pychemstation 0.10.8.dev3__py3-none-any.whl → 0.10.9__py3-none-any.whl

pychemstation/analysis/process_report.py

@@ -83,7 +83,9 @@ class CSVProcessor(ReportProcessor):
                 if "00" in name and file_extension.lower() == "csv":
                     prefix, _, _ = name.partition("00")
                     return prefix
-        raise FileNotFoundError("Couldn't find the prefix for CSV")
+        raise FileNotFoundError(
+            "Couldn't find the prefix for CSV, please make sure the post-run settings generate a CSV."
+        )
 
     def report_contains(self, labels: List[str], want: List[str]):
         for label in labels:

pychemstation/control/controllers/data_aq/method.py

@@ -3,7 +3,7 @@ from __future__ import annotations
 import os
 import time
 import warnings
-from typing import Dict, List, Optional, Set, Union, Tuple
+from typing import Dict, List, Optional, Union, Tuple
 
 from result import Err, Ok, Result
 
@@ -51,9 +51,7 @@ class MethodController(RunController):
         )
 
     def get_current_method_name(self) -> str:
-        time.sleep(2)
-        self.send(Command.GET_METHOD_CMD)
-        time.sleep(2)
+        self.sleepy_send(Command.GET_METHOD_CMD)
         res = self.receive()
         if res.is_ok():
             return res.ok_value.string_response
@@ -192,7 +190,6 @@ class MethodController(RunController):
                 method_dir=method_dir, method_name=method_name
             )
         )
-
         time.sleep(2)
         self.send(Command.GET_METHOD_CMD)
         time.sleep(2)
@@ -341,7 +338,7 @@ class MethodController(RunController):
         )
         if isinstance(method_param.chemstation_key, list):
             for register_flag in method_param.chemstation_key:
-                self.send(
+                self.sleepy_send(
                     setting_command.value.format(
                         register=register,
                         register_flag=register_flag,
@@ -349,20 +346,17 @@ class MethodController(RunController):
                     )
                 )
         else:
-            self.send(
+            self.sleepy_send(
                 setting_command.value.format(
                     register=register,
                     register_flag=method_param.chemstation_key,
                     val=method_param.val,
                 )
             )
-        time.sleep(2)
         self.download()
 
     def download(self):
-        self.send("Sleep 1")
         self.sleepy_send("DownloadRCMethod PMP1")
-        self.send("Sleep 1")
 
     def _edit_row(
         self,
@@ -579,10 +573,10 @@ class MethodController(RunController):
             else:
                 warnings.warn(run_completed.err_value)
         else:
-            folder = self._fuzzy_match_most_recent_folder(self.data_files[-1], None)
+            folder = self._fuzzy_match_most_recent_folder(self.data_files[-1])
             i = 0
             while folder.is_err() and i < 10:
-                folder = self._fuzzy_match_most_recent_folder(self.data_files[-1], None)
+                folder = self._fuzzy_match_most_recent_folder(self.data_files[-1])
                 i += 1
             if folder.is_ok():
                 self.data_files[-1] = folder.ok_value
@@ -591,11 +585,11 @@ class MethodController(RunController):
                 warnings.warn(warning)
 
     def _fuzzy_match_most_recent_folder(
-        self, most_recent_folder: T, child_dirs: Optional[Set[str]]
+        self, most_recent_folder: T
     ) -> Result[str, str]:
         if isinstance(most_recent_folder, str) or isinstance(most_recent_folder, bytes):
             if os.path.exists(most_recent_folder):
-                return Ok(most_recent_folder)
+                return Ok(str(most_recent_folder))
             return Err("Folder not found!")
         raise ValueError("Folder is not a str or byte type.")
 

pychemstation/control/controllers/data_aq/sequence.py

@@ -3,7 +3,7 @@ from __future__ import annotations
 import os
 import time
 import warnings
-from typing import Any, Dict, List, Optional, Union, Set, Tuple
+from typing import Any, Dict, List, Optional, Union, Tuple
 
 from result import Err, Ok, Result
 from typing_extensions import override
@@ -301,11 +301,6 @@ class SequenceController(RunController):
         under the <data_dir>/<sequence table name> folder.
         Device must be ready.
         """
-        if self.controller:
-            self.controller.send(Command.SAVE_METHOD_CMD)
-            self.controller.send(Command.SAVE_SEQUENCE_CMD)
-        else:
-            raise ValueError("Controller is offline!")
 
