pychemstation 0.10.7__tar.gz → 0.10.8.dev1__tar.gz

{pychemstation-0.10.7 → pychemstation-0.10.8.dev1}/.gitlab-ci.yml

@@ -13,4 +13,6 @@ pages:
     - mv doc/ ./public/
   artifacts:
     paths:
-    - public
+    - public
+  rules:
+    - if: $CI_COMMIT_BRANCH == "v0.10.x"

{pychemstation-0.10.7 → pychemstation-0.10.8.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.10.7
+Version: 0.10.8.dev1
 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
@@ -13,19 +13,13 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.10
 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>=3.5.0
-Requires-Dist: pytest>=7.3.5
 Requires-Dist: rainbow-api>=1.0.10
 Requires-Dist: result>=0.17.0
 Requires-Dist: scipy>=1.10.1
-Requires-Dist: seabreeze>=2.9.2
-Requires-Dist: setuptools>=75.3.2
-Requires-Dist: twine>=6.1.0
 Requires-Dist: xsdata>=24.9
 Description-Content-Type: text/markdown
 

pychemstation-0.10.8.dev1/branch-rename.sh

@@ -0,0 +1,23 @@
+# Names of things - allows you to copy/paste commands
+old_name=nightly
+new_name=finn-python38-support
+remote=origin
+
+# Rename the local branch to the new name
+git branch -m $old_name $new_name
+
+# Delete the old branch on remote
+git push $remote --delete $old_name
+
+# Or shorter way to delete remote branch [:]
+git push $remote :$old_name
+
+# Prevent git from using the old name when pushing in the next step.
+# Otherwise, git will use the old upstream name instead of $new_name.
+git branch --unset-upstream $new_name
+
+# Push the new branch to remote
+git push $remote $new_name
+
+# Reset the upstream branch for the new_name local branch
+git push $remote -u $new_name

{pychemstation-0.10.7 → pychemstation-0.10.8.dev1}/pychemstation/analysis/base_spectrum.py

@@ -2,6 +2,7 @@ import logging
 import os
 import pickle
 from abc import ABC, abstractmethod
+from typing import Optional, Union
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -43,16 +44,15 @@ class AbstractSpectrum(ABC):
         "baseline",
     }
 
-    def __init__(self, path=None, autosaving=True):
+    def __init__(
+        self, path: Optional[Union[str, bool]] = None, autosaving: Optional[bool] = True
+    ):
         """Default constructor, loads properties into instance namespace.
 
         Can be redefined in ancestor classes.
 
-        Args:
-            path (Union[str, bool], optional): Valid path to save data to.
-                If omitted, uses ".//spectrum". If False - no folder created.
-            autosaving (bool, optional): If the True (default) will save the
-                spectrum when the new one is loaded. Will drop otherwise.
+        :param path: Valid path to save data to.  If omitted, uses ".//spectrum". If False - no folder created.
+        :param autosaving: If the True (default) will save the  spectrum when the new one is loaded. Will drop otherwise.
         """
 
         self.autosaving = autosaving
@@ -70,10 +70,10 @@ class AbstractSpectrum(ABC):
             self.path = os.path.join(".", "spectrum")
             os.makedirs(self.path, exist_ok=True)
         else:
-            try:
+            if isinstance(path, str):
                 os.makedirs(path, exist_ok=True)
                 self.path = path
-            except TypeError:  # type(path) -> bool
+            else:
                 self.path = "."
 
         # creating logger
@@ -86,15 +86,14 @@ class AbstractSpectrum(ABC):
         self.__init__(path=self.path, autosaving=self.autosaving)
 
     @abstractmethod
-    def load_spectrum(self, x, y, timestamp):
+    def load_spectrum(self, x: np.ndarray, y: np.ndarray, timestamp: float):
         """Loads the spectral data.
 
         This method must be redefined in ancestor classes.
 
