Audit disabled lint rules and adopt the low-risk subset

pyproject.toml

@@ -291,10 +291,12 @@ select = [
   'SIM', # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
   #'SLF',   # https://docs.astral.sh/ruff/rules/#flake8-self-slf
   'SLOT', # https://docs.astral.sh/ruff/rules/#flake8-slots-slot
-  #'T20',   # https://docs.astral.sh/ruff/rules/#flake8-print-t20
-  'TC', # https://docs.astral.sh/ruff/rules/#flake8-type-checking-tc
+  'T20',  # https://docs.astral.sh/ruff/rules/#flake8-print-t20
+  'TC',   # https://docs.astral.sh/ruff/rules/#flake8-type-checking-tc
   #'TD',    # https://docs.astral.sh/ruff/rules/#flake8-todos-td
-  'TID', # https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid
+  'TD004', # https://docs.astral.sh/ruff/rules/missing-todo-colon/ (TODO-format subset)
+  'TD005', # https://docs.astral.sh/ruff/rules/missing-todo-description/ (TODO-format subset)
+  'TID',   # https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid
 ]
 
 # Exceptions to the linting rules
@@ -306,10 +308,6 @@ ignore = [
   'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc
   # Disable, as [tool.format_docstring] split one-line docstrings into the canonical multi-line layout
   'D200', # https://docs.astral.sh/ruff/rules/unnecessary-multiline-docstring/
-  # Temporary:
-  'D100',   # https://docs.astral.sh/ruff/rules/undocumented-public-module/#undocumented-publi-module-d100
-  'D104',   # https://docs.astral.sh/ruff/rules/undocumented-public-package/#undocumented-public-package-d104
-  'DTZ005', # https://docs.astral.sh/ruff/rules/call-datetime-now-without-tzinfo/#call-datetime-now-without-tzinfo-dtz005
 ]
 
 # Ignore specific rules in certain files or directories
@@ -325,25 +323,26 @@ ignore = [
   'RUF012', # https://docs.astral.sh/ruff/rules/mutable-class-default/ (test stubs use mutable defaults)
   'RUF069', # https://docs.astral.sh/ruff/rules/unreliable-float-equality/ (exact comparisons in assertions)
   'S101',   # https://docs.astral.sh/ruff/rules/assert/
+  'T20',    # tests may print debug/scaffolding output
   # Temporary:
   'ARG001',
   'ARG002',
   'ARG004',
   'ARG005',
-  'B011',
-  'B017',
   'B018',
-  'E501',
   'E741',
-  'F841',
-  'I001',
   'N801',
-  'N805',
   'N812',
   'PLC',
-  'PLE',
-  'PLR',
-  'PLW',
+  # Keep the test idioms (PLR2004 magic values, PLR6301 no-self-use) and
+  # the ADR-governed complexity rules ignored; the rest of PLR (e.g.
+  # PLR0402/PLR1711/PLR6104) is enforced. PLW is fully enforced.
+  'PLR0913',
+  'PLR0914',
+  'PLR0915',
+  'PLR0917',
+  'PLR2004',
+  'PLR6301',
   'SIM117',
   'SLF',
   'TRY',
@@ -356,13 +355,20 @@ ignore = [
   'RUF003', # https://docs.astral.sh/ruff/rules/ambiguous-unicode-character-comment/ (en-dashes in headings)
   'T201',   # https://docs.astral.sh/ruff/rules/print/
   # Temporary:
-  'ANN',
   'D',
   'W',
 ]
 'docs/docs/tutorials/**' = [
   'E402', # https://docs.astral.sh/ruff/rules/module-import-not-at-top-of-file/
 ]
+# Intentional terminal rendering: these write raw/ASCII output that
+# `Console.print` would garble, so `print` is deliberate here.
+'src/easydiffraction/display/plotters/ascii.py' = [
+  'T201', # https://docs.astral.sh/ruff/rules/print/
+]
+'src/easydiffraction/project/display.py' = [
+  'T201', # https://docs.astral.sh/ruff/rules/print/
+]
 
