Organized files for less clutering

src/eeg_research/simulators/cleaner_pipelines.py → src/eeg_research/preprocessing/pipelines/cleaner_pipelines.py

@@ -47,7 +47,7 @@
 )
 from eeg_research.preprocessing.tools.utils import read_raw_eeg
 from eeg_research.simulators.decorators import pipe
-from eeg_research.simulators.simulate_data import simulate_eeg_data
+from eeg_research.simulators.eeg_simulator import simulate_eeg_data
 
 
 class CleanerPipelines:

src/eeg_research/simulators/main_cleaner_pipelines.py → src/eeg_research/preprocessing/pipelines/main_cleaner_pipelines.py

@@ -28,7 +28,7 @@
 
 import bids
 
-from eeg_research.simulators.cleaner_pipelines import CleanerPipelines
+from eeg_research.preprocessing.pipelines.cleaner_pipelines import CleanerPipelines
 
 
 def run_cbin_cleaner(cleaner: CleanerPipelines) -> CleanerPipelines:

src/eeg_research/simulators/bids_simulator.py

@@ -1,21 +1,106 @@
 """Create a temporary BIDS dataset to test data handling scripts."""
 
 import json
+import os
 import shutil
 import tempfile
 from pathlib import Path
+from typing import Generator, Any
 
 import mne
 import numpy as np
 import pandas as pd
 
-from eeg_research.simulators.path_handler import DirectoryTree
-from eeg_research.simulators.simulate_data import (
+from eeg_research.simulators.eeg_simulator import (
     simulate_eeg_data,
     simulate_light_eeg_data,
 )
 
 
+class DirectoryTree:
+    """The class to handle the directory tree."""
+
+    def __init__(self, root_dir: str | os.PathLike) -> None:
+        """Initialize the class with the root directory."""
+        self.root_dir = os.path.abspath(root_dir)
+        self.current_dir = self.root_dir
+
+    def generate_tree(
+        self: "DirectoryTree",
+    ) -> Generator[tuple[str, list[str], list[str]], None, None]:
+        """A generator method to walk through the directory tree.
+
+        It starts from the root directory. Yields tuples of (path, dirs, files)
+        for each directory in the tree.
+        """
+        for dirpath, dirnames, filenames in os.walk(self.root_dir):
+            yield dirpath, dirnames, filenames
+
+    def list_directory_contents(
+        self: "DirectoryTree",
+    ) -> tuple[list[str] | str, list[str]]:
+        """List the contents of the current directory."""
+        try:
+            with os.scandir(self.current_dir) as it:
+                dirs = [entry.name for entry in it if entry.is_dir()]
+                files = [entry.name for entry in it if entry.is_file()]
+            return dirs, files
+        except PermissionError as e:
+            return f"Permission denied: {e}", []
+
+    def change_directory(self, target_dir: str | os.PathLike) -> str | os.PathLike:
+        """Change the current directory to target_dir.
+
+        Change the current directory if it's a subdirectory
+        of current_dir or a valid path.
+
+        Args:
+            target_dir (str | os.PathLike): The target directory path.
+        """
+        new_dir = os.path.abspath(os.path.join(self.current_dir, target_dir))
+        if os.path.commonpath([self.root_dir, new_dir]) != self.root_dir:
+            return f"Error: {new_dir} is not a subdirectory of the root directory."
+        if os.path.isdir(new_dir):
+            self.current_dir = new_dir
+            return f"Changed current directory to {self.current_dir}"
+        else:
+            return f"Error: Directory {new_dir} does not exist."
+
+    def print_tree(
+        self: "DirectoryTree",
+        start_path: str | os.PathLike = "",
+        prefix: str | os.PathLike = "",
+    ) -> None:
+        """Print the tree in a formated way.
+
+        Recursively prints the directory tree starting f
+        rom start_path with proper formatting.
+
+        Args:
+            start_path (str | os.PathLike, optional): The starting path.
+                                                      Defaults to ''.
+            prefix (str | os.PathLike, optional): The prefix to be added.
+                                                  Defaults to ''.
+        """
+        if start_path == "":
+            start_path = self.root_dir
+            print(start_path + "/")
+
+        entries = [entry for entry in os.scandir(str(start_path))]
+        entries = sorted(entries, key=lambda e: (e.is_file(), e.name))
+        last_index = len(entries) - 1
+
+        for index, entry in enumerate(entries):
+            connector = "├──" if index != last_index else "└──"
+            if entry.is_dir():
+                print(f"{prefix}{connector} {entry.name}/")
+                extension = "│   " if index != last_index else "    "
+                self.print_tree(
+                    os.path.join(start_path, entry.name), str(prefix) + str(extension)
+                )
+            else:
+                print(f"{prefix}{connector} {entry.name}")
+
 class DummyDataset:
     """A class to create a dummy BIDS dataset for EEG data.
 