-        Args:
-            x (:obj: np.array): An array with data to be plotted as "x" axis.
-            y (:obj: np.array): An array with data to be plotted as "y" axis.
-            timestamp (float): Timestamp to the corresponding spectrum.
+        :param x: An array with data to be plotted as "x" axis.
+        :param y: An array with data to be plotted as "y" axis.
+        :param timestamp: Timestamp to the corresponding spectrum.
         """
 
         try:
@@ -107,8 +106,8 @@ class AbstractSpectrum(ABC):
                 self.save_data()
             self._dump()
 
-        self.x = x
-        self.y = y
+        self.x: np.ndarray = x
+        self.y: np.ndarray = y
         self.timestamp = timestamp
 
     def save_data(self, filename=None, verbose=False):

{pychemstation-0.10.7 → pychemstation-0.10.8.dev1}/pychemstation/analysis/chromatogram.py

@@ -3,7 +3,7 @@
 import os
 import time
 from dataclasses import dataclass
-from typing import Dict
+from typing import Dict, Tuple
 
 import numpy as np
 
@@ -80,15 +80,14 @@ class AgilentHPLCChromatogram(AbstractSpectrum):
 
     ### PUBLIC METHODS TO LOAD RAW DATA ###
 
-    def extract_rawdata(self, experiment_dir: str, channel: str):
-        """
-        Reads raw data from Chemstation .CH files.
+    def extract_rawdata(
+        self, experiment_dir: str, channel: str
+    ) -> Tuple[np.ndarray, np.ndarray]:
+        """Reads raw data from Chemstation .CH files.
 
-        Args:
-            experiment_dir: .D directory with the .CH files
+        :param experiment_dir: .D directory with the .CH files
 
-        Returns:
-            np.array(times), np.array(values)   Raw chromatogram data
+        :returns: np.array(times), np.array(values)   Raw chromatogram data
         """
         filename = os.path.join(experiment_dir, f"DAD1{channel}")
         npz_file = filename + ".npz"

{pychemstation-0.10.7 → pychemstation-0.10.8.dev1}/pychemstation/analysis/process_report.py

@@ -65,8 +65,7 @@ class ReportProcessor(abc.ABC):
 
 class CSVProcessor(ReportProcessor):
     def __init__(self, path: str):
-        """
-        Class to process reports in CSV form.
+        """Class to process reports in CSV form.
 
         :param path: the parent folder that contains the CSV report(s) to parse.
         """
@@ -104,8 +103,7 @@ class CSVProcessor(ReportProcessor):
         return all_labels_seen
 
     def process_report(self) -> Result[AgilentReport, AnyStr]:
-        """
-        Method to parse details from CSV report.
+        """Method to parse details from CSV report.
 
         :return: subset of complete report details, specifically the sample location, solvents in pumps,
          and list of peaks at each wavelength channel.
@@ -176,9 +174,7 @@ class CSVProcessor(ReportProcessor):
 
 
 class TXTProcessor(ReportProcessor):
-    """
-    Regex matches for column and unit combinations, courtesy of Veronica Lai.
-    """
+    """Regex matches for column and unit combinations, courtesy of Veronica Lai."""
 
     _column_re_dictionary = {
         "Peak": {  # peak index
@@ -212,8 +208,7 @@ class TXTProcessor(ReportProcessor):
         max_ret_time: int = 999,
         target_wavelength_range=None,
     ):
-        """
-        Class to process reports in CSV form.
+        """Class to process reports in CSV form.
 
         :param path: the parent folder that contains the CSV report(s) to parse.
         :param min_ret_time: peaks after this value (min) will be returned
@@ -228,8 +223,7 @@ class TXTProcessor(ReportProcessor):
         super().__init__(path)
 
     def process_report(self) -> Result[AgilentReport, Union[AnyStr, Exception]]:
-        """
-        Method to parse details from CSV report.
+        """Method to parse details from CSV report.
         If you want more functionality, use `aghplctools`.
         `from aghplctools.ingestion.text import pull_hplc_area_from_txt`
         `signals = pull_hplc_area_from_txt(file_path)`
@@ -281,8 +275,7 @@ class TXTProcessor(ReportProcessor):
             return Err(e)
 
     def parse_area_report(self, report_text: str) -> Dict:
-        """
-        Interprets report text and parses the area report section, converting it to dictionary.
+        """Interprets report text and parses the area report section, converting it to dictionary.
         Courtesy of Veronica Lai.
 
         :param report_text: plain text version of the report.
@@ -340,8 +333,7 @@ class TXTProcessor(ReportProcessor):
         return signals
 
     def build_peak_regex(self, signal_table: str) -> Pattern[str] | None:
-        """
-        Builds a peak regex from a signal table. Courtesy of Veronica Lai.
+        """Builds a peak regex from a signal table. Courtesy of Veronica Lai.
 