 # Specific options for certain rules
 

src/easydiffraction/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2025 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""EasyDiffraction public API for diffraction analysis."""
 
 from __future__ import annotations
 

src/easydiffraction/__main__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2025 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Typer command-line interface for the EasyDiffraction library."""
 
 from __future__ import annotations
 

src/easydiffraction/analysis/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2025 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Fitting analysis: minimizers, fit parameters, and results."""
 
 from easydiffraction.analysis.analysis import UndoFitOutcome
 from easydiffraction.analysis.categories.fit_parameter_correlations import (

src/easydiffraction/analysis/analysis.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2025 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Analysis orchestration of fitting, parameters, and results."""
 
 from __future__ import annotations
 

src/easydiffraction/analysis/calculators/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""CrysFML, CrysPy, and PDFfit calculation backends."""
 
 from easydiffraction.analysis.calculators.crysfml import CrysfmlCalculator
 from easydiffraction.analysis.calculators.cryspy import CryspyCalculator

src/easydiffraction/analysis/calculators/base.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2025 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Abstract base API for diffraction calculation backends."""
 
 from __future__ import annotations
 

src/easydiffraction/analysis/calculators/crysfml.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""CrysFML calculation backend for powder diffraction patterns."""
 
 from __future__ import annotations
 
@@ -12,6 +13,7 @@
 from easydiffraction.analysis.calculators.factory import CalculatorFactory
 from easydiffraction.core.metadata import TypeInfo
 from easydiffraction.datablocks.experiment.item.enums import BeamModeEnum
+from easydiffraction.utils.logging import log
 
 if TYPE_CHECKING:
     from easydiffraction.datablocks.experiment.collection import Experiments
@@ -137,7 +139,7 @@
         try:
             y = self._calculate_adjusted_pattern(crysfml_dict, experiment)
         except KeyError:
-            print('[CrysfmlCalculator] Error: No calculated data')
+            log.warning('[CrysfmlCalculator] No calculated data')
             y = []
         return np.asarray(y)
 
@@ -164,10 +166,8 @@
         if experiment.type.beam_mode.value == BeamModeEnum.TIME_OF_FLIGHT:
             _, y = cfml_py_utilities.tof_powder_pattern_from_dict(crysfml_dict)
             return y
-        print(
-            f'[CrysfmlCalculator] Error: Unsupported beam mode {experiment.type.beam_mode.value}'
-        )
+        log.warning(f'[CrysfmlCalculator] Unsupported beam mode {experiment.type.beam_mode.value}')
         return None
 
     def _adjust_pattern_length(  # noqa: PLR6301
         self,

src/easydiffraction/analysis/calculators/cryspy.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""CrysPy calculation backend for diffraction patterns."""
 
 from __future__ import annotations
 
@@ -18,6 +19,7 @@
 from easydiffraction.datablocks.experiment.item.enums import BeamModeEnum
 from easydiffraction.datablocks.experiment.item.enums import PeakProfileTypeEnum
 from easydiffraction.datablocks.experiment.item.enums import SampleFormEnum
+from easydiffraction.utils.logging import log
 from easydiffraction.utils.utils import sin_theta_over_lambda_to_d_spacing
 
 if TYPE_CHECKING:
@@ -165,7 +167,7 @@
             y_calc = cryspy_in_out_dict[cryspy_block_name]['intensity_calc']
             stol = cryspy_in_out_dict[cryspy_block_name]['sthovl']
         except KeyError:
-            print(f'[CryspyCalculator] Error: No calculated data for {cryspy_block_name}')
+            log.warning(f'[CryspyCalculator] No calculated data for {cryspy_block_name}')
             return [], []
 
