collective code refactory, updated module and class name convention a…

…nd polish the code style

.dockerignore

@@ -6,6 +6,7 @@ env
 
 **/__pycache__
 **/.pytest_cache
+**/.mypy_cache
 
 .idea/**
 
@@ -16,4 +17,5 @@ env
 tests/*
 paper
 
-.DS_Store
+.DS_Store
+

.github/pull_request_template.md

@@ -6,4 +6,4 @@ Changes proposed in this pull request:
 -
 
 
-@BrkRaw/Bruker
+@BrkRaw/brkraw

README.md

@@ -4,7 +4,6 @@
 
 ## BrkRaw: A comprehensive tool to access raw Bruker Biospin MRI data
 #### Version: 0.3.11
-
 ### Description
 
 The ‘BrkRaw’ is a python module designed to provide a comprehensive tool to access raw data acquired from 

brkraw/api/__init__.py

@@ -1,4 +1,4 @@
 from .data import Study
-from ..config import ConfigManager
+from .config import Manager as ConfigManager
 
 __all__ = ['Study', 'ConfigManager']

brkraw/api/config/__init__.py

@@ -0,0 +1,3 @@
+from .manager import Manager
+
+__all__ = ['Manager']

brkraw/api/config/config.yaml

@@ -0,0 +1,24 @@
+# default configuration for brkraw
+plugin:
+  repo: 
+  - https://github.com/brkraw/brkraw-plugin.git/plugin
+  template:
+  - boilerplate
+
+preset:
+  repo:
+  - https://github.com/brkraw/brkraw-plugin.git/preset
+  template:
+  - boilerplate
+
+bids:
+  spec:
+    repo:
+    - https://github.com/brkraw/brkraw-bids.git/spec
+  recipes:
+    repo:
+    - https://github.com/brkraw/brkraw-bids.git/recipes
+
+app:
+  tonifti:
+    output_format: <study_name>_<scan_name>_<scan_id>_<reco_id>

