Add time-of-flight verification examples (single crystal & DREAM) and refresh the features overview

.github/workflows/docs.yml

@@ -88,6 +88,13 @@ jobs:
       # Note: The gh-pages branch is fetched separately later for mike deployment.
       - name: Checkout repository
         uses: actions/checkout@v6
+        with:
+          # Full history with tags so versioningit derives the real
+          # version (e.g. 0.18.0+dev40) instead of the v999.0.0 fallback
+          # (tool.versioningit.vcs default-tag), which would otherwise
+          # appear as "edi 999" in the executed notebook outputs rendered
+          # to HTML.
+          fetch-depth: 0
 
       # Activate dark mode to create documentation with Plotly charts in dark mode
       # Need a better solution to automatically switch the chart colour theme based on the mkdocs material switcher

.github/workflows/nightly-test.yml

@@ -27,6 +27,10 @@ jobs:
     steps:
       - name: Check-out repository
         uses: actions/checkout@v6
+        with:
+          # Full history with tags so versioningit derives the real
+          # version instead of the v999.0.0 fallback in notebook output.
+          fetch-depth: 0
 
       - name: Set up pixi
         uses: ./.github/actions/setup-pixi

.github/workflows/tutorial-tests.yml

@@ -41,6 +41,10 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v6
+        with:
+          # Full history with tags so versioningit derives the real
+          # version instead of the v999.0.0 fallback in notebook output.
+          fetch-depth: 0
 
