Release: merge develop into master#179
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* Move essdiffraction to dev deps and simplify test * Add dev and user features to pixi.toml * Apply latest templates * Isolate tagged docs deployments from dev runs * Remove resolved dev documentation * Remove resolved ADP implementation plan
* Add Bayesian analysis design note * Add arviz for Bayesian analysis * Remove old package structure documentation * Update package structure docs with refln reorganization * Plan Bayesian DREAM implementation * Register BUMPS DREAM minimizer * Add Bayesian fit result models * Thread random seed through fitting * Implement DREAM sampling * Add Bayesian fit result display * Plot Bayesian parameter correlations * Add posterior ArviZ plots * Add posterior predictive plots * Refine Bayesian fit UX * Fix DREAM sampler progress reporting * Fix posterior pair plot axis sharing * Improve Bayesian demo parameter choices * Expose DREAM sampler settings * Render posterior marginals as KDE curves * Add posterior pair density contours * Switch Bayesian demo to correlated pair * Add Bayesian tracking and posterior plot updates * Add posterior draws and log-posterior tracking * Use population mean log-posterior for progress tracking * Polish Bayesian progress and posterior plots * Fix DREAM diagnostics and posterior KDEs * Refine posterior plot styling * Improve posterior pair plot UX * Add uncertainty-based fit bounds method * Tighten posterior pair plot layout * Make fit bounds helper a setter * Refine posterior contour layering * Fix posterior contour layering * Preserve pair plot sample hover * Enforce pair plot trace z-order * Restore pair plot axis frames * Split posterior diagnostic warnings * Strengthen pair plot axis borders * Free broad_gauss and set bounds from uncertainty * Draw explicit pair plot borders * Align pair plot y-axis titles * Unify plot axis border colors * Lock posterior pair axis ranges * Align pair plot title with modebar * Update diagonal subplot axis styling * Expose DREAM init and align pair labels * Tighten fit bounds multiplier from 5 to 4 * Match pair plot axis title font sizes * Disable Rich highlighting in Bayesian summaries * Tune DREAM and model parameters in fit * Expand Bayesian tutorial walkthrough * Apply linting rules and formatting * Add LBCO Bayesian tutorial * Make posterior pair plots responsive * Add DREAM bound validation and flexible parameter selection * Adopt fixed-aspect CSS for posterior pair plots * Add posterior pair plot rendering modes * Add multiline axis titles to posterior pair plots * Redesign correlation heatmap display * Simplify tutorial parameter loops and bounds * Improve hover template readability * Improve posterior plot binning and styling * Refactor posterior x-axis range to static method * Change posterior predictive default style to band * Add separate caching for band summaries * Reduce sampling steps and adjust plot ranges * Update posterior pair plot marker and background * Update notebooks * Fix docstring errors in Plotter class * Standardize axis title font size * Improve Bayesian fit summary display * Improve Bayesian fit result display * Adjust posterior and band fill transparency * Update fit bounds and plot range in ed-21 * Improve posterior table diagnostic notes * Add parallel DREAM sampling * Add parallel=0 description to DREAM tutorial * Fix test expectations for r-hat and parallel=0 * Add Bayesian DREAM to architecture * Clean up * Fix Bayesian diagnostics and DREAM cleanup edge cases * Fix square matrix plot spacing and aspect ratio * Apply the latest templates * Bump setup-pixi to v0.9.5 * Bump dependencies * Bump pixi.lock from v6 to v7 * Add correlation-based limits to posterior pair plots * Improve posterior summary plot styling * Add single-crystal posterior predictive scatter plot * Add Tb2TiO7 Bayesian tutorial * Set default correlation and pair-plot limit to six * Bump copier template to v0.11.3 * Update tutorials * Adjust posterior pair plot margins and title shift * Generalize pair-plot layout to square matrix * Switch DREAM defaults and refine Bayesian fit displays * Show uncertainty multiplier in pair plot titles * Refine Bayesian tutorial examples * Shorten fit-bounds multiplier constant name * Bump dependencies * Add ADR documents * Improve CI and codecov settings * Fix structure factor support for X-ray * Increase integration coverage for Bayesian fit helpers * Remove unused benchmark dependency and track serial benchmarks * Normalize styled console output in Windows integration tests
* Add display UX ADR and plan * Rename display settings category to rendering * Add grouped display facade * Move constraint display and standardize CIF helpers * Refine display pattern routing * Implement state-aware pattern display * Update display UX documentation * Complete display UX verification and test updates * Address display UX review fixes * Fix single-crystal display availability checks
