Global evaluation rewrite

.github/workflows/build_deploy_pdoc.yml

@@ -44,7 +44,7 @@ jobs:
           export PETSC_DIR="/home/runner/micromamba/envs/uw3_test/lib"
           VERSION=`python3 setup.py --version`
           echo "UW - version " ${VERSION}
-          ./compile.sh
+          ./scripts/compile.sh
 
       - name: Build docs with pdoc
         shell: bash -l {0}
@@ -53,7 +53,7 @@ jobs:
           echo "VERSION=$(echo $VERSION)" >> $GITHUB_ENV
           # mkdir -p docs
           pip install pdoc3
-          ./build_api_docs.sh
+          ./scripts/build_api_docs.sh
 
       # There is an action to build the jupyter book to a different directory
       # and then they can be uploaded side by side

.github/workflows/build_uw3_and_test.yml

@@ -34,10 +34,10 @@ jobs:
           VERSION=`python3 setup.py --version`
           echo "UW - version " ${VERSION}
 
-          ## TODO. Use compile.sh once it is in development
+          ## TODO. Use scripts/compile.sh once it is in development
           pip install -e . --no-build-isolation
 
-      - name: Run tests 
+      - name: Run tests
         shell: bash -l {0}
         run: |
-          ./test.sh
+          ./scripts/test.sh --p 2

.github/workflows/publish.yml

@@ -29,20 +29,20 @@ jobs:
           post-cleanup: "all"
           create-args: quarto
 
-      - name: Render docs with quarto
+      - name: Render unified docs with quarto
         shell: bash -l {0}
         run: |
           quarto install tinytex
-          cd docs/user
+          cd docs
           quarto render --cache-refresh --log-level info
       ## Always deploy to version directory
-      - name: Deploy quarto book
+      - name: Deploy unified documentation
         uses: peaceiris/actions-gh-pages@v3
 
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          destination_dir: ${{ github.ref_name }}/_quickstart
-          publish_dir: docs/user/_build/book
+          destination_dir: ${{ github.ref_name }}/docs
+          publish_dir: docs/_build
 
       # - name: Deploy quarto lectures
       #   uses: peaceiris/actions-gh-pages@v3

.gitignore

@@ -10,6 +10,7 @@ maths.c
 swarm.c
 *_debug.txt
 compile.log
+*.log
 .env
 **/__pycache__
 *.so
@@ -27,10 +28,89 @@ old
 keep/*
 *.swp
 nohup.out
-src/underworld3/_uwid.py
-*.png # Add these explicitly if you want to keep them 
-
-# quarto build relics
+src/underworld3/_uwid.py 
+
+# TeX/LaTeX/PDF build artifacts (comprehensive)
+*.aux
+*.lof
+*.log
+*.lot
+*.fls
+*.out
+*.toc
+*.fmt
+*.fot
+*.cb
+*.cb2
+.*.lb
+*.bbl
+*.bcf
+*.blg
+*-blx.aux
+*-blx.bib
+*.run.xml
+*.fdb_latexmk
+*.synctex
+*.synctex(busy)
+*.synctex.gz
+*.synctex.gz(busy)
+*.pdfsync
+*.nav
+*.snm
+*.vrb
+*.xdv
+*.idx
+*.ilg
+*.ind
+*.glg
+*.glo
+*.gls
+*.ist
+*.acn
+*.acr
+*.alg
+*.glsdefs
+*.lzo
+*.lzs
+*.slg
+*.slo
+*.sls
+
+# Quarto build artifacts (comprehensive coverage for all docs subdirectories)
+docs/_build/
+docs/.quarto/
+docs/_freeze/
+docs/*/_build/
+docs/*/.quarto/
+docs/*/_freeze/
+docs/*/*/_build/
+docs/*/*/.quarto/
+docs/*/*/_freeze/
+docs/**/*.pdf
+docs/**/*.tex
+docs/**/*.aux
+docs/**/*.log
+docs/**/*.toc
+docs/**/*.out
+docs/**/*.fls
+docs/**/*.fdb_latexmk
+docs/**/*.synctex.gz
+docs/**/*.nav
+docs/**/*.snm
+docs/**/*.vrb
+
+# Additional documentation build artifacts
+docs/**/.ipynb_checkpoints/
+docs/**/site_libs/
+docs/**/libs/
+docs/**/_site/
+docs/**/dist/
+docs/**/node_modules/
+docs/**/.sass-cache/
+docs/**/.jekyll-cache/
+docs/**/.jekyll-metadata
+docs/**/*.rdb
+docs/**/*.rdx
 
