labmate 0.10.4__py3-none-any.whl → 0.10.6__py3-none-any.whl

labmate/acquisition_notebook/acquisition_analysis_manager.py

@@ -19,10 +19,12 @@ from ..acquisition import AcquisitionManager, AnalysisData
 from ..logger import logger
 from . import display_widget
 
+
 if TYPE_CHECKING:
     from dh5.path import Path
 
     from ..acquisition import FigureProtocol
+    from ..acquisition.backend import AcquisitionBackend
     from ..acquisition.config_file import ConfigFile
 
     # from ..logger import Logger
@@ -65,7 +67,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
     _analysis_cell_str = None
     _is_old_data = False
     _last_fig_name = None
-    _default_config_files: Tuple[str, ...] = tuple()
+    _default_config_files: Tuple[str, ...] = ()
     _acquisition_started = 0
     _linting_external_vars = None
     _analysis_cell_prerun_hook: Optional[Tuple[_CallableWithNoArgs, ...]] = None
@@ -83,6 +85,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
         save_on_edit_analysis: Optional[bool] = None,
         save_fig_inside_h5: bool = False,
         shell: Any = True,
+        backend: Optional[Union["AcquisitionBackend", Iterable["AcquisitionBackend"]]] = None,
     ):
         """
         AcquisitionAnalysisManager.
@@ -115,7 +118,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
             self.shell = shell
 
         if use_magic:
-            from .acquisition_magic_class import load_ipython_extension
+            from .acquisition_magic_class import load_ipython_extension  # pyright: ignore[reportMissingImports]  # noqa: I001
 
             load_ipython_extension(aqm=self, shell=self.shell)
 
@@ -131,6 +134,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
             config_files=config_files,
             save_files=save_files,
             save_on_edit=save_on_edit,
+            backend=backend,
         )
 
     @property
@@ -173,7 +177,8 @@ class AcquisitionAnalysisManager(AcquisitionManager):
         Args:
             fig (Figure, optional): Figure that should be saved. Figure could be any class with
              function save_fig implemented. By default gets plt.gcf().
-            name (str, optional): Name of the fig. It's a suffix that will be added to the filename. Defaults to None.
+            name (str, optional): Name of the fig. It's a suffix that will be added to the filename.
+                Defaults to None.
             extensions(str, optional): Extensions of the file. Defaults to `pdf`.
             tight_layout(bool, optional): True to call fig.tight_layout(). Defaults to True.
 
@@ -220,6 +225,10 @@ class AcquisitionAnalysisManager(AcquisitionManager):
                 fig = fig or fig_or_name
         self.save_fig_only(fig=fig, name=name, **kwds)
         self.save_analysis_cell(name=name, cell=cell)
+
+        if self.current_acquisition is not None:
+            self._schedule_backend_save(self.current_acquisition)
+
         if self._connected_widgets:
             display_widget.display_widgets(
                 self._connected_widgets,
@@ -248,15 +257,12 @@ class AcquisitionAnalysisManager(AcquisitionManager):
         acquisition_finished = time.time()
         if not self._once_saved:
             additional_info: Dict[str, Any] = {
-                "acquisition_duration": acquisition_finished
-                - self._acquisition_started,
+                "acquisition_duration": acquisition_finished - self._acquisition_started,
                 "logs": self.logger.getvalue(),
                 "prints": self.logger.get_stdout(),
             }
             if self._default_config_files:
-                additional_info.update(
-                    {"default_config_files": self._default_config_files}
-                )
+                additional_info.update({"default_config_files": self._default_config_files})
             kwds.update({"info": additional_info})
 
         super().save_acquisition(update_, file_suffix=file_suffix, **kwds)
@@ -292,9 +298,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
             - If default configuration files are provided, they are set in the loaded data.
         """
         filename = self._get_full_filename(filename)
-        if not os.path.exists(
-            filename if filename.endswith(".h5") else filename + ".h5"
-        ):
+        if not os.path.exists(filename if filename.endswith(".h5") else filename + ".h5"):  # noqa: PTH110
             raise ValueError(f"File {filename} cannot be found")
 