         return stol, y_calc
@@ -255,7 +257,7 @@
         if beam_mode in prefixes:
             cryspy_block_name = f'{prefixes[beam_mode]}_{experiment.name}'
         else:
-            print(f'[CryspyCalculator] Error: Unknown beam mode {experiment.type.beam_mode.value}')
+            log.warning(f'[CryspyCalculator] Unknown beam mode {experiment.type.beam_mode.value}')
             return []
 
         try:
@@ -267,7 +269,7 @@
                 f'dict_in_out_{structure.name}'
             )
         except KeyError:
-            print(f'[CryspyCalculator] Error: No calculated data for {cryspy_block_name}')
+            log.warning(f'[CryspyCalculator] No calculated data for {cryspy_block_name}')
             return []
 
         return y_calc

src/easydiffraction/analysis/calculators/pdffit.py

@@ -19,6 +19,7 @@
 from easydiffraction.analysis.calculators.base import CalculatorBase
 from easydiffraction.analysis.calculators.factory import CalculatorFactory
 from easydiffraction.core.metadata import TypeInfo
+from easydiffraction.utils.logging import log
 
 if TYPE_CHECKING:
     from easydiffraction.datablocks.experiment.item.base import ExperimentBase
@@ -89,7 +90,7 @@ def calculate_structure_factors(  # noqa: PLR6301
         # PDF doesn't compute HKL but we keep interface consistent
         # Intentionally unused, required by public API/signature
         del structures, experiments
-        print('[pdffit] Calculating HKLs (not applicable)...')
+        log.debug('[pdffit] Calculating HKLs (not applicable)')
         return []
 
     def calculate_pattern(  # noqa: PLR6301

src/easydiffraction/analysis/categories/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""CIF categories for fitting analysis configuration."""
 
 from easydiffraction.analysis.categories.aliases import Alias
 from easydiffraction.analysis.categories.aliases import Aliases

src/easydiffraction/analysis/categories/aliases/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Parameter alias categories for fit expressions."""
 
 from easydiffraction.analysis.categories.aliases.default import Alias
 from easydiffraction.analysis.categories.aliases.default import Aliases

src/easydiffraction/analysis/categories/aliases/default.py

@@ -40,7 +40,7 @@ def __init__(self) -> None:
             name='label',
             description='Human-readable alias for a parameter.',
             value_spec=AttributeSpec(
-                default='_',  # TODO, Maybe None?
+                default='_',  # TODO: Maybe None?
                 validator=RegexValidator(pattern=r'^[A-Za-z_][A-Za-z0-9_]*$'),
             ),
             cif_handler=CifHandler(

src/easydiffraction/analysis/categories/constraints/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Parameter constraint categories for fitting."""
 
 from easydiffraction.analysis.categories.constraints.default import Constraint
 from easydiffraction.analysis.categories.constraints.default import Constraints

src/easydiffraction/analysis/categories/constraints/default.py

@@ -48,7 +48,7 @@ def __init__(self) -> None:
             name='expression',
             description='Constraint equation, e.g. "occ_Ba = 1 - occ_La".',
             value_spec=AttributeSpec(
-                default='_',  # TODO, Maybe None?
+                default='_',  # TODO: Maybe None?
                 validator=RegexValidator(pattern=r'.*'),
             ),
             cif_handler=CifHandler(

src/easydiffraction/analysis/categories/fit_parameter_correlations/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Fit parameter correlation categories from fit results."""
 
 from easydiffraction.analysis.categories.fit_parameter_correlations.default import (
     FitParameterCorrelationItem,

src/easydiffraction/analysis/categories/fit_parameters/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Refined fit parameter categories with values and errors."""
 
 from easydiffraction.analysis.categories.fit_parameters.default import FitParameterItem
 from easydiffraction.analysis.categories.fit_parameters.default import FitParameters

src/easydiffraction/analysis/categories/fit_result/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Fit-result categories for least-squares and Bayesian fits."""
 
 from easydiffraction.analysis.categories.fit_result.base import FitResultBase
 from easydiffraction.analysis.categories.fit_result.bayesian import BayesianFitResult

src/easydiffraction/analysis/categories/joint_fit/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Joint-fit categories for fitting multiple experiments together."""
 