         :param signal_table: block of lines associated with an area table
         :return: peak line regex object (<=3.6 _sre.SRE_PATTERN, >=3.7 re.Pattern)

{pychemstation-0.10.7 → pychemstation-0.10.8.dev1}/pychemstation/control/README.md

@@ -70,7 +70,7 @@ seq_table = SequenceTable(
             inj_source=InjectionSource.MANUAL
         ),
         SequenceEntry(
-            vial_location=TenVialColumn.ONE,
+            vial_location=VialBar.ONE,
             method="General-Poroshell",
             num_inj=1,
             inj_vol=1,

{pychemstation-0.10.7 → pychemstation-0.10.8.dev1}/pychemstation/control/controllers/__init__.py

@@ -4,5 +4,6 @@
 
 from .comm import CommunicationController
 from . import data_aq
+from . import devices
 
-__all__ = ["CommunicationController", "data_aq"]
+__all__ = ["CommunicationController", "data_aq", "devices"]

{pychemstation-0.10.7 → pychemstation-0.10.8.dev1}/pychemstation/control/controllers/comm.py

@@ -15,18 +15,23 @@ from typing import Optional, Union, Tuple, List
 
 from result import Err, Ok, Result
 
+from ...utils.abc_tables.abc_comm import ABCCommunicationController
 from ...utils.macro import (
     Command,
     HPLCErrorStatus,
     Status,
     str_to_status,
 )
-from .abc_tables.abc_comm import ABCCommunicationController
 
 
 class CommunicationController(ABCCommunicationController):
-    """
-    Class that communicates with Agilent using Macros
+    """Class that communicates with Agilent using Macros
+
+    :param comm_dir: the complete directory path that was used in the MACRO file, common file that pychemstation and Chemstation use to communicate.
+    :param cmd_file: name of the write file that pychemstation writes MACROs to, in `comm_dir`
+    :param reply_file: name of the read file that Chemstation replies to, in `comm_dir
+    :param offline: whether or not communication with Chemstation is to be established
+    :param debug: if True, prints all send MACROs to an out.txt file
     """
 
     def __init__(
@@ -37,12 +42,6 @@ class CommunicationController(ABCCommunicationController):
         offline: bool = False,
         debug: bool = False,
     ):
-        """
-        :param comm_dir:
-        :param cmd_file: Name of command file
-        :param reply_file: Name of reply file
-        :param debug: whether to save log of sent commands
-        """
         super().__init__(comm_dir, cmd_file, reply_file, offline, debug)
 
     def get_num_val(self, cmd: str) -> Union[int, float]:
@@ -151,21 +150,28 @@ class CommunicationController(ABCCommunicationController):
 
     def get_chemstation_dirs(self) -> Tuple[str, str, List[str]]:
         method_dir, sequence_dir, data_dirs = None, None, None
-        self.send(Command.GET_METHOD_DIR)
-        res = self.receive()
-        if res.is_ok():
-            method_dir = res.ok_value.string_response
-        self.send(Command.GET_SEQUENCE_DIR)
-        res = self.receive()
-        if res.is_ok():
-            sequence_dir = res.ok_value.string_response
-        self.send(Command.GET_DATA_DIRS)
-        res = self.receive()
-        if res.is_ok():
-            data_dirs = res.ok().string_response.split("|")
-        if method_dir and sequence_dir and data_dirs:
-            return method_dir, sequence_dir, data_dirs
-        else:
-            raise ValueError(
-                "Please provide the method, sequence and data directories, could not be found."
-            )
+        for _ in range(10):
+            self.send(Command.GET_METHOD_DIR)
+            res = self.receive()
+            if res.is_ok():
+                method_dir = res.ok_value.string_response
+            self.send(Command.GET_SEQUENCE_DIR)
+            res = self.receive()
+            if res.is_ok():
+                sequence_dir = res.ok_value.string_response
+            self.send(Command.GET_DATA_DIRS)
+            res = self.receive()
+            if res.is_ok():
+                data_dirs = res.ok().string_response.split("|")
+            if method_dir and sequence_dir and data_dirs:
+                if not sequence_dir[0].isalpha():
+                    sequence_dir = "C:" + sequence_dir
+                if not method_dir[0].isalpha():
+                    method_dir = "C:" + method_dir
+                for i, data_dir in enumerate(data_dirs):
+                    if not data_dir[0].isalpha():
+                        data_dirs[i] = "C:" + data_dir
+                return method_dir, sequence_dir, data_dirs
+        raise ValueError(
+            f"One of the method: {method_dir}, sequence: {sequence_dir} or data directories: {data_dirs} could not be found, please provide your own."
+        )

