labmate 0.8.3__tar.gz → 0.8.4__tar.gz

{labmate-0.8.3/labmate.egg-info → labmate-0.8.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: labmate
-Version: 0.8.3
+Version: 0.8.4
 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-0.8.3 → labmate-0.8.4}/labmate/__config__.py

@@ -1,3 +1,3 @@
 """This file contains all package constants."""
 
-__version__ = "0.8.3"
+__version__ = "0.8.4"

{labmate-0.8.3 → labmate-0.8.4}/labmate/acquisition/acquisition_data.py

@@ -1,9 +1,10 @@
 """Module that contains NotebookAcquisitionData class."""
+
 from typing import Dict, List, Optional, Union
 
 from dh5 import DH5
-from ..utils.file_read import read_files
 
+from ..utils.file_read import read_files
 from .logger_setup import logger
 
 
@@ -14,6 +15,9 @@ class NotebookAcquisitionData(DH5):
     `cell` is a str. It saves using `save_cell` function that will save it to `..._CELL.py` file
     """
 
+    _current_step: int
+    _cells: Dict[int, Optional[str]]
+
     def __init__(
         self,
         filepath: str,
@@ -58,10 +62,11 @@ class NotebookAcquisitionData(DH5):
         self._config = configs
         self.save_configs()
 
-        self._cell = cell
-        self.save_cell(cell=cell)
+        self._cells = {1: cell}
+        self.save_cell(cell=cell, suffix="1")
 
         self.experiment_name = experiment_name
+        self.current_step = 1
 
         self["useful"] = False
 
@@ -95,7 +100,12 @@ class NotebookAcquisitionData(DH5):
             with open(filepath + "_" + name, "w", encoding="utf-8") as file:
                 file.write(value)
 
-    def save_cell(self, cell: Optional[str] = None, filepath: Optional[str] = None):
+    def save_cell(
+        self,
+        cell: Optional[str] = None,
+        filepath: Optional[str] = None,
+        suffix: Optional[str] = None,
+    ):
         """Save the cell code to the h5 file and possibly to a file.
 
         If `save_files` during init was set to True, then it will create a '.py' file near
@@ -108,14 +118,15 @@ class NotebookAcquisitionData(DH5):
              the desired location, i.e. it should end with the file prefix to which the suffix and
              'py' extension will be added. Defaults to save filepath as h5 file.
         """
-        cell = cell or self._cell
         if cell == "none":
             return
         if cell is None or cell == "":
             logger.warning("Acquisition cell is not set. Nothing to save")
             return
-
-        self["acquisition_cell"] = cell
+        if suffix is not None:
+            self[f"acquisition_cell/{suffix}"] = cell
+        else:
+            self["acquisition_cell/0"] = cell
 
         if not self._save_files:
             return
@@ -124,13 +135,26 @@ class NotebookAcquisitionData(DH5):
         with open(filepath + "_CELL.py", "w", encoding="utf-8") as file:
             file.write(cell)
 
+    def save_cells(
+        self,
+        cells: Optional[Dict[int, Optional[str]]] = None,
+        filepath: Optional[str] = None,
+    ):
+        """Save all sells that are provided or pushed into self._cells array."""
+        cells = cells or self._cells
+        # if len(cells) == 1:
+        #     self.save_cell(cells.popitem()[1], filepath)
+        #     return
+        for i, cell in cells.items():
+            self.save_cell(cell, filepath, suffix=str(i))
+
     def save_additional_info(self):
         """Save all additional information, i.e. cell code, configs. Put useful key to True."""
         self["useful"] = True
 
         if not self._save_files:
             return
-        self.save_cell()
+        self.save_cells()
         self.save_configs()
 
     def save_acquisition(self, **kwds) -> "NotebookAcquisitionData":
@@ -140,3 +164,18 @@ class NotebookAcquisitionData(DH5):
         if self.save_on_edit is False:
             self.save()
         return self
+
+    @property
+    def current_step(self):
+        """Return the current step of the acquisition."""
+        return self._current_step
+
+    @current_step.setter
+    def current_step(self, value: int):
+        self._current_step = value
+
+    def set_cell(self, cell: Optional[str], step: Optional[int] = None):
+        """Set the cell code."""
+        if step is None:
+            step = self.current_step
+        self._cells[step] = cell

{labmate-0.8.3 → labmate-0.8.4}/labmate/acquisition/acquisition_loop.py

@@ -185,9 +185,7 @@ class AcquisitionLoop(DH5):
                 )
                 self[key][iteration] = value
         else:
-            if isinstance(value, (complex, np.complex_)) or (  # type: ignore
-                isinstance(value, (np.ndarray,)) and value.dtype == np.complex_
-            ):
+            if np.iscomplexobj(value):
                 self[key] = SyncNp(np.zeros(key_shape, dtype=np.complex128))
             else:
                 self[key] = SyncNp(np.zeros(key_shape))

{labmate-0.8.3 → labmate-0.8.4}/labmate/acquisition/acquisition_manager.py

@@ -132,6 +132,9 @@ class AcquisitionManager:
             filename = [str(filename)]
 
         self.config_files = list(filename)
+        self._config_files_names_to_path = {
+            os.path.basename(file): file for file in self.config_files
+        }
 
         for config_file in self.config_files:
             if not os.path.exists(config_file):

{labmate-0.8.3 → labmate-0.8.4}/labmate/acquisition_notebook/acquisition_analysis_manager.py

@@ -290,6 +290,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
         cell: Optional[str] = None,
         prerun: Optional[Union[_CallableWithNoArgs, List[_CallableWithNoArgs]]] = None,
         save_on_edit: Optional[bool] = None,
+        step: int = 1,
     ) -> "AcquisitionAnalysisManager":
         self._analysis_cell_str = None
         self._analysis_data = None
@@ -297,8 +298,19 @@ class AcquisitionAnalysisManager(AcquisitionManager):
         self._acquisition_started = time.time()
 
         cell = cell or get_current_cell(self.shell)
-
-        self.new_acquisition(name=name, cell=cell, save_on_edit=save_on_edit)
+        if step != 1 and self._current_acquisition is not None:
+            if self._current_acquisition.experiment_name != name:
+                raise ValueError(
+                    f"Current acquisition ('{self.current_experiment_name}') "
+                    f"isn't the one expected ('{name}') for this acquisition. "
+                    f"Possible solutions: run acquisition '{name}' with step 1; "
+                    f"or change current acquisition name to '{self.current_experiment_name}'"
+                )
+            self._current_acquisition.current_step = step
+            self._current_acquisition.set_cell(cell, step=step)
+            self._current_acquisition.save_cell(cell, suffix=str(step))
+        else:
+            self.new_acquisition(name=name, cell=cell, save_on_edit=save_on_edit)
 
         logger.info(self.current_filepath.basename)
 
@@ -528,6 +540,7 @@ class AcquisitionAnalysisManager(AcquisitionManager):
                 )
                 continue
             file, line_no = res
+            file = self._config_files_names_to_path.get(file, file)
             link = display.links.create_link(param_text, file, line_no, after_text)
             links += link + "<br/>"
         return display.display_html(links)

{labmate-0.8.3 → labmate-0.8.4/labmate.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: labmate
-Version: 0.8.3
+Version: 0.8.4
 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