[pre-commit.ci] pre-commit autoupdate

.gitignore

@@ -22,4 +22,4 @@ dist/*
 .pixi/*
 !.pixi/config.toml
 
-notebooks/pleiades_logs
+notebooks/pleiades_logs

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: "^pixi.lock$"
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-added-large-files
         args: [--maxkb=8192]
@@ -16,21 +16,21 @@ repos:
       - id: trailing-whitespace
         exclude: "notebooks/.*\\.ipynb$"
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.14.10
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
         exclude: "notebooks/.*\\.ipynb$"
       - id: ruff-format
         exclude: "notebooks/.*\\.ipynb$"
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         exclude: "notebooks/.*\\.ipynb$"
         args: ["--skip=*.js,*.html,*.css"]
   - repo: https://github.com/adrienverge/yamllint
-    rev: v1.35.1
+    rev: v1.37.1
     hooks:
       - id: yamllint
   - repo: https://github.com/ComPWA/taplo-pre-commit

notebooks/__code/_utilities/array.py

@@ -33,7 +33,11 @@ def reject_outliers(array=None):
     if len(array) < 3:
         return array
 
-    new_array = [_value for _value in array if (not (_value == np.min(array))) and (not (_value == np.max(array)))]
+    new_array = [
+        _value
+        for _value in array
+        if (not (_value == np.min(array))) and (not (_value == np.max(array)))
+    ]
     return new_array
 
 

notebooks/__code/_utilities/file.py

@@ -192,7 +192,9 @@ def make_or_increment_folder_name(folder_name):
     if not os.path.exists(folder_name):
         os.makedirs(folder_name)
     else:
-        new_folder_name = "_".join([folder_name, get_current_time_in_special_file_name_format()])
+        new_folder_name = "_".join(
+            [folder_name, get_current_time_in_special_file_name_format()]
+        )
         if os.path.exists(new_folder_name):
             os.removedirs(new_folder_name)
         os.makedirs(new_folder_name)
@@ -205,7 +207,9 @@ def copy_files_to_folder(list_files=[], output_folder=""):
         shutil.copy(_file, output_folder)
 
 
-def copy_and_rename_files_to_folder(list_files=[], new_list_files_names=[], output_folder=""):
+def copy_and_rename_files_to_folder(
+    list_files=[], new_list_files_names=[], output_folder=""
+):
     for _index_file, _original_file in enumerate(list_files):
         _new_file = os.path.join(output_folder, new_list_files_names[_index_file])
         shutil.copy(_original_file, _new_file)
@@ -250,7 +254,9 @@ def append_to_file(data=[], output_file_name=""):
             f.write(_line + "\n")
 
 
-def make_ascii_file_from_2dim_array(metadata=None, col1=None, col2=None, output_file_name=None, sep=", "):
+def make_ascii_file_from_2dim_array(
+    metadata=None, col1=None, col2=None, output_file_name=None, sep=", "
+):
     with open(output_file_name, "w") as f:
         for _meta in metadata:
             _line = _meta + "\n"
@@ -315,7 +321,9 @@ def retrieve_metadata_from_dsc_list_files(list_files=[]):
 
     metadata = {}
     for _index, _file in enumerate(list_files):
-        metadata[os.path.basename(_file)] = retrieve_metadata_from_dsc_file(filename=_file)
+        metadata[os.path.basename(_file)] = retrieve_metadata_from_dsc_file(
+            filename=_file
+        )
         w.value = _index + 1
 