{pychemstation-0.10.7 → pychemstation-0.10.8.dev1}/pychemstation/control/controllers/data_aq/method.py

@@ -7,7 +7,6 @@ from typing import List, Optional, Union, Dict, Set
 
 from result import Err, Ok, Result
 
-from ..abc_tables.run import RunController
 from ....analysis.process_report import AgilentReport, ReportType
 from ....control.controllers import CommunicationController
 from pychemstation.analysis.chromatogram import (
@@ -15,6 +14,7 @@ from pychemstation.analysis.chromatogram import (
     AgilentChannelChromatogramData,
     AgilentHPLCChromatogram,
 )
+from ....utils.abc_tables.run import RunController
 from ....utils.macro import Command
 from ....utils.method_types import (
     HPLCMethodParams,
@@ -28,15 +28,13 @@ from ..devices.injector import InjectorController
 
 
 class MethodController(RunController):
-    """
-    Class containing method related logic
-    """
+    """Class containing method related logic."""
 
     def __init__(
         self,
-        controller: CommunicationController,
-        src: str,
-        data_dirs: List[str],
+        controller: Optional[CommunicationController],
+        src: Optional[str],
+        data_dirs: Optional[List[str]],
         table: Table,
         offline: bool,
         injector_controller: InjectorController,
@@ -51,7 +49,7 @@ class MethodController(RunController):
             offline=offline,
         )
 
-    def check(self) -> str:
+    def get_current_method_name(self) -> str:
         time.sleep(2)
         self.send(Command.GET_METHOD_CMD)
         time.sleep(2)
@@ -441,18 +439,20 @@ class MethodController(RunController):
             if run_completed.is_ok():
                 self.data_files[-1] = run_completed.ok_value
             else:
-                raise RuntimeError(f"Run error has occurred:{run_completed.err_value}.")
+                warnings.warn(run_completed.err_value)
         else:
-            folder = self.fuzzy_match_most_recent_folder(self.data_files[-1], None)
-            while folder.is_err():
-                folder = self.fuzzy_match_most_recent_folder(self.data_files[-1], None)
+            folder = self._fuzzy_match_most_recent_folder(self.data_files[-1], None)
+            i = 0
+            while folder.is_err() and i < 10:
+                folder = self._fuzzy_match_most_recent_folder(self.data_files[-1], None)
+                i += 1
             if folder.is_ok():
                 self.data_files[-1] = folder.ok_value
             else:
                 warning = f"Data folder {self.data_files[-1]} may not exist, returning and will check again after run is done."
                 warnings.warn(warning)
 
-    def fuzzy_match_most_recent_folder(
+    def _fuzzy_match_most_recent_folder(
         self, most_recent_folder: T, child_dirs: Optional[Set[str]]
     ) -> Result[str, str]:
         if isinstance(most_recent_folder, str) or isinstance(most_recent_folder, bytes):

{pychemstation-0.10.7 → pychemstation-0.10.8.dev1}/pychemstation/control/controllers/data_aq/sequence.py

@@ -13,6 +13,7 @@ from pychemstation.analysis.chromatogram import (
 
 from ....analysis.process_report import AgilentReport, ReportType
 from ....control.controllers.comm import CommunicationController
+from ....utils.abc_tables.run import RunController
 from ....utils.macro import Command
 from ....utils.sequence_types import (
     InjectionSource,
@@ -22,8 +23,7 @@ from ....utils.sequence_types import (
     SequenceTable,
 )
 from ....utils.table_types import RegisterFlag, T, Table
-from ....utils.tray_types import FiftyFourVialPlate, TenVialColumn, Tray
-from ..abc_tables.run import RunController
+from ....utils.tray_types import FiftyFourVialPlate, VialBar, Tray
 from . import MethodController
 
 
@@ -36,8 +36,8 @@ class SequenceController(RunController):
         self,
         controller: Optional[CommunicationController],
         method_controller: MethodController,
-        src: str,
-        data_dirs: List[str],
+        src: Optional[str],
+        data_dirs: Optional[List[str]],
         table: Table,
         offline: bool,
     ):
@@ -80,11 +80,7 @@ class SequenceController(RunController):
 
     def try_vial_location(self, val: Any) -> Tray:
         try:
-            return (
-                TenVialColumn(val)
-                if val <= 10
-                else FiftyFourVialPlate.from_int(num=val)
-            )
+            return VialBar(val) if val <= 10 else FiftyFourVialPlate.from_int(num=val)
         except ValueError:
             raise ValueError("Expected vial location, is empty.")
 
