Add single-crystal diffraction support via cryspy (#127)

* Implement the extinction category

* Implement the linked crystal category

* Add base class for single crystal experiments

* Clarify sy handling; move background property

* Update BraggScExperiment class

* Add SC Bragg reflection data and linked crystal

* Add single-crystal Bragg CW data mapping

* Remove unused linked crystal validator

* Add minimizer flag to calculator API

* Remove lru_cache; update data index hash

* Add single-crystal Tb2TiO7 HEiDi tutorial

* Add TODO about sy handling when loading CIF

* Add single-crystal support to Cryspy calculator

* Add stol propagation and d-spacing for SC data

* Add d-spacing computation and fix plotting checks

* Update SC tutorial

* Use Cryspy-calculated intensity output

* Update SC tutorial

* Update data index checksum

* Add new SC-TOF tutorial

* Add TOF single-crystal support via Cryspy

* Apply formatting

* Cache tutorials index; adjust Bragg SC test

* Add single-crystal F2 meas-vs-calc plot

* Update SG tutorials

* Add Single Crystal Diffraction section to docs

* Update SC tutorial

* Lower coverage threshold to 60%

* Clarify Miller index and intensity descriptions

* Add TODOs and fix docstring

* Remove ED tutorial data; tidy pyproject comments

* Remove kwargs from Refln init; add return type

* Add units to extinction parameters

* Add single-crystal neutron fitting tests

* Reduce Ruff excludes; lint/format tests

* Simplify single-crystal category initializers

* Rename refln_id to id per coreCIF

* Add CW/TOF SC ASCII import with wavelength

* Rename plot_sg to plot_sc for single-crystal

* Add single-crystal scatter comparison plotting

* Extract scatter trace creation to helper

* Rename traces for powder and single-crystal

* Use Plotly autorange; drop fixed axis limits

* Extract Plotly config to helper

* Centralize Plotly figure display logic

* Refactor Plotly figure creation and formatting

* Draw identity line in paper coordinates

* Add reusable Plotly layout helper

* Extract diagonal reference line helper

* Rename plot methods for powder/single-crystal

* Reformat Plotly plotter for readability

* Clarify diffraction plotter docstrings

* Add single-crystal plotting tests

* Remove deprecated plot alias; update tests

* Add sin(theta)/lambda to d-spacing conversion

* Update SC data API; compute d-spacing via util

* Fix reflection index attribute names

* Add single-crystal support to plotter base

* Unify powder/SC plotting with axis auto-detect

* Unify plotting API; replace d_spacing with x

* Rename all_x to unfiltered_x

* Rename meas/calc to intensity_*; add axis aliases

* Rename TotalData module to total_pd

* Update tests for sample-form and intensity API

* Log read/validation errors; import numpy globally

* Move instrument and extinction to SC base

* Split Bragg SC into CWL/TOF; update factory

* Refactor single-crystal instrument support

* Move instrument init to BraggPdExperiment

* Update tests for Pd/Sc instrument classes

* Add scattering-type aware x-axis defaults

* Increase CIF float precision to 8 decimals

* Update pixi lock

* Update docs code examples for style consistency

* Pin scipp for ARM macOS; use editable local pkg

* Refactor plotting; unify axis and data prep

* Add macOS 14.0 minimum version requirement

* Update plot_meas_vs_calc calls to use 'x' parameter for d_spacing

Author: AndrewSazonov

docs/mkdocs.yml

@@ -73,12 +73,15 @@ nav:
           - LBCO quick code: tutorials/ed-2.ipynb
           - LBCO basic: tutorials/ed-3.ipynb
           - PbSO4 advanced: tutorials/ed-4.ipynb
-      - Standard Diffraction:
+      - Powder Diffraction:
           - Co2SiO4 pd-neut-cwl: tutorials/ed-5.ipynb
           - HS pd-neut-cwl: tutorials/ed-6.ipynb
           - Si pd-neut-tof: tutorials/ed-7.ipynb
           - NCAF pd-neut-tof: tutorials/ed-8.ipynb
           - LBCO+Si McStas: tutorials/ed-9.ipynb
+      - Single Crystal Diffraction:
+          - Tb2TiO7 sg-neut-cwl: tutorials/ed-14.ipynb
+          - Taurine sg-neut-tof: tutorials/ed-15.ipynb
       - Pair Distribution Function:
           - Ni pd-neut-cwl: tutorials/ed-10.ipynb
           - Si pd-neut-tof: tutorials/ed-11.ipynb

