pychemstation 0.10.3__tar.gz → 0.10.4__tar.gz

pychemstation-0.10.4/.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.11.2
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format

{pychemstation-0.10.3 → pychemstation-0.10.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.10.3
+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
@@ -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

{pychemstation-0.10.3/build/lib → pychemstation-0.10.4}/pychemstation/__init__.py

@@ -1,3 +1,3 @@
 """
 .. include:: ../README.md
-"""
+"""

pychemstation-0.10.4/pychemstation/analysis/__init__.py

@@ -0,0 +1,4 @@
+from .process_report import CSVProcessor
+from .process_report import TXTProcessor
+
+__all__ = ["CSVProcessor", "TXTProcessor"]

{pychemstation-0.10.3/build/lib → pychemstation-0.10.4}/pychemstation/analysis/base_spectrum.py

@@ -197,10 +197,10 @@ class AbstractSpectrum(ABC):
             return (self.x.copy()[full_mask], self.y.copy()[full_mask])
 
     def show_spectrum(
-            self,
-            filename=None,
-            title=None,
-            label=None,
+        self,
+        filename=None,
+        title=None,
+        label=None,
     ):
         """Plots the spectral data using matplotlib.pyplot module.
 
@@ -249,7 +249,7 @@ class AbstractSpectrum(ABC):
             os.makedirs(path, exist_ok=True)
             fig.savefig(os.path.join(path, f"{filename}.png"), dpi=150)
 
-    def find_peaks(self, threshold=1, min_width=.1, min_dist=None, area=None):
+    def find_peaks(self, threshold=1, min_width=0.1, min_dist=None, area=None):
         """Finds all peaks above the threshold with at least min_width width.
 
         Args:
@@ -385,12 +385,12 @@ class AbstractSpectrum(ABC):
 
         if rule == "trapz":
             return integrate.trapz(
-                self.y[left_idx: right_idx + 1], self.x[left_idx: right_idx + 1]
+                self.y[left_idx : right_idx + 1], self.x[left_idx : right_idx + 1]
             )
 
         elif rule == "simps":
             return integrate.simps(
-                self.y[left_idx: right_idx + 1], self.x[left_idx: right_idx + 1]
+                self.y[left_idx : right_idx + 1], self.x[left_idx : right_idx + 1]
             )
 
         else:

{pychemstation-0.10.3/build/lib/pychemstation/utils → pychemstation-0.10.4/pychemstation/analysis}/chromatogram.py

@@ -6,8 +6,9 @@ from dataclasses import dataclass
 
 import numpy as np
 
-from ..analysis import AbstractSpectrum
-from .parsing import CHFile
+
+from ..utils.parsing import CHFile
+from ..analysis.base_spectrum import AbstractSpectrum
 
 ACQUISITION_PARAMETERS = "acq.txt"
 
@@ -36,12 +37,11 @@ class AgilentHPLCChromatogram(AbstractSpectrum):
     }
 
     def __init__(self, path=None, autosaving=False):
-
         if path is not None:
             os.makedirs(path, exist_ok=True)
             self.path = path
         else:
-            self.path = os.path.join(".", "hplc_data")
+            self.path = os.path.join("../utils", "hplc_data")
             os.makedirs(self.path, exist_ok=True)
 
         super().__init__(path=path, autosaving=autosaving)

{pychemstation-0.10.3 → pychemstation-0.10.4}/pychemstation/analysis/process_report.py

@@ -17,8 +17,8 @@ from aghplctools.ingestion.text import (
 )
 from result import Err, Ok, Result
 
-from pychemstation.utils.chromatogram import AgilentHPLCChromatogram
-from pychemstation.utils.tray_types import FiftyFourVialPlate, Tray
+from ..analysis.chromatogram import AgilentHPLCChromatogram
+from ..utils.tray_types import FiftyFourVialPlate, Tray
 
