Release: merge develop into master#132
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AndrewSazonov merged 6 commits intomasterfrom Mar 31, 2026
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* 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
…ble-category API (#128) * Refactor validation imports and remove unused DataTypes references * Refactor value specification to use 'data_type' instead of 'type_' in AttributeSpec * Refactor content_validator to validator in AttributeSpec * Refactor Cell class constructor to use default parameters and simplify attribute setting * Refactor AtomSite and SpaceGroup initializers to remove parameters and improve clarity * Refactor constructors in multiple classes to remove parameters and use property setters * Refactor add method to accept only keyword arguments for improved clarity * Refactor initialization of descriptors in multiple classes for consistency * Remove value initialization from validation class constructor * Refactor parameter value specification to remove DataTypes dependency * Refactor parameter initialization and property methods in mixin files * Refactor: streamline CIF handler initialization and add public property comments * Refactor ExperimentType initialization to use property setters * Refactor ExperimentType initialization to use property setters * Add temporary test script * Initialize parent class in guard.py constructor * Refactor peak-profile mixins to remove unused broadening and asymmetry methods * Refactor broadening parameter comments and remove unused initializations in TofPeak * Refactor parameter definitions to streamline unit assignments in various modules * Refactor CIF handler initialization for clarity and consistency * Refactor constructors in PdDataPoint mixins to remove kwargs * Refactor parameters module to variable module; update imports across multiple files * Refactor import statements for consistency and clarity * Refactor sample models to structures in project and related files * Refactor terminology from "sample" to "structure" in documentation and code comments * More refactoring from sample models to structures * Refactor factory methods, etc. * Refactor method names from `add_from_scratch` to `create` for consistency across collections * Rebuild classes structure * Refactor validation module by removing unused type checking decorator * Refactor PeakProfileTypeEnum to consider auto-extraction of peak profile info * Add revised design for all factories * Improve revised design for all factories * Add copilot instructions for EasyDiffraction project * Update all init files * Refactor metadata handling * Refactor type hints for optional parameters in collection.py * Add per-file ignores for __init__.py in Ruff configuration * Add TOF instrument and peak profile classes with compatibility and calculator support * Clarify usage of keyword arguments in copilot instructions * Add metadata dataclasses for factory-created classes * Refactor setter methods for improved readability and consistency * Refactor formatting of beam_mode and calculators in Chebyshev class * Update copilot instructions to clarify beta project guidelines * Update copilot instructions to clarify refactoring guidelines * Add architecture documentation for EasyDiffraction library * Refactor calculator management for joint and sequential fitting in experiments * Refactor code blocks in architecture.md to specify shell syntax highlighting * Document current and potential architectural issues in the codebase * Document current and potential issues in architecture * Document limitations of `FactoryBase` regarding constructor-variant registrations * Refactor calculator and minimizer factory methods for consistency and clarity * Refactor architecture documentation for improved clarity and consistency * Refactor logging and docstring formatting in analysis and factory modules * Refactor calculator and minimizer factory to use tag strings; update tests accordingly * Refactor core factory structure to eliminate duplication and unify metadata handling * Add initial experiment setup and analysis workflow for hrpt project * Update easydiffraction version and SHA-256 hash in pixi.lock * Refactor architecture documentation to clarify factory structures and display methods * Remove unused exports from __init__.py to streamline module interface * Refactor string quotes in test.py for consistency and readability * unify CollectionBase key resolution, add __contains__ and remove() * Make ExperimentType immutable after creation * Make peak and background read-only public properties * Document editable vs read-only property convention with _set_ private methods * Standardize switchable-category naming convention * Apply formatting * Refactor Analysis class to instantiate calculator in __init__ and remove class-level attribute * Remove duplicated symmetry methods from Structure * Route constraint updates through validated setter * Override _key_for in CategoryCollection and DatablockCollection * Warn when switching background or peak profile type * Document why minimisers bypass the value setter * Replace 'lmfit (leastsq)' with 'lmfit' in tests, tutorials, and docs * Consolidate revised-design-v5.md into architecture.md * Apply formatting * Update copilot instructions for linting and testing workflow * Enable dirty-flag guard via _set_value_from_minimizer * Add factory.py and metadata.py to package structure documentation * Consolidate all issues into issues.md and update copilot instructions * Move calculator from global Analysis to per-experiment * Add Bragg+PDF joint tutorial, multi-experiment docs section, and test * Temporarily disable Bragg+PDF joint fit until test is improved * Add universal factories for Extinction and LinkedCrystal * Add universal factories for all remaining categories * Update tutorial #14 * Add switchable-category API to all factory-created categories * Add switchable-category API