Save tutorial projects consistently and verify their fit results

.copier-answers.yml

@@ -1,6 +1,6 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.11.4
+_commit: v0.12.0
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/diffraction-app
 app_doi: 10.5281/zenodo.18163581

.github/workflows/coverage.yml

@@ -63,32 +63,8 @@ jobs:
           files: ./coverage-unit.xml
           token: ${{ secrets.CODECOV_TOKEN }}
 
-  # Job 2: Run integration tests with coverage and upload to Codecov
-  integration-tests-coverage:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Check-out repository
-        uses: actions/checkout@v6
-
-      - name: Set up pixi
-        uses: ./.github/actions/setup-pixi
-
-      - name: Run integration tests with coverage
-        run:
-          pixi run integration-tests-coverage --cov-report=xml:coverage-integration.xml
-
-      - name: Upload integration tests coverage to Codecov
-        if: ${{ !cancelled() }}
-        uses: ./.github/actions/upload-codecov
-        with:
-          name: integration-tests-job
-          flags: integration
-          files: ./coverage-integration.xml
-          token: ${{ secrets.CODECOV_TOKEN }}
-
   # Job 4: Build and publish dashboard (reusable workflow)
   run-reusable-workflows:
-    needs: [docstring-coverage, unit-tests-coverage, integration-tests-coverage] # depend on the previous jobs
+    needs: [docstring-coverage, unit-tests-coverage] # depend on the previous jobs
     uses: ./.github/workflows/dashboard.yml
     secrets: inherit

.github/workflows/tutorial-tests.yml

@@ -47,15 +47,15 @@ jobs:
 
       - name: Test tutorials as python scripts
         shell: bash
-        run: pixi run script-tests
+        run: pixi run script-tests-checked
 
       - name: Prepare notebooks
         shell: bash
         run: pixi run notebook-prepare
 
       - name: Test tutorials as notebooks
         shell: bash
-        run: pixi run notebook-tests
+        run: pixi run notebook-tests-checked
 
   # Job 2: Build and publish dashboard (reusable workflow)
   run-reusable-workflows:

.prettierignore

@@ -31,6 +31,9 @@ src/easydiffraction/report/templates/html/vendor/
 src/easydiffraction/report/templates/tex/styles/
 src/easydiffraction/utils/_vendored/jupyter_dark_detect/
 
+# Tox
+.tox
+
 # Misc
 .benchmarks
 .cache

docs/dev/adrs/accepted/crysview-structure-visualization.md

@@ -158,8 +158,7 @@ representation); like the HTML report it can also write a standalone
 HTML file to a path. The exact return and save signature is left to the
 implementation plan.
 
-Content selection mirrors `pattern(include=...)` rather than inventing a
-new vocabulary:
+Content selection uses an `include=` argument:
 
 ```python
 project.display.structure(struct_name='lbco')
@@ -181,13 +180,11 @@ toggles the same features after the initial view is drawn, so `include`
 sets the starting state and the modebar refines it.
 
 A companion `project.display.show_structure_options(struct_name=...)`
-mirrors the existing `show_pattern_options(expt_name=...)`: it lists
-each `include=` option with whether the active engine and the current
-structure state support it, and the reason when they do not — for
-example `moments` is unavailable until the structure model carries
+lists each `include=` option with whether the active engine and the
+current structure state support it, and the reason when they do not —
+for example `moments` is unavailable until the structure model carries
 moment fields, and the `ascii` engine reports the features only the 3D
-engines draw. This gives the structure view the same per-option
-discoverability the pattern view already offers.
+engines draw. This gives the structure view per-option discoverability.
 
 The view also has a spatial extent: which symmetry-equivalent atoms the
 scene contains. The scene builder takes the unique (asymmetric-unit)
@@ -613,11 +610,11 @@ a per-call request behave predictably:
 ## Consequences
 
 - `project.display` gains a spatial view (`structure()`) that
-  complements the 1D `pattern()` view and reuses the `include=`
-  vocabulary.
-- `project.display` also gains `show_structure_options()`, parallel to
-  `show_pattern_options()`, so the supported content for a given
-  structure and engine is discoverable with reasons.
+  complements the 1D `pattern()` view with an `include=` feature
+  selector.
+- `project.display` also gains `show_structure_options()`, so the
+  supported content for a given structure and engine is discoverable
+  with reasons.
 - Keeping crystallography in the scene builder and out of renderers lets
   several front-ends (Three.js now, Qt Quick 3D later) share one model.
 - A switchable `rendering_structure` category

docs/dev/adrs/accepted/display-ux.md

@@ -82,8 +82,6 @@ project.display.fit.series(param, versus='diffrn.ambient_temperature')
 project.display.posterior.pairs()
 project.display.posterior.distribution(param)
 project.display.posterior.predictive(expt_name='hrpt')
-
-project.display.show_pattern_options(expt_name='hrpt')
 ```
 