 documentation/index.aux
 documentation/index.pdf
@@ -61,15 +141,35 @@ joss-paper/paper.pdf
 .ash_history
 
 
-# Mesh files etc
+# Example output files (comprehensive exclusion)
 
+# Mesh files
 uw_*.msh
-*.msh # unless we really want to add some examples
+*.msh
 *.h5
 *.xdmf
 *.vtk
 *.pbin
 
+# Visualization outputs (exclude generated, allow curated assets)
+docs/examples/**/output/**
+docs/examples/**/*.png
+docs/examples/**/*.jpg
+docs/examples/**/*.gif
+docs/examples/**/*.mp4
+docs/examples/**/*.html
+# But allow curated documentation images
+!docs/examples/assets/**
+
+# Additional example artifacts
+docs/examples/**/*.txt
+docs/examples/**/*.dat
+docs/examples/**/*.csv
+docs/examples/**/*.log
+docs/examples/**/checkpoint_*
+docs/examples/**/restart_*
+docs/examples/**/.meshes/
+
 # Any checkpoints from notebooks (since .md files can be run in setups with 
 # jupytext and will produce spurious/unexpected checkpoints.
 
@@ -101,3 +201,47 @@ Jupyterbook/.DS_Store
 Jupyterbook/Notebooks/.DS_Store
 Jupyterbook/Notebooks/Examples-NavierStokes/order_1/NS_test_Re_250_0.06_step_0.png
 Documentation/index.aux
+
+# Claude Code files
+CLAUDE.md
+.claude/
+
+# Prevent future markdown clutter in root (allow essential docs only)
+/*_ANALYSIS.md
+/*_REPORT.md
+/*_SUMMARY.md
+/*_STATUS.md
+/*_PROGRESS.md
+/*_REVIEW.md
+/*_PLAN.md
+/*_FIXES.md
+/SESSION_SUMMARY*.md
+/PHASE_*.md
+# Exceptions for essential docs
+!TODO.md
+!README.md
+!CLAUDE.md
+!CONTRIBUTING.md
+!CHANGES.md
+!SPELLING_CONVENTION.md
+!LICENSE.md
+
+# Temporary test files (can be deleted)
+temp_tests_deletable/
+debug_*.py
+/test_*.py
+# Allow legitimate test files in tests/ directory
+!tests/**/test_*.py
+
+# IDE and editor artifacts
+.ropeproject/
+.vscode/
+
+# Mesh cache directory
+.meshes/
+
+# Additional cache directories
+.pytest_cache/
+
+# Visualization output files (generated during notebook execution)
+docs/beginner/tutorials/html5/*.html

