🎉 Release: merge develop into master#192
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* Draft minimizer category consolidation ADR * Add plans for minimizer consolidation and emcee * Add agent instructions and plan review workflow * Update minimizer consolidation plan after reviews * Move PosteriorParameterSummary to core * Add Parameter.posterior attribute * Add InitializationMethodEnum for samplers * Add MinimizerCategoryBase * Add concrete minimizer category classes * Resolve CIF '?' to descriptor default on load * Wire minimizer selector on Analysis owner * Serialize minimizer category to _minimizer.* CIF tags * Persist parameter posterior via _fit_parameter columns * Use Analysis.minimizer_type in non-analysis modules * Overwrite results.h5 on new fit with user warning * Absorb deterministic_result fields into LSQ minimizers * Read posterior plots from results.h5 groups * Remove obsolete Bayesian and fitting categories * Update tutorials for analysis.minimizer API * Promote minimizer-category-consolidation ADR * Complete Phase 1 review gate * Limit random seed category field to Bayesian minimizers * Prune unsupported LSQ minimizer descriptors * Address minimizer consolidation review comments * Remove obsolete minimizer category tests * Migrate tests to analysis minimizer selectors * Migrate project-load tests to minimizer state * Assert Bayesian projection sidecar payloads * Rewrite sidecar tests for consolidated results * Migrate fit-state tests to consolidated categories * Add minimizer category unit tests * Update Phase 2 test migration status * Apply Phase 2 fix and check updates * Update Phase 2 unit-test status * Stabilize DREAM integration tests * Update Phase 2 script-test status * Plan Phase-2 follow-ups P2.6-P2.10 from Review 8 * Compare FitResultKindEnum member in _should_use_sidecar results_sidecar._should_use_sidecar used a hard-coded 'bayesian' literal. Use FitResultKindEnum.BAYESIAN.value to follow the project convention of comparing against enum members. Implements P2.6 / F2. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * Default LSQ result descriptors to None for clean round-trip * Add reviewer constraint: no tests * Format minimizer-swap warning as removed/added lines * Validate Bayesian minimizer matches result_kind on restore * Tidy review-8 follow-ups (lint, hoisted F5 guard) * Reformat review-8 markdown files with prettier * Mark P2.10 verification complete * Propose switchable-category-owned-selectors ADR * Exempt review files from formatting pass * Incorporate switchable-category ADR review responses * Accept switchable category selector plan * Record accepted selector plan reply * Add SwitchableCategoryBase behavior-only mixin * Support collection-level scalar descriptors * Add owner-side switchable hook scaffolding * Wire analysis.minimizer to category-owned selector * Wire experiment.peak to category-owned selector * Wire experiment.background to category-owned selector * Wire experiment.extinction to category-owned selector * Rename Calculation to Calculator and wire to mixin * Split Rendering into Chart and Table sibling categories * Promote fitting_mode to FittingMode category * Drop persisted optimizer_name/method_name; add metadata dict * Remove owner-level selector shims and obsolete CIF tags * Update tutorials for category-owned selectors * Promote switchable-category-owned-selectors ADR * Complete Phase 1 review gate * Finalize fit timer before projecting result categories * Migrate tests to category-owned selectors * Run Phase 2 static fixes * Mark Phase 2 unit tests complete * Mark Phase 2 integration tests complete * Mark Phase 2 script tests complete * Collapse owner shadow state onto category descriptors * Simplify help() tables: drop # column, hide ✗, drop title * Raise on invalid category.type assignment * Validate chart/table types up-front and require parent on from_cif * Dispatch experiment filter context per switchable category * Narrow ed-24 archive normaliser to ID 35 with deletion roadmap * Delete completed consolidation and selector plan files * Delete obsolete switchable-selector ADR review/reply files * Apply formatting * Update tests to expect raise on invalid category.type * Adjust help-table tests for simplified row structure * Update pixi dependencies --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* Propose minimizer input/output split ADR * Address review 1 findings on minimizer input/output split * Address review 2: demote credible intervals; clarify context table * Address review 3: fix context list for credible-interval fields * Reply to review 4: all findings already addressed in earlier replies * Reply to review 5: both findings already addressed * Reply to review 6: single finding already addressed in reply 3 * Reply to review 7: clean signoff, no findings * Draft minimizer input/output split implementation plan * Address plan review 1: reset paths, defaults, imports, factory * Address plan review 2: migration map, reset hooks, CIF ordering * Address plan review 3: lead P1.11 with no-reordering rule * Rename FitResult to FitResultBase, add reset hooks * Add LeastSquaresFitResult class * Add BayesianFitResult class * Register fit-result family classes with factory * Declare paired _fit_result_class on minimizer bases * Wire fit_result swap and reset paths to paired class * Route LSQ result writers to fit_result * Route Bayesian result writers to fit_result * Remove LSQ output descriptors from minimizer base * Remove Bayesian output descriptors from minimizer base * Serialize fit outputs to _fit_result.* tags * Confirm fit_result paired instance flows through serializer * Add settings-used block to fit.results display * Amend affected ADRs for minimizer input/output split * Update tutorials to read outputs from fit_result * Remove essdiffraction dependency * Promote minimizer-input-output-split ADR * Complete Phase 1 minimizer split review gate * Propose IUCr CIF tag alignment for fit outputs * Add review 4 of input/output split post-Phase 1 * Reply to minimizer input-output review 4 * Complete minimizer input-output Phase 2 * Reply to minimizer input-output review 5 * Reply to minimizer input-output review 6 * Reply to minimizer input-output review 7 * Drop minimizer-input-output-split review/reply files
* Refresh emcee plan for post-merge surface * Document /draft-adr /review-adr /draft-plan /review-plan shortcuts * Sync copilot-instructions with current API and branch conventions * Refine shortcut triggers and loop behavior * Add emcee minimizer implementation plan * Add /implement-plan and switch shortcuts to sentinel-based handoff * Clean up and formatting * Add emcee runtime dependency * Register emcee minimizer enum value * Remove emcee version pin * Add EmceeMinimizer category class * Add EmceeMinimizer engine class * Wire emcee resume through fit stack * Append-on-save plus explicit truncate-on-new-fit prep * Route emcee posterior through fit_result and sidecar * Add ed-25 emcee tutorial * Mark emcee phase 1 review gate * Improve emcee sampler progress reporting * Restore emcee default parallel sampling * Align emcee sampling progress totals * Trim deterministic fit-parameter CIF columns * Omit empty fit bounds multiplier column * Suppress duplicate LSQ exit reason * Persist Bayesian runtime seed and timing * Add notebook stop control for fitting * Use Jupyter server interrupt for stop fitting * Clear stop fitting button on interrupt * Default emcee resume steps from minimizer settings * Fallback to fresh emcee fit when resume chain is missing * Resume emcee from persisted sampler state * Update emcee default proposal moves and thinning * Introduce emcee minimizer tutorials * Format switch warnings as bullet lists * Improve fitting output and peak warnings * Add ADR on fit results display naming * Replace arviz with custom diagnostics * Update tutorial archives and reduce steps * Update notebooks * Share emcee minimizer defaults * Remove unused sidecar warning wrapper * Keep DREAM parallel worker syncing * Use native emcee sampler setting keys * Document emcee tutorial split * Use eager emcee sidecar imports * Clarify emcee integration test phase * Remove redundant emcee initialization map * Apply non-py formatting * Update notebooks * Add emcee phase 2 verification tests * Apply pixi run fix auto-fixes * Apply remaining pixi run fix auto-fixes * Complete emcee static checks * Record emcee unit test verification * Fix emcee result synchronization * Add live elapsed time to benchmark runs * Isolate sequential tutorial project path * Document emcee fit options refinement * Record emcee Phase 2 bug-fix note * Document emcee benchmark tooling note * Expand emcee minimizer category tests * Document emcee tutorial verification note * Improve benchmark tutorial progress table * Update tutorial benchmarks for emcee minimizer * Clean up * Formatting
* Add tutorial benchmark results * Add undo-fit ADR suggestion * Split fit-state save gate from _fit_parameter rows * Use _fit_result.result_kind as the fit-state load marker * Decouple live-bound restoration from fit-result flag * Add Analysis.undo_fit() rollback operation * Wire CLI undo to Analysis.undo_fit() * Promote undo-fit ADR to accepted * Reach Phase 1 review gate * Re-export undo-fit outcome type * Align undo CLI example with ASCII output * Clarify undo rollback start-value filter * Apply pixi run fix auto-fixes * Document undo outcome attributes * Add undo-fit verification coverage * Assert all undo posterior fields clear * Make tutorial artifact-root assertion path portable * Document undo command in user-facing docs * Interpret empty parentheses as no esd * Clarify empty parentheses comment * Remove undo-fit implementation plan
