Restructure fitting components into dedicated analysis/fitting module (#89)

* Create a new fitting module directory

* Reorganizes fitting tracker module structure

* Refactors minimizer structure and imports

* Refactors reliability factors into metrics module

* Reorganizes import statements for clarity

* Enforces absolute imports for consistency

* Updates pixi.lock

* Pins dependencies in pixi.toml

* Reorganizes import statements in minimization module

Author: AndrewSazonov

pixi.lock

@@ -20,14 +20,14 @@ channels = ["conda-forge"]
 # Default feature configuration
 
 [dependencies] # == [feature.default.dependencies]
-pip = "*"        # Required to install from PyPI
-jupyterlab = "*" # JupyterLab for notebooks
+pip = ">=25.2,<26"        # Required to install from PyPI
+jupyterlab = ">=4.4.7,<5" # JupyterLab for notebooks
 
 [target.win-64.dependencies]
 libcblas = "*" # CBLAS library for linear algebra. Required for pdffit2.
 
 [pypi-dependencies] # == [feature.default.pypi-dependencies]
-pixi-kernel = "*" # Pixi Jupyter kernel integration
+pixi-kernel = ">=0.6.6, <0.7" # Pixi Jupyter kernel integration
 
 # Extra features for different Python versions
 

pixi.toml

@@ -142,18 +142,22 @@ line-length = 127
 
 [tool.ruff.lint]
 select = [
-  'E',   # General PEP 8 style errors
-  'E9',  # Runtime errors (e.g., syntax errors, undefined names)
-  'F',   # Pyflakes-specific checks (e.g., unused variables, imports)
-  'F63', # Issues related to invalid escape sequences in strings
-  'F7',  # Type-related errors (e.g., mismatched argument types, unsupported operations)
-  'F82', # Import-related errors (e.g., unresolved imports, reimported modules)
-  'I',   # Import sorting issues (e.g., unsorted imports)
-  'S',   # Security-related issues (e.g., use of insecure functions or libraries)
-  'W',   # General PEP 8 warnings (e.g., lines too long, trailing whitespace)
-  'TCH', # Type checking issues (e.g., incompatible types, missing type annotations)
+  'E',      # General PEP 8 style errors
+  'E9',     # Runtime errors (e.g., syntax errors, undefined names)
+  'F',      # Pyflakes-specific checks (e.g., unused variables, imports)
+  'F63',    # Issues related to invalid escape sequences in strings
+  'F7',     # Type-related errors (e.g., mismatched argument types, unsupported operations)
+  'F82',    # Import-related errors (e.g., unresolved imports, reimported modules)
+  'I',      # Import sorting issues (e.g., unsorted imports)
+  'S',      # Security-related issues (e.g., use of insecure functions or libraries)
+  'W',      # General PEP 8 warnings (e.g., lines too long, trailing whitespace)
+  'TCH',    # Type checking issues (e.g., incompatible types, missing type annotations)
+  'TID252', # Enforces absolute imports over relative imports
 ]
 
+[tool.ruff.lint.flake8-tidy-imports]
+ban-relative-imports = 'all'
+
 [tool.ruff.lint.isort]
 force-single-line = true
 

pyproject.toml

@@ -7,6 +7,12 @@
 
 import pandas as pd
 
+from easydiffraction.analysis.calculators.calculator_factory import CalculatorFactory
+from easydiffraction.analysis.collections.aliases import Aliases
+from easydiffraction.analysis.collections.constraints import Constraints
+from easydiffraction.analysis.collections.joint_fit_experiments import JointFitExperiments
+from easydiffraction.analysis.minimization import DiffractionMinimizer
+from easydiffraction.analysis.minimizers.minimizer_factory import MinimizerFactory
 from easydiffraction.core.objects import Descriptor
 from easydiffraction.core.objects import Parameter
 from easydiffraction.core.singletons import ConstraintsHandler
@@ -16,13 +22,6 @@
 from easydiffraction.utils.utils import render_cif
 from easydiffraction.utils.utils import render_table
 