     return metadata
@@ -426,7 +434,9 @@ def retrieve_time_stamp(list_images, label=""):
     box = widgets.HBox(
         [
             widgets.Label(message, layout=widgets.Layout(width="20%")),
-            widgets.IntProgress(min=0, max=len(list_images), value=0, layout=widgets.Layout(width="50%")),
+            widgets.IntProgress(
+                min=0, max=len(list_images), value=0, layout=widgets.Layout(width="50%")
+            ),
         ]
     )
     progress_bar = box.children[1]
@@ -494,21 +504,33 @@ def read_bragg_edge_fitting_ascii_format(full_file_name):
                 regular = r"^#fitting peak range in file index: \[(?P<left_index>\d+), (?P<right_index>\d+)\]$"
                 m = re.search(regular, line.strip())
                 if m:
-                    metadata["bragg_edge_range"] = [int(m.group("left_index")), int(m.group("right_index"))]
+                    metadata["bragg_edge_range"] = [
+                        int(m.group("left_index")),
+                        int(m.group("right_index")),
+                    ]
                 else:
                     metadata["bragg_edge_range"] = [None, None]
                 line_number += 1
                 continue
             if "#distance detector-sample: " in line:
-                metadata["distance_detector_sample"] = line.split("#distance detector-sample: ")[1].strip()
+                metadata["distance_detector_sample"] = line.split(
+                    "#distance detector-sample: "
+                )[1].strip()
                 line_number += 1
                 continue
             if "#detector offset: " in line:
-                metadata["detector_offset"] = line.split("#detector offset: ")[1].strip()
+                metadata["detector_offset"] = line.split("#detector offset: ")[
+                    1
+                ].strip()
                 line_number += 1
                 continue
             if "#kropff fitting procedure started: " in line:
-                result = True if line.split("#kropff fitting procedure started: ")[1].strip() == "True" else False
+                result = (
+                    True
+                    if line.split("#kropff fitting procedure started: ")[1].strip()
+                    == "True"
+                    else False
+                )
                 metadata["kropff fitting procedure started"] = result
                 line_number += 1
                 continue
@@ -524,7 +546,12 @@ def read_bragg_edge_fitting_ascii_format(full_file_name):
                 continue
             if "#march-dollase fitting procedure started: " in line:
                 result = (
-                    True if line.split("#march-dollase fitting procedure started: ")[1].strip() == "True" else False
+                    True
+                    if line.split("#march-dollase fitting procedure started: ")[
+                        1
+                    ].strip()
+                    == "True"
+                    else False
                 )
                 metadata["march-dollase fitting procedure started"] = result
                 line_number += 1
@@ -533,11 +560,17 @@ def read_bragg_edge_fitting_ascii_format(full_file_name):
                 regular = r"^#Bragg peak selection range: \[(?P<left_index>\d+), (?P<right_index>\d+)\]$"
                 m = re.search(regular, line.strip())
                 if m:
-                    metadata["bragg_peak_selection_range"] = [int(m.group("left_index")), int(m.group("right_index"))]
+                    metadata["bragg_peak_selection_range"] = [
+                        int(m.group("left_index")),
+                        int(m.group("right_index")),
+                    ]
                 line_number += 1
                 continue
             if "#kropff " in line:
-                regular = r"^#kropff (?P<type>\w+) selection range: \[(?P<left_index>\d+), " r"(?P<right_index>\d+)\]$"
+                regular = (
+                    r"^#kropff (?P<type>\w+) selection range: \[(?P<left_index>\d+), "
+                    r"(?P<right_index>\d+)\]$"
+                )
                 m = re.search(regular, line.strip())
                 if m:
                     metadata["kropff_{}".format(m.group("type"))] = [
@@ -547,17 +580,23 @@ def read_bragg_edge_fitting_ascii_format(full_file_name):
                 line_number += 1
                 continue
             if "#fitting algorithm selected: " in line:
-                metadata["fitting_algorithm_selected"] = line.split("#fitting algorithm selected: ")[1].strip()
+                metadata["fitting_algorithm_selected"] = line.split(
+                    "#fitting algorithm selected: "
+                )[1].strip()
                 line_number += 1
                 continue
             if "#march-dollase history table row " in line:
-                _row_and_list_flag = line.split("#march-dollase history table row ")[1].strip()
+                _row_and_list_flag = line.split("#march-dollase history table row ")[
+                    1
+                ].strip()
                 [_row, list_flag] = _row_and_list_flag.split(":")
                 march_history_table[_row] = list_flag
                 line_number += 1
                 continue
             if "#march-dollase history init " in line:
-                _parameter_and_value = line.split("#march-dollase history init ")[1].strip()
+                _parameter_and_value = line.split("#march-dollase history init ")[
+                    1
+                ].strip()
                 [_parameter, _value] = _parameter_and_value.split(":")
                 march_history_init[_parameter] = _value
                 line_number += 1
@@ -648,7 +687,9 @@ def read_bragg_edge_fitting_ascii_format(full_file_name):
         metadata["march-dollase history table"] = march_history_table
         metadata["march-dollase history init"] = march_history_init
 