.zenodo.json

@@ -1,59 +1,64 @@
 {
-    "creators": [
-        {
-            "name": "Louis Moresi",
-            "affiliation": "Research School of Earth Sciences, The Australian National University",
-            "orcid": "0000-0003-3685-174X"
-        },
-        {
-            "name": "John Mansour",
-            "affiliation": "School of Earth, Atmospheric & Environmental Science, Monash University",
-            "orcid": "0000-0001-5865-1664"
-        },
-        {
-            "name": "Julian Giordani",
-            "affiliation": "School of Earth Science, The University of Sydney",
-            "orcid": "0000-0003-4515-9296"
-        },
-        {
-            "name": "Matt Knepley",
-            "orcid": "0000-0002-2292-0735",
-            "affiliation": "Computer Science and Engineering, University at Buffalo"
-        },
-        {
-            "name": "Ben Knight",
-            "affiliation": "School of Earth and Planetary Sciences, Curtin University",
-            "orcid": "0000-0001-7919-2575"
-        },
-        {
-            "name": "Juan Carlos Graciosa",
-            "orcid": "0000-0003-0817-354X",
-            "affiliation": "Research School of Earth Sciences, The Australian National University"
-        },
-        {
-            "name": "Thyagarajulu Gollapalli",
-            "orcid": "0000-0001-9394-4104",
-            "affiliation": "School of Earth, Atmospheric & Environmental Science, Monash University"
-        },
-        {
-            "name": "Neng Lu",
-            "affiliation": "Research School of Earth Sciences, The Australian National University",
-            "orcid": "0000-0001-9424-2315"
-        },
-        {
-            "name": "Romain Beucher",
-            "affiliation": "Research School of Earth Sciences, The Australian National University",
-            "orcid": "0000-0003-3891-5444"
-        }
-    ],
-    "license": "lgpl-3.0",
-    "title": "Underworld3: Mathematically Self-Describing Modelling in Python for Desktop, HPC and Cloud",
-    "upload_type": "software",
-    "access_right": "open",
-    "keywords": [
-        "geodynamics",
-        "finite elements",
-        "particle-in-cell",
-        "symbolic computation"
-    ]
+  "creators": [
+    {
+      "name": "Louis Moresi",
+      "affiliation": "Research School of Earth Sciences, The Australian National University",
+      "orcid": "0000-0003-3685-174X"
+    },
+    {
+      "name": "Julian Giordani",
+      "affiliation": "School of Earth Science, The University of Sydney",
+      "orcid": "0000-0003-4515-9296"
+    },
+    {
+      "name": "Matt Knepley",
+      "orcid": "0000-0002-2292-0735",
+      "affiliation": "Computer Science and Engineering, University at Buffalo"
+    },
+    {
+      "name": "Romain Beucher",
+      "affiliation": "Research School of Earth Sciences, The Australian National University",
+      "orcid": "0000-0003-3891-5444"
+    },
+    {
+      "name": "Thyagarajulu Gollapalli",
+      "orcid": "0000-0001-9394-4104",
+      "affiliation": "School of Earth, Atmospheric & Environmental Science, Monash University"
+    },
+    {
+      "name": "Juan Carlos Graciosa",
+      "orcid": "0000-0003-0817-354X",
+      "affiliation": "Research School of Earth Sciences, The Australian National University"
+    },
+    {
+      "name": "Ben Knight",
+      "affiliation": "School of Earth and Planetary Sciences, Curtin University, Australia",
+      "orcid": "0000-0001-7919-2575"
+    },
+    {
+      "name": "Neng Lu",
+      "affiliation": "Research School of Earth Sciences, The Australian National University",
+      "orcid": "0000-0001-9424-2315"
+    },
+    {
+      "name": "John Mansour",
+      "affiliation": "School of Earth, Atmospheric & Environmental Science, Monash University",
+      "orcid": "0000-0001-5865-1664"
+    },
+    {
+      "name": "Romain Beucher",
+      "affiliation": "Research School of Earth Sciences, The Australian National University",
+      "orcid": "0000-0003-3891-5444"
+    }
+  ],
+  "license": "lgpl-3.0",
+  "title": "Underworld3: Mathematically Self-Describing Modelling in Python for Desktop, HPC and Cloud",
+  "upload_type": "software",
+  "access_right": "open",
+  "keywords": [
+    "geodynamics",
+    "finite elements",
+    "particle-in-cell",
+    "symbolic computation"
+  ]
 }