         data = AnalysisData(
@@ -386,9 +390,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
                 display_warning("Old data analysis")
 
             filename = str(filepath or self._get_full_filename(filename))  # type: ignore
-            filename = (
-                (filename.rsplit(".h5", 1)[0]) if filename.endswith(".h5") else filename
-            )
+            filename = (filename.rsplit(".h5", 1)[0]) if filename.endswith(".h5") else filename
 
         else:
             self._is_old_data = False
@@ -403,8 +405,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
                     )
                     or (
                         acquisition_name[0] == r"^"
-                        and re.match(acquisition_name, self.current_experiment_name)
-                        is None
+                        and re.match(acquisition_name, self.current_experiment_name) is None
                     )
                 ):
                     raise ValueError(
@@ -413,14 +414,14 @@ class AcquisitionAnalysisManager(AcquisitionManager):
                     )
 
             filename = str(self.current_filepath)  # without h5
-        self.logger.info(os.path.basename(filename))
+        self.logger.info(os.path.basename(filename))  # noqa: PTH119
 
         if (
             (not self._is_old_data)
             and (self.shell is not None)
             and (
-                "acquisition_cell(" in self.shell.last_execution_result.info.raw_cell
-                and not self.shell.last_execution_result.success
+                "acquisition_cell(" in self.shell.last_execution_result.info.raw_cell  # type: ignore
+                and not self.shell.last_execution_result.success  # type: ignore
             )
         ):
             raise ChildProcessError(
@@ -428,7 +429,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
                 "Check if everything is ok and executive again"
             )
 
-        if os.path.exists(filename + ".h5"):
+        if os.path.exists(filename + ".h5"):  # noqa: PTH110
             self._load_analysis_data(filename)
         else:
             if self._is_old_data:
@@ -438,9 +439,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
         if cell is not None:
             self.save_analysis_cell(cell=cell)
 
-        if (self._analysis_cell_str is not None) and (
-            self._linting_external_vars is not None
-        ):
+        if (self._analysis_cell_str is not None) and (self._linting_external_vars is not None):
             from ..acquisition import custom_lint
             from ..utils import lint
 
@@ -453,9 +452,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
                 run_on_call=custom_lint.on_call_functions,
             )
             for var in lint_result.external_vars:
-                self.logger.warning(
-                    "External variable used inside the analysis code: %s", var
-                )
+                self.logger.warning("External variable used inside the analysis code: %s", var)
             for error in lint_result.errors:
                 self.logger.warning(error)
 
@@ -480,15 +477,13 @@ class AcquisitionAnalysisManager(AcquisitionManager):
 
         filepath = utils.get_path_from_filename(filename)
         if isinstance(filepath, tuple):
-            return os.path.join(self.data_directory, *filepath)
+            return os.path.join(self.data_directory, *filepath)  # noqa: PTH118
         return filepath
 
     def parse_config_file(self, config_file_name: str, /) -> "ConfigFile":
         return self.data.parse_config_file(config_file_name)
 
-    def parse_config(
-        self, config_files: Optional[Tuple[str, ...]] = None
-    ) -> "ConfigFile":
+    def parse_config(self, config_files: Optional[Tuple[str, ...]] = None) -> "ConfigFile":
         return self.data.parse_config(config_files=config_files)
 
     @property
@@ -510,16 +505,12 @@ class AcquisitionAnalysisManager(AcquisitionManager):
     ):
         from ..utils import lint
 
-        allowed_variables = (
-            set() if allowed_variables is None else set(allowed_variables)
-        )
+        allowed_variables = set() if allowed_variables is None else set(allowed_variables)
         if init_file is not None:
             allowed_variables.update(lint.find_variables_from_file(init_file)[0])
         self._linting_external_vars = allowed_variables
 