       - name: Set up pixi
         uses: ./.github/actions/setup-pixi

docs/dev/adrs/accepted/development-docs-structure.md

@@ -37,14 +37,19 @@ docs/dev/
 |   |-- accepted/
 |   `-- suggestions/
 |-- issues/
-|   |-- open.md
-|   `-- closed.md
+|   |-- index.md
+|   |-- open/
+|   `-- closed/
 |-- package-structure/
 |   |-- full.md
 |   `-- short.md
 `-- plans/
 ```
 
+Issues are one Markdown file per issue under `issues/open/` and
+`issues/closed/`, with `issues/index.md` as the table of contents (not
+flat `open.md` / `closed.md` files).
+
 Use lowercase directory names for new development-doc folders. The
 feature/roadmap matrix is published directly in the user documentation
 at `docs/docs/features/index.md` (single source of truth for both

docs/dev/adrs/accepted/edstar-project-persistence.md

@@ -437,6 +437,13 @@ For type-neutral ADPs, `edi_names` stays the neutral
 `_atom_site.adp_iso` (so the Edi save is always type-neutral) while the
 type-specific B/U order is applied to `cif_names` for export.
 
+The "generated inventory" referenced throughout this ADR (the full set
+of `TagSpec`/`CifHandler` entries used as the migration and
+parameter-docs audit) is produced by
+[`tools/edi_handler_inventory.py`](../../../../tools/edi_handler_inventory.py)
+and written to the sidecar `handler-inventory.json` next to this file.
+Regenerate it with that tool rather than hand-editing the JSON.
+
 ## Consequences
 
 ### Positive

docs/dev/adrs/accepted/minimizer-category-consolidation.md

@@ -115,7 +115,7 @@ owner, category as a read-only attribute that gets swapped.
 ### 3. Per-parameter posterior data lives on `Parameter.posterior`
 
 Adopt the proposal from
-[`parameter-posterior-summary.md`](../suggestions/parameter-posterior-summary.md):
+[`parameter-posterior-summary.md`](parameter-posterior-summary.md):
 `GenericParameter.posterior` is `None` for deterministic fits and a
 `PosteriorParameterSummary` for Bayesian fits. The
 `_bayesian_parameter_posterior` CIF loop is removed; posterior summary
@@ -466,9 +466,9 @@ category's class-level `_engine_metadata` dict.
 
 ### Suggestions superseded or absorbed
 
-- [`parameter-posterior-summary.md`](../suggestions/parameter-posterior-summary.md)
-  — absorbed by §3 of this ADR. When this ADR is accepted, that
-  suggestion can be closed and a pointer added.
+- [`parameter-posterior-summary.md`](parameter-posterior-summary.md) —
+  absorbed by §3 of this ADR. When this ADR is accepted, that suggestion
+  can be closed and a pointer added.
 
 ## Alternatives Considered
 

docs/dev/adrs/accepted/peak-profile-cutoff.md

@@ -46,7 +46,7 @@ unsafe (too aggressive for some data). Users therefore need a per-
 experiment knob, mirroring FullProf's `.pcr` `WDT`.
 
 This relates to the upstream capability-request workflow
-([`upstream-capability-request-evidence.md`](../suggestions/upstream-capability-request-evidence.md)):
+([`upstream-capability-request-evidence.md`](upstream-capability-request-evidence.md)):
 the literal cutoff was proposed upstream and released in cryspy 0.12.0,
 so EasyDiffraction drives it through the released `profile_cutoff_fwhm`
 key without requiring a cryspy CIF-schema change.

docs/dev/adrs/suggestions/upstream-capability-request-evidence.md → docs/dev/adrs/accepted/upstream-capability-request-evidence.md

@@ -2,7 +2,7 @@
 
 ## Status
 
-Proposed.
+Accepted.
 
 ## Date
 

docs/dev/adrs/suggestions/verification-example-lifecycle.md → docs/dev/adrs/accepted/verification-example-lifecycle.md

@@ -2,7 +2,7 @@
 
 ## Status
 
-Proposed.
+Accepted.
 
 ## Date
 

docs/dev/issues/closed/add-single-crystal-tof-fit-verification-example.md

@@ -0,0 +1,18 @@
+# 190. Add a Single-Crystal TOF Fit Verification Example
+
+**Closed:** added the single-crystal time-of-flight verification example
+`docs/docs/verification/sc-neut-tof_taurine_basic.py` (and generated
+`.ipynb`), built from a FullProf reference for Taurine (P 2₁/c, neutron
+TOF single-crystal data, SENJU @ J-PARC).
+
+The FullProf model has extinction set to zero (Ext1 = 0, unrefined) so
+the comparison focuses on the structure-factor physics shared by cryspy
+and FullProf. After refining the overall scale only, edi-cryspy matches
+the FullProf F²cal to ~0.01% (profile diff and max deviation), with area
+ratio 1.0000 and shape correlation 1.0000.
+
+Reference files live in
+`docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/`; the
+example is listed under the **Single Crystal** section of
+`docs/docs/verification/index.md` and linked from the features page
+(§2.2 single-crystal Time-of-Flight row).

docs/dev/issues/closed/reconcile-git-ignored-agents-md-claude-md-with-their-checked-in-role.md

@@ -4,9 +4,12 @@ Resolved by an explicit project-owner decision: `AGENTS.md` and
 `CLAUDE.md` are **intentionally git-ignored** and kept local-only, not
 committed repository artifacts. The `.gitignore` `# Agents` block keeps
 both files ignored, and a note at the top of `AGENTS.md` (plus a clause
-in §Change Discipline) records that they are deliberately local-only and
-that their `AGENTS_review-N.md` / `AGENTS_reply-N.md` artifacts are
-likewise untracked and may be cleaned up once a review cycle closes.
-This removes the earlier contradiction (the document described itself as
-checked-in while being ignored) by adopting the local-only branch rather
-than committing the files.
