labmate 0.10.2__tar.gz → 0.10.3__tar.gz

{labmate-0.10.2/labmate.egg-info → labmate-0.10.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: labmate
-Version: 0.10.2
+Version: 0.10.3
 Summary: Data management library to save data and plots to hdf5 files
 Home-page: https://github.com/kyrylo-gr/labmate
 Author: kyrylo.gr | LKB-OMQ

{labmate-0.10.2 → labmate-0.10.3}/labmate/__config__.py

@@ -1,3 +1,3 @@
 """This file contains all package constants."""
 
-__version__ = "0.10.2"
+__version__ = "0.10.3"

{labmate-0.10.2 → labmate-0.10.3}/labmate/acquisition/acquisition_manager.py

@@ -167,18 +167,22 @@ class AcquisitionManager:
         experiment_path = Path(data_directory) / str(dic.experiment_name)
         if not experiment_path.exists():
             experiment_path.makedirs()
+        # Copy init_analyses code to the experiment directory if it does not exist
         if self._init_code and not os.path.exists(experiment_path / "init_analyse.py"):
             with open(
                 experiment_path / "init_analyse.py", "w", encoding="utf-8"
             ) as file:
                 file.write(self._init_code)
+
         filepath_original = filepath = (
             experiment_path / f"{dic.time_stamp}__{dic.experiment_name}"
         )
+
+        # If ignore existence is True, no check is required
         if ignore_existence:
             return filepath
-
-        index = 0
+        # If the file already exists, add a suffix to the name
+        index = 1
         while os.path.exists(filepath + ".h5"):
             filepath = filepath_original + f"__{index}"
             index += 1
@@ -307,7 +311,7 @@ class AcquisitionManager:
             experiment_name=acquisition_tmp_data.experiment_name,
         )
 
-    def save_acquisition(self, **kwds) -> "AcquisitionManager":
+    def save_acquisition(self, update_: bool = True, /, **kwds) -> "AcquisitionManager":
         acq_data = self.current_acquisition
         if acq_data is None:
             raise ValueError(
@@ -315,6 +319,10 @@ class AcquisitionManager:
                 Possibly because you have never run `acquisition_cell(..)` or it's an old data"
                 ""
             )
+        if update_ is False:
+            for key in list(kwds.keys()):
+                if key in acq_data:
+                    del kwds[key]
 
         acq_data.update(**kwds)
         acq_data.save_additional_info()

{labmate-0.10.2 → labmate-0.10.3}/labmate/acquisition/analysis_data.py

@@ -81,6 +81,7 @@ class AnalysisData(DH5):
         save_files: bool = False,
         save_on_edit: bool = True,
         save_fig_inside_h5: bool = False,
+        open_on_init: Optional[bool] = None,
     ):
         """Load data from a filepath and lock it to prevent any changes.
 
@@ -106,6 +107,7 @@ class AnalysisData(DH5):
             overwrite=False,
             read_only=False,
             save_on_edit=save_on_edit,
+            open_on_init=open_on_init,
         )
 
         self.lock_data()
@@ -305,16 +307,16 @@ class AnalysisData(DH5):
                         key_value, filename, key_units, key_format
                     )
                 )
-            elif key_value in config_data:
+            elif key_value in self:
                 keys_with_values.append(
                     utils.title_parsing.ValueForPrint(
-                        key_value, config_data[key_value], key_units, key_format
+                        key_value, self[key_value], key_units, key_format
                     )
                 )
-            elif key_value in self:
+            elif key_value in config_data:
                 keys_with_values.append(
                     utils.title_parsing.ValueForPrint(
-                        key_value, self[key_value], key_units, key_format
+                        key_value, config_data[key_value], key_units, key_format
                     )
                 )
             else:
@@ -382,7 +384,11 @@ class AnalysisData(DH5):
         )
 
     def get_analysis_code(
-        self, name: str = "default", /, update_code: bool = True
+        self,
+        name: str = "default",
+        /,
+        update_code: bool = True,
+        replace: Optional[dict] = None,
     ) -> str:
         code: Optional[dict] = self.get("analysis_cells")
         if code is None:
@@ -403,6 +409,9 @@ class AnalysisData(DH5):
             code_str = code_str.replace(
                 "aqm.analysis_cell()", f"aqm.analysis_cell('{self.filepath}')"
             )
+        if replace is not None:
+            for key, value in replace.items():
+                code_str = code_str.replace(key, value)
         return code_str
 
     def open_figs(self) -> list:

{labmate-0.10.2 → labmate-0.10.3}/labmate/acquisition_notebook/acquisition_analysis_manager.py

@@ -240,9 +240,11 @@ class AcquisitionAnalysisManager(AcquisitionManager):
                 "Cannot save data to acquisition as current acquisition is None."
                 "Possibly because you have never run `acquisition_cell(..)` or it's an old data"
             )
-        acq_data[__key] = __value
+        acq_data[__key] = __value  # pylint: disable=E1137
 