-from .calculators.calculator_factory import CalculatorFactory
-from .collections.aliases import Aliases
-from .collections.constraints import Constraints
-from .collections.joint_fit_experiments import JointFitExperiments
-from .minimization import DiffractionMinimizer
-from .minimizers.minimizer_factory import MinimizerFactory
-
 
 class Analysis:
     _calculator = CalculatorFactory.create_calculator('cryspy')

src/easydiffraction/analysis/analysis.py

@@ -5,12 +5,11 @@
 from typing import List
 from typing import Optional
 
+from easydiffraction.analysis.calculators.calculator_factory import CalculatorFactory
 from easydiffraction.experiments.experiment import Experiment
 from easydiffraction.experiments.experiments import Experiments
 from easydiffraction.sample_models.sample_models import SampleModels
 
-from .calculators.calculator_factory import CalculatorFactory
-
 
 class DiffractionCalculator:
     """

src/easydiffraction/analysis/calculation.py

@@ -8,13 +8,12 @@
 
 import numpy as np
 
+from easydiffraction.analysis.calculators.calculator_base import CalculatorBase
 from easydiffraction.experiments.experiment import Experiment
 from easydiffraction.experiments.experiments import Experiments
 from easydiffraction.sample_models.sample_models import SampleModel
 from easydiffraction.sample_models.sample_models import SampleModels
 
-from .calculator_base import CalculatorBase
-
 try:
     from pycrysfml import cfml_py_utilities
 

src/easydiffraction/analysis/calculators/calculator_crysfml.py

@@ -11,12 +11,11 @@
 
 import numpy as np
 
+from easydiffraction.analysis.calculators.calculator_base import CalculatorBase
 from easydiffraction.experiments.components.experiment_type import BeamModeEnum
 from easydiffraction.experiments.experiment import Experiment
 from easydiffraction.sample_models.sample_model import SampleModel
 
-from .calculator_base import CalculatorBase
-
 try:
     import cryspy
     from cryspy.H_functions_global.function_1_cryspy_objects import str_to_globaln

src/easydiffraction/analysis/calculators/calculator_cryspy.py

@@ -7,15 +7,14 @@
 from typing import Type
 from typing import Union
 
+from easydiffraction.analysis.calculators.calculator_base import CalculatorBase
+from easydiffraction.analysis.calculators.calculator_crysfml import CrysfmlCalculator
+from easydiffraction.analysis.calculators.calculator_cryspy import CryspyCalculator
+from easydiffraction.analysis.calculators.calculator_pdffit import PdffitCalculator
 from easydiffraction.utils.formatting import error
 from easydiffraction.utils.formatting import paragraph
 from easydiffraction.utils.utils import render_table
 
-from .calculator_base import CalculatorBase
-from .calculator_crysfml import CrysfmlCalculator
-from .calculator_cryspy import CryspyCalculator
-from .calculator_pdffit import PdffitCalculator
-
 
 class CalculatorFactory:
     _potential_calculators: Dict[str, Dict[str, Union[str, Type[CalculatorBase]]]] = {

src/easydiffraction/analysis/calculators/calculator_factory.py

@@ -6,11 +6,10 @@
 
 import numpy as np
 
+from easydiffraction.analysis.calculators.calculator_base import CalculatorBase
 from easydiffraction.experiments.experiment import Experiment
 from easydiffraction.sample_models.sample_model import SampleModel
 
-from .calculator_base import CalculatorBase
-
 try:
     from diffpy.pdffit2 import PdfFit as pdffit
     from diffpy.pdffit2 import redirect_stdout

src/easydiffraction/analysis/calculators/calculator_pdffit.py

@@ -0,0 +1,3 @@
+# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction Python Library contributors <https://github.com/easyscience/diffraction-lib>
+# SPDX-License-Identifier: BSD-3-Clause
+