 `project.analysis.display` is removed from the primary public API. Its
@@ -116,77 +114,14 @@ project.display.pattern(expt_name='hrpt')
 project.display.pattern(expt_name='hrpt', x_min=40, x_max=55)
 ```
 
-By default, `pattern()` uses `include='auto'` and displays as much
-useful information as the project state supports:
-
-- measured data if present
-- calculated data if linked structure state and calculated intensities
-  are available
-- background if powder Bragg measured and calculated data plus defined
-  background points are available
-- Bragg ticks if powder Bragg measured and calculated data plus
-  reflection rows are available
-- residual if both measured and calculated data are available and the
-  experiment type supports a residual panel
-- excluded regions if available on the experiment
-- uncertainty bands where posterior predictive data exists and the chart
-  engine supports them
-
-Specific subsets are selected with `include`:
-
-```python
-project.display.pattern(expt_name='hrpt', include='auto')
-project.display.pattern(expt_name='hrpt', include='measured')
-project.display.pattern(expt_name='hrpt', include='calculated')
-project.display.pattern(
-    expt_name='hrpt',
-    include=('measured', 'calculated', 'background', 'residual', 'bragg'),
-)
-```
-
-`include` was chosen over alternatives:
-
-| Name          | Reason not selected                             |
-| ------------- | ----------------------------------------------- |
-| `layers`      | Sounds graphical rather than user intent.       |
-| `components`  | Precise, but longer.                            |
-| `content`     | Too broad.                                      |
-| `view`        | Better for presets than arbitrary combinations. |
-| `series`      | Does not fit residual rows or Bragg ticks well. |
-| boolean flags | Explicit, but scales poorly.                    |
-
-Add discovery for supported pattern content:
-
-```python
-project.display.show_pattern_options(expt_name='hrpt')
-```
-
-The table shows option name, description, availability for the
-experiment, whether `include='auto'` includes it, and the reason an
-option is unavailable.
-
-Pattern option names:
-
-- `auto`
-- `measured`
-- `calculated`
-- `background`
-- `residual`
-- `bragg`
-- `excluded`
-- `uncertainty`
-
-`uncertainty` is available where posterior predictive data exists for a
-supported experiment and the active chart engine can render bands. It is
-unavailable, with a clear reason, when no posterior predictive data is
-present.
-
-Explicit combinations are validated against the same project state used
-by `include='auto'`. `background`, `bragg`, and `residual` require both
-measured and calculated data in the same view. `excluded` requires
-measured, calculated, or uncertainty content in the same view, and
-excluded-region overlays currently require the experiment's default
-x-axis.
+`pattern()` renders every kind of data the project state supports —
+measured, calculated, residual, Bragg ticks, background, excluded
+regions, and posterior predictive uncertainty, each shown when
+available. It takes no view-selection argument. The content rules, the
+removed `include` / `show_pattern_options` design, and the shared
+single- and multi-panel figure sizing are recorded in the
+[Unified Pattern View](pattern-display-unification.md) ADR, which
+supersedes the `include`-based pattern design once described here.
 
 ## Deterministic And Bayesian Consistency
 
@@ -230,8 +165,9 @@ users should not need to decide the output type before asking for
 information. Some outputs may render as a chart or a table depending on
 backend and state.
 
-Separate `measured()` and `calculated()` methods were rejected because
-they duplicate `pattern(..., include=...)`.
+Separate `measured()` and `calculated()` methods are unnecessary:
+`pattern()` shows every available kind of data directly, so there is no
+subset for them to select.
 
 ## Consequences
 

docs/dev/adrs/accepted/pattern-display-unification.md

@@ -0,0 +1,92 @@
+# ADR: Unified Pattern View
+
+## Status
+
+Accepted and implemented.
+
+## Date
+
+2026-06-04
+
+## Context
+
+`project.display.pattern()` was originally specified by the
+[Display UX Facade](display-ux.md) ADR with an `include=` argument that
