Refactors CryspyCalculator and updates SPDX compliance

Author: AndrewSazonov

src/easydiffraction/analysis/calculators/cryspy.py

@@ -160,6 +160,8 @@ def _recreate_cryspy_dict(
         cryspy_model_id = f'crystal_{sample_model.name}'
         cryspy_model_dict = cryspy_dict[cryspy_model_id]
 
+        # Update sample model parameters
+
         # Cell
         cryspy_cell = cryspy_model_dict['unit_cell_parameters']
         cryspy_cell[0] = sample_model.cell.length_a.value
@@ -186,15 +188,18 @@ def _recreate_cryspy_dict(
         for idx, atom_site in enumerate(sample_model.atom_sites):
             cryspy_biso[idx] = atom_site.b_iso.value
 
-        # ---------- Update experiment parameters ----------
+        # Update experiment parameters
+
         if experiment.type.beam_mode.value == BeamModeEnum.CONSTANT_WAVELENGTH:
             cryspy_expt_name = f'pd_{experiment.name}'
             cryspy_expt_dict = cryspy_dict[cryspy_expt_name]
+
             # Instrument
             cryspy_expt_dict['offset_ttheta'][0] = np.deg2rad(
                 experiment.instrument.calib_twotheta_offset.value
             )
             cryspy_expt_dict['wavelength'][0] = experiment.instrument.setup_wavelength.value
+
             # Peak
             cryspy_resolution = cryspy_expt_dict['resolution_parameters']
             cryspy_resolution[0] = experiment.peak.broad_gauss_u.value
@@ -206,13 +211,15 @@ def _recreate_cryspy_dict(
         elif experiment.type.beam_mode.value == BeamModeEnum.TIME_OF_FLIGHT:
             cryspy_expt_name = f'tof_{experiment.name}'
             cryspy_expt_dict = cryspy_dict[cryspy_expt_name]
+
             # Instrument
             cryspy_expt_dict['zero'][0] = experiment.instrument.calib_d_to_tof_offset.value
             cryspy_expt_dict['dtt1'][0] = experiment.instrument.calib_d_to_tof_linear.value
             cryspy_expt_dict['dtt2'][0] = experiment.instrument.calib_d_to_tof_quad.value
             cryspy_expt_dict['ttheta_bank'] = np.deg2rad(
                 experiment.instrument.setup_twotheta_bank.value
             )
+
             # Peak
             cryspy_sigma = cryspy_expt_dict['profile_sigmas']
             cryspy_sigma[0] = experiment.peak.broad_gauss_sigma_0.value

src/easydiffraction/analysis/calculators/pdffit.py

@@ -1,10 +1,10 @@
+# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-License-Identifier: BSD-3-Clause
 """PDF calculation backend using diffpy.pdffit2 if available.
 
 The class adapts the engine to EasyDiffraction calculator interface and
 silences stdio on import to avoid noisy output in notebooks and logs.
 """
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
-# SPDX-License-Identifier: BSD-3-Clause
 
 import os
 import re

src/easydiffraction/analysis/categories/aliases.py

@@ -1,10 +1,10 @@
+# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-License-Identifier: BSD-3-Clause
 """Alias category for mapping friendly names to parameter UIDs.
 
 Defines a small record type used by analysis configuration to refer to
 parameters via readable labels instead of raw unique identifiers.
 """
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
-# SPDX-License-Identifier: BSD-3-Clause
 
 from easydiffraction.core.category import CategoryCollection
 from easydiffraction.core.category import CategoryItem

src/easydiffraction/analysis/categories/constraints.py

@@ -1,10 +1,10 @@
+# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-License-Identifier: BSD-3-Clause
 """Simple symbolic constraint between parameters.
 
 Represents an equation of the form ``lhs_alias = rhs_expr`` where
 ``rhs_expr`` is evaluated elsewhere by the analysis engine.
 """
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
-# SPDX-License-Identifier: BSD-3-Clause
 
 from easydiffraction.core.category import CategoryCollection
 from easydiffraction.core.category import CategoryItem

src/easydiffraction/analysis/categories/joint_fit_experiments.py

@@ -1,10 +1,10 @@
+# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-License-Identifier: BSD-3-Clause
 """Joint-fit experiment weighting configuration.
 
 Stores per-experiment weights to be used when multiple experiments are
 fitted simultaneously.
 """
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
-# SPDX-License-Identifier: BSD-3-Clause
 
 from easydiffraction.core.category import CategoryCollection
 from easydiffraction.core.category import CategoryItem

src/easydiffraction/experiments/categories/experiment_type.py

@@ -1,11 +1,11 @@
+# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
+# SPDX-License-Identifier: BSD-3-Clause
 """Experiment type descriptor (form, beam, probe, scattering).
 
 This lightweight container stores the categorical attributes defining
 an experiment configuration and handles CIF serialization via
 ``CifHandler``.
 """
-# SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
-# SPDX-License-Identifier: BSD-3-Clause
 
 from easydiffraction.core.category import CategoryItem
 from easydiffraction.core.parameters import StringDescriptor

src/easydiffraction/experiments/experiment/bragg_sc.py

@@ -1,7 +1,6 @@
-"""Single crystal experiment types and helpers."""
-
 # SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
+"""Single crystal experiment types and helpers."""
 
 from __future__ import annotations
 

src/easydiffraction/sample_models/sample_models.py

@@ -1,7 +1,6 @@
 # SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
-
 from typeguard import typechecked
 
 from easydiffraction.core.datablock import DatablockCollection

src/easydiffraction/utils/utils.py

@@ -1,7 +1,6 @@
 # SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
-import importlib
 import io
 import json
 import os
@@ -10,6 +9,7 @@
 import zipfile
 from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version
+from importlib.util import find_spec
 from typing import List
 from typing import Optional
 from urllib.parse import urlparse
@@ -409,7 +409,7 @@ def is_colab() -> bool:
         bool: True if running in Google Colab PyCharm, False otherwise.
     """
     try:
-        return importlib.util.find_spec('google.colab') is not None
+        return find_spec('google.colab') is not None
     except ModuleNotFoundError:
         return False
 

tests/unit/easydiffraction/analysis/calculators/test_cryspy.py

@@ -1,7 +1,6 @@
 # SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
-
 def test_module_import():
     import easydiffraction.analysis.calculators.cryspy as MUT