@@ -322,7 +407,7 @@ def flush(self, check: bool = True) -> None:
             print("Content being removed:")
             tree.print_tree()
 
-            shutil.rmtree(self.root, ignore_errors=True, onerror=None)
+            shutil.rmtree(str(self.root))
             post_removal_checker = self.root.exists()
             if post_removal_checker:
                 print("The tree was not removed.")

src/eeg_research/simulators/decorators.py

@@ -8,7 +8,7 @@
 
 import bids
 
-from eeg_research.simulators.simulate_data import DummyDataset
+from eeg_research.simulators.eeg_simulator import DummyDataset
 
 FunctionType = TypeVar("FunctionType", bound=Callable[..., Any])
 

src/eeg_research/simulators/simulate_data.py → src/eeg_research/simulators/eeg_simulator.py

@@ -54,7 +54,6 @@ def simulate_light_eeg_data(
 
     return raw
 
-
 def simulate_eeg_data(
     n_channels: int = 16,
     duration: int = 2,

src/eeg_research/simulators/path_handler.py

@@ -1,89 +1 @@
 """The module to handle the directory tree."""
-
-import os
-from typing import Generator
-
-
-class DirectoryTree:
-    """The class to handle the directory tree."""
-
-    def __init__(self, root_dir: str | os.PathLike) -> None:
-        """Initialize the class with the root directory."""
-        self.root_dir = os.path.abspath(root_dir)
-        self.current_dir = self.root_dir
-
-    def generate_tree(
-        self: "DirectoryTree",
-    ) -> Generator[tuple[str, list[str], list[str]], None, None]:
-        """A generator method to walk through the directory tree.
-
-        It starts from the root directory. Yields tuples of (path, dirs, files)
-        for each directory in the tree.
-        """
-        for dirpath, dirnames, filenames in os.walk(self.root_dir):
-            yield dirpath, dirnames, filenames
-
-    def list_directory_contents(
-        self: "DirectoryTree",
-    ) -> tuple[list[str] | str, list[str]]:
-        """List the contents of the current directory."""
-        try:
-            with os.scandir(self.current_dir) as it:
-                dirs = [entry.name for entry in it if entry.is_dir()]
-                files = [entry.name for entry in it if entry.is_file()]
-            return dirs, files
-        except PermissionError as e:
-            return f"Permission denied: {e}", []
-
-    def change_directory(self, target_dir: str | os.PathLike) -> str | os.PathLike:
-        """Change the current directory to target_dir.
-
-        Change the current directory if it's a subdirectory
-        of current_dir or a valid path.
-
-        Args:
-            target_dir (str | os.PathLike): The target directory path.
-        """
-        new_dir = os.path.abspath(os.path.join(self.current_dir, target_dir))
-        if os.path.commonpath([self.root_dir, new_dir]) != self.root_dir:
-            return f"Error: {new_dir} is not a subdirectory of the root directory."
-        if os.path.isdir(new_dir):
-            self.current_dir = new_dir
-            return f"Changed current directory to {self.current_dir}"
-        else:
-            return f"Error: Directory {new_dir} does not exist."
-
-    def print_tree(
-        self: "DirectoryTree",
-        start_path: str | os.PathLike = "",
-        prefix: str | os.PathLike = "",
-    ) -> None:
-        """Print the tree in a formated way.
-
-        Recursively prints the directory tree starting f
-        rom start_path with proper formatting.
-
-        Args:
-            start_path (str | os.PathLike, optional): The starting path.
-                                                      Defaults to ''.
-            prefix (str | os.PathLike, optional): The prefix to be added.
-                                                  Defaults to ''.
-        """
-        if start_path == "":
-            start_path = self.root_dir
-            print(start_path + "/")
-
-        entries = [entry for entry in os.scandir(str(start_path))]
-        entries = sorted(entries, key=lambda e: (e.is_file(), e.name))
-        last_index = len(entries) - 1
-
-        for index, entry in enumerate(entries):
-            connector = "├──" if index != last_index else "└──"
-            if entry.is_dir():
-                print(f"{prefix}{connector} {entry.name}/")
-                extension = "│   " if index != last_index else "    "
-                self.print_tree(
-                    os.path.join(start_path, entry.name), str(prefix) + str(extension)
-                )
-            else:
-                print(f"{prefix}{connector} {entry.name}")

tests/analysis/tools/test_freq_analysis.py

@@ -32,7 +32,7 @@
 from mne.io import RawArray
 
 import eeg_research.analysis.tools.freq_analysis as script
-from eeg_research.simulators.simulate_data import simulate_light_eeg_data
+from eeg_research.simulators.eeg_simulator import simulate_light_eeg_data
 
 
 @pytest.fixture