Release: merge develop into master #109
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* Simplifies branch processing and installs badgery * Adds flag for unit test coverage in .badgery.yaml * Updates dependencies and easydiffraction shortcuts * Adds dashboard build trigger post-tutorial tests * Updates tutorial command names in workflow script * Simplifies installation by using all extras * Adds dashboard build trigger after PyPI tests * Refactors sample model creation architecture * Updates sample model API in tests * Updates sample model API in tutorials * Refactors argument validation and simplifies CIF reading * Update SampleModel API and adjust linked phases check * Increase McCabe complexity limit and add dependency * Fixes dev-install command in pixi.toml * Adds centralized logging utility * Adds function to parse CIF-style numeric strings to ufloat * Refactors core object model for improved structure * Refactors ID attributes to use entry_name consistently * Refactors alias and constraint classes * Refactors core objects to enhance category handling * Refactors core components and structures for enhanced clarity * Adds CIF alias utility functions to enhance data handling * Add test suite for SampleModels components and fix imports * Updates package versions in dependency lock file * Introduce allowed attributes and update collection initialization * Adds allowed attributes to mixins for parameter handling * Refactors CIF conversion by removing method calls * Enhances attribute validation in CryspyCalculator * Allow editing of uncertainty and free attributes * Refines CIF data parsing and handling logic * Modifies model initialization and linking * Refines instrument and peak attribute handling * Fixes bug in parameter setting logic * Refactors parameter attributes and access methods * Enhances background and model flexibility * Rename error handling methods and adjust datablock management * Refactors entry name handling in core classes * Standardizes 'entry_name' to 'category_entry_name' * Enhances sample model and plotting configuration * Enhances item management in CategoryCollection * Adds allowed attributes to SingleCrystalExperiment * Replaces human-readable ID generation with property access * Comments out unit test step from pre-push hook * Disables physical parameter bounds * Refines physical constraints and simplifies code * Refactors method calls to use add_from_args for clarity * Refactors method calls and updates numeric constants * Updates parameter bound handling and method naming * Refactors method calls to improve clarity * Refines attribute access and updates test methods * Refactors item addition in CategoryCollection * Refactors unit tests to use full_cif_names * Refactors parameter access and method calls * Refines attribute naming for clarity in background model * Adjusts default renderer for PyCharm environment * Updates attribute checks, adds data files, renames scripts * Adds extra test configuration and refines unit tests * Refactors attribute access and control logic * Enhances logging and error handling mechanism * Simplifies error handling in logging with 'raise from' * Refactors core objects for modular design * Improves logging behavior during pytest * Simplifies py-format-fix command * Refactors parameter descriptor hierarchy * Enhances logging and documents parameter abstraction * Refactors test cases to align with new API and data structures * Cleans up test imports and simplifies assertions * Refactors singleton tests for consistency * Refines descriptor/parameter handling logic * First attempt to add CifMixin to parameter classes * Updates CifMixin.cif_uid to use full_name * Refactors parameter abstraction layer * Enhances Logger configuration with environment variables * Refactors lazy loading in __init__.py for efficiency * Consolidates attribute guard mixins and refactors logic * Move mixins to guarded base class * Refactors core component architecture * Replace enforce_type with typeguard for runtime type checking * Remove legacy signature from add method and update tests * Enhances category item renaming logic (ugly temporary workaround) * Refactors attribute handling in parameter classes * Enhances Project class with type-checking and encapsulation * Refines __str__ method and fixes super call * Enhances collection handling by implementing AbstractCollection * Enhances type safety with generics for collections * Add SPDX license headers to source files * Initialize base class in CollectionBase constructor * Refactors parameter access for consistency * Removes unnecessary Generic typing * Work in progress * Enhances identity resolution and string representation * Improves parameter retrieval in collections * Adds `full_name` property to multiple classes * Simplifies attribute handling in GuardedBase * Renames full_name property to unique_name * Refines validation logging messages * Adds configurable error reaction in Logger * Enhances type error diagnostics in checktype decorator * Giant refactoring * Refactors parameter handling in FitResults * Refactors descriptor properties and enhances validation * Removes unused TODO comments and corrects assertions * Adds SPDX license headers to source files * Enhances space group validation logic * Refactors validation logic for atom site properties * Adds missing newline in atom_sites.py * Refactors CIF conversion and updates test format * Reformats code for consistency and clarity * Refines parameter handling and improves validation * Refactors tests to improve readability and maintainability * Enhances atom site configuration in tutorials * Enhances x-axis data selection for plotting * Refactors atom site addition for clarity and consistency * Fixes parameter limit handling * Fixes attribute assignment and model access * Refactors data extraction with list comprehensions * Refactors constraint handling and data access methods * Enhances peak profile type handling in experiments * Removes unused public attributes method * Improves logging settings and Python path resolution * Refines validators