-    def save_acquisition(self, **kwds) -> "AcquisitionAnalysisManager":
+    def save_acquisition(
+        self, update_: bool = True, /, file_suffix: Optional[str] = None, **kwds
+    ) -> "AcquisitionAnalysisManager":
         acquisition_finished = time.time()
         if not self._once_saved:
             additional_info: Dict[str, Any] = {
@@ -255,10 +257,9 @@ class AcquisitionAnalysisManager(AcquisitionManager):
                 additional_info.update(
                     {"default_config_files": self._default_config_files}
                 )
-
             kwds.update({"info": additional_info})
 
-        super().save_acquisition(**kwds)
+        super().save_acquisition(update_, file_suffix=file_suffix, **kwds)
         self._load_analysis_data()
         return self
 
@@ -273,6 +274,23 @@ class AcquisitionAnalysisManager(AcquisitionManager):
         return self._analysis_data
 
     def load_file(self, filename) -> "AnalysisData":
+        """
+        Loads an analysis data file.
+
+        Args:
+            filename (str): The name of the file to load.
+
+        Returns:
+            AnalysisData: An instance of AnalysisData containing the loaded data.
+
+        Raises:
+            ValueError: If the file cannot be found.
+
+        Notes:
+            - The method checks if the file exists with a ".h5" extension.
+            - If the data does not have a "useful" attribute set to True, it updates this attribute.
+            - 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"
@@ -284,6 +302,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
             save_files=self._save_files,
             save_on_edit=self._save_on_edit_analysis,
             save_fig_inside_h5=self._save_fig_inside_h5,
+            open_on_init=False,
         )
 
         if not data.get("useful", True):
@@ -308,7 +327,16 @@ class AcquisitionAnalysisManager(AcquisitionManager):
         self._acquisition_started = time.time()
 
         cell = cell or get_current_cell(self.shell)
-        if step != 1 and self._current_acquisition is not None:
+        if step == 1:
+            self.logger.reset()
+            self.new_acquisition(name=name, cell=cell, save_on_edit=save_on_edit)
+        elif self._current_acquisition is None:
+            raise ValueError("Acquisition should start from step 1")
+        elif self._current_acquisition.current_step == step:
+            raise ValueError(
+                "This step was already run. Please run the next step or restart from step 1"
+            )
+        else:
             if self._current_acquisition.experiment_name != name:
                 raise ValueError(
                     f"Current acquisition ('{self.current_experiment_name}') "
@@ -326,9 +354,6 @@ class AcquisitionAnalysisManager(AcquisitionManager):
                     "Please rerun the acquisition from the first step."
                 )
             self.logger.stdout_flush()
-        else:
-            self.logger.reset()
-            self.new_acquisition(name=name, cell=cell, save_on_edit=save_on_edit)
 
         self.logger.info(  # pylint: disable=W1203
             f"{step}:{self.current_filepath.basename}"
@@ -571,6 +596,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
     def display_cfg_link(
         self,
         parameters: Dict[str, Any],
+        update_button: bool = False,
     ):
         from labmate.display import html_output
 
@@ -589,9 +615,15 @@ class AcquisitionAnalysisManager(AcquisitionManager):
             def update_value(param, value):
                 self.update_config_params_on_disk({param: value})
 
-            buttons = [
-                display.buttons.create_button(update_value, param, value, name="Update")
-            ]
+            buttons = (
+                [
+                    display.buttons.create_button(
+                        update_value, param, value, name="Update"
+                    )
+                ]
+                if update_button
+                else None
+            )
 
             link = html_output.create_link_row(
                 link_text=f"{param} = ",

{labmate-0.10.2 → labmate-0.10.3}/labmate/display/main.py

@@ -24,7 +24,7 @@ try:
 
     display = display.display_functions.display
 
-except ImportError:
+except (ImportError, AttributeError):
     # For testing purposes every IPython function should have a simpler version.
     # pylint: disable=C0115, C0103, R0903
 
@@ -56,8 +56,8 @@ except ImportError:
         class CoreWidget:  # noqa: D106
             pass
 
-        class Layout:
-            def __init__(self, *args, **kwargs) -> None:
+        class Layout:  # noqa: D106
+            def __init__(self, *args, **kwargs) -> None:  # noqa: D107
                 del args, kwargs
 
     # pylint: enable=C0115, C0103, R0903

{labmate-0.10.2 → labmate-0.10.3}/labmate/parsing/parsed_value.py

@@ -84,6 +84,9 @@ class ParsedValue:
     def __float__(self) -> float:
         return float(self.value)  # type: ignore
 
+    def __neg__(self) -> float:
+        return -self.value  # type: ignore
+
     def __add__(self, other):
         other = self._convert_other(other)
         return self.value + other

{labmate-0.10.2 → labmate-0.10.3}/labmate/utils/file_read.py

@@ -67,6 +67,7 @@ def update_file_variable(file, params: Dict[str, Any]):
     brackets = BracketsScore()
     current_param: Optional[str] = None
     # print(lines)
+    start_line = 0
     for line in lines:
         # print(line)
         if len(line) == 0:

{labmate-0.10.2 → labmate-0.10.3/labmate.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: labmate
-Version: 0.10.2
+Version: 0.10.3
 Summary: Data management library to save data and plots to hdf5 files
 Home-page: https://github.com/kyrylo-gr/labmate
 Author: kyrylo.gr | LKB-OMQ