+in §Change Discipline) records that they are deliberately local-only.
+The `.gitignore` block ignores only `AGENTS.md` / `CLAUDE.md` themselves
+— **not** their `AGENTS_review-N.md` / `AGENTS_reply-N.md` artifacts —
+so those review/reply files stay visible in `git status` by design, a
+deliberate reminder that they are temporary and must be cleaned up once
+a review cycle closes (the agent never `git add`s them). This removes
+the earlier contradiction (the document described itself as checked-in
+while being ignored) by adopting the local-only branch rather than
+committing the files.

docs/dev/issues/index.md

@@ -23,7 +23,6 @@ individual issue files** — not here.
 | 167 | [Add CrysFML `WDT` Parameter to Peak Shapes](open/highest_add-crysfml-wdt-parameter-to-peak-shapes.md)                                                                         | `[priority] highest` | Performance / Engine feature                                |
 | 168 | [Decide X-ray Anomalous Scattering Table Source](open/highest_decide-x-ray-anomalous-scattering-table-source.md)                                                               | `[priority] highest` | Correctness / External backend / Verification               |
 | 170 | [Document CrysFML X-ray Polarization as EasyDiffraction-Custom](open/highest_document-crysfml-x-ray-polarization-is-easydiffraction-custom.md)                                 | `[priority] highest` | Correctness / External backend / Verification               |
-| 180 | [Nuclear-Only Reflection Filter Drops Valid Peaks (Breaks HS HRPT)](open/highest_nuclear-only-reflection-filter-drops-valid-peaks.md)                                          | `[priority] highest` | Correctness / External backend                              |
 | 8   | [Add Explicit `create()` Signatures on Collections](open/high_add-explicit-create-signatures-on-collections.md)                                                                | `[priority] high`    | API safety                                                  |
 | 61  | [Clarify Logger Default Reaction Mode](open/high_clarify-logger-default-reaction-mode.md)                                                                                      | `[priority] high`    | Design                                                      |
 | 66  | [Decide Error-Handling Strategy: `log.error` vs `raise`](open/high_decide-error-handling-strategy-log-error-vs-raise.md)                                                       | `[priority] high`    | Design                                                      |
@@ -72,6 +71,9 @@ individual issue files** — not here.
 | 174 | [Bulk Write-Back of Calculated Intensity During Fits](open/medium_bulk-write-back-of-calculated-intensity-during-fits.md)                                                      | `[priority] medium`  | Performance                                                 |
 | 175 | [Avoid the CIF Round-Trip on Every Public `calculate()`](open/medium_avoid-cif-round-trip-on-every-public-calculate.md)                                                        | `[priority] medium`  | Performance                                                 |
 | 179 | [Investigate a Better Automatic `cutoff_fwhm` Detection Mechanism](open/medium_better-automatic-cutoff-fwhm-detection.md)                                                      | `[priority] medium`  | Performance / Engine feature                                |
+| 182 | [Display `engine` Setter Swallows `ValueError` and Is Off-Contract](open/medium_display-engine-setter-swallows-valueerror-and-is-off-contract.md)                              | `[priority] medium`  | Robustness / Architecture                                   |
+| 183 | [Add Mixin Tests for TOF Size/Strain Parameters](open/medium_add-mixin-tests-for-tof-size-strain-parameters.md)                                                                | `[priority] medium`  | Test coverage                                               |
+| 187 | [`fork()` in a Multi-Threaded Process (BUMPS/DREAM)](open/medium_fork-in-multi-threaded-process-deprecation-in-bumps-dream.md)                                                 | `[priority] medium`  | Forward-compatibility / Concurrency                         |
 | 9   | [Add Future Enum Extensions](open/low_add-future-enum-extensions.md)                                                                                                           | `[priority] low`     | Design improvement                                          |
 | 10  | [Unify Project-Level Update Orchestration](open/low_unify-project-level-update-orchestration.md)                                                                               | `[priority] low`     | Maintainability                                             |
 | 11  | [Document Category `_update` Contract](open/low_document-category-update-contract.md)                                                                                          | `[priority] low`     | Maintainability                                             |
@@ -153,10 +155,17 @@ individual issue files** — not here.
 | 159 | [Narrow Defensive getattr-Chain in Aniso ADP Unit Resolution](open/low_narrow-defensive-getattr-chain-in-aniso-adp-unit-resolution.md)                                         | `[priority] low`     | Maintainability                                             |