with enhanced logging * Adds parameter validation and logging enhancements * Replaces diagnostics and validators with an enhanced implementation * Adds Diagnostics for Type Override and Enhances Collections * Enhances validation and logging mechanisms * Refactors validator and identity handling * Replaces RegexValidator with AttributeSpec for validation * Maintain parent linkage for nested objects * Corrects attribute access in identity resolution * Refactors validation types to use DataTypes enum * Refines type validation logic in diagnostics * Replace UUID with secure random UID generation * Refines atom site validations and logging * Enhances validation logic and diagnostics handling * Relocates CifHandler to new IO module for clarity * Refactors experiment enums structure * Updates peak mixin imports for better organization * Refactors instrument setup for improved modularity * Refactors background module implementation * Refactors CIF serialization methods * Refactors CIF serialization to centralized functions * Removes obsolete CIF conversion methods * Restructures experiment type classes for modular design * Refactors instrument handling and restructures sample models * Reorganizes import paths to category_items * Refactors component naming for better clarity * Refactors code to categorize collections * Reorganizes import paths to use category_collections modules * Refactors background type handling for clarity * Refactors background handling and reorganizes enums * Refactors background and instrument modules organization * Refactors instrument and peak base class imports * Refactors argument validation in ExperimentFactory * Refactors import paths for consistency * Refactors datastore architecture for segregation of types * Fixes property getter for uncertainty * Add and update SPDX license headers across files * Adds package structure documentation generator * Renames datastore type modules for clarity * Refactors package structure for clarity * Renames and restructures package directories for clarity * Renames core modules for consistency * New unit tests * Refactors factory method usage in test suite * Add unit tests for various components in easydiffraction * Adds unit test for crystallographic and experimental data * Enables macOS h5py dependency for validation * Replaces scaffold tests with concrete test implementations * Replaces test scaffolds with concrete tests * Adds comprehensive test coverage for core modules * Format tests * Enhances SPDX header update for tests directory * Cleans up tests and refines pytest configuration * Refines config and reorganizes files for tmp exclusion * Adds comprehensive docstrings to Analysis classes and descriptors * Enhances experiment class documentation * Updates .gitignore for test and linter caches * Removes Python cache before packaging artifacts * Updates python_socketio and mkdocs-jupyter dependencies * Adds multiple Python cache removal steps * Adds dev-install step in GitHub workflow * Removes redundant dev-install command from workflow * Reorganizes dependency configuration * Refactors Python cache removal in workflow * Refactors to use Factory classes for model and experiment creation * Enhances enums with descriptive methods * Enhances documentation with docstrings * Add missing documentation for core modules * Adds docstrings for improved code documentation * Updates pytest configuration for test management * Refactors CryspyCalculator and updates SPDX compliance * Remove commented code and add documentation placeholders * Adds environment variable for CI branch
* Converts print statements to logging * Refactors plotting module to display module * Refines parameter handling and logging functionality * Refines CIF serialization and updates docs * Refines renderer architecture and error handling * Refines logging and utils import structure * Refines table rendering and error handling logic * Enhances logging with customizable rich formatting * Refactors plotting modules and updates test expectations * Refactors logger and environment detection functions * Switches logging from log to console * Improves axis scaling for asciichartpy * Refactors logging utility with enhanced features * Renames utils module for clarity * Enhances display and tracking in analysis module * Disable Jupyter notebook output scrolling * Rename environment checks for clarity * Remove redundant type ignores and streamline exception handling * Improves console width detection for flexible environments * Refactors logging modes and console output methods * Enhances logging utilities with improved docs * Removes unused imports and obsolete functions * Refactors logging architecture for clarity * Removes unused show_index parameter * Refactors logger configuration setup * Reorders render_table arguments for clarity * Refactors parameter table rendering and identity handling * Removes redundant header handling in render_table * Adds structure refinement example scripts * Refactors test environment detection logic * Enhances table styling with padding and font size * Refactors logger imports and removes lazy loading * Suppresses user warnings in pytest configuration * Adds SPDX license headers to utils.py * Reorganizes display and logging structure * Refines logging initialization and aliases * Activates commented pre-commit hooks * Adds SPDX license identifiers to init files * Enhances Pandas table styling * Removes Jupyter-specific logic from CIF renderer * Updates deps * Temporarily disable Jupyter scroll in MkDocs * Improves table styling for enhanced readability * Add conditional doc build for branch environments