         current_sequence_name = self.get_current_sequence_name()
         if not self.table_state or self.table_state.name not in current_sequence_name:
@@ -333,6 +328,8 @@ class SequenceController(RunController):
         timestamp = time.strftime(SEQUENCE_TIME_FORMAT)
         folder_name = f"{self.table_state.name} {timestamp}"
 
+        self.send(Command.SAVE_METHOD_CMD)
+        self.send(Command.SAVE_SEQUENCE_CMD)
         self.send(Command.RUN_SEQUENCE_CMD.value)
         self.timeout = total_runtime * 60
 
@@ -344,12 +341,11 @@ class SequenceController(RunController):
                 break
 
         if hplc_running:
-            current_sample_file, full_path_name = self.try_getting_run_info(folder_name)
+            full_path_name, current_sample_file = self.try_getting_run_info(folder_name)
             if full_path_name and current_sample_file:
                 data_file = SequenceDataFiles(
                     sequence_name=self.table_state.name,
                     dir=full_path_name,
-                    _data_files=[r.data_file for r in self.table_state.rows],
                     child_dirs=[os.path.join(full_path_name, current_sample_file)],
                 )
                 self.data_files.append(data_file)
@@ -374,64 +370,25 @@ class SequenceController(RunController):
                 )
             except ValueError:
                 pass
-        if full_path_name and folder_name in full_path_name:
-            pass
-        else:
-            if self.controller:
-                self.controller.send(Command.GET_RUNNING_SEQUENCE_DIR)
-                res = self.controller.receive()
-                if res.is_ok():
-                    if os.path.isdir(res.ok_value.string_response):
-                        if folder_name in res.ok_value.string_response:
-                            full_path_name = res.ok_value.string_response
-                else:
-                    raise ValueError("Could not get sequence data folder.")
-            else:
-                raise ValueError("Controller is offline.")
-        if current_sample_file and full_path_name:
-            return full_path_name, current_sample_file
-        elif full_path_name:
-            return full_path_name, None
-        else:
-            raise ValueError("Could not get sequence data folder")
+            if current_sample_file and full_path_name:
+                return full_path_name, current_sample_file
+            elif full_path_name:
+                return full_path_name, None
+        raise ValueError("Could not get sequence data folder")
 
     @override
     def _fuzzy_match_most_recent_folder(
-        self, most_recent_folder: T, child_dirs: Optional[Set[str]]
+        self, most_recent_folder: T
     ) -> Result[SequenceDataFiles, str]:
         if isinstance(most_recent_folder, SequenceDataFiles):
             try:
                 if most_recent_folder.dir and os.path.isdir(most_recent_folder.dir):
                     subdirs = [x[0] for x in os.walk(most_recent_folder.dir)]
-                    if (
-                        child_dirs
-                        and len(child_dirs) > 0
-                        and set(most_recent_folder._data_files) == child_dirs
-                    ):
-                        most_recent_folder.child_dirs = [
-                            os.path.join(most_recent_folder.dir, f)
-                            if not os.path.isdir(f)
-                            else f
-                            for f in child_dirs
-                        ]
-                        for d in most_recent_folder.child_dirs:
-                            assert os.path.isdir(d)
-                    else:
-                        potential_folders: List[str] = sorted(
-                            list(
-                                filter(
-                                    lambda d: most_recent_folder.dir in d,
-                                    subdirs,
-                                )
-                            )
-                        )
-                        most_recent_folder.child_dirs = [
-                            f
-                            for f in potential_folders
-                            if most_recent_folder.dir in f
-                            and ".M" not in f
-                            and ".D" in f
-                        ]
+                    most_recent_folder.child_dirs = [
+                        f
+                        for f in subdirs
+                        if most_recent_folder.dir in f and ".D" in f and f[-1] == "D"
+                    ]
                     return Ok(most_recent_folder)
                 else:
                     return Err("No sequence folder found, please give the full path.")
@@ -446,14 +403,11 @@ class SequenceController(RunController):
             if custom_path
             else self.data_files[-1]
         )
-        if len(seq_data_dir.child_dirs) == 0:
-            search_folder = self._fuzzy_match_most_recent_folder(
-                seq_data_dir, set(seq_data_dir.child_dirs)
-            )
-            if search_folder.is_ok():
-                seq_data_dir = search_folder.ok_value
-            else:
-                raise FileNotFoundError(search_folder.err_value)
+        search_folder = self._fuzzy_match_most_recent_folder(seq_data_dir)
+        if search_folder.is_ok():
+            seq_data_dir = search_folder.ok_value
+        else:
+            raise FileNotFoundError(search_folder.err_value)
         all_w_spectra: List[Dict[int, AgilentHPLCChromatogram]] = []
         for row in seq_data_dir.child_dirs:
             all_w_spectra.append(self.get_data_uv(custom_path=row))
@@ -477,10 +431,9 @@ class SequenceController(RunController):
             if custom_path
             else self.data_files[-1]
         )
-        if len(seq_file_dir.child_dirs) == 0:
-            self.data_files[-1] = self._fuzzy_match_most_recent_folder(
-                seq_file_dir, set(seq_file_dir.child_dirs)
-            ).ok_value
+        self.data_files[-1] = self._fuzzy_match_most_recent_folder(
+            seq_file_dir
+        ).ok_value
         spectra: List[AgilentChannelChromatogramData] = []
         for row in self.data_files[-1].child_dirs:
             self.get_spectrum_at_channels(row)
@@ -499,17 +452,13 @@ class SequenceController(RunController):
                         dir=custom_path,
                         sequence_name="NA",
                     ),
-                    child_dirs=None,
                 ).ok_value
             )
         parent_dir = self.data_files[-1]
-        if (
-            len(parent_dir._data_files) != len(parent_dir.child_dirs)
-            or len(parent_dir.child_dirs) == 0
-        ):
-            parent_dir = self._fuzzy_match_most_recent_folder(
-                most_recent_folder=parent_dir, child_dirs=None
-            )
+        parent_dir = self._fuzzy_match_most_recent_folder(
+            most_recent_folder=parent_dir,
+        ).ok_value
+        assert len(parent_dir.child_dirs) != 0
         spectra = self.get_data()
         reports = []
         for i, child_dir in enumerate(parent_dir.child_dirs):