…ut (#172) * Reorganize dev documentation files * Hide refln in parameter summary displays * Exclude symmetry-fixed parameters from fittable displays * Rename parameter constraint state flags * Adopt bulk-created loop items into collections * Add help methods to display facades * Add help discovery helpers to analysis display * Add activity indicator implementation plan * Omit empty CIF fragments from serialization * Add Quick Reference page to docs * Uncomment display calls, simplify save in tutorial
* Add shared activity indicator helper * Wire fit tracker activity indicator * Reuse activity indicator for sequential fitting * Restore shared display handle compatibility * Show processing indicator for posterior displays * Prevent notebook progress table stretching * Add activity label constants and styling * Refine progress indicator styling * Refactor progress indicator context manager * Format posterior predictive call * Rename 95% interval, remove 68% interval * Refactor progress indicator to use dynamic renderable * Share display handle across multi-experiment fits * Add timed progress updates for fit tracking * Prevent progress indicator errors on exception * Remove completed progress indicator plan
* Use full samples for pair-plot marginal KDEs * Support posterior distribution defaults * Support ASCII posterior predictive plots * Add ASCII posterior density plots * Update console heading color to deep_sky_blue3 * Guard DREAM multiprocessing for direct script entry points * Remove unused colorama and tabulate dependencies * Normalize docstring formatting * Add DREAM multiprocessing CLI workflow issue * Resample ASCII plots to terminal width * Simplify posterior distribution display in tutorials * Fit ASCII plot range to terminal width * Use 'processing' label for sampler tracking * Clean up code formatting * Add posterior display documentation * Refactor plotting and ASCII chart constants * Simplify posterior display calls in tutorials
* Rename Bayesian MAP labels to best posterior sample * Add ADR for fit mode categories * Refine fit-mode categories ADR with active-sibling pattern * Add open questions and drop fitting.mode mirror in ADR * Add implementation plan for fit-mode-categories ADR * Rename CIF field _fitting.mode to _fitting.mode_type * Tighten high-risk steps in fit-mode-categories plan * Add BoolDescriptor for CIF-bound boolean values * Add fitting category replacing fit configuration surface * Add fitting_mode_type selector and fitting accessor on Analysis * Rename joint_fit_experiments category to joint_fit * Add sequential_fit category with persisted scan settings * Add sequential_fit_extract category for scan metadata rules * Replace fit category with Analysis.fit() method * Drive sequential fitting from sequential_fit settings * Auto-populate joint_fit rows and validate before fitting * Add instance-aware help filter and hide inactive mode categories * Serialize only active mode-specific analysis categories * Restore mode before mode-specific analysis sections * Update tutorials, docs, and exports for new fitting API * Resolve ZIP extraction relative to saved project * Add live progress tables for sequential fitting * Set sequential fitting mode and save project * Complete fit-mode categories and refactor progress * Fix sequential replay, styling, and docs * Simplify sequential progress table headers * Add progress and time columns to sequential tables * Unify sequential and single fit spinners on ActivityIndicator * Fix spacing in chunk file range display * Render sequential progress as bordered table with index column * Render sequential progress with shared single-fit table renderable * Add fit.series_all to plot every fitted parameter * Unify fit.series to plot single or all fitted parameters * Encapsulate chunk progress in dataclass * Use string paths for versus parameter * Unify ASCII plot width handling across terminal charts * Sort ASCII parameter series by x before plotting * Skip fit reports for sequential mode * List all analysis files on save * Bump dependencies * Add resumed sequential-fit tutorial for Co2SiO4 * Update data index reference and hash * Clear sequential fit state and make ZIP extraction explicit * Update data index reference and hash * Normalize sequential CSV paths for resumed fits * Update data index reference and hash * Add resume fit tutorial and fix paths * Normalize CSV relative paths to POSIX style * Remove project save step from tutorial * Accept fit-mode categories ADR * Move Quick Reference to end of nav * Lower coverage threshold to 65%
