Implement project reports in HTML, PDF, and CIF (#185)

* 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

Author: AndrewSazonov

.codecov.yml

@@ -4,6 +4,11 @@
 github_checks:
   annotations: true
 
+ignore:
+  - 'src/easydiffraction/report/templates/html/vendor/**'
+  - 'src/easydiffraction/report/templates/tex/styles/**'
+  - 'src/easydiffraction/utils/_vendored/jupyter_dark_detect/**'
+
 comment:
   layout: 'reach, diff, flags, files'
   behavior: default

.codefactorignore

@@ -1,11 +1,13 @@
 # CodeFactor exclude patterns configuration must be done online:
 # https://www.codefactor.io/repository/github/easyscience/diffraction-lib/ignore
 #
-# Last updated: 2026-01-05
+# Last updated: 2026-05-29
 #
 # Exclude patterns:
 # deps/**
 # docs/**
+# src/easydiffraction/report/templates/html/vendor/**
+# src/easydiffraction/report/templates/tex/styles/**
 # src/easydiffraction/utils/_vendored/jupyter_dark_detect/**
 # tests/**
 # tmp/**

.prettierignore

@@ -25,6 +25,11 @@ docs/docs/assets/
 # Node
 node_modules
 
+# Vendored snapshots
+src/easydiffraction/report/templates/html/vendor/
+src/easydiffraction/report/templates/tex/styles/
+src/easydiffraction/utils/_vendored/jupyter_dark_detect/
+
 # Misc
 .benchmarks
 .cache

THIRD_PARTY_LICENSES.md

@@ -0,0 +1,13 @@
+# Third-Party Licenses
+
+This file indexes third-party assets vendored in this repository.
+
+## Report LaTeX Styles
+
+The vendored report LaTeX style files are documented in
+`src/easydiffraction/report/templates/tex/styles/LICENSES.md`.
+
+## Report HTML Assets
+
+The vendored report HTML assets are documented in
+`src/easydiffraction/report/templates/html/vendor/LICENSES.md`.

docs/dev/adrs/accepted/analysis-cif-fit-state.md

@@ -25,6 +25,7 @@ Analysis-owned fit state needs to persist:
 - fit bounds and bound provenance
 - pre-fit scalar snapshots for recovery workflows
 - compact status metadata for the latest saved fit projection
+- software-provenance snapshot for the latest successful fit
 - deterministic correlation summaries
 - minimizer-specific fit outputs on the paired `_fit_result.*` category
 - per-parameter posterior summaries on `_fit_parameter`
@@ -104,6 +105,34 @@ round-trip project schema remains common.
 correlation summaries keyed by a persisted `id`. Only unique parameter
 pairs are stored.
 
+### Software provenance
+
+`_software` stores the runtime software snapshot recorded after a
+successful fit. It is part of the project save / load contract and feeds
+report rendering plus the IUCr export software labels. It is not a user
+configuration category.
+
+The category stores name, version, and URL triples for:
+
+- `framework`
+- `calculator`
+- `minimizer`
+
+Each role is persisted as scalar items on the same category:
+
+- `<role>_name`
+- `<role>_version`
+- `<role>_url`
+
+The category also stores:
+
+- `timestamp`
+
+`timestamp` is an ISO-8601 UTC string for the fit that produced the
+snapshot. Projects saved before this category existed load with all
+software fields unset and `timestamp` set to `None`; rerunning a fit
+populates the snapshot.
+
 ### Minimizer fit projection
 
 The active `_minimizer.*` category stores user-selected solver inputs
@@ -230,9 +259,10 @@ Load order is:
 
 1. standard analysis configuration
 2. `_minimizer.*` settings according to the active `_minimizer.type`
-3. common and family-specific `_fit_result.*` fields on the paired class
-4. `_fit_parameter` and `_fit_parameter_correlation`
-5. posterior sidecar arrays when a Bayesian result is expected
+3. `_software.*` provenance fields when present
+4. common and family-specific `_fit_result.*` fields on the paired class
+5. `_fit_parameter` and `_fit_parameter_correlation`
+6. posterior sidecar arrays when a Bayesian result is expected
 
 Persist backend runtime objects, optimizer instances, and raw driver
 payloads nowhere in this design.

docs/dev/adrs/accepted/iucr-cif-tag-alignment.md

@@ -16,7 +16,8 @@ Persistence.
 
 `Project` is the top-level user facade. It owns project metadata,
 structures, experiments, rendering preferences, display helpers,
-analysis, report helpers, verbosity, and save/load behavior.
+analysis, report helpers, publication metadata, verbosity, and save/load
+behavior.
 
 A later proposal considered renaming this facade to `Workspace` so that
 `project` could be reserved for the scientific project information
@@ -50,9 +51,18 @@ through `project.report` and written only when requested, using
 `reports/<project>.cif`; default project saves do not write
 `summary.cif`.
 
-Expose submission-report helpers as `project.report`. The previous
-`project.summary` placeholder and its `summary.cif` output are not part
-of the persistence layout.
+Expose submission-report helpers as `project.report`. This facade is a
+hybrid surface: its scalar output configuration persists to
+`project.cif` as `_report.*`, while its methods render report artifacts
+under `reports/`. The previous `project.summary` placeholder and its
+`summary.cif` output are not part of the persistence layout.
+
+Expose journal-submission metadata as `project.publication`. It is a
+top-level owner with CIF-aligned sibling categories for `_journal.*`,
+`_journal_date.*`, `_journal_coeditor.*`, `_publ_contact_author.*`,
+`_publ_body.*`, and the `_publ_author.*` loop. These singleton
+publication categories persist in `project.cif` and feed report exports;
+`reports/<project>.cif` remains export-only.
 
 Keep project information available as `project.info`. The Python name
 avoids a confusing `project.project` access path, while the persisted
@@ -79,6 +89,11 @@ The saved project directory path is runtime file-I/O state, not a
 serialized project-information field. If the path is exposed in Python,
 it must not emit a `_project.path` CIF item.
 
+The project-level singleton categories currently persisted in
+`project.cif` are `_project.*`, `_chart.*`, `_report.*`, `_table.*`,
+`_verbosity.*`, `_journal.*`, `_journal_date.*`, `_journal_coeditor.*`,
+`_publ_contact_author.*`, `_publ_body.*`, and the `_publ_author.*` loop.
+
 ## Consequences
 
 The saved layout mirrors the current object graph while preserving the