 
 @dataclass
@@ -76,9 +76,11 @@ class CSVProcessor(ReportProcessor):
         :return: subset of complete report details, specifically the sample location, solvents in pumps,
          and list of peaks at each wavelength channel.
         """
-        labels = os.path.join(self.path, 'REPORT00.CSV')
+        labels = os.path.join(self.path, "REPORT00.CSV")
         if os.path.exists(labels):
-            df_labels: Dict[int, Dict[int: AnyStr]] = pd.read_csv(labels, encoding="utf-16", header=None).to_dict()
+            df_labels: Dict[int, Dict[int:AnyStr]] = pd.read_csv(
+                labels, encoding="utf-16", header=None
+            ).to_dict()
             vial_location = []
             signals = {}
             solvents = {}
@@ -91,18 +93,28 @@ class CSVProcessor(ReportProcessor):
                 elif val == "Number of Signals":
                     num_signals = int(df_labels[1][pos])
                     for s in range(1, num_signals + 1):
-                        df = pd.read_csv(os.path.join(self.path, f'REPORT0{s}.CSV'),
-                                         encoding="utf-16", header=None)
+                        df = pd.read_csv(
+                            os.path.join(self.path, f"REPORT0{s}.CSV"),
+                            encoding="utf-16",
+                            header=None,
+                        )
                         peaks = df.apply(lambda row: AgilentPeak(*row), axis=1)
-                        wavelength = df_labels[1][pos + s].partition(",4 Ref=off")[0][-3:]
+                        wavelength = df_labels[1][pos + s].partition(",4 Ref=off")[0][
+                            -3:
+                        ]
                         signals[wavelength] = list(peaks)
                     break
 
-            return Ok(AgilentReport(
-                signals=[Signals(wavelength=int(w), peaks=s, data=None) for w, s in signals.items()],
-                vial_location=FiftyFourVialPlate.from_int(int(vial_location)),
-                solvents=solvents
-            ))
+            return Ok(
+                AgilentReport(
+                    signals=[
+                        Signals(wavelength=int(w), peaks=s, data=None)
+                        for w, s in signals.items()
+                    ],
+                    vial_location=FiftyFourVialPlate.from_int(int(vial_location)),
+                    solvents=solvents,
+                )
+            )
 
         return Err("No report found")
 
@@ -111,34 +123,39 @@ class TXTProcessor(ReportProcessor):
     """
     Regex matches for column and unit combinations, courtesy of Veronica Lai.
     """
+
     _column_re_dictionary = {
-        'Peak': {  # peak index
-            '#': '[ ]+(?P<Peak>[\d]+)',  # number
+        "Peak": {  # peak index
+            "#": "[ ]+(?P<Peak>[\d]+)",  # number
         },
-        'RetTime': {  # retention time
-            '[min]': '(?P<RetTime>[\d]+.[\d]+)',  # minutes
+        "RetTime": {  # retention time
+            "[min]": "(?P<RetTime>[\d]+.[\d]+)",  # minutes
         },
-        'Type': {  # peak type
-            '': '(?P<Type>[A-Z]{1,3}(?: [A-Z]{1,2})*)',  # todo this is different from <4.8.8 aghplc tools
+        "Type": {  # peak type
+            "": "(?P<Type>[A-Z]{1,3}(?: [A-Z]{1,2})*)",  # todo this is different from <4.8.8 aghplc tools
         },
-        'Width': {  # peak width
-            '[min]': '(?P<Width>[\d]+.[\d]+[e+-]*[\d]+)',
+        "Width": {  # peak width
+            "[min]": "(?P<Width>[\d]+.[\d]+[e+-]*[\d]+)",
         },
-        'Area': {  # peak area
-            '[mAU*s]': '(?P<Area>[\d]+.[\d]+[e+-]*[\d]+)',  # area units
-            '%': '(?P<percent>[\d]+.[\d]+[e+-]*[\d]+)',  # percent
+        "Area": {  # peak area
+            "[mAU*s]": "(?P<Area>[\d]+.[\d]+[e+-]*[\d]+)",  # area units
+            "%": "(?P<percent>[\d]+.[\d]+[e+-]*[\d]+)",  # percent
         },
-        'Height': {  # peak height
-            '[mAU]': '(?P<Height>[\d]+.[\d]+[e+-]*[\d]+)',
+        "Height": {  # peak height
+            "[mAU]": "(?P<Height>[\d]+.[\d]+[e+-]*[\d]+)",
         },
-        'Name': {
-            '': '(?P<Name>[^\s]+(?:\s[^\s]+)*)',  # peak name
+        "Name": {
+            "": "(?P<Name>[^\s]+(?:\s[^\s]+)*)",  # peak name
         },
     }
 
-    def __init__(self, path: str, min_ret_time: int = 0,
-                 max_ret_time: int = 999,
-                 target_wavelength_range: List[int] = range(200, 300)):
+    def __init__(
+        self,
+        path: str,
+        min_ret_time: int = 0,
+        max_ret_time: int = 999,
+        target_wavelength_range: List[int] = range(200, 300),
+    ):
         """
         Class to process reports in CSV form.
 