+assembled a view from named layers (`measured`, `calculated`,
+`background`, `residual`, `bragg`, `excluded`, `uncertainty`), plus a
+`show_pattern_options()` discovery table. `include='auto'` already chose
+the most informative combination from project state.
+
+In practice this surfaced several problems:
+
+- The single-panel path (`plot_meas`/`plot_calc` → `plot_powder`) and
+  the composite path (`build_powder_meas_vs_calc_figure`) computed
+  figure height and x-range independently, so they drifted. A
+  measured-only view rendered at the full three-panel height in the lazy
+  docs runtime — the
+  [Plotting & Docs Performance](plotting-docs-performance.md) skeleton
+  fell back to `DEFAULT_HEIGHT * PLOTLY_HEIGHT_PER_UNIT` — and gained
+  stray left/right autoscale padding the composite did not have.
+- `'excluded'` was an opt-in overlay, but excluded regions are a
+  property of the experiment, not a viewing choice; `include='measured'`
+  and `include=('measured', 'excluded')` produced different plots of the
+  same data, which read as redundant.
+- For a scientist audience, choosing layers is friction. The project
+  state already determines what is meaningful to show, which is exactly
+  what `include='auto'` computed.
+
+## Decision
+
+`pattern(expt_name, x_min=None, x_max=None, *, x=None)` always renders
+every kind of data the project state supports — the former
+`include='auto'` behaviour is now the only behaviour. The `include`
+parameter, the `show_pattern_options()` method, and the option-status
+discovery table are removed. Strict-subset views (for example
+measured-only once a calculation exists) are intentionally no longer
+offered; zooming (`x_min`/`x_max`) and the x-axis variable (`x`) remain.
+
+Excluded regions are always shaded when defined on the experiment,
+skipped only when a custom `x` axis variable is selected, because the
+overlay cannot be mapped onto an arbitrary axis.
+
+Single-panel and composite charts share one figure-sizing and x-range
+core. `plot_powder` builds its layout with the same
+`_single_main_panel_height_pixels(...)` height and tight
+`_composite_x_range(...)` as the composite main row, and `_get_layout`
+already applies the composite margins. A one-row chart is therefore the
+top row of the multi-row chart pixel for pixel, by construction, so the
+two paths cannot diverge again.
+
+This supersedes the `include`-based pattern design in the
+[Display UX Facade](display-ux.md) ADR. The remainder of that ADR — the
+facade grouping, renderer categories, and naming rules — still stands.
+
+## Consequences
+
+- `pattern(expt_name=...)` is the whole pattern API surface; tutorials,
+  docs, and tests no longer pass `include=`.
+- The project is in beta, so this replaces the previous API with no
+  compatibility shim; tutorials and tests are updated to the current
+  API.
+- Sizing and range differences between one- and three-panel views are
+  prevented structurally, not patched per call.
+- `structure(include=...)` and `show_structure_options()` are
+  unaffected: choosing which 3D features to draw remains a genuine
+  viewing choice (see
+  [Crystal Structure 3D Visualization](crysview-structure-visualization.md)).
+
+## Alternatives Considered
+
+Keeping `include` as the view-selection vocabulary (the original
+design). `include` had been chosen over `layers`, `components`,
+`content`, `view`, `series`, and boolean flags because it read as user
+intent and fit residual rows and Bragg ticks. It is removed now because
+the only combination users reached for in practice was the automatic
+"show everything available" view; the subset combinations added API
+surface and a discovery table without a matching workflow, and the
+parallel single-panel rendering path was the source of the sizing and
+range divergence.
+
+Keeping `'excluded'` as an opt-in overlay, or as a redundant no-op
+token, was rejected: excluded regions belong to the experiment, so
+shading them is automatic whenever they are present.

docs/dev/adrs/accepted/wyckoff-letter-detection.md

@@ -2,6 +2,14 @@
 
 **Status:** Accepted **Date:** 2026-06-01
 
+> **Amendment (2026-06-04):** the derived `space_group_Wyckoff` loop is
+> now **code-only** — it is excluded from IUCr/report output as well as