* Add project-summary-rendering ADR suggestion * Add project-summary-rendering implementation plan * Add ReportFormatEnum and ReportStyleEnum * Refactor Report into a ProjectConfig CategoryItem * Load _report.* from project.cif with legacy defaults * Move IUCr CIF validation inside the writer * Remove public Report.check() and check=True flag * Add per-format save methods and Report.save dispatch * Lock empty-config behaviour in Report API * Add analysis.software category and engine URL constants * Populate analysis.software at fit time and emit fit_datetime * Amend analysis-cif-fit-state for analysis.software * Amend iucr-cif-tag-alignment for project.report * Add project.publication facade and sub-categories * Persist project.publication to project.cif * Add Publication.load TOML JSON entry point * Read publication metadata in IUCr writer * Add ReportDataContext builder and Jinja base macros * Add HTML renderer with CDN and offline Plotly modes * Vendor LaTeX styles with licenses and add report deps * Add LaTeX renderer and save_tex with vendored styles * Add opportunistic PDF compilation via TeX subprocess * Add crystal_system and measured_range properties for reports * Add ed save-report CLI subcommand * Update tutorials and user-guide docs for project.report * Promote project-summary-rendering ADR to accepted * Reach Phase 1 review gate * Document Kaleido browser bootstrap option * Make dictionary validation optional and fix TeX braces * Preserve report uncertainties in exported formats * Reuse TeX bundle for PDF generation * Replace report formats list with booleans * Accept project summary rendering migration plan * Drop ReportStyleEnum and _report.style field * Drop style parameter from report save commands * Drop REVTeX style files from vendored bundle * Rename TeX template to canonical report name * Drop kaleido runtime dependency * Add DisplayHandler value object * Wire display metadata into descriptors * Add units vocabulary validation * Migrate descriptor units to display handlers * Read report labels through display handlers * Vendor MathJax bundle for offline reports * Inline MathJax for offline HTML reports * Add x_descriptor and fit_data_arrays on ExperimentBase * Replace fit_data payload with descriptor-driven shape * Emit pgfplots CSV and replace includegraphics with pgfplots blocks * Build Plotly fit figures from fit_data context * Replace stale figures references with data * Update report tutorials for single-style output * Reach Phase 1 review gate * Fix TeX report axis label template syntax * Keep fit running when PDF reporting fails * Escape plain labels in TeX reports * Update report templates with composite fit plots * Fix TeX report ytick brace escaping * Promote project-summary-rendering ADR to accepted * Add project-summary-rendering implementation plan * Emit standalone pgfplots figures included as PDF * Serialize report Plotly figures via shared notebook path * Match pgfplots figure geometry to Plotly layout * Reach Phase 1 review gate * Scale pgfplots axes to Plotly panel ratios * Align report plot styling with Plotly output * Keep all points in pgfplots figures * Align numeric report table columns * Restore pgfplots report line widths * Render category-driven reports with aligned tables * Harmonize report styling * Tighten section number spacing * Replace report format list with boolean flags * Fix console report lattice rows * Remove orphaned report module tests * Return intended PDF report path * Load IUCr dictionaries lazily * Warn on skipped IUCr dictionary loads * Use powder phase id tag in IUCr refln loop * Remove dead PDF compiler helpers * Apply pixi run fix auto-fixes * Apply ruff format auto-fixes * Fix Phase 2 lint failures * Restore lazy report import * Align Phase 2 tests with report configuration * Handle nonnumeric descriptors without units * Apply Phase 2 formatting fixes * Add Phase 2 structure coverage tests * Apply docstring formatting cleanup * Apply final Phase 2 formatting * Update report integration save test * Exclude vendored files from project checks * Remove standalone report CLI commands * Document PDF compiler exception handling * Clarify report display mixin responsibility * Explain TeX subprocess lint suppressions * Complete PDF compiler helper docstring * Use active ADP labels in reports * Record software package name without minimizer method * Remove console report display from Report category * Show report timestamp in human-readable format * Add display labels to analysis result descriptors * Add project metadata to tutorial * Render analysis section from categories * Use lowercase software analysis subsection title * Center and brace string columns in TeX tables * Use longtable macro and