pychemstation/control/hplc.py

@@ -252,7 +252,6 @@ class HPLCController:
         if len(self.sequence_controller.data_files):
             self.sequence_controller._fuzzy_match_most_recent_folder(
                 most_recent_folder=self.sequence_controller.data_files[-1],
-                child_dirs=set(),
             )
             return self.sequence_controller.data_files[-1]
         else:

pychemstation/utils/abc_tables/abc_comm.py

@@ -88,10 +88,15 @@ class ABCCommunicationController(abc.ABC):
         :return: whether the HPLC machine is in a safe state to retrieve data back."""
         self.set_status()
         hplc_avail = isinstance(self._most_recent_hplc_status, HPLCAvailStatus)
-        time.sleep(5)
+        time.sleep(10)
         self.set_status()
         hplc_actually_avail = isinstance(self._most_recent_hplc_status, HPLCAvailStatus)
-        return hplc_avail and hplc_actually_avail
+        time.sleep(10)
+        self.set_status()
+        hplc_final_check_avail = isinstance(
+            self._most_recent_hplc_status, HPLCAvailStatus
+        )
+        return hplc_avail and hplc_actually_avail and hplc_final_check_avail
 
     def sleepy_send(self, cmd: Union[Command, str]):
         self.send("Sleep 0.1")

pychemstation/utils/abc_tables/run.py

@@ -94,9 +94,7 @@ class RunController(ABCTableController, abc.ABC):
         return object.__new__(cls)
 
     @abc.abstractmethod
-    def _fuzzy_match_most_recent_folder(
-        self, most_recent_folder: T, child_dirs: Set[str]
-    ) -> Result[T, str]:
+    def _fuzzy_match_most_recent_folder(self, most_recent_folder: T) -> Result[T, str]:
         pass
 
     @abc.abstractmethod
@@ -192,9 +190,7 @@ class RunController(ABCTableController, abc.ABC):
         else:
             raise ValueError("Timeout value is None, no comparison can be made.")
 
-        check_folder = self._fuzzy_match_most_recent_folder(
-            self.data_files[-1], self.current_run_child_files
-        )
+        check_folder = self._fuzzy_match_most_recent_folder(self.data_files[-1])
         if check_folder.is_ok() and finished_run:
             return check_folder
         elif check_folder.is_ok():

pychemstation/utils/device_types.py

@@ -0,0 +1,7 @@
+from dataclasses import dataclass
+
+
+@dataclass
+class SignalRead:
+    on: bool
+    wavelength: int

pychemstation/utils/sequence_types.py

@@ -13,13 +13,11 @@ class SequenceDataFiles:
 
     :param sequence_name: the name of the sequence that is running
     :param dir: the complete path of the directory generated for the sequence
-    :param _data_files: the names of the files of the sequence runs, ends with ".D"
     :param child_dirs: the complete path of the files for sequence runs, contains the Chemstation data, `dir` and the sample run file.
     """
 
     sequence_name: str
     dir: str
-    _data_files: List[str] = field(default_factory=list)
     child_dirs: List[str] = field(default_factory=list)
 
 

{pychemstation-0.10.8.dev3.dist-info → pychemstation-0.10.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.10.8.dev3
+Version: 0.10.9
 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
@@ -30,8 +30,7 @@ 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.**9**.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!
+> If you are running Python **>=3.10**, use version 0.**10**.x. Older versions of pychemstation are not the most feature-rich and bug-free. Please consider upgrading to using Python 3.10!
 
