)

pychemstation-0.10.7.dist-info/RECORD

@@ -0,0 +1,42 @@
+pychemstation/__init__.py,sha256=Sc4z8LRVFMwJUoc_DPVUriSXTZ6PO9MaJ80PhRbKyB8,34
+pychemstation/analysis/__init__.py,sha256=mPNnp0TmkoUxrTGcT6wNKMyCiOar5vC0cTPmFLrDU1Q,313
+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=yVMhIOq3YL-8EzqZDWGXt36GzSjzqiI4fwkJ35bAzD0,3130
+pychemstation/control/__init__.py,sha256=7lSkY7Qa7Ikdz82-2FESc_oqktv7JndsjltCkiMqnMI,147
+pychemstation/control/hplc.py,sha256=PY6P_GTnVxL3rAwPHtJmiAm5iTw9X6xjYghyKpBpYFM,13063
+pychemstation/control/controllers/README.md,sha256=S5cd4NJmPjs6TUH98BtPJJhiS1Lu-mxLCNS786ogOrQ,32
+pychemstation/control/controllers/__init__.py,sha256=EWvvITwY6RID5b1ilVsPowP85uzmIt3LYW0rvyN-3x0,146
+pychemstation/control/controllers/comm.py,sha256=a3qp_u2vm_UO3VTDwKEEkJfHIWgF4Gxne0h03dQe0A8,5878
+pychemstation/control/controllers/abc_tables/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pychemstation/control/controllers/abc_tables/abc_comm.py,sha256=G2JSCNwLrLYPYBdcf_WuIl6dvJORmmQe5wih6TdvPiU,5226
+pychemstation/control/controllers/abc_tables/device.py,sha256=ZJQID_M53bUwVSleBL5MjFJFrExZO1xdYKRFn5VToug,641
+pychemstation/control/controllers/abc_tables/run.py,sha256=L958yy3vBxN0qxHVfMb7wgxxHAvSQq4zggWlon6vPs4,9294
+pychemstation/control/controllers/abc_tables/table.py,sha256=4c4W_9OzrY-SfH_oV6oBZkfn1Vp5XvNYbWUvbGY3G2s,7699
+pychemstation/control/controllers/data_aq/__init__.py,sha256=w-Zgbit10niOQfz780ZmRHjUFxV1hMkdui7fOMPqeLA,132
+pychemstation/control/controllers/data_aq/method.py,sha256=BqAW2XdlJJQj08P282h_NPTJofdBKiNJgdis9j0c9lc,18183
+pychemstation/control/controllers/data_aq/sequence.py,sha256=here444uwwIH9m08ls8_wapA9088uvqX5DYCHFsarcU,17422
+pychemstation/control/controllers/devices/__init__.py,sha256=QpgGnLXyWiB96KIB98wMccEi8oOUUaLxvBCyevJzcOg,75
+pychemstation/control/controllers/devices/injector.py,sha256=OxrF-SbV006bCh_j9o-clavc_d8Loh3myhFerbvjLg4,4033
+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=z2iWwTklGm0GRDCL9pnPCovQrwyRwxv8w5w5Xh7Pj3U,1152
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+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=Bf_oGm-adRejDUmYrzV2GEx16NIO6jlH_ZMIYVKl8gg,1981
+pychemstation/utils/spec_utils.py,sha256=lS27Xi4mFNDWBfmBqOoxTcVchPAkLK2mSdoaWDOfaPI,10211
+pychemstation/utils/table_types.py,sha256=I5xy7tpmMWOMb6tFfWVE1r4wnSsgky5sZU9oNtHU9BE,3451
+pychemstation/utils/tray_types.py,sha256=FUjCUnozt5ZjCl5Vg9FioPHGTdKa43SQI1QPVkoBmV0,6078
+pychemstation/utils/mocking/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pychemstation/utils/mocking/mock_comm.py,sha256=4DcKmUxp-LYNXjywT_za1_GpqKa4sFTj7F2V3r_qsA0,156
+pychemstation/utils/mocking/mock_hplc.py,sha256=Hx6127C7d3miYGCZYxbN-Q3PU8kpMgXYX2n6we2Twgw,25
+pychemstation-0.10.7.dist-info/METADATA,sha256=oDYpd4ohtIgRyHstF4Pdnn-EP5YSN0ozESFeAQLu_CE,5939
+pychemstation-0.10.7.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+pychemstation-0.10.7.dist-info/licenses/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
+pychemstation-0.10.7.dist-info/RECORD,,

pychemstation/control/controllers/devices/device.py

@@ -1,74 +0,0 @@
-from __future__ import annotations
-
-import abc
-from typing import Union
-
-from result import Err, Ok
-
-from ....control.controllers import CommunicationController
-from ....utils.macro import Command, Response
-from ....utils.table_types import RegisterFlag, Table, TableOperation
-
-
-class DeviceController(abc.ABC):
-    def __init__(
-        self, controller: CommunicationController, table: Table, offline: bool
-    ):
-        self.table_locator = table
-        self.controller = controller
-        self.offline = offline
-
-    @abc.abstractmethod
-    def get_row(self, row: int):
-        pass
-
-    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,
-            )
-        )
-
-    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,
-            )
-        )
-
-    def get_num_rows(self) -> Ok[Response] | Err[str]:
-        self.send(
-            TableOperation.GET_NUM_ROWS.value.format(
-                register=self.table_locator.register,
-                table_name=self.table_locator.name,
-                col_name=RegisterFlag.NUM_ROWS,
-            )
-        )
-        self.send(
-            Command.GET_ROWS_CMD.value.format(
-                register=self.table_locator.register,
-                table_name=self.table_locator.name,
-                col_name=RegisterFlag.NUM_ROWS,
-            )
-        )
-        res = self.controller.receive()
-
-        if res.is_ok():
-            self.send("Sleep 0.1")
-            self.send("Print Rows")
-            return res
-        else:
-            return Err("No rows could be read.")
-
-    def send(self, cmd: Union[Command, str]):
-        if not self.controller:
-            raise RuntimeError(
-                "Communication controller must be initialized before sending command. It is currently in offline mode."
-            )
-        self.controller.send(cmd)

pychemstation-0.10.5.dist-info/RECORD

@@ -1,36 +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=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
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-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,,