drop CIF validation * Update ADRs to reflect removed gemmi validation * Remove commented-out show_report line * Clean up docs after validation removal * Add open issue for CIF report dictionary-validation test * Split single-crystal refln into CWL and TOF variants * Left-align loop tables and center item strings in TeX report * Style PDF report links to match HTML * Remove TeX intermediate after PDF-only report build * Enable HTML report output by default * Add single-crystal agreement chart to HTML report * Add single-crystal agreement scatter to PDF report * Apply pixi run fix auto-fixes * Update refln tests for CWL/TOF split * Update report renderer tests for analysis section and longtable * Update save tests for default HTML report output * Update data_context tests for analysis split and centered columns * Assert absent refln wavelength via class, not guarded instance * Disable HTML default in CIF report integration test * Drop removed show_report call from tutorials * Document default HTML report and TeX-bundle cleanup * Regenerate tutorial notebooks without show_report * Regenerate ed-3 notebook without show_report * Fix mangled mkdocstrings directive on report API page
* Add crysview-structure-visualization ADR suggestion * Add crysview-structure-visualization implementation plan * Add crysview viewer and styling enums * Add renderer-neutral structure scene model * Add orthogonalization and ADP eigendecomposition helpers * Add extended element database for radii and colours * Add structure scene builder * Add ASCII structure renderer * Add Viewer facade and factory with ASCII engine * Add style category for structure view styling * Use six scalar descriptors for the view range * Add switchable view category for renderer selection * Wire project.view and project.style with CIF persistence * Add per-structure geom bond-cutoff category * Align single-crystal scatter axes and style in HTML and PDF * Add structure() and show_structure_options() display surface * Add tests for single-crystal scatter range, ticks, and diagonal Cover the new single_crystal_axis_range / single_crystal_tick_step helpers, the data-coordinate diagonal and smaller markers/error bars in the Plotly trace, and the shared x/y range, tick step, and diagonal colour in the report fit-plot context. * Vendor pinned Three.js assets * Add Three.js structure renderer * Embed structure figure in HTML report under html_offline * Document structure view in tutorials and reference * Reach Phase 1 review gate * Resync tutorial notebooks with sources * Default structure view engine to environment-aware auto * Document auto default for structure view engine * Fix single-crystal tick rounding and lighten markers and bars Round the shared tick step to the nearest 1/2/5 power of ten and anchor ticks at 0, so both axes read 0, 500, ..., 2500 (was 750-spaced from the padded minimum). Colour the marker stroke like the fill to drop the ring, and thin the error-bar line and caps. * Test single-crystal tick step rounding and marker stroke Add a regression that the padded heidi range rounds to a 500 step (not 750) and assert the marker stroke colour matches the fill. * Remove unimplemented Structure.show() superseded by display.structure() * Wrap Three.js import map in required imports key * Add import-map regression guard to Phase 2 test plan * Force light theme for structure view in HTML reports * Match structure-view modebar and layout to reference demo * Add atom_scale and per-axis axis lengths to structure scene * Thicken axes, tighten zoom, add PNG download and mixed-site legend * Document atom_scale style option * Rename rendering selectors to rendering_plot/structure/table * Fall back to identity symmetry for unlisted space groups * Update ADRs to renamed rendering_plot/table selectors * Reconcile crysview ADR/plan prose with renamed selectors * Square-root compress atom ball sizes and lower default scale * Halve bond cylinder radius for ball-and-stick balance * Lower default bond increment to 0.25 A for cleaner bonding * Default to a trimetric c-axis-up structure view * Note near-neighbour auto-bonding as a future improvement * Prune bonds to first coordination shell * Reduce default zoom ~20% and left-align legend text * Document first-shell bond prune in ADR, plan, and issues * Write rendering_structure and style sections to project.cif * Add TikZ structure figure to TeX/PDF reports * Document TikZ structure figure in ADR and user guide * Clip TikZ bonds to atom surfaces for correct occlusion * Depth-segment cell edges and overlay axis triad in TikZ figure * Use depth-occluded axes in TeX structure figure * Replace TikZ structure figures with raster PNG * Merge atom_shape and radius_model into atom_view setting * Render true ADP ellipsoids in the raster figure * Demonstrate ADP atom view