Merge pull request #192 from easyscience/develop

🎉 Release: merge develop into master

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/**

.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/copilot-instructions.md

@@ -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/coverage.yml

@@ -121,6 +121,12 @@ jobs:
         # if: false # Temporarily disabled to speed up the docs build
         run: pixi run notebook-exec-ci
 
+      # Sync the canonical Three.js snapshot into the docs assets so
+      # MkDocs can serve it (belt-and-braces; docs-build also depends on
+      # this task).
+      - name: Sync vendored JS into docs assets
+        run: pixi run docs-sync-vendored-js
+
       # Build the static files for the documentation site for local inspection
       # Input: docs/ directory containing the Markdown files
       # Output: site/ directory containing the generated HTML files

.github/workflows/docs.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:

.github/workflows/tutorial-tests.yml

@@ -15,6 +15,10 @@ build/
 # MkDocs
 docs/site/
 
+# Generated docs-serving copy of the canonical Three.js (synced from
+# src/ by `pixi run docs-sync-vendored-js`; the source of truth is src/)
+docs/docs/assets/javascripts/vendor/threejs/
+
 # Jupyter Notebooks
 .ipynb_checkpoints
 
@@ -45,6 +49,10 @@ CMakeLists.txt.user*
 *.log
 *.zip
 
+# Agents
+AGENTS.md
+CLAUDE.md
+
 # ED
 # Used to fetch tutorials data during their runtime. Need to have '/' at
 # the beginning to avoid ignoring 'data' module in the src/.

.gitignore

@@ -25,6 +25,15 @@ docs/docs/assets/
 # Node
 node_modules
 
+# Vendored snapshots
+src/easydiffraction/display/structure/renderers/vendor/
+src/easydiffraction/report/templates/html/vendor/
+src/easydiffraction/report/templates/tex/styles/
+src/easydiffraction/utils/_vendored/jupyter_dark_detect/
+
+# Tox
+.tox
+
 # Misc
 .benchmarks
 .cache

.prettierignore

@@ -0,0 +1,25 @@
+# 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`.
+
+## Structure-View Three.js
+
+The vendored Three.js assets for the crysview structure view (MIT) are
+documented in
+`src/easydiffraction/display/structure/renderers/vendor/threejs/LICENSES.md`.
+
+## Structure-View Element Data
+
+The bundled per-element radii and colour palettes (with per-source
+provenance) are documented in
+`src/easydiffraction/display/structure/assets/LICENSES.md`.