docs/tutorials/index.md

@@ -42,7 +42,7 @@ The tutorials are organized into the following categories.
   refinement of the PbSO4 crystal structure based on the joint fit of both X-ray
   and neutron diffraction data.
 
-## Standard Diffraction
+## Powder Diffraction
 
 - [Co2SiO4 `pd-neut-cwl`](ed-5.ipynb) – Demonstrates a Rietveld refinement of
   the Co2SiO4 crystal structure using constant wavelength neutron powder
@@ -61,6 +61,15 @@ The tutorials are organized into the following categories.
   secondary phase using time-of-flight neutron powder diffraction data simulated
   with McStas.
 
+## Single Crystal Diffraction
+
+- [Tb2TiO7 `sg-neut-cwl`](ed-14.ipynb) – Demonstrates structure refinement of
+  Tb2TiO7 using constant wavelength neutron single crystal diffraction data from
+  HEiDi at FRM II.
+- [Taurine `sg-neut-tof`](ed-15.ipynb) – Demonstrates structure refinement of
+  Taurine using time-of-flight neutron single crystal diffraction data from
+  SENJU at J-PARC.
+
 ## Pair Distribution Function (PDF)
 
 - [Ni `pd-neut-cwl`](ed-10.ipynb) – Demonstrates a PDF analysis of Ni using data

docs/user-guide/analysis-workflow/analysis.md

@@ -271,21 +271,21 @@ An example of setting aliases for parameters in a sample model:
 # Set aliases for the atomic displacement parameters
 project.analysis.aliases.add(
     label='biso_La',
-    param_uid=project.sample_models['lbco'].atom_sites['La'].b_iso.uid
+    param_uid=project.sample_models['lbco'].atom_sites['La'].b_iso.uid,
 )
 project.analysis.aliases.add(
     label='biso_Ba',
-    param_uid=project.sample_models['lbco'].atom_sites['Ba'].b_iso.uid
+    param_uid=project.sample_models['lbco'].atom_sites['Ba'].b_iso.uid,
 )
 
 # Set aliases for the occupancies of the atom sites
 project.analysis.aliases.add(
     label='occ_La',
-    param_uid=project.sample_models['lbco'].atom_sites['La'].occupancy.uid
+    param_uid=project.sample_models['lbco'].atom_sites['La'].occupancy.uid,
 )
 project.analysis.aliases.add(
     label='occ_Ba',
-    param_uid=project.sample_models['lbco'].atom_sites['Ba'].occupancy.uid
+    param_uid=project.sample_models['lbco'].atom_sites['Ba'].occupancy.uid,
 )
 ```
 
@@ -302,12 +302,12 @@ An example of setting constraints for the aliases defined above:
 ```python
 project.analysis.constraints.add(
     lhs_alias='biso_Ba',
-    rhs_expr='biso_La'
+    rhs_expr='biso_La',
 )
 
 project.analysis.constraints.add(
     lhs_alias='occ_Ba',
-    rhs_expr='1 - occ_La'
+    rhs_expr='1 - occ_La',
 )
 ```
 

docs/user-guide/analysis-workflow/experiment.md

@@ -105,20 +105,24 @@ explicitly defined:
 
 ```python
 # Add an experiment with default parameters, based on the specified type.
-project.experiments.add_from_data_path(name='hrpt',
-                                       data_path='data/hrpt_lbco.xye',
-                                       sample_form='powder',
-                                       beam_mode='constant wavelength',
-                                       radiation_probe='neutron',
-                                       scattering_type='bragg')
+project.experiments.add_from_data_path(
+    name='hrpt',
+    data_path='data/hrpt_lbco.xye',
+    sample_form='powder',
+    beam_mode='constant wavelength',
+    radiation_probe='neutron',
+    scattering_type='bragg',
+)
 ```
 
 To add an experiment of default type, you can simply do:
 