-    def set_default_config_files(
-        self, config_files: Union[str, Tuple[str, ...], List[str]], /
-    ):
+    def set_default_config_files(self, config_files: Union[str, Tuple[str, ...], List[str]], /):
         self._default_config_files = (
             (config_files,) if isinstance(config_files, str) else tuple(config_files)
         )
@@ -566,7 +557,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
         if after_text is not None:
             if not isinstance(params, str):
                 raise ValueError(
-                    "Cannot use after_text with multiple params"
+                    "Cannot use after_text with multiple params. "
                     "Use params=[(param, after_text), ...] instead."
                 )
             return self.display_param_link(params=[(params, after_text)], title=title)
@@ -616,11 +607,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
                 self.update_config_params_on_disk({param: value})
 
             buttons = (
-                [
-                    display.buttons.create_button(
-                        update_value, param, value, name="Update"
-                    )
-                ]
+                [display.buttons.create_button(update_value, param, value, name="Update")]
                 if update_button
                 else None
             )
@@ -653,9 +640,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
 
     def connect_default_widget(
         self,
-        objs: Union[
-            "display_widget.WidgetProtocol", List["display_widget.WidgetProtocol"]
-        ],
+        objs: Union["display_widget.WidgetProtocol", List["display_widget.WidgetProtocol"]],
     ):
         if not isinstance(objs, (list, tuple)):
             objs = [objs]

labmate/acquisition_notebook/display_widget.py

@@ -4,6 +4,7 @@ from typing import TYPE_CHECKING, List, Optional, Protocol, TypeVar
 from .. import display as lm_display
 from ..display import platform_utils
 
+
 if TYPE_CHECKING:
     from labmate.acquisition_notebook import AcquisitionAnalysisManager
 
@@ -19,12 +20,11 @@ def _create_file_link(aqm: "AcquisitionAnalysisManager", level_up) -> str:
     filepath = _get_filepath(aqm)
     if filepath is None:
         return ""
-    link_name = os.path.basename(filepath)
-    link = "/".join(
-        os.path.abspath(filepath).replace("\\", "/").split("/")[-level_up:]
-    ).replace(" ", "%20")
-    link = f"[{link_name}](//kyrylo-gr.github.io/h5viewer/open?url={link})"
-    return link
+    link_name = os.path.basename(filepath)  # noqa: PTH119
+    link = "/".join(os.path.abspath(filepath).replace("\\", "/").split("/")[-level_up:]).replace(  # noqa: PTH100
+        " ", "%20"
+    )
+    return f"[{link_name}](//kyrylo-gr.github.io/h5viewer/open?url={link})"
 
 
 def display_widgets(objs: List["WidgetProtocol"], *args, **kwargs):
@@ -193,14 +193,14 @@ class OpenFinderButton(BaseWidget):
         import sys
 
         def open_finder():
-            path = os.path.abspath(filepath) + ".h5"
+            path = os.path.abspath(filepath) + ".h5"  # noqa: PTH100
             if sys.platform == "win32":
                 path = path.replace("/", "\\")
                 subprocess.run(["explorer", "/select,", path], shell=True)
             elif sys.platform == "darwin":
-                subprocess.Popen(["open", "-R", os.path.dirname(path)])
+                subprocess.Popen(["open", "-R", os.path.dirname(path)])  # noqa: PTH120
             else:
-                subprocess.Popen(["nautilus", "--select", os.path.dirname(path)])
+                subprocess.Popen(["nautilus", "--select", os.path.dirname(path)])  # noqa: PTH120
 
         self.widget = lm_display.buttons.create_button(open_finder, name="Open finder")
         return self.widget

labmate/attrdict/attrdict_class.py

@@ -92,21 +92,15 @@ class AttrDict(dict):
         keys_with_values = self.__get_value_for_output(keys)
         return utils_parse.format_title(keys_with_values, max_length=max_length)
 