for instrument and data on experiments * Filter show_supported_instrument_types by experiment context * Add target-audience and reliability instructions to copilot config * Convert fit_mode to CategoryItem * Convert fit_mode to factory-based category with enum comparison * Add flat category structure rule to architecture.md * Consolidate architecture docs and fix stale references * Restructure help() to show Parameters, Properties, and Methods tables * Auto-populate Analysis.help() from class introspection * Refine eager-imports rule to document lazy-import exceptions * Update tutorial structure in mkdocs.yml for clarity and consistency * Update issues list * Add instruction to run tutorial tests after changes * Refactor background type naming for consistency * Delete test.py * Fix tutorial failures and stale calculator cache with excluded regions * Update issues * Update tutorial names and copyright year
* Apply new templates * pixi run nonpy-format-fix * pixi run py-lint-fix * Disable some rules temporary * pixi run py-format-fix * Temporarily disable pydoclint until we are ready * Update license headers * Convert notebooks * Clean up * Add missing deps to test workflow * Add parameter-property consistency checker * Use structural type extraction in param consistency checker * Enhance property docstrings and type hints for clarity and consistency * Enhance docstrings by including type annotations for setter arguments * Ignore E501 lint rule in favor of formatter and W505 * Update line length settings in pyproject.toml for consistency and clarity * Simplify property docstring template and checker * Wrap long property docstrings to satisfy max-doc-length * Switch from docformatter to format-docstring * Apply formatting * Apply formatting * Convert docstrings from google to numpy style: Step 1 * Remove docstring-format-check * Convert docstrings from google to numpy style: Step 2 * Convert docstrings from google to numpy style: Step 3 * Enable ANN rules * Apply linting and formatting * Run docstring format fix for src/ only * Add types to the Parameters sections in docstrings * Apply docstrings formatting * More rules * Bump dependencies * Add some missing docstrings to public methods * New combination of rules * Make all docstring summaries to take single line * More docstring fixes * Remove unused script * Fix D401: use imperative mood in all docstring summaries * More formatting and linting * More fromatting * Add missing D101 class docstrings across 9 files * Add missing D105 magic method docstrings across 3 files * Minor changes * Fix broken nav entry, tutorial links, and anchor in docs * Bump dependencies * Refactor tutorial display to remove description and update title in index * Add platform-specific dependencies for GNU Scientific Library and libc++ on macOS * Consolidate GNU Scientific Library dependency for macOS in pixi.toml and test.yml
* Create and use load_numeric_block method in io/ascii.py * Disable some rules for docs/ * Initial implementation of the new tutorial * Add add_from_zip_path to Experiments collection * Update data index hash * Use data from web repo * Use another dataset * Save project after every fit * Clean up * Initial implementation of plotting parameter evolution * Replace conditions category with diffrn using CIF naming * Simplify extract_metadata API and make data loading explicit * Fix fit_results to store snapshot parameters per experiment * Clean up tutorial ed-17.py duplicate plot_param calls * Fix test to use save_as() matching current ProjectInfo.path default * Add integer index support to CollectionBase.__getitem__ * Rename plot_param to plot_param_series with versus descriptor * Clean up tutorial * Update docs with new notebook * Simplify constraints API to single expression string * Fix docstring lint errors in CollectionBase.__getitem__ * New dataset and update tutorials * Update T-scan notebook * Fix Windows CI UnicodeDecodeError in script test runner
* Create and use load_numeric_block method in io/ascii.py * Disable some rules for docs/ * Initial implementation of the new tutorial * Add add_from_zip_path to Experiments collection * Update data index hash * Use data from web repo * Use another dataset * Save project after every fit * Clean up * Initial implementation of plotting parameter evolution * Replace conditions category with diffrn using CIF naming * Simplify extract_metadata API and make data loading explicit * Fix fit_results to store snapshot parameters per experiment * Clean up tutorial ed-17.py duplicate plot_param calls * Fix test to use save_as() matching current ProjectInfo.path default * Add integer index support to CollectionBase.__getitem__ * Rename plot_param to plot_param_series with versus descriptor * Clean up tutorial * Update docs with new notebook * Simplify constraints API to single expression string * Fix docstring lint errors in CollectionBase.__getitem__ * New dataset and update tutorials * Update T-scan notebook * Add fit verbosity parameter with full, short and silent modes * Update notebook * Add project-level verbosity with full, short and silent modes * Improve grammar and consistency in ed-17 tutorial * Fix docstring lint errors in data loading methods * Increase notebook cell timeout to 1200s for T-scan tutorial
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #132 +/- ##
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- Coverage 82.93% 82.04% -0.90%
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Files 89 133 +44
Lines 5463 6916 +1453
Branches 453 581 +128
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+ Hits 4531 5674 +1143
- Misses 761 1037 +276
- Partials 171 205 +34
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This PR is created automatically to trigger the release pipeline. It merges the accumulated changes from
developintomaster.It is labeled
[maintainer] auto-pull-requestand is excluded from release notes and version bump logic.