in ed-14 tutorial * Add colour-scheme selector to the structure view * Render atoms by ADP shape with relative-proportion wedges * Fix anisotropic ADP orientation and reciprocal c-axis * Speed up structure-view zoom; stack the hint in three rows * Add specular highlights to the raster structure figure * Add HTML specular, bond recolour and asymmetric-unit toggle * Drop atomic radius, improve rendering consistency * Fix structure-view distortion at off-axis camera angles * Default view: longest axis horizontal, second-longest up * Rebuild axis arrows at a constant on-screen size * Hide a/b/c axis labels with the axes toggle * Note crysview Phase 2 coverage and superseded prose * Add value-selector-discovery ADR suggestion * Add structure-view-settings implementation plan * Add EnumDescriptor with show_supported listing * Classify enumerated selectors for discovery * Add default and description to value-selector enums * Use EnumDescriptor for experiment_type axes * Use EnumDescriptor for atom_sites adp_type * Use EnumDescriptor for verbosity selector * Use EnumDescriptor for fit_result result_kind * Use EnumDescriptor for fit_parameter_correlations source_kind * Use EnumDescriptor for extinction model selector * Add structure_view content/region category * Add structure_style appearance category * Read structure view and style from new categories * Remove the old style and rendering_structure surfaces * Move model.md structure styling to structure_style * Show occupancy split as a vertical camera-facing pie * Update crysview ADR for the structure-view category split * Reach Phase 1 review gate * Reopen Phase 1 gate pending tutorial migration * Migrate tutorials to structure_style and regenerate notebooks * Reach Phase 1 review gate * Apply pixi run fix auto-fixes * Pin Logger to WARN in rendering_plot invalid-type test * Regenerate drifted tutorial notebooks * Ignore vendored structure renderers * Reorder tutorial rendering and fix jupytext metadata * Reduce report margin to 2cm * Call theme_colors by keyword in Three.js renderer * Refactor and annotate structure display modules for lint * Annotate project view categories and config for lint * Add unit tests for structure display and view categories * Repoint stale tests to renamed and split categories * Reflow docs and regenerate package structure * Update ed-17 tutorial to demonstrate structure_style * Add structure view to remaining tutorials * Frame the raster structure image with a container border * Flatten report headings and widen the structure figure * Frame structure figure within half page height, full width * Document report figure layout in summary-rendering ADR * Refresh structures before display scene building * Clean up implemented ADR and plan docs * Change default atom view to covalent * Document clean report CIF metadata policy * Simplify CIF block naming in reports * Polish structure view dark mode and labels toggle * Refine structure view controls and report axes * Clean report CIF metadata and block references * Keep report datablock names unique * Apply pixi run fix auto-fixes * Add tutorial benchmarks * Finalize Python-CIF category correspondence ADR * Refresh user guide docs for current API * Add documentation CI ADR suggestion * Contain structure view overlays in docs * Format refreshed user guide docs * Render pretty units in fit parameter tables * Sync Plotly and structure themes in docs * Remove redundant line in tutorial docs * Normalize structure toolbar select sizing * Use unified dark plot background * Use transparent plot backgrounds * Clarify structure-view settings ADR coverage * Centralize display theme styling * Add DisplayThemeColors class * Clean up Python-CIF ADR review artifacts * Reset zoom on view reset * Remove implemented plan records * Add responsive resizing for Plotly plots * Remove unused reason column and standardize titles * Add Python-CIF correspondence implementation plan * Promote Python-CIF correspondence ADR * Reach Python-CIF correspondence Phase 1 review gate * Make Plotly backgrounds transparent * Apply pixi run fix auto-fixes * Sync tutorials index.json with index.md and add ed-23 to ed-26 * Add optional width parameter to table rendering * Show plain tutorial title in Jupyter * Specify instrument and data type in tutorials * Consume Pandas table width argument * Add table rendering follow-ups to open issues * Make Plotly modebar background transparent in both themes * Tweak axis frame and grid colors * Size correlation matrix cells to 16 label characters * Merge atoms and asymmetric-unit into a cycle button * Refine theme legend, grid, and frame colors * Sync Plotly theme to annotations, shapes, heatmaps * Sort notebook cell_metadata_filter to avoid diff churn * Use display units in parameter tables * Adjust Three.js structure overlay styling * Keep structure-view secondary axis upright