-    def __get_value_for_output(
-        self, keys: List[str]
-    ) -> List[utils_parse.ValueForPrint]:
-        """Prepare the values for output. Returns list of ValueForPrint(key, value, unit, format))."""
+    def __get_value_for_output(self, keys: List[str]) -> List[utils_parse.ValueForPrint]:
+        """Prepare values for output. Returns list of ValueForPrint(key, value, unit, format)."""
         keys_with_values = []
         for key in keys:
             key_value, key_units, key_format = utils_parse.parse_get_format(key)
             if key_value in self:
                 keys_with_values.append(
-                    utils_parse.ValueForPrint(
-                        key_value, self[key_value], key_units, key_format
-                    )
+                    utils_parse.ValueForPrint(key_value, self[key_value], key_units, key_format)
                 )
             else:
-                raise ValueError(
-                    f"Cannot find key={key} inside {self.__class__.__name__}"
-                )
+                raise ValueError(f"Cannot find key={key} inside {self.__class__.__name__}")
         return keys_with_values

labmate/display/__init__.py

@@ -10,6 +10,7 @@ from .main import (
     logger,
 )
 
+
 __all__ = ["links", "buttons", "logger", "html_output"]
 
 
@@ -20,9 +21,7 @@ class _LazyModule:
 
     def __getattr__(self, name):
         if self.__module is None:
-            self.__module = importlib.import_module(
-                f".{self.__name}", package=__package__
-            )
+            self.__module = importlib.import_module(f".{self.__name}", package=__package__)
         return getattr(self.__module, name)
 
     # @property

labmate/display/buttons.py

@@ -4,6 +4,7 @@ from typing import TypeVar
 
 from .main import display, widgets
 
+
 # from functools import wraps
 # def add_display_method(func):
 #     """If a function changes the data it should be saved.

labmate/display/links.py

@@ -23,5 +23,6 @@ def create_link(
     after_text = after_text if after_text else ""
     return (
         f"<a href='{file}:{line_no}' target='_blank' style='margin: 0!; padding:0!;'>"
-        f"{link_text}</a> {after_text}"
+        f"{link_text}"
+        f"</a> {after_text}"
     )

labmate/display/main.py

@@ -4,6 +4,7 @@ import logging
 import sys
 from typing import Callable, List
 
+
 logging.basicConfig(format="%(levelname)s:%(message)s", level=logging.WARNING)
 logger = logging.getLogger(__name__)
 handler = logging.StreamHandler()
@@ -28,13 +29,13 @@ except (ImportError, AttributeError):
     # For testing purposes every IPython function should have a simpler version.
     # pylint: disable=C0115, C0103, R0903
 
-    def HTML(text):  # noqa: D103
+    def HTML(text):  # noqa: D103, N802
         return text
 
     def display(text):  # noqa: D103
         logger.info(text)
 
-    class widgets:  # noqa: D101
+    class widgets:  # noqa: D101, N801
         class Button:  # noqa: D106
             func: str
             description: str

labmate/display/platform_utils/__init__.py

@@ -2,9 +2,11 @@
 
 The goal it to have a single interface for all such functions.
 """
+
 import os
-import sys
 import subprocess
+import sys
+
 
 if os.name == "nt":
     from . import windows_utils as current_utils

labmate/display/platform_utils/windows_utils.py

@@ -1,9 +1,7 @@
 """This submodule contains functions that are specific for windows."""
 
 
-def copy_fig(
-    fig=None, format_=None, text_to_copy=None, **kwargs
-):  # pragma: no cover <--
+def copy_fig(fig=None, format_=None, text_to_copy=None, **kwargs):  # pragma: no cover <--
     """Copy fig to the clipboard.
 