 ```python
 # Add an experiment of default type
-project.experiments.add_from_data_path(name='hrpt',
-                                       data_path='data/hrpt_lbco.xye')
+project.experiments.add_from_data_path(
+    name='hrpt',
+    data_path='data/hrpt_lbco.xye',
+)
 ```
 
 If you do not have measured data for fitting and only want to view the simulated
@@ -127,10 +131,12 @@ pattern, you can define an experiment without measured data using the
 
 ```python
 # Add an experiment without measured data
-project.experiments.add_without_data(name='hrpt',
-                                     sample_form='powder',
-                                     beam_mode='constant wavelength',
-                                     radiation_probe='x-ray')
+project.experiments.add_without_data(
+    name='hrpt',
+    sample_form='powder',
+    beam_mode='constant wavelength',
+    radiation_probe='x-ray',
+)
 ```
 
 Finally, you can also add an experiment by passing the experiment object
@@ -139,11 +145,14 @@ directly using the `add` method:
 ```python
 # Add an experiment by passing the experiment object directly
 from easydiffraction import Experiment
-experiment = Experiment(name='hrpt',
-                        sample_form='powder',
-                        beam_mode='constant wavelength',
-                        radiation_probe='neutron',
-                        scattering_type='bragg')
+
+experiment = Experiment(
+    name='hrpt',
+    sample_form='powder',
+    beam_mode='constant wavelength',
+    radiation_probe='neutron',
+    scattering_type='bragg',
+)
 project.experiments.add(experiment)
 ```
 

docs/user-guide/analysis-workflow/model.md

@@ -104,7 +104,7 @@ project.sample_models['nacl'].atom_sites.append(
     fract_y=0,
     fract_z=0,
     occupancy=1,
-    b_iso_or_equiv=0.5
+    b_iso_or_equiv=0.5,
 )
 project.sample_models['nacl'].atom_sites.append(
     label='Cl',
@@ -113,7 +113,7 @@ project.sample_models['nacl'].atom_sites.append(
     fract_y=0,
     fract_z=0.5,
     occupancy=1,
-    b_iso_or_equiv=0.5
+    b_iso_or_equiv=0.5,
 )
 ```
 

docs/user-guide/analysis-workflow/project.md

@@ -30,10 +30,10 @@ project = ed.Project(name='lbco_hrpt')
 
 # Define project info
 project.info.title = 'La0.5Ba0.5CoO3 from neutron diffraction at HRPT@PSI'
-project.info.description = '''This project demonstrates a standard refinement
+project.info.description = """This project demonstrates a standard refinement
 of La0.5Ba0.5CoO3, which crystallizes in a perovskite-type structure, using
 neutron powder diffraction data collected in constant wavelength mode at the
-HRPT diffractometer (PSI).'''
+HRPT diffractometer (PSI)."""
 ```
 
 ## Saving a Project

docs/user-guide/first-steps.md

@@ -41,12 +41,10 @@ example, you can import the `Project`, `SampleModel`, `Experiment` classes and
 `download_from_repository` method like this:
 
 ```python
-from easydiffraction import (
-    Project,
-    SampleModel,
-    Experiment,
-    download_from_repository
-)
+from easydiffraction import Project
+from easydiffraction import SampleModel
+from easydiffraction import Experiment
+from easydiffraction import download_from_repository
 ```
 
 This enables you to use these classes and methods directly without the package
@@ -73,9 +71,11 @@ For example, you can download a sample data file like this:
 ```python
 import easydiffraction as ed
 
-ed.download_from_repository('hrpt_lbco.xye',
-                            branch='docs',
-                            destination='data')
+ed.download_from_repository(
+    'hrpt_lbco.xye',
+    branch='docs',
+    destination='data',
+)
 ```
 
 This command will download the `hrpt_lbco.xye` file from the `docs` branch of