* Add CategoryOwner ADR and migration plan * Add category-owner baseline tests * Add CategoryOwner base class * Make DatablockItem inherit CategoryOwner * Split category-owner CIF serialization * Make Analysis inherit CategoryOwner * Generalize dirty-flag lookup to CategoryOwner * Document CategoryOwner architecture changes * Move project info into ProjectConfig categories * Plan Project-to-Workspace rename * Finalize CategoryOwner refactor * Standardize project.save_as usage in tutorials * Ignore projects directory * Mark verification steps as complete * Accept CategoryOwner ADR and remove migration plan
* Document verbosity category and workspace.cif layout * Reorganize development documentation structure * Tighten workspace migration plan for autonomous implementation * Consolidate ADR index into single table * Add loop category key identity ADR and plan * Add declarative category identity resolution * Declare category identities on current items * Persist explicit constraint identifiers * Update ADR for declarative category identity * Verify declarative category identity behavior
* Split persistence ADR and add fit output ADR * Add artifact root for reproducible tutorials * Finalize Project facade decision * Store auto rendering defaults in project config * Accept loop category key identity ADR * Add project save to ed-2 tutorial * Remove extraneous blank line * Add project fit verbosity category * Add analysis fit state implementation plan * Reformat documentation tables and line breaks * Add project fit verbosity verification * Clarify analysis fit-state ADR schema * Add common analysis fit-state categories * Add deterministic fit-result categories * Add Bayesian fit-result metadata categories * Add Bayesian fit-cache manifest categories * Add project save step to tutorial * Wire analysis fit-state CIF restore * Linting and formatting * Add h5py dependency * Capture persisted fit-state projections * Persist Bayesian fit arrays in results sidecar * Restore fit results from saved analysis state * Align persisted fit-state schema with review feedback * Persist Bayesian plot caches in sidecar * Add integer type and skip redundant processing * Update tutorial notebooks with consistent IDs and saves * Add pre/post-processing tracking to Bayesian fits * Add project-first CLI commands for saved projects * Fix missing pre-processing row in DREAM progress table * Add CLI commands for example data downloads * Remove pattern display from tutorial * Group saved-project tutorials under Load Project * Consolidate download and extract in tutorials * Refactor Bayesian fit-state manifest create APIs * Remove deterministic parameter-result persistence * Update data index reference and hash * Consolidate saved project tutorials to download_data * Remove deterministic_parameter_results from docs * Revise docs for CLI syntax and project loading * Update undo command to show it's a placeholder * Harden fit-state sidecar paths and finalize ADR * Reorder CLI command definitions * Restore saved DREAM sampler settings on project load * Restore legacy DREAM sampler settings before CLI fit * Clarify DREAM multiprocessing issue for direct scripts * Update data index ref and hash * Add DREAM multiprocessing issue #95 * Remove obsolete package references from docs * Update CIF serializer test for long descriptions * Update ADR suggestions for implemented fit-state work * Accept parameter correlation persistence ADR * Rename sequential fit result CSV columns * Add overwrite option to Project.save_as * Improve code formatting and docstrings * Update data index reference and hash * Simplify tutorial with API shortcuts * Improve tutorial index descriptions * Accept str or list for column_names * Fix fit tracking finalization cleanup * Add tutorial benchmark runner and pixi task * Write benchmark results incrementally * Reduce tutorial computation time and fix data ID * Simplify tutorial titles for consistency * Honor max_iterations in BUMPS fits * Add tutorial benchmark results * Refactor BumpsMinimizer evaluation limit handling * Plot fit quality vs temperature * Improve output formatting and add logging * Optimize tutorial execution time * Add newline before saved path * Remove notebook timeout, add CI artifact root
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## master #179 +/- ##
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- Coverage 88.52% 85.77% -2.76%
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Files 154 210 +56
Lines 9475 15884 +6409
Branches 990 1831 +841
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+ Hits 8388 13624 +5236
- Misses 764 1548 +784
- Partials 323 712 +389
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This PR is created automatically to trigger the release pipeline. It merges the accumulated changes from
developintomaster.[bot] releaseand is excluded from release notes and version bump logic.