@@ -163,7 +180,9 @@ class TXTProcessor(ReportProcessor):
          and list of peaks at each wavelength channel.
         """
 
-        with open(os.path.join(self.path, "REPORT.TXT"), 'r', encoding='utf-16') as openfile:
+        with open(
+            os.path.join(self.path, "REPORT.TXT"), "r", encoding="utf-16"
+        ) as openfile:
             text = openfile.read()
 
         try:
@@ -171,25 +190,33 @@ class TXTProcessor(ReportProcessor):
         except ValueError as e:
             return Err("No peaks found: " + str(e))
 
-        signals = {key: signals[key] for key in self.target_wavelength_range if key in signals}
+        signals = {
+            key: signals[key] for key in self.target_wavelength_range if key in signals
+        }
 
         parsed_signals = []
         for wavelength, wavelength_dict in signals.items():
-            current_wavelength_signals = Signals(wavelength=int(wavelength), peaks=[], data=None)
+            current_wavelength_signals = Signals(
+                wavelength=int(wavelength), peaks=[], data=None
+            )
             for ret_time, ret_time_dict in wavelength_dict.items():
                 if self.min_ret_time <= ret_time <= self.max_ret_time:
-                    current_wavelength_signals.peaks.append(AgilentPeak(retention_time=ret_time,
-                                                                        area=ret_time_dict['Area'],
-                                                                        width=ret_time_dict['Width'],
-                                                                        height=ret_time_dict['Height'],
-                                                                        peak_number=None,
-                                                                        peak_type=ret_time_dict['Type'],
-                                                                        area_percent=None))
+                    current_wavelength_signals.peaks.append(
+                        AgilentPeak(
+                            retention_time=ret_time,
+                            area=ret_time_dict["Area"],
+                            width=ret_time_dict["Width"],
+                            height=ret_time_dict["Height"],
+                            peak_number=None,
+                            peak_type=ret_time_dict["Type"],
+                            area_percent=None,
+                        )
+                    )
             parsed_signals.append(current_wavelength_signals)
 
-        return Ok(AgilentReport(vial_location=None,
-                                solvents=None,
-                                signals=parsed_signals))
+        return Ok(
+            AgilentReport(vial_location=None, solvents=None, signals=parsed_signals)
+        )
 
     def parse_area_report(self, report_text: str) -> Dict:
         """
@@ -205,7 +232,7 @@ class TXTProcessor(ReportProcessor):
         should be able to use the `parse_area_report` method of aghplctools v4.8.8
         """
         if re.search(_no_peaks_re, report_text):  # There are no peaks in Report.txt
-            raise ValueError('No peaks found in Report.txt')
+            raise ValueError("No peaks found in Report.txt")
         blocks = _header_block_re.split(report_text)
         signals = {}  # output dictionary
         for ind, block in enumerate(blocks):
@@ -218,23 +245,28 @@ class TXTProcessor(ReportProcessor):
                     si = _signal_info_re.match(table)
                     if si is not None:
                         # some error state (e.g. 'not found')
-                        if si.group('error') != '':
+                        if si.group("error") != "":
                             continue
-                        wavelength = float(si.group('wavelength'))
+                        wavelength = float(si.group("wavelength"))
                         if wavelength in signals:
                             # placeholder error raise just in case (this probably won't happen)
                             raise KeyError(
-                                f'The wavelength {float(si.group("wavelength"))} is already in the signals dictionary')
+                                f"The wavelength {float(si.group('wavelength'))} is already in the signals dictionary"
+                            )
                         signals[wavelength] = {}
                         # build peak regex
                         peak_re = self.build_peak_regex(table)
-                        if peak_re is None:  # if there are no columns (empty table), continue
+                        if (
+                            peak_re is None
+                        ):  # if there are no columns (empty table), continue
                             continue
-                        for line in table.split('\n'):
+                        for line in table.split("\n"):
                             peak = peak_re.match(line)
                             if peak is not None:
-                                signals[wavelength][float(peak.group('RetTime'))] = {}
-                                current = signals[wavelength][float(peak.group('RetTime'))]
+                                signals[wavelength][float(peak.group("RetTime"))] = {}
+                                current = signals[wavelength][
+                                    float(peak.group("RetTime"))
+                                ]
                                 for key in self._column_re_dictionary:
                                     if key in peak.re.groupindex:
                                         try:  # try float conversion, otherwise continue
@@ -253,30 +285,35 @@ class TXTProcessor(ReportProcessor):
         :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)
         """
-        split_table = signal_table.split('\n')
+        split_table = signal_table.split("\n")
         if len(split_table) <= 4:  # catch peak table with no values
             return None
         # todo verify that these indicies are always true
         column_line = split_table[2]  # table column line
         unit_line = split_table[3]  # column unit line
-        length_line = [len(val) + 1 for val in split_table[4].split('|')]  # length line
+        length_line = [len(val) + 1 for val in split_table[4].split("|")]  # length line
 