     Parameters
@@ -73,9 +71,7 @@ def copy_fig(
                 im = Image.open(buf)
                 with BytesIO() as output:
                     im.convert("RGB").save(output, "BMP")
-                    data = output.getvalue()[
-                        14:
-                    ]  # The file header off-set of BMP is 14 bytes
+                    data = output.getvalue()[14:]  # The file header off-set of BMP is 14 bytes
                     format_id = win32clipboard.CF_DIB  # DIB = device independent bitmap
 
             except ImportError:
@@ -89,8 +85,6 @@ def copy_fig(
     win32clipboard.EmptyClipboard()
     win32clipboard.SetClipboardData(format_id, data)
     if text_to_copy:
-        win32clipboard.SetClipboardData(
-            win32clipboard.CF_TEXT, text_to_copy.encode("utf-8")
-        )
+        win32clipboard.SetClipboardData(win32clipboard.CF_TEXT, text_to_copy.encode("utf-8"))
 
     win32clipboard.CloseClipboard()

labmate/parsing/__init__.py

@@ -10,10 +10,11 @@ Examples:
 
 
 """
+
 from typing import Dict
 
-from .parsed_value import ParsedValue
 from .brackets_score import BracketsScore
+from .parsed_value import ParsedValue
 
 
 def parse_str(file: str, /) -> Dict[str, ParsedValue]:
@@ -36,10 +37,7 @@ def parse_str(file: str, /) -> Dict[str, ParsedValue]:
         if not brackets.is_zero():
             continue
 
-        if "# value: " in value:
-            value_eval = value[value.rfind("# value: ") + 9 :]
-        else:
-            value_eval = None
+        value_eval = value[value.rfind("# value: ") + 9 :] if ("# value: " in value) else None
 
         value = value.split("#")[0].strip()
 

labmate/parsing/parsed_value.py

@@ -2,6 +2,8 @@
 
 from typing import Any, Union
 
+import numpy as np
+
 
 def parse_value(value: str) -> Union[str, int, float]:
     """Convert str to int or float if possible."""
@@ -16,14 +18,14 @@ def parse_value(value: str) -> Union[str, int, float]:
             value_without_underscores[0] == "-" and value[1:].isdigit()
         ):
             return int(value)
-        elif value_without_underscores.replace(".", "").isdigit() or (
-            value[0] == "-" and value_without_underscores[1:].replace(".", "").isdigit()
-        ):
-            return float(value)
         elif (
-            (value[0].isdigit() or (value[0] == "-" and value[1].isdigit()))
-            and value[-1].isdigit()
-            and "e" in value
+            value_without_underscores.replace(".", "").isdigit()
+            or (value[0] == "-" and value_without_underscores[1:].replace(".", "").isdigit())
+            or (
+                (value[0].isdigit() or (value[0] == "-" and value[1].isdigit()))
+                and value[-1].isdigit()
+                and "e" in value
+            )
         ):
             return float(value)
     except ValueError:
@@ -44,9 +46,11 @@ class ParsedValue:
 
     Examples:
         >>> v1 = ParsedValue("1", 1)
-        >>> v2 = ParsedValue("2", 2)
+        >>> v2 = ParsedValue("6/3", 2)
         >>> v1 + v2
         3
+        >>> v2.unpack()
+        ('6/3', 2)
 
     """
 
@@ -63,8 +67,11 @@ class ParsedValue:
         self.original = parse_value(original)
         self.value = parse_value(value)
 
-    def __iter__(self):
-        return iter((self.original, self.value))
+    # def __iter__(self):
+    #     return iter((self.original, self.value))
+
+    def unpack(self):
+        return self.original, self.value
 
     def __str__(self) -> str:
         return str(self.value)
@@ -81,9 +88,18 @@ class ParsedValue:
     def __abs__(self) -> float:
         return abs(self.value)  # type: ignore
 
+    def __int__(self) -> int:
+        return int(self.value)  # type: ignore
+
     def __float__(self) -> float:
         return float(self.value)  # type: ignore
 
+    def __array__(self, dtype=None, **kwargs):
+        # So numpy/matplotlib can use it: np.asarray(obj) works
+        if dtype is not None:
+            return np.array(self.value, dtype=dtype, **kwargs)
+        return np.array(self.value, **kwargs)
+
     def __neg__(self) -> float:
         return -self.value  # type: ignore
 
@@ -195,3 +211,7 @@ class ParsedValue:
         if isinstance(other, ParsedValue):
             return other.value
         return other
+
+    def __hash__(self) -> int:
+        return hash(self.value)
+        # return hash((self.original, self.value))

labmate/parsing/saving.py

@@ -27,9 +27,7 @@ def append_values_from_modules_to_files(
     return configs
 
 
-def append_values_from_module_to_file(
-    body: str, module, separator="  # value: "
-) -> str:
+def append_values_from_module_to_file(body: str, module, separator="  # value: ") -> str:
     """Add values from a module to a given file body.
 