+> from project CIF. Wording below that calls the loop "report-facing" or
+> says the report writer "emits" it (the §"`space_group_Wyckoff` loop"
+> decision and the matching Consequences bullet) is superseded: the
+> table is reachable in code via `structure.space_group_wyckoff` but is
+> never serialized.
+
 ## Group
 
 Structure model.
@@ -447,13 +455,17 @@ which fall out naturally below.
   already emits the resolved `Wyckoff_symbol` for every atom and now
   also emits `_atom_site.site_symmetry_multiplicity`.
 - **`space_group_Wyckoff` loop.** The derived category is model-owned
-  and report-facing, but it is not persisted in project CIF. `Structure`
-  explicitly excludes it from project-save serialization via
-  `_serializable_categories()`, overriding `CategoryOwner`'s default of
-  serializing all owned categories. The IUCr/report writer emits the
-  `_space_group_Wyckoff.*` loop from the derived category because that
-  loop is useful report output even though it is redundant persisted
-  state.
+  and code-facing only; it is not serialized. The collection suppresses
+  its own output through `_skip_cif_serialization()` returning `True`,
+  the same collection-owned hook `atom_site_aniso` uses (conditionally);
+  every serialization path that consults it honours the suppression —
+  `category_collection_to_cif` (project CIF) and the report data context
+  — so the `_space_group_Wyckoff.*` loop never appears in project CIF or
+  HTML/TeX reports, and the hand-rolled IUCr writer does not emit it
+  either. The decision lives on the category, so `Structure` needs no
+  `_serializable_categories()` override. The table is redundant derived
+  state, reachable in code via `structure.space_group_wyckoff` (amended
+  2026-06-04).
 - **Derived values on read.** Multiplicity is recomputed from the
   letter, so any incoming `_atom_site.site_symmetry_multiplicity` is
   ignored rather than trusted; the `space_group_Wyckoff` category is
@@ -677,8 +689,8 @@ may miss:
   structure's space group (each entry's letter / multiplicity /
   site_symmetry / coords match `SPACE_GROUPS`), rebuilds when the space
   group changes, refuses all public mutation paths, is empty for an
-  absent group, is omitted from project CIF, and is emitted in
-  IUCr/report output;
+  absent group, and is omitted from both project CIF and IUCr/report
+  output (code-only, reachable via `structure.space_group_wyckoff`);
 - CIF round-trip stability — a written letter reloads verbatim, an
   omitted one re-derives to the same value, and an unsupported-group row
   keeps `None` multiplicity whether its letter is empty, explicitly

docs/dev/adrs/index.md

@@ -56,4 +56,5 @@ folders.
 | User-facing API      | Accepted   | String Paths and Live Descriptors                   | Separates persisted field selectors from references to live model parameters.                                         | [`string-paths-and-live-descriptors.md`](accepted/string-paths-and-live-descriptors.md)     |
 | User-facing API      | Accepted   | Switchable Category API                             | Places multi-type category selectors on the owner and omits public selectors for fixed or single-type categories.     | [`switchable-category-api.md`](accepted/switchable-category-api.md)                         |
 | User-facing API      | Accepted   | Switchable Category Owned Selectors                 | Moves the writable `type` selector and `show_supported()` onto the category itself; collapses the CIF duplication.    | [`switchable-category-owned-selectors.md`](accepted/switchable-category-owned-selectors.md) |
+| User-facing API      | Accepted   | Unified Pattern View                                | `pattern()` always renders available data, drops `include`, and unifies single- and three-panel figure sizing.        | [`pattern-display-unification.md`](accepted/pattern-display-unification.md)                 |
 | User-facing API      | Accepted   | Value-Selector Discovery                            | Gives enumerated value fields a per-descriptor `show_supported()`, beside the three category-level selector families. | [`value-selector-discovery.md`](accepted/value-selector-discovery.md)                       |