Merge pull request #26 from BAMresearch/fix_formatting_for_tox

Fix formatting for tox

Author: ahoermann

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/process_step.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/validators.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/io/hdf/__init__.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

src/modacor/math/variance_calculations.py

@@ -70,6 +70,6 @@ def divide(x, vx, y, vy=0):
                     ∂/∂y = -x / y^2
     """
     result = x / y
-    dx_, dy_ = 1 / y, -x / (y ** 2)
+    dx_, dy_ = 1 / y, -x / (y**2)
     variance = dx_**2 * vx + dy_**2 * vy
     return result, variance

src/modacor/tests/test_processstep.py

@@ -1,99 +1,12 @@
-from datetime import datetime, timedelta, timezone
-from pathlib import Path
+from modacor.dataclasses.process_step import ProcessStep
+from modacor.io import IoSources
 
-import pytest
-
-from ..dataclasses.process_step import ProcessStep
-
-
-# Dummy BaseData for testing execute() since ProcessStep.execute() requires it.
-class DummyBaseData:
-    pass
+TEST_IO_SOURCES = IoSources()
 
 
 def test_minimal_instantiation():
     """
     Test that a ProcessStep can be instantiated with only the minimal arguments.
     """
-    ps = ProcessStep(
-        calling_name="Test Process",
-        calling_id="proc_001",
-        calling_module_path=Path("src/modacor/modules/some_module.py"),
-        calling_version="1.0",
-    )
-    assert ps is not None
-
-
-def test_full_instantiation():
-    """
-    Test that a ProcessStep can be instantiated with all arguments.
-    """
-    ps = ProcessStep(
-        calling_name="Test Process",
-        calling_id="proc_002",
-        calling_module_path=Path("src/modacor/modules/some_module.py"),
-        calling_version="1.0",
-        required_data_keys=["fish", "cake"],
-        calling_arguments={"fish": "salmon", "cake": "chocolate"},
-        step_keywords=["test", "full"],
-        step_doc="Test full instantiation",
-        step_reference="doi: 10.1234/5678",
-        step_note="I am a note.",
-        # produced_values={},  # this is internally generated
-        use_frames_cache=["fish"],
-        use_overall_cache=["cake"],
-        saved={"cake": "/path/to/cake"},
-    )
-    ps.start()
-    ps.stop()
-    assert ps is not None
-
-
-def test_missing_required_input():
-    """
-    Test that a ProcessStep can be instantiated with all arguments.
-    """
-    with pytest.raises(
-        ValueError, match=r"Missing required data keys in calling_arguments: ['bread']"
-    ):
-        ProcessStep(
-            calling_name="Test Process",
-            calling_id="proc_002",
-            calling_module_path=Path("src/modacor/modules/some_module.py"),
-            calling_version="1.0",
-            required_data_keys=["fish", "cake", "bread"],
-            calling_arguments={"fish": "salmon", "cake": "chocolate"},
-            step_keywords=["test", "full"],
-            step_doc="Test full instantiation",
-            step_reference="doi: 10.1234/5678",
-            step_note="I am a note.",
-            # produced_values={},  # this is internally generated
-            use_frames_cache=["fish"],
-            use_overall_cache=["cake"],
-            saved={"cake": "/path/to/cake"},
-        )
-
-
-def test_duration_calculation():
-    """
-    Test that the duration property correctly computes elapsed time.
-    """
-    ps = ProcessStep(
-        calling_name="Test Process",
-        calling_id="proc_003",
-        calling_module_path=Path("src/modacor/modules/some_module.py"),
-        calling_version="1.0",
-        required_data_keys=[],
-        calling_arguments={},
-        step_keywords=["test", "duration"],
-        step_doc="Test duration calculation",
-        step_reference="",
-        step_note=None,
-        produced_values={},
-        use_frames_cache=[],
-    )
-    # Manually set start_time 5 seconds before now.
-    ps.start_time = datetime.now(timezone.utc) - timedelta(seconds=5)
-    ps.stop()  # Sets stop_time to now.
-    duration = ps.duration
-    assert duration is not None and duration >= 5
+    ps = ProcessStep(TEST_IO_SOURCES)
+    assert isinstance(ps, ProcessStep)

src/modacor/tests/test_variance_calculations.py

@@ -6,15 +6,19 @@
 `uncertainties` package. Randomly generated arrays simulate real-world numeric data
 with associated variances.
 """
+
 import numpy as np
+from uncertainties.unumpy import nominal_values, std_devs, uarray
+
 import modacor.math.variance_calculations as varc
-from uncertainties.unumpy import uarray, nominal_values, std_devs
 
 samples = 1000
 
+
 def generate_samples(size, low=1, high=1.0e9):
     return np.random.uniform(low, high, size)
 
+
 def generate_error(values, add_zero_errors=False):
     s = np.sqrt(values)
     if add_zero_errors:  # to check if scalars will work
@@ -35,7 +39,7 @@ def test_add():
     result, variances = varc.add(x, dx**2, y, dy**2)
 
     assert np.allclose(result, nominal_values(expected))
-    assert np.allclose(variances, std_devs(expected)**2)
+    assert np.allclose(variances, std_devs(expected) ** 2)
 
 
 def test_subtract():
@@ -51,7 +55,7 @@ def test_subtract():
     result, variances = varc.subtract(x, dx**2, y, dy**2)
 
     assert np.allclose(result, nominal_values(expected))
-    assert np.allclose(variances, std_devs(expected)**2)
+    assert np.allclose(variances, std_devs(expected) ** 2)
 
 
 def test_multiply():
@@ -67,7 +71,7 @@ def test_multiply():
     result, variances = varc.multiply(x, dx**2, y, dy**2)
 
     assert np.allclose(result, nominal_values(expected))
-    assert np.allclose(variances, std_devs(expected)**2)
+    assert np.allclose(variances, std_devs(expected) ** 2)
 
 
 def test_divide():
@@ -83,4 +87,4 @@ def test_divide():
     result, variances = varc.divide(x, dx**2, y, dy**2)
 
     assert np.allclose(result, nominal_values(expected))
-    assert np.allclose(variances, std_devs(expected)**2)
+    assert np.allclose(variances, std_devs(expected) ** 2)