         # iterate over header values and units to build peak table regex
         peak_re_string = []
         for header, unit in zip(
-                chunk_string(column_line, length_line),
-                chunk_string(unit_line, length_line)
+            chunk_string(column_line, length_line), chunk_string(unit_line, length_line)
         ):
-            if header == '':  # todo create a better catch for an undefined header
+            if header == "":  # todo create a better catch for an undefined header
                 continue
             try:
                 peak_re_string.append(
-                    self._column_re_dictionary[header][unit]  # append the appropriate regex
+                    self._column_re_dictionary[header][
+                        unit
+                    ]  # append the appropriate regex
                 )
             except KeyError:  # catch for undefined regexes (need to be built)
-                raise KeyError(f'The header/unit combination "{header}" "{unit}" is not defined in the peak regex '
-                               f'dictionary. Let Lars know.')
+                raise KeyError(
+                    f'The header/unit combination "{header}" "{unit}" is not defined in the peak regex '
+                    f"dictionary. Let Lars know."
+                )
         return re.compile(
-            '[ ]+'.join(peak_re_string)  # constructed string delimited by 1 or more spaces
-            + '[\s]*'  # and any remaining white space
+            "[ ]+".join(
+                peak_re_string
+            )  # constructed string delimited by 1 or more spaces
+            + "[\s]*"  # and any remaining white space
         )

{pychemstation-0.10.3 → pychemstation-0.10.4}/pychemstation/control/__init__.py

@@ -1,8 +1,9 @@
 """
 .. include:: README.md
 """
+
 from .hplc import HPLCController
 
 __all__ = [
-    'HPLCController',
-]
+    "HPLCController",
+]

{pychemstation-0.10.3/build/lib → pychemstation-0.10.4}/pychemstation/control/controllers/__init__.py

@@ -6,8 +6,4 @@ from .comm import CommunicationController
 from .tables.method import MethodController
 from .tables.sequence import SequenceController
 
-__all__ = [
-    'CommunicationController',
-    'MethodController',
-    'SequenceController'
-]
+__all__ = ["CommunicationController", "MethodController", "SequenceController"]

{pychemstation-0.10.3/build/lib → pychemstation-0.10.4}/pychemstation/control/controllers/comm.py

@@ -9,6 +9,7 @@ been processed.
 
 Authors: Alexander Hammer, Hessam Mehr, Lucy Hao
 """
+
 import os
 import time
 from typing import Optional, Union
@@ -34,11 +35,11 @@ class CommunicationController:
     MAX_CMD_NO = 255
 
     def __init__(
-            self,
-            comm_dir: str,
-            cmd_file: str = "cmd",
-            reply_file: str = "reply",
-            debug: bool = False
+        self,
+        comm_dir: str,
+        cmd_file: str = "cmd",
+        reply_file: str = "reply",
+        debug: bool = False,
     ):
         """
         :param comm_dir:
@@ -62,7 +63,7 @@ class CommunicationController:
         self.reset_cmd_counter()
 
         # Initialize row counter for table operations
-        self.send('Local Rows')
+        self.send("Local Rows")
 
     def get_num_val(self, cmd: str) -> Union[int, float]:
         tries = 5
@@ -194,7 +195,7 @@ class CommunicationController:
     def receive(self) -> Result[Response, str]:
         """Returns messages received in reply file.
 
-        :return: ChemStation response 
+        :return: ChemStation response
         """
         num_response_prefix = "Numerical Responses:"
         str_response_prefix = "String Responses:"
@@ -203,10 +204,18 @@ class CommunicationController:
             lines = possible_response.ok_value.splitlines()
             for line in lines:
                 if str_response_prefix in line and num_response_prefix in line:
-                    string_responses_dirty, _, numerical_responses = line.partition(num_response_prefix)
-                    _, _, string_responses = string_responses_dirty.partition(str_response_prefix)
-                    return Ok(Response(string_response=string_responses.strip(),
-                                       num_response=float(numerical_responses.strip())))
+                    string_responses_dirty, _, numerical_responses = line.partition(
+                        num_response_prefix
+                    )
+                    _, _, string_responses = string_responses_dirty.partition(
+                        str_response_prefix
+                    )
+                    return Ok(
+                        Response(
+                            string_response=string_responses.strip(),
+                            num_response=float(numerical_responses.strip()),
+                        )
+                    )
             return Err("Could not retrieve HPLC response")
         else:
             return Err(f"Could not establish response to HPLC: {possible_response}")