 | 160 | [Replace No-Op `assert True` in `test_logging.py`](open/low_replace-no-op-assert-true-in-test-logging-py.md)                                                                   | `[priority] low`     | Test coverage                                               |
 | 161 | [Add Boundary Tests for `verification.py` FullProf/IGOR Parsers](open/low_add-boundary-tests-for-verification-py-fullprof-igor-parsers.md)                                     | `[priority] low`     | Test coverage                                               |
-| 163 | [Fix `.gitignore` Gaps and Remove the Stale `absorption/` Package](open/low_fix-gitignore-gaps-and-remove-the-stale-absorption-package.md)                                     | `[priority] low`     | Hygiene                                                     |
+| 163 | [Fix `.gitignore` Gaps (`.pyc` Pattern and `benchmark.json`)](open/low_fix-gitignore-pyc-and-benchmark-gaps.md)                                                                | `[priority] low`     | Hygiene                                                     |
 | 165 | [cryspy Backend Hardcodes `flag_only_nuclear` (No Magnetic Structures)](open/low_cryspy-backend-hardcodes-flag-only-nuclear-no-magnetic-structures.md)                         | `[priority] low`     | Engine limitation                                           |
 | 176 | [Reuse Reflection Record Objects Across Fit Iterations](open/low_reuse-reflection-record-objects-across-fit-iterations.md)                                                     | `[priority] low`     | Performance                                                 |
 | 177 | [Reduce Per-Point Data-Model Overhead in Fits](open/low_reduce-per-point-data-model-overhead-in-fits.md)                                                                       | `[priority] low`     | Performance                                                 |
+| 180 | [Re-enable `flag_only_nuclear` Pre-Filter After Upstream cryspy Fix](open/low_re-enable-nuclear-only-pre-filter-after-cryspy-fix.md)                                           | `[priority] low`     | Correctness / External backend                              |
+| 181 | [Add `from __future__ import annotations` to All Modules](open/low_add-from-future-annotations-to-all-modules.md)                                                              | `[priority] low`     | Hygiene / Consistency                                       |
+| 184 | [Replace String-Dispatch `getattr` in `core/identity.py`](open/low_replace-string-dispatch-getattr-in-core-identity.md)                                                        | `[priority] low`     | Code style                                                  |
+| 185 | [Replace `**kwargs` in `Logger.print`](open/low_replace-kwargs-in-logger-print.md)                                                                                             | `[priority] low`     | Code style                                                  |
+| 186 | [Test `AdpTypeEnum.description()`](open/low_test-adptypeenum-description.md)                                                                                                   | `[priority] low`     | Test coverage                                               |
+| 188 | [Track `diffpy.Structure` Deprecation Warning](open/low_track-diffpy-structure-deprecation-warning.md)                                                                         | `[priority] low`     | Dependency / Deprecation                                    |
+| 189 | [Quiet Expected pytest Warnings (benchmark/xdist and BUMPS)](open/low_quiet-expected-pytest-warnings-benchmark-xdist-and-bumps.md)                                             | `[priority] low`     | Test hygiene / CI noise                                     |
 | 88  | [Fix Dataset 26 Description (47 Files, Not 57)](open/lowest_fix-dataset-26-description-47-files-not-57.md)                                                                     | `[priority] lowest`  | Data                                                        |
 | 91  | [Disable TODO Comment Checks in CodeFactor PRs](open/lowest_disable-todo-comment-checks-in-codefactor-prs.md)                                                                  | `[priority] lowest`  | CI / Tooling                                                |
 | 117 | [Live-Notebook Plotly Delivery: Loader vs Native Mimetype](open/lowest_live-notebook-plotly-delivery-loader-vs-native-mimetype.md)                                             | `[priority] lowest`  | Display / Architecture                                      |
@@ -188,3 +197,4 @@ individual issue files** — not here.
 | 164 | [Reconcile Git-Ignored `AGENTS.md` / `CLAUDE.md` With Their Checked-In Role](closed/reconcile-git-ignored-agents-md-claude-md-with-their-checked-in-role.md) |
 | 172 | [Cache Wyckoff Orbit Templates to Speed Up Refinement](closed/cache-wyckoff-orbit-templates-to-speed-up-refinement.md)                                       |
 | 173 | [Avoid Rebuilding the Included-Point Mask Every Fit Iteration](closed/avoid-rebuilding-included-point-mask-every-fit-iteration.md)                           |
+| 190 | [Add a Single-Crystal TOF Fit Verification Example](closed/add-single-crystal-tof-fit-verification-example.md)                                               |