* Adds CIF parsing capabilities to Category and Parameter classes * Refines error logging using _log_name * Refactors for CIF parsing functionality * Enhances CIF parsing support in experiments: 1st step * Enhances CIF parsing in SampleModelFactory * Refactors CIF handling in SampleModelFactory and enhances DatablockItem with categories property * Enhances CIF handling in SampleModelFactory * Refactors ExperimentType initialization to use default values and updates experiment handling in factory methods * Refactors dependencies section in pixi.toml * More refactoring of old datastore towards new data * Refactors symmetry constraint methods in AtomSites and Cell classes for clarity and consistency * Refactors category update handling and updates CIF serialization methods * Refactors update methods and intruduces update_priority attribute * Refactors category update calls in CalculatorBase and Fitter classes for consistency * Refactors calculation methods and updates category handling in analysis and experiment modules * Refactors PdCwlData and PdDataBase classes for improved structure and clarity * Refactors category update handling in Project class and consolidates update logic for plotting methods * Refactors PdDataBase and PdCwlData classes to introduce d-spacing calculations and update methods for improved data handling * Refactors CIF serialization methods by removing unused datastore functions and simplifying experiment data handling * Adds Refln and ReflnData classes for single crystal diffraction data handling; removes obsolete ScDatastore class * Refactors data handling by replacing 'datastore' references with 'data' * Clean up code across multiple modules * Refactors Analysis class by removing unused calculator variable and simplifies fitting method; deletes obsolete datastore test files * Refactors add methods in various classes * Refactors LineSegment and ExcludedRegion classes to add 'id' parameter * Refactors one of the tutorials to fit new API * Refactors PolynomialTerm, LineSegment, and ExcludedRegion classes to add 'id' parameter * Add missing SPDX license headers * Refactor PolynomialTerm, LineSegment, and ExcludedRegion classes to set default values for parameters * Mark parameters as free if uncertainty is present in CIF deserialization * Update Biso values in lbco.cif to include uncertainty and remove unnecessary data * Add minimal example for Rietveld refinement using LBCO and HRPT data * Remove unnecessary blank line before showing project summary report * Refactor minimal example to streamline project and experiment definitions, removing unnecessary logging and aliases * Remove trailing whitespace from multiple files * Refactor joint_fit_experiments method call to use 'add' instead of 'add_from_args' * Refactor add method in Experiments and SampleModels to allow explicit sample/experiment input * Refactor Chebyshev and LineSegment models to include identifier descriptors and improve documentation * Refactor PdDataPoint classes to update point_id type and adjust mixin order * Refactor SampleModelFactory to introduce _create_minimal method for creating default models * Update tutorials * Add new data classes for powder diffraction and total scattering experiments * Temporary disable unit tests hook from pre-push checks * Add d_spacing property to PdDataBase for calculated d values * Refactor tutorials * Refactor format_value function to improve value formatting and precision handling * Refactor category_collection_to_cif function for improved readability and structure * Add analysis output for free parameters in project * Fix category_entry_name handling to ensure it defaults to an empty string * Update default values in ExperimentType to use enum values directly * Update functional tests following API changes * Update unit tests following new API * Refactor sample model and experiment addition methods * Enhance Chebyshev and LineSegment classes with improved background handling and id property * Refactor Chebyshev and LineSegment background tests to use mock parent data structure * Enhance Analysis and Fitter classes to update categories during fitting process * Refactor CategoryCollection to optimize child instance creation logic * Refactor test_fit_neutron_pd_cwl_hs to improve background data handling and enhance project setup * Refactor sample model addition in tutorials to use updated method * Fix fill_value in LineSegmentBackground interpolation to use correct y values * Update category handling in Fitter * Refactor time-of-flight to follow new API * More fixes of the functional tests * Refactor test_joint_fit * More refactoring in fitting tests * More refactoring of the tutorials to follow new API * Fix formatting * Update unit tests to follow new API * Refactor CIF string handling in Experiment and SampleModel factories * Refactor package structure by removing obsolete files and adding new data modules * Add '_pd_proc.intensity_norm' and '_pd_proc.intensity_norm_su' to CIF handler * Add integration tests for reading CIF files from Scipp * Rename functional tests to integration tests * Add SPDX license headers to test_scipp-cif.py * Extend tutorial section in docs * Refactor test for reading CIF files from Scipp * Bump deps * Pin pdffit2 to be <1.5.2 due to the issues or changed API in the latest versions * Add temporary workaround for pdffit2 installation in CI workflow * Update dependencies in pixi.toml and pyproject.toml for pdffit2 compatibility * Remove temporary workaround for pdffit2 installation in CI workflow * Add id-based data download API; update tutorials * Adopts download_data in tests; prunes local data * Excludes TOF regions in neutron PD fit test * Removes repo download util; updates index hash * Updates tutorial to new data download API * Adapts tests to index-based download_data * Uses returned data paths instead of hardcoded ones * Debugging (3089,) (3098,) (3089,) * Runs script tests serially (temporarily?) * More debugging * Runs tutorial scripts in isolated subprocesses * Streamlines tutorial tests in CI workflow * Justifies subprocess use in tests; adds noqa tags
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## master #109 +/- ##
===========================================
+ Coverage 71.57% 82.26% +10.68%
===========================================
Files 47 88 +41
Lines 3550 5451 +1901
Branches 373 454 +81
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+ Hits 2541 4484 +1943
+ Misses 894 802 -92
- Partials 115 165 +50
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