pychemstation-0.10.4/pychemstation/control/controllers/devices/device.py

@@ -0,0 +1,49 @@
+import abc
+from typing import List, Union, Dict, Optional
+
+from result import Result
+
+from ....analysis.process_report import AgilentReport, ReportType
+from ....control.controllers import CommunicationController
+from ....control.controllers.tables.table import TableController
+from pychemstation.analysis.chromatogram import (
+    AgilentChannelChromatogramData,
+    AgilentHPLCChromatogram,
+)
+from ....utils.table_types import T, Table
+
+
+class DeviceController(TableController, abc.ABC):
+    def __init__(
+        self, controller: CommunicationController, table: Table, offline: bool
+    ):
+        super().__init__(
+            controller=controller, src=None, data_dirs=[], table=table, offline=offline
+        )
+
+    @abc.abstractmethod
+    def get_row(self, row: int):
+        pass
+
+    def retrieve_recent_data_files(self):
+        raise NotImplementedError
+
+    def fuzzy_match_most_recent_folder(self, most_recent_folder: T) -> Result[T, str]:
+        raise NotImplementedError
+
+    def get_report(
+        self, report_type: ReportType = ReportType.TXT
+    ) -> List[AgilentReport]:
+        raise NotImplementedError
+
+    def get_data_uv(
+        self,
+    ) -> Union[
+        List[Dict[str, AgilentHPLCChromatogram]], Dict[str, AgilentHPLCChromatogram]
+    ]:
+        raise NotImplementedError
+
+    def get_data(
+        self, custom_path: Optional[str] = None
+    ) -> Union[List[AgilentChannelChromatogramData], AgilentChannelChromatogramData]:
+        raise NotImplementedError

{pychemstation-0.10.3 → pychemstation-0.10.4}/pychemstation/control/controllers/devices/injector.py

@@ -1,4 +1,3 @@
-
 from ....control.controllers import CommunicationController
 from ....utils.injector_types import (
     Draw,
@@ -17,8 +16,9 @@ from .device import DeviceController
 
 
 class InjectorController(DeviceController):
-
-    def __init__(self, controller: CommunicationController, table: Table, offline: bool):
+    def __init__(
+        self, controller: CommunicationController, table: Table, offline: bool
+    ):
         super().__init__(controller, table, offline)
 
     def get_row(self, row: int) -> InjectorFunction:
@@ -34,17 +34,28 @@ class InjectorController(DeviceController):
             # TODO: better error handling
             is_source = SourceType(self.get_text(row, RegisterFlag.DRAW_SOURCE))
             is_volume = Mode(self.get_text(row, RegisterFlag.DRAW_VOLUME))
-            vol = self.get_num(row, RegisterFlag.DRAW_VOLUME_VALUE) if is_volume == Mode.SET else None
+            vol = (
+                self.get_num(row, RegisterFlag.DRAW_VOLUME_VALUE)
+                if is_volume == Mode.SET
+                else None
+            )
             if is_source is SourceType.SPECIFIC_LOCATION:
                 return Draw(amount=vol, source=return_tray_loc())
             elif is_source is SourceType.LOCATION:
-                return Draw(amount=vol, location=self.get_text(row, RegisterFlag.DRAW_LOCATION))
+                return Draw(
+                    amount=vol, location=self.get_text(row, RegisterFlag.DRAW_LOCATION)
+                )
         elif function == "Remote":
-            return Remote(command=RemoteCommand(self.get_text(row, RegisterFlag.REMOTE)),
-                          duration=self.get_num(row, RegisterFlag.REMOTE_DUR))
+            return Remote(
+                command=RemoteCommand(self.get_text(row, RegisterFlag.REMOTE)),
+                duration=self.get_num(row, RegisterFlag.REMOTE_DUR),
+            )
 
     def load(self) -> InjectorTable:
         rows = self.get_num_rows()
         if rows.is_ok():
-            return InjectorTable(functions=[self.get_row(i) for i in range(int(rows.ok_value.num_response))])
-
+            return InjectorTable(
+                functions=[
+                    self.get_row(i) for i in range(int(rows.ok_value.num_response))
+                ]
+            )