* Add space-group-database ADR suggestion * Add space-group-database implementation plan * Add cctbx-based space-group table extraction * Add multi-source cross-check and disagreement report * Generate initial space-group disagreement report * Localize space-group curation artifacts * Move crysview demo to subdirectory * Add curated space-group overrides * Generate complete space_groups.json.gz with recorded provenance * Load space groups from JSON and drop restricted unpickler * Reach Phase 1 review gate * Cover public space-group coordinate aliases * Add space-group database ADR index row * Add Phase 2 space-group database tests and packaging check * Apply pixi run fix auto-fixes * Alias runtime coordinate codes in space-group database * Apply prettier formatting to space-group-database ADR * Make packaging check inspect the wheel directly * Unify Plotly tooltip styling and fix white Bragg hover * Guard optional IPython import in table backend base * Pin space-group record count in tests and wheel check * Update Plotly hover test and fix overlong comment * Update tutorial links to latest docs * Add Wyckoff letter detection ADR
* Promote space-group-database ADR to accepted * Promote plotting-docs-performance ADR to accepted * Add plotting-docs-performance implementation plan * Add FigureEmbedMode enum and env resolver * Add vendored-JS bump script and pixi task * Vendor plotly-cartesian and refresh three.js * Add docs-sync-vendored-js task and wiring * Add shared ed-figures.js lazy figure loader * Wire docs runtime assets and page importmap * Add SHARED embedding mode to Plotly serializer * Add SHARED embedding mode to Three.js renderer * Pass STANDALONE mode from report renderer * Route docs notebook execution to SHARED mode * Reach Phase 1 review gate * Guard LICENSES.md drift in vendor-check-js * Downcast SHARED figure data to float32 * Finalize Wyckoff letter detection ADR * Record and bound float32 display-precision decision * Drop broken cif-numeric-precision ADR links * Apply pixi run fix lint and format fixes * Add Phase 2 tests for embedding mode and float32 * Resolve RequireJS open question (kept, removal deferred) * Add float32 fidelity, report STANDALONE, and bump drift tests * Finalize Wyckoff ADR, add CIF precision ADR * Add match to resolver test pytest.raises (PT011) * Record Phase 2 verification results in plan * Add plotting-docs-performance ADR index row * Rewrap documentation paragraphs * Document Wyckoff coords_xyz operator-form regression and fix * Make axes and scene background opaque, paper transparent * Display squared degrees as deg² instead of deg^2 * Standardize tutorial section headings * Limit tutorial notebook TOC to two levels * Theme modebar icons; clear background outside correlation cells * Inset Plotly plot legend from the top-right corner * Use #212121 for dark background inside the axes * Theme modebar icons via native Plotly colors, drop CSS hack * Match Plotly legend top inset to its right inset * Exclude vendored JS licenses from docs nav * Paint structure scene background via WebGL clear color * Theme modebar icons via class CSS overriding Plotly inline fill * Add themed code-cell border colors to docs extra.css * Convert shared figure-height fallback from units to pixels * Sync Plotly tooltip border to axis-frame in docs loader * Update report style test for new axis-frame color * Fall back to baked theme for modebar when host theme hidden * Refine chart theme background and grid colors * Blend shared-mode loading skeleton with page background * Size posterior distribution plots to single main panel * Size posterior distribution plots to single main panel
* Add space-group-database canonical-templates phase * Refine canonical-templates phase to re-source from cryspy * Refine canonical-templates CT1 to fix generator and re-run * Settle canonical-templates phase on cctbx-free post-process * Canonicalize space-group coords_xyz templates * Assert canonical coords_xyz in packaged DB check * Record canonical coords_xyz invariant and provenance * Reach canonical-templates Phase 1 review gate * Keep pattern-plot top and bottom panels at fixed height * Test fixed pattern-plot panel heights across row layouts * Inline composite row-height max() and trim docstring * Keep TeX report panels fixed when rows are hidden * Store full canonical Wyckoff orbits via exact check * Document two-stage canonical rebuild as invariant step * Build full Wyckoff orbits from cryspy primitive and centering * Fix plan references to obsolete generator coords source * Validate canonical coords_xyz and coupled constraints * Note plotting-module docstring fix for Phase 2 review * Mark Phase 2 verification complete * Assert R-3m special positions stay on-site after fit * Confirm wyckoff