@@ -109,15 +105,6 @@ class SequenceController(RunController):
             data_file=data_file,
         )
 
-    def check(self) -> str:
-        time.sleep(2)
-        self.send(Command.GET_SEQUENCE_CMD)
-        time.sleep(2)
-        res = self.receive()
-        if res.is_ok():
-            return res.ok_value.string_response
-        return "ERROR"
-
     def switch(self, seq_name: str):
         """
         Switch to the specified sequence. The sequence name does not need the '.S' extension.
@@ -249,7 +236,7 @@ class SequenceController(RunController):
 
     def edit_vial_location(self, loc: Tray, row_num: int, save: bool = True):
         loc_num = -1
-        if isinstance(loc, TenVialColumn):
+        if isinstance(loc, VialBar):
             loc_num = loc.value
         elif isinstance(loc, FiftyFourVialPlate):
             loc_num = loc.value()
@@ -322,6 +309,7 @@ class SequenceController(RunController):
                     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)
             else:
@@ -332,12 +320,12 @@ class SequenceController(RunController):
                 if run_completed.is_ok():
                     self.data_files[-1] = run_completed.ok_value
                 else:
-                    warnings.warn("Run may have not completed.")
+                    warnings.warn(run_completed.err_value)
         else:
             raise RuntimeError("Sequence run may not have started.")
 
     @override
-    def fuzzy_match_most_recent_folder(
+    def _fuzzy_match_most_recent_folder(
         self, most_recent_folder: T, child_dirs: Optional[Set[str]]
     ) -> Result[SequenceDataFiles, str]:
         if isinstance(most_recent_folder, SequenceDataFiles):
@@ -383,7 +371,7 @@ class SequenceController(RunController):
             else self.data_files[-1]
         )
         if len(seq_data_dir.child_dirs) == 0:
-            search_folder = self.fuzzy_match_most_recent_folder(
+            search_folder = self._fuzzy_match_most_recent_folder(
                 seq_data_dir, set(seq_data_dir.child_dirs)
             )
             if search_folder.is_ok():
@@ -414,7 +402,7 @@ class SequenceController(RunController):
             else self.data_files[-1]
         )
         if len(seq_file_dir.child_dirs) == 0:
-            self.data_files[-1] = self.fuzzy_match_most_recent_folder(
+            self.data_files[-1] = self._fuzzy_match_most_recent_folder(
                 seq_file_dir, set(seq_file_dir.child_dirs)
             ).ok_value
         spectra: List[AgilentChannelChromatogramData] = []
@@ -430,7 +418,7 @@ class SequenceController(RunController):
     ) -> List[AgilentReport]:
         if custom_path:
             self.data_files.append(
-                self.fuzzy_match_most_recent_folder(
+                self._fuzzy_match_most_recent_folder(
                     most_recent_folder=SequenceDataFiles(
                         dir=custom_path,
                         sequence_name="NA",

{pychemstation-0.10.7 → pychemstation-0.10.8.dev1}/pychemstation/control/controllers/devices/injector.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
-from ..abc_tables.device import DeviceController
 from ....control.controllers import CommunicationController
+from ....utils.abc_tables.device import DeviceController
 from ....utils.injector_types import (
     Draw,
     Inject,
@@ -17,7 +17,7 @@ from ....utils.injector_types import (
 )
 from ....utils.macro import Response
 from ....utils.table_types import RegisterFlag, Table
-from ....utils.tray_types import Tray, FiftyFourVialPlate, TenVialColumn, LocationPlus
+from ....utils.tray_types import Tray, FiftyFourVialPlate, VialBar, LocationPlus
 
 
 class InjectorController(DeviceController):
@@ -31,7 +31,7 @@ class InjectorController(DeviceController):
             return FiftyFourVialPlate.from_str(val)
         except Exception:
             try:
-                return TenVialColumn(int(val))
+                return VialBar(int(val))
             except Exception:
                 raise ValueError("Location could not be identified.")