-    pd_data = pd.read_csv(full_file_name, skiprows=line_number, header=0, names=col_label)
+    pd_data = pd.read_csv(
+        full_file_name, skiprows=line_number, header=0, names=col_label
+    )
     return {"data": pd_data, "metadata": metadata}
 
 
@@ -661,7 +702,9 @@ def __init__(self, working_dir=""):
     def get_list_of_files(self):
         list_of_input_files = glob.glob(os.path.join(self.working_dir, "*"))
         list_of_input_files.sort()
-        self.list_of_base_name = [os.path.basename(_file) for _file in list_of_input_files]
+        self.list_of_base_name = [
+            os.path.basename(_file) for _file in list_of_input_files
+        ]
 
     def get_counter_of_extension(self):
         counter_extension = Counter()
@@ -686,7 +729,11 @@ def get_dominant_extension(self):
 
     def check_uniqueness_of_dominant_extension(self):
         # check if there are several ext with the same max number
-        indices = [i for i, x in enumerate(self.list_of_number_of_ext) if x == self.dominant_number]
+        indices = [
+            i
+            for i, x in enumerate(self.list_of_number_of_ext)
+            if x == self.dominant_number
+        ]
         if len(indices) > 1:  # found several majority ext
             self.uniqueness = False
         else:
@@ -701,21 +748,34 @@ def calculate(self):
 
     def retrieve_parameters(self):
         if self.uniqueness:
-            list_of_input_files = glob.glob(os.path.join(self.working_dir, "*" + self.dominant_extension))
+            list_of_input_files = glob.glob(
+                os.path.join(self.working_dir, "*" + self.dominant_extension)
+            )
             list_of_input_files.sort()
 
-            self.result = self.Result(list_files=list_of_input_files, ext=self.dominant_extension, uniqueness=True)
+            self.result = self.Result(
+                list_files=list_of_input_files,
+                ext=self.dominant_extension,
+                uniqueness=True,
+            )
 
         else:
             list_of_maj_ext = [
-                _ext for _ext in self.counter_extension.keys() if self.counter_extension[_ext] == self.dominant_number
+                _ext
+                for _ext in self.counter_extension.keys()
+                if self.counter_extension[_ext] == self.dominant_number
             ]
 
             box = widgets.HBox(
                 [
-                    widgets.Label("Select Extension to work with", layout=widgets.Layout(width="20%")),
+                    widgets.Label(
+                        "Select Extension to work with",
+                        layout=widgets.Layout(width="20%"),
+                    ),
                     widgets.Dropdown(
-                        options=list_of_maj_ext, layout=widgets.Layout(width="20%"), value=list_of_maj_ext[0]
+                        options=list_of_maj_ext,
+                        layout=widgets.Layout(width="20%"),
+                        value=list_of_maj_ext[0],
                     ),
                 ]
             )
@@ -728,7 +788,13 @@ def get_files_of_selected_ext(self):
 
         else:
             _ext_selected = self.dropdown_ui.value
-            list_of_input_files = glob.glob(os.path.join(self.working_dir, "*" + _ext_selected))
+            list_of_input_files = glob.glob(
+                os.path.join(self.working_dir, "*" + _ext_selected)
+            )
             list_of_input_files.sort()
 