letter detection ADR gate * Add Wyckoff orbit detection to crystallography module * Record free-param-solving Wyckoff snap decision for P1.6 * Add derived space group Wyckoff category * Wire derived Wyckoff table into Structure * Add read-only multiplicity to AtomSite * Derive allowed Wyckoff letters from the space group * Add Wyckoff coordinate snap helper to crystallography module * Detect and track Wyckoff letters in the update flow * Read multiplicity from the model in the cryspy calculator * Serialize Wyckoff multiplicity and report Wyckoff table * Promote wyckoff-letter-detection ADR and close issue #51 * Reach Phase 1 review gate * Preserve explicit Wyckoff letter until a later edit * Build space-group Wyckoff id from multiplicity and letter * Rebuild Wyckoff index and parent links on replace * Reject item assignment and deletion on Wyckoff collection * Resolve None-coord-code groups in Wyckoff constraint helper * Sync top-level plan status with completed Phase 1 * Raise ValueError for Wyckoff read-only mutation per ADR * Remove wyckoff_letter from tutorial examples * Apply pixi run fix auto-fixes * Resolve ruff lint findings in Wyckoff Phase 1 code * Update tests for Wyckoff detection behavior changes * Add tests for derived space_group_wyckoff category * Add detection and lookup tests for Wyckoff crystallography * Assert canonical Wyckoff representative templates in data * Add atom-site Wyckoff detection behavior tests * Add tutorial-corpus Wyckoff detection regression * Satisfy pydoclint and ruff for Wyckoff Phase 2 tests * Fix ed-13 Si to the 8a diamond position * Regenerate tutorial notebooks after Wyckoff letter removal * Restore tutorial-corpus coverage with explicit ground-truth table * Match Fd-3m corpus ground truth to corrected ed-13 Si site * Mark Phase 2 verification complete in plan
We make nightly releases of reduced files on github now, so no need for this R2 bucket :) https://github.com/scipp/ess/releases/tag/reduced_data_nightly
* Standardize tutorial project save paths * Seed and standardize save paths for Bayesian tutorials * Regenerate tutorial notebooks * Add tutorial-output regression test against fit baseline * Apply pixi run fix auto-fixes * Assert persisted result_kind in tutorial-output test * Run tutorial-output checks in CI * Clean saved tutorial projects before tutorial tests * Skip numeric baseline for platform-sensitive tutorials * Set non-zero defaults for TOF profiles * Trim platform-sensitive skip message * Update tutorial Si structure and doc URLs * Add pattern-display-unification implementation plan * Add top margin above structure scene rectangle * Match single-panel pattern height and x-range to composite * Always render available pattern content; drop include * Amend display-ux ADR for always-on pattern view * Apply formatter to pattern docstring and docs * Drop include= from tutorials for unified pattern view * Reach Phase 1 review gate * Add Raises section to pattern docstring * Set single-panel height via layout construction * Update unit tests for unified pattern view * Remove py3Dmol, relax pillow constraint * Update integration plotting tests for dropped include * Mark Phase 2 verification complete * Record pattern unification as a dedicated ADR * Show pretty units in parameter repr * Omit space_group_Wyckoff loop from IUCr reports * Hide space_group_Wyckoff via _skip_cif_serialization hook * Make Wyckoff skip-serialization hook a staticmethod * Update Wyckoff plan for serialization-hook refactor * Apply latest templates * Assert crysfml engine is loaded in switch-calculator test * Reformat builtins as multiline list * Increase page max-width to 118em * Point report API page at easydiffraction.report package * Track host theme in 3D-view loading box, relabel to plot * Size fit-series scatter plot to the pattern top panel * Increase page and content max-widths * Hide space_group_Wyckoff from parameter tables * Render integer descriptors in parameter table * Pre-bin posterior distribution histogram, not raw samples * Move notebook action buttons to top left above title * Drop duplicate pair scatter hover layer, halve sample cap * Apply ruff format to distribution histogram test * Include integer descriptors in remaining parameter tables * Add regression tests for parameter table rendering * Name tutorial projects to match their save directories * Render pandas tables as inline-styled HTML * Remove dead table theme-sync leftovers * Neutralize MkDocs Material table CSS rules * Rename tutorial projects to match save directories * Temporarily mark all structures as nuclear-only * Match project outputs to save directories * Validate refined tutorial parameters from model and experiment CIFs * Update tutorial projects and remove structure display
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