 Unofficial Python package to control Agilent Chemstation; we are not affiliated with Agilent.
 Check out the [docs](https://pychemstation-e5a086.gitlab.io/pychemstation.html) for usage instructions. This project is under
@@ -73,21 +72,17 @@ HPLCTalk_Run
 ## Example Usage
 
 ```python
+import time
 from pychemstation.control import HPLCController
 from pychemstation.utils.method_types import *
 import pandas as pd
 
-DEFAULT_METHOD_DIR = "C:\\ChemStation\\1\\Methods\\"
-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"
+CUSTOM_DATA_DIR = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data\\MyData"
 
 # Initialize HPLC Controller
-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)
+hplc_controller = HPLCController(extra_data_dirs=[CUSTOM_DATA_DIR],
+                                 comm_dir=DEFAULT_COMMAND_PATH)
 
 # Switching a method
 hplc_controller.switch_method("General-Poroshell")
@@ -116,7 +111,17 @@ new_method = MethodDetails(
 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")
+hplc_controller.run_method(experiment_name="test_experiment", stall_while_running=False)
+time_left, done = hplc_controller.check_method_complete()
+while not done:
+    print(time_left)
+    time.sleep(time_left/2)
+    time_left, done = hplc_controller.check_method_complete()
+    
+# Save the path the HPLC data for later!  
+file_path = hplc_controller.get_last_run_method_file_path()
+
+# Make sure CSV reports are being generated in the post-run MACRO!
 report = hplc_controller.get_last_run_method_report()
 vial_location = report.vial_location
 

{pychemstation-0.10.8.dev3.dist-info → pychemstation-0.10.9.dist-info}/RECORD

@@ -2,40 +2,41 @@ pychemstation/__init__.py,sha256=Sc4z8LRVFMwJUoc_DPVUriSXTZ6PO9MaJ80PhRbKyB8,34
 pychemstation/analysis/__init__.py,sha256=mPNnp0TmkoUxrTGcT6wNKMyCiOar5vC0cTPmFLrDU1Q,313
 pychemstation/analysis/base_spectrum.py,sha256=HjbTPoueR7XB1_puCcmx7zbQmeT5SH6_HVwHrYhNXhA,16537
 pychemstation/analysis/chromatogram.py,sha256=Jk6xOMHA6kSV597fJDZgrFRlvVorldvK4zerPASZrug,3969
-pychemstation/analysis/process_report.py,sha256=aTsW6u5-0iwsH3jQtkoKE9jbsy5NAUG6l7O-I49B8kY,14650
+pychemstation/analysis/process_report.py,sha256=GEazFm1asY1FZO87siiV9kWu2Wnbu7xwx86nlPeRexk,14728
 pychemstation/control/README.md,sha256=ohPn3xhgjFyPraQqR4x9aZhurQVAOYuYHv-E8sj0eK4,3124
 pychemstation/control/__init__.py,sha256=7lSkY7Qa7Ikdz82-2FESc_oqktv7JndsjltCkiMqnMI,147
-pychemstation/control/hplc.py,sha256=JrfkQ5Jt9K9kf5l2X5wQzuYaQvPEnDa_aAkCVeMBk0o,14244
+pychemstation/control/hplc.py,sha256=Nw5rJAOsmW1W6faq4jRuMJlEoGda91kD9GqkRX2jcgk,14210
 pychemstation/control/controllers/README.md,sha256=S5cd4NJmPjs6TUH98BtPJJhiS1Lu-mxLCNS786ogOrQ,32
 pychemstation/control/controllers/__init__.py,sha256=q2TUEie3J-OLlxcGLkG7vIy8fazCEhHm61OGzJPbhD0,179