brkraw/api/config/manager.py

@@ -0,0 +1,145 @@
+from __future__ import annotations
+import yaml
+from pathlib import Path
+from brkraw import __version__
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    from typing import Literal
+
+class Manager:
+    """
+    Make this configuration works internally without create file but if user use cli to create, do it so (create on home folder)
+    Manage the configuration settings.
+
+    Notes:
+        - Provides methods to ensure the existence of the config directory, load or create the configuration, 
+        set configuration values, and retrieve configuration values.
+    """
+    def __init__(self):
+        """
+        Initialize the configuration object.
+
+        Notes:
+            - Sets up the home directory, config directory, and config file paths.
+            - Ensures the existence of the config directory and loads or creates the configuration.
+        """
+        self.home = Path.home()
+        self.package = Path(__file__).absolute().parent
+        self.local_dir = Path.cwd()
+        self.global_dir = self.home_dir / '.brkraw'
+        self.fname = 'config.yaml'
+
+    def config_file(self, target: Literal['local', 'global'] = 'global'):
+        dir = self.global_dir if target == 'global' else self.local_dir
+        if dir.exists() and (dir / self.fname).exists():
+            return dir / self.fname
+        else:
+            return self.package / self.fname            
+
+    def ensure_config_dir_exists(self):
+        """
+        Ensure the existence of the configuration directory.
+
+        Notes:
+            - Creates the config directory if it does not already exist.
+            - Also creates 'plugin' and 'bids' directories within the config directory.
+        """
+        if not self.config_dir.exists():
+            self.config_dir.mkdir()
+            (self.config_dir / 'plugin').mkdir()
+            (self.config_dir / 'preset').mkdir()
+            (self.config_dir / 'bids').mkdir()
+
+    def load(self, target: Literal['local', 'global'] = 'global'):
+        """
+        Load an existing configuration file or create a new one if it does not exist.
+
+        Notes:
+            - If the config file does not exist, a default configuration is created and saved.
+            - Otherwise, the existing configuration is loaded from the file.
+        """
+        if not self.config_file.exists():
+            with open(self.installed_dir / 'config.yalm') as f:
+                self.config = yaml.safe_load(f)
+
+    def create(self, target: Literal['local', 'global'] = 'global'):
+        """_summary_
+
+        Returns:
+            _type_: _description_
+        """
+
+    # use default config if no configure created,
+    # for downloading location, if no configuration folder created (~/.brkraw), use local folder
+    # also check local folder first (plugin, preset, bids), where you run a command
+    def set(self, key, value):
+        """
+        Set a key-value pair in the configuration and save the updated configuration to the file.
+
+        Args:
+            key: The key to set in the configuration.
+            value: The value to associate with the key.
+
+        Notes:
+            - Updates the configuration with the provided key-value pair.
+            - Persists the updated configuration to the config file.
+        """
+        self.config[key] = value
+        with open(self.config_file, 'w') as f:
+            yaml.dump(self.config, f, sort_keys=False)
+
+    def get(self, key):
+        """
+        Retrieve the value associated with the given key from the configuration.
+
+        Args:
+            key: The key to retrieve the value for.
+
+        Returns:
+            The value associated with the key in the configuration, or None if the key is not found.
+
+        Notes:
+            - Returns the value corresponding to the provided key from the configuration.
+        """
+        return self.config.get(key)
+
+# def get_scan_time(self, visu_pars=None):
+#         import datetime as dt
+#         subject_date = get_value(self._subject, 'SUBJECT_date')
+#         subject_date = subject_date[0] if isinstance(subject_date, list) else subject_date
+#         pattern_1 = r'(\d{2}:\d{2}:\d{2})\s+(\d+\s\w+\s\d{4})'
+#         pattern_2 = r'(\d{4}-\d{2}-\d{2})[T](\d{2}:\d{2}:\d{2})'
+#         if re.match(pattern_1, subject_date):
+#             # start time
+#             start_time = dt.time(*map(int, re.sub(pattern_1, r'\1', subject_date).split(':')))
+#             # date
+#             date = dt.datetime.strptime(re.sub(pattern_1, r'\2', subject_date), '%d %b %Y').date()
+#             # end time
+#             if visu_pars != None:
+#                 last_scan_time = get_value(visu_pars, 'VisuAcqDate')
+#                 last_scan_time = dt.time(*map(int, re.sub(pattern_1, r'\1', last_scan_time).split(':')))
+#                 acq_time = get_value(visu_pars, 'VisuAcqScanTime') / 1000.0
+#                 time_delta = dt.timedelta(0, acq_time)
+#                 scan_time = (dt.datetime.combine(date, last_scan_time) + time_delta).time()
+#                 return dict(date=date,
+#                             start_time=start_time,
+#                             scan_time=scan_time)
+#         elif re.match(pattern_2, subject_date):
+#             # start time
+#             # subject_date = get_value(self._subject, 'SUBJECT_date')[0]
+#             start_time = dt.time(*map(int, re.sub(pattern_2, r'\2', subject_date).split(':')))
+#             # date
+#             date = dt.date(*map(int, re.sub(pattern_2, r'\1', subject_date).split('-')))
+
+#             # end date
+#             if visu_pars != None:
+#                 scan_time = get_value(visu_pars, 'VisuCreationDate')[0]
+#                 scan_time = dt.time(*map(int, re.sub(pattern_2, r'\2', scan_time).split(':')))
+#                 return dict(date=date,
+#                             start_time=start_time,
+#                             scan_time=scan_time)
+#         else:
+#             raise Exception(ERROR_MESSAGES['NotIntegrated'])
+
+#         return dict(date=date,
+#                     start_time=start_time)

brkraw/api/data/__init__.py

@@ -1,4 +1,24 @@
+"""Initializes and exports the main components of the MRI study and scan management package.
+
+This package module consolidates and provides easy access to the primary classes involved in managing
+and analyzing MRI study and scan data. The classes exported here facilitate the interfacing with MRI
+data at both the study and scan levels, supporting detailed data manipulation and analysis.
+
+Exports:
+    Study: A class that manages MRI study operations, extending functionalities for detailed study data handling.
+    Scan: A class representing individual MRI scans, capable of detailed scan data analysis and management.
+    ScanInfo: A class for managing basic information and warnings related to MRI scans.
+
+The `__init__.py` module ensures that these classes are readily accessible when the package is imported,
+making the package easier to use and integrate into larger projects or applications.
+
+Example:
+    from your_package_name import Study, Scan, ScanInfo
+
+This enables straightforward access to these classes for further development and deployment in MRI data analysis tasks.
+"""
+
 from .study import Study
 from .scan import Scan, ScanInfo
 
-__all__ = ['Study', 'Scan', 'ScanInfo']
+__all__ = ['Study', 'Scan', 'ScanInfo']