-            return self.Result(list_files=list_of_input_files, ext=self.dominant_extension, uniqueness=True)
+            return self.Result(
+                list_files=list_of_input_files,
+                ext=self.dominant_extension,
+                uniqueness=True,
+            )

notebooks/__code/_utilities/folder.py

@@ -5,7 +5,9 @@
 import numpy as np
 
 
-def get_list_of_folders_with_specified_file_type(list_of_folders_to_check=None, file_extension=["tiff", "tif"]):
+def get_list_of_folders_with_specified_file_type(
+    list_of_folders_to_check=None, file_extension=["tiff", "tif"]
+):
     """
     check in the list of folder given (list_of_folders_to_check) if files of the type specified are there.
     If no file can be found in that folder with that type, the folder name is removed from the list

notebooks/__code/_utilities/images.py

@@ -16,7 +16,9 @@ def _init_arr_from_stack(list_files, ext=".tiff", slc=None):
         _arr = dxchange.read_tiff(first_file)
         f_type = "tif"
     else:
-        raise ValueError(f"'{first_file}', only '.tif/.tiff' and '.fits' are supported.")
+        raise ValueError(
+            f"'{first_file}', only '.tif/.tiff' and '.fits' are supported."
+        )
     size = (number_of_files, _arr.shape[0], _arr.shape[1])
     return np.empty(size, dtype=_arr.dtype), f_type
 

notebooks/__code/_utilities/legend.py

@@ -5,9 +5,13 @@
 def legend() -> None:
     display(HTML("<hr style='height:2px'/>"))
     display(HTML("<h2>Legend</h2>"))
-    display(HTML("<ul>"
-                    "<li><b><font color='red'>Mandatory steps</font></b> must be performed to ensure proper data processing.</li>"
-                    "<li><b><font color='orange'>Optional but recommended steps</font></b> are not mandatory but should be performed to ensure proper data processing.</li>"
-                    "<li><b><font color='purple'>Optional steps</font></b> are not mandatory but highly recommended to improve the quality of your data processing.</li>"
-                    "</ul>"))
-    display(HTML("<hr style='height:2px'/>"))
+    display(
+        HTML(
+            "<ul>"
+            "<li><b><font color='red'>Mandatory steps</font></b> must be performed to ensure proper data processing.</li>"
+            "<li><b><font color='orange'>Optional but recommended steps</font></b> are not mandatory but should be performed to ensure proper data processing.</li>"
+            "<li><b><font color='purple'>Optional steps</font></b> are not mandatory but highly recommended to improve the quality of your data processing.</li>"
+            "</ul>"
+        )
+    )
+    display(HTML("<hr style='height:2px'/>"))

notebooks/__code/_utilities/list.py

@@ -25,7 +25,9 @@ def are_those_two_lists_identical_within_tolerance(list1, list2, tolerance=0.01)
     return True
 
 
-def are_those_two_lists_of_lists_identical_within_tolerance(list1, list2, tolerance=0.01):
+def are_those_two_lists_of_lists_identical_within_tolerance(
+    list1, list2, tolerance=0.01
+):
     """
     check that 2 lists composed of lists are identical
 
@@ -44,7 +46,9 @@ def are_those_two_lists_of_lists_identical_within_tolerance(list1, list2, tolera
         return True
 
     for list_item1, list_item2 in zip(list1, list2, strict=False):
-        if not are_those_two_lists_identical_within_tolerance(list_item1, list_item2, tolerance=tolerance):
+        if not are_those_two_lists_identical_within_tolerance(
+            list_item1, list_item2, tolerance=tolerance
+        ):
             return False
 
     return True
@@ -60,10 +64,14 @@ def is_this_list_already_in_those_lists_within_tolerance(list1, list2, tolerance
     :return:
     """
     if (not (type(list1) == list)) or (not (type(list2) == list)):
-        raise TypeError("First argument should be a list of floats, second argument a list of lists")
+        raise TypeError(
+            "First argument should be a list of floats, second argument a list of lists"
+        )
 
     for target_list in list2:
-        if are_those_two_lists_identical_within_tolerance(list1, target_list, tolerance=tolerance):
+        if are_those_two_lists_identical_within_tolerance(
+            list1, target_list, tolerance=tolerance
+        ):
             return True
 
     return False

notebooks/__code/_utilities/logger.py

@@ -2,7 +2,6 @@
 
 
 def display_dictionary_in_logging(dictionary):
-
     for key, value in dictionary.items():
         logging.info(f"\t {key}: {value}")
     logging.info("")  # Add an empty line for better readability