Merge remote-tracking branch 'origin/main' into modifying_databundle_and_associates

Author: toqduj

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+ignore = E203, E266, E501, W503, F403, F401, F405
+max-line-length = 120
+max-complexity = 18
+select = C,E,F,W,B,B950

.pre-commit-config.yaml

@@ -22,3 +22,4 @@ repos:
     rev: 6.0.0
     hooks:
       - id: flake8
+        args: [--config=.flake8]

docs/conf.py

@@ -85,5 +85,5 @@
     + r".*",
     # attempted fix of '406 Client Error: Not Acceptable for url'
     # https://github.com/sphinx-doc/sphinx/issues/1331
-    join(project_meta["project"]["urls"]["repository"], "commit", r"[0-9a-fA-F]+")
+    join(project_meta["project"]["urls"]["repository"], "commit", r"[0-9a-fA-F]+"),
 ]

requirements.txt

@@ -1,5 +1,4 @@
 attrs
-dask
 entrypoints
 matplotlib
 numpy
@@ -8,6 +7,6 @@ h5py
 pint
 pytest
 stamina
-tiled
 tox
 scipy
+uncertainties

src/modacor/__init__.py

@@ -1,12 +1,13 @@
 # -*- coding: utf-8 -*-
 # __init__.py
 
-__version__ = '0.0.0'
+__version__ = "0.0.0"
 
 from pint import UnitRegistry, set_application_registry
-ureg = UnitRegistry(system='SI')
+
+ureg = UnitRegistry(system="SI")
 Q_ = ureg.Quantity
-# recommended for pickling and unpickling: 
+# recommended for pickling and unpickling:
 set_application_registry(ureg)
 ureg.formatter.default_format = "~P"
 ureg.setup_matplotlib(True)

src/modacor/dataclasses/messagehandler.py

@@ -2,6 +2,7 @@
 # # -*- coding: utf-8 -*-
 
 import logging
+
 logger = logging.getLogger(__name__)
 
 
@@ -13,7 +14,8 @@ class MessageHandler:
     Args:
         level (int): The logging level to use. Defaults to logging.INFO.
     """
-    def __init__(self, level: int = logging.INFO, name: str = 'MoDaCor', **kwargs):
+
+    def __init__(self, level: int = logging.INFO, name: str = "MoDaCor", **kwargs):
         self.level = level
         self.name = name
 
@@ -23,7 +25,7 @@ def __init__(self, level: int = logging.INFO, name: str = 'MoDaCor', **kwargs):
         self.consoleLogHandler = logging.StreamHandler()
         self.consoleLogHandler.setLevel(level)
 
-        formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+        formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
         self.consoleLogHandler.setFormatter(formatter)
         self.logger.addHandler(self.consoleLogHandler)
 
@@ -33,20 +35,20 @@ def log(self, message: str, level: int = None, name: str = None):
 
         if name is None:
             name = self.name
-        
+
         self.logger(message, level=level, name=name)
 
     def info(self, message: str):
-        self.log(message, level=logging.INFO, name='MoDaCor')
+        self.log(message, level=logging.INFO, name="MoDaCor")
 
     def warning(self, message: str):
-        self.log(message, level=logging.WARNING, name='MoDaCor')
+        self.log(message, level=logging.WARNING, name="MoDaCor")
 
     def error(self, message: str):
-        self.log(message, level=logging.ERROR, name='MoDaCor')
+        self.log(message, level=logging.ERROR, name="MoDaCor")
 
     def critical(self, message: str):
-        self.log(message, level=logging.CRITICAL, name='MoDaCor')
-    
+        self.log(message, level=logging.CRITICAL, name="MoDaCor")
+
     def debug(self, message: str):
-        self.log(message, level=logging.DEBUG, name='MoDaCor')
+        self.log(message, level=logging.DEBUG, name="MoDaCor")

src/modacor/dataclasses/pipelinedata.py

@@ -3,10 +3,12 @@
 
 __all__ = ["ProcessStep"]
 __license__ = "BSD-3-Clause"
+__version__ = "0.0.1"
 
 
 from abc import abstractmethod
 from numbers import Integral
+from pathlib import Path
 from typing import Any
 
 from attrs import define, field
@@ -26,7 +28,12 @@ class ProcessStep:
     io_sources: IoSources = field()
 
     # class attribute for a machine-readable description of the process step
-    documentation: ProcessStepDescriber
+    documentation = ProcessStepDescriber(
+        calling_name="Generic Process step",
+        calling_id=None,
+        calling_module_path=Path(__file__),
+        calling_version=__version__,
+    )
 
     # dynamic instance configuration
     configuration: dict = field(factory=dict, validator=v.instance_of(dict))
@@ -45,9 +52,8 @@ class ProcessStep:
         default=MessageHandler(), validator=v.instance_of(MessageHandler)
     )
 
-    # a list of data keys that are modified by this process
-    def __attrs_post_init__(self):
-        self.__prepared = False
+    # internal variables:
+    __prepared: bool = field(default=False, validator=v.instance_of(bool))
 
     def prepare_execution(self):
         """
@@ -94,5 +100,5 @@ def modify_config(self, key: str, value: Any):
         if key in self.configuration:
             self.configuration[key] = value
         else:
-            raise KeyError(f"Key {key} not found in configuration")
+            raise KeyError(f"Key {key} not found in configuration")  # noqa
         self.__prepared = False

src/modacor/dataclasses/process_step.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 from numbers import Integral
-from typing import Any
+from typing import Any, Type
 
 import pint
 
@@ -19,7 +19,7 @@
 ]
 
 
-def is_list_of_ints(value: Any):
+def is_list_of_ints(instance: Type, attribute: str, value: Any):
     """
     Check if the value is a list of integers.
     """

src/modacor/dataclasses/validators.py

@@ -25,7 +25,3 @@
 __license__ = "BSD-3-Clause"
 __copyright__ = "Copyright 2025 MoDaCor Authors"
 __status__ = "Alpha"
-
-
-from ..io_source import IoSource
-from ..io_sources import IoSources