 pychemstation/control/controllers/comm.py,sha256=ySjgMBIfJ11sygXiZSPp9Rf6ABM4t6JhZRONRj1u2Cc,6652
 pychemstation/control/controllers/data_aq/__init__.py,sha256=w-Zgbit10niOQfz780ZmRHjUFxV1hMkdui7fOMPqeLA,132
-pychemstation/control/controllers/data_aq/method.py,sha256=KFKL8yt3lHxpgND52z4gN6TeMvnNaAOVetpO2su1GlU,24935
-pychemstation/control/controllers/data_aq/sequence.py,sha256=CgNPc-IaPXCHkkWjhb2UrxhDmAltUz7rPCiZa4O6ATw,20967
+pychemstation/control/controllers/data_aq/method.py,sha256=sWtMjmBV-oY8dCxQbnksKvTVUtiH7rcq9cF1t-yoAKY,24787
+pychemstation/control/controllers/data_aq/sequence.py,sha256=5JpXDWpS3JR2Cawn9RdUwOIYSipQPeB3OR7KW6muO6U,18623
 pychemstation/control/controllers/devices/__init__.py,sha256=QpgGnLXyWiB96KIB98wMccEi8oOUUaLxvBCyevJzcOg,75
 pychemstation/control/controllers/devices/injector.py,sha256=LyubM-fqf5ruseGx32deTDK-yevmaTOvdo6YKg2PF7I,4029
 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=GZJyDzkhzrlMguxZTUpgthq72pA3YV23DJIR2Q63PCk,449
+pychemstation/utils/device_types.py,sha256=X8LFRdZpOK3bmdLgKKpsi8N9T27bI0Tg6_qEG9QJEBs,98
 pychemstation/utils/injector_types.py,sha256=z2iWwTklGm0GRDCL9pnPCovQrwyRwxv8w5w5Xh7Pj3U,1152
 pychemstation/utils/macro.py,sha256=VGOU380ruJSKQhXJFI1g--qg4Xgx-e0D8z5FDPGe0cA,3433
 pychemstation/utils/method_types.py,sha256=ck8I4dRGhHXCUfBf3AT1OU1eCcSSZPgnlhvlLTfezEM,1562
 pychemstation/utils/num_utils.py,sha256=OpqZwMPoxTYkpjpinA1CcoQAXDY_0sie6d-hTU547uo,2087
 pychemstation/utils/parsing.py,sha256=mzdpxrH5ux4-_i4CwZvnIYnIwAnRnOptKb3fZyYJcx0,9307
-pychemstation/utils/sequence_types.py,sha256=JLGL7kCkPouHN7iBsnZfWe-nSjzF8XqFKzBPyF4SulE,2724
+pychemstation/utils/sequence_types.py,sha256=H9htO2thyU9_KYOFBsGjlmA-4Nyd6aLd4D0MDLaXNCQ,2583
 pychemstation/utils/spec_utils.py,sha256=BtXgQndZy4kVKsrgEDxwNd0HctypnAt5upB9SOk1D9w,9700
 pychemstation/utils/table_types.py,sha256=ZmV52Vl1cYG_C1PEmVGB02mC3Dhfi7QMkUZwe0ujzAg,3748
 pychemstation/utils/tray_types.py,sha256=UeHM0hUYaNc9giT96ZiGpyWBPQwG-SyLA0rVGzDDAJk,6618
 pychemstation/utils/abc_tables/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pychemstation/utils/abc_tables/abc_comm.py,sha256=gLvCiD8hDHXlMsiUzZX__g2kgFCeNnUIK7_nsLwI7Hc,5465
+pychemstation/utils/abc_tables/abc_comm.py,sha256=7ywcufQZ7UWfNQdEEsfHqkA2CpRkt6ZlKYuLt9MXjvs,5656
 pychemstation/utils/abc_tables/device.py,sha256=v8MNFvymbKe4hWsqzO6Z_qsVvju_rISYtnPgaftecyE,919
-pychemstation/utils/abc_tables/run.py,sha256=Sr6Iz_YrwJ78HTNHFv6fTA-Kca8gP3Dic_-7-AriyOw,10140
+pychemstation/utils/abc_tables/run.py,sha256=uURDl66Mga8NAMffOUsG6prKhjpLo1-p2Y2PUTY1hY0,10052
 pychemstation/utils/abc_tables/table.py,sha256=AbuitDcBHODV-KpxjL7ZPoE-TSa6gyG2uqXXY90Mv2o,7992
 pychemstation/utils/mocking/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pychemstation/utils/mocking/mock_comm.py,sha256=vZeYBXaKBZOlJmhn4TSbkov62gqlkfztqf3MSFU9kLE,800
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