 from __future__ import annotations
 

src/easydiffraction/analysis/categories/joint_fit/default.py

@@ -32,7 +32,7 @@ def __init__(self) -> None:
 
         self._experiment_id: StringDescriptor = StringDescriptor(
             name='experiment_id',
-            description='Experiment identifier',  # TODO
+            description='Experiment identifier',  # TODO: revisit description
             value_spec=AttributeSpec(
                 default='_',
                 validator=RegexValidator(pattern=r'^[A-Za-z_][A-Za-z0-9_]*$'),
@@ -44,7 +44,7 @@ def __init__(self) -> None:
         )
         self._weight: NumericDescriptor = NumericDescriptor(
             name='weight',
-            description='Weight factor',  # TODO
+            description='Weight factor',  # TODO: revisit description
             value_spec=AttributeSpec(
                 default=0.0,
                 validator=RangeValidator(),

src/easydiffraction/analysis/categories/sequential_fit/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Sequential-fit category for fitting experiments one by one."""
 
 from __future__ import annotations
 

src/easydiffraction/analysis/categories/sequential_fit_extract/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Categories for extracted results of a sequential fit."""
 
 from __future__ import annotations
 

src/easydiffraction/analysis/fit_helpers/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Fit-result reporting and Bayesian posterior summaries."""
 
 from easydiffraction.analysis.fit_helpers.bayesian import BayesianFitResults
 from easydiffraction.analysis.fit_helpers.bayesian import PosteriorPredictiveSummary

src/easydiffraction/analysis/fit_helpers/metrics.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""R-factor and reduced chi-square fit-quality metrics."""
 
 from __future__ import annotations
 

src/easydiffraction/analysis/fit_helpers/reporting.py

@@ -1,6 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
-
+"""Least-squares fit-result container and summary rendering."""
 
 from easydiffraction.analysis.fit_helpers.metrics import calculate_r_factor
 from easydiffraction.analysis.fit_helpers.metrics import calculate_r_factor_squared

src/easydiffraction/analysis/fit_helpers/tracking.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Track and display fit and sampler progress during optimization."""
 
 from __future__ import annotations
 

src/easydiffraction/analysis/fitting.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Fitter orchestrating model refinement via a pluggable minimizer."""
 
 from __future__ import annotations
 
@@ -16,6 +17,7 @@
 from easydiffraction.core.variable import Parameter
 from easydiffraction.datablocks.experiment.item.base import intensity_category_for
 from easydiffraction.utils.enums import VerbosityEnum
+from easydiffraction.utils.logging import log
 
 if TYPE_CHECKING:
     from easydiffraction.analysis.fit_helpers.reporting import FitResults
@@ -218,7 +220,7 @@ def fit(
                 analysis._clear_persisted_fit_state()
                 analysis.fit_results = None
             self.results = None
-            print('⚠️ No parameters selected for fitting.')
+            log.warning('No parameters selected for fitting.')
             return
 
         if analysis is not None and not fit_options.resume:

src/easydiffraction/analysis/minimizers/__init__.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2025 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Minimizer adapters for lmfit, bumps, dfo-ls and emcee."""
 
 from easydiffraction.analysis.minimizers.bumps import BumpsMinimizer
 from easydiffraction.analysis.minimizers.bumps_amoeba import BumpsAmoebaMinimizer

src/easydiffraction/analysis/minimizers/base.py

@@ -1,5 +1,6 @@
 # SPDX-FileCopyrightText: 2025 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Abstract base class for pluggable least-squares minimizers."""
 
 from abc import ABC
 from abc import abstractmethod

src/easydiffraction/analysis/minimizers/dfols.py

@@ -1,6 +1,6 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
-
+"""Derivative-free least-squares minimizer built on DFO-LS."""
 
 import numpy as np
 from dfols import solve