     Args:
@@ -68,9 +66,7 @@ def append_values_from_module_to_file(
         for key, (val, _) in parse_str(line).items():
             real_val = variables.get(key, "")
             if (
-                isinstance(val, str)
-                and isinstance(real_val, str)
-                and real_val != val.strip("\"'")
+                isinstance(val, str) and isinstance(real_val, str) and real_val != val.strip("\"'")
             ) or (
                 isinstance(val, str)
                 and isinstance(real_val, (float, int, complex))

labmate/utils/async_utils.py

@@ -1,4 +1,5 @@
 """Async utilities."""
+
 from dh5.utils.async_utils import (  # pylint: disable=unused-import # noqa: F401
     sleep,
 )

labmate/utils/autoreload.py

@@ -12,8 +12,10 @@ import labmate.utils.autoreload
 ```
 
 """
+
 from IPython.core.getipython import get_ipython
 
+
 shell = get_ipython()
 if shell:
     shell.run_cell("%load_ext autoreload")

labmate/utils/file_read.py

@@ -1,8 +1,8 @@
 """Different method to read files."""
 
 import json
-import os
 import re
+from pathlib import Path
 from typing import Any, Dict, List, Optional
 
 from ..parsing.brackets_score import BracketsScore
@@ -20,13 +20,13 @@ def read_file(file: str, /) -> str:
     Raises:
         ValueError: If the file does not exist or is not a file.
     """
-    if not os.path.isfile(file):
+    if not Path(file).is_file():
         raise ValueError(
-            "Cannot read a file if it doesn't exist or it's not a file."
-            f"Path: {os.path.abspath(file)}"
+            "Cannot read a file if it doesn't exist or it's not a file. "
+            f"Path: {Path(file).absolute()}"
         )
 
-    with open(file, "r", encoding="utf-8") as file_opened:
+    with open(file, encoding="utf-8") as file_opened:
         return file_opened.read()
 
 
@@ -40,15 +40,16 @@ def read_files(files: List[str], /) -> Dict[str, str]:
         A dictionary where the keys are the file names and the values are the contents of the files.
 
     Raises:
-        ValueError: If some of the files have the same name, which would cause a key collision in the dictionary.
+        ValueError: If some of the files have the same name,
+            which would cause a key collision in the dict.
     """
     configs: Dict[str, str] = {}
     for config_file in files:
-        config_file_name = os.path.basename(config_file)
+        config_file_name = Path(config_file).name
         if config_file_name in configs:
             raise ValueError(
-                "Some of the files have the same name. So it cannot be pushed into dictionary to"
-                " preserve unique key"
+                "Some of the files have the same name. "
+                "So it cannot be pushed into dict to preserve unique key"
             )
         configs[config_file_name] = read_file(config_file)
     return configs
@@ -62,7 +63,7 @@ def update_file_variable(file, params: Dict[str, Any]):
         file (str): The path to the file to update.
         params (Dict[str, Any]): The parameters to update the file with.
     """
-    with open(file, "r", encoding="utf-8") as file_opened:
+    with open(file, encoding="utf-8") as file_opened:
         lines = file_opened.readlines()
     brackets = BracketsScore()
     current_param: Optional[str] = None
@@ -87,9 +88,7 @@ def update_file_variable(file, params: Dict[str, Any]):
             value_str = json.JSONEncoder().encode(params[current_param])
 
             print("value_str", value_str)
-            if re.match(
-                r"^['\"]?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?['\"]?$", value_str
-            ):
+            if re.match(r"^['\"]?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?['\"]?$", value_str):
                 value_str = value_str.replace('"', "")
 
             lines.insert(