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Jukka Aho 626266c990 docs: Reorganize documentation into three-tier structure

**Three Manuals for Three Audiences:**

1. **User Manual** (docs/user/) - "Just Get It Done"
   - For end users, engineers, students
   - Simple, practical, step-by-step
   - Quick start, tutorials, examples, troubleshooting
   - Philosophy: Show me how to solve my problem

2. **Contributor Manual** (docs/contributor/) - "Show Me the Code"
   - For developers, contributors, advanced users
   - Technical, detailed, design rationale
   - Testing, architecture, performance, CI/CD
   - Philosophy: Explain HOW and WHY

3. **The JuliaFEM Book** (docs/book/) - "Let Me Show You How I Think"
   - For researchers, theory nerds, and Jukka
   - Comprehensive, educational, opinionated, personal
   - Math foundations, design philosophy, history, research
   - Philosophy: Mix theory, code, and personal experience

**Reorganization:**
- Moved: TESTING_PHILOSOPHY.md → contributor/testing_philosophy.md
- Moved: STATUS.md → contributor/status.md
- Moved: TEST_FIXES_NEEDED.md → contributor/test_fixes_needed.md
- Moved: lagrange_basis_functions.md → book/lagrange_basis_functions.md
- Moved: benchmarks/ → book/benchmarks/
- Created: docs/README.md (main index explaining structure)
- Created: README.md in each section explaining audience and contents
- Updated: All references in scripts and source files

**Naming:** All docs now lowercase (testing_philosophy not TESTING_PHILOSOPHY)

**Benefits:**
- Clear separation of concerns
- Users don't get overwhelmed with implementation details
- Contributors get technical depth
- Book preserves deep theory and personal insights
- Each manual optimized for its audience

**Next:** Populate each section with appropriate content

2025-11-09 04:38:28 +02:00

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Test Fixes Needed

Date: November 8, 2025
Status: 5 passing, 49 failing (infrastructure now in place)

Summary

Tests are failing due to API evolution between Julia 0.6/1.0 (2018) and Julia 1.12 (2025), not fundamental architectural problems. Package loads successfully and core functionality works.

Main Issues

1. Missing `aster_read_mesh` (14 tests)

Problem: Tests use aster_read_mesh() from IO submodule, but it requires HDF5
Files affected: Most 3D elasticity tests, med file tests
Fix options:

A) Add HDF5 as optional dependency (Julia 1.9+ package extensions)
B) Skip tests that need .med files for now
C) Convert test meshes to .inp format (ABAQUS, which we support)

Recommendation: Option C - convert test meshes to .inp format

2. `eval_basis!` Signature Mismatch (2 tests)

Problem: eval_basis!(::Type{Seg2}, ::Matrix, ::Tuple{Float64})
Current: eval_basis!(::Seg2, ::Vector, ::Tuple{Float64}, time::Float64)
Location: vendor/FEMBasis.jl

Fix: Update signature in FEMBasis or fix call sites

3. `jacobian` Signature Mismatch (~20 tests)

Problem: Tests call jacobian(element_type, X, xi) with old signatures
Current API: Different parameter order or types
Location: vendor/FEMBasis.jl/src/jacobian.jl

Fix: Consolidate FEMBasis into src/basis/ with modern API

4. `allocate_buffer` Missing (2 tests)

Problem: allocate_buffer(::Problem{Elasticity}, ::Vector{Element})
Status: Method doesn't exist in current codebase
Fix: Either restore method or update tests to not need it

5. `Analysis` Missing (5 tests) - ✅ FIXED

Status: Now exported, these tests should pass

6. Statistics Package Missing (1 test) - ✅ FIXED

Status: Now in test dependencies

Test Categories

✅ Passing (5 tests)

Virtual work test
Contact 2D/3D tests
Mortar 2D tests
Heat transfer (basic)

❌ Failing - Missing HDF5 (~14 tests)

test_elasticity_2d_nonlinear_with_surface_load.jl
test_elasticity_3d_unit_block.jl
test_elasticity_med_pyr5_point_load.jl
test_elasticity_plane_strain.jl
test_elasticity_pyr5_point_load.jl
Many more...

❌ Failing - API Mismatches (~30 tests)

eval_basis! signature (2)
jacobian signature (~20)
allocate_buffer missing (2)
Various others (6)

Action Plan

Phase 1: Low-Hanging Fruit (1-2 hours)

✅ Export Analysis types
✅ Add Statistics to test deps
⏳ Skip/comment out HDF5-dependent tests temporarily
⏳ Re-run tests, see how many pass

Phase 2: API Fixes (4-6 hours)

Fix eval_basis! signature in FEMBasis
Fix jacobian signature in FEMBasis
Either restore allocate_buffer or update tests
Fix any remaining signature mismatches

Phase 3: Mesh Conversion (2-4 hours)

Find all .med test meshes
Convert to .inp format using Code Aster or similar
Update test files to use .inp instead of .med
Re-run tests

Phase 4: Verify All Pass (1 hour)

Run full test suite
Fix any remaining issues
Update CI to run tests automatically
Celebrate! 🎉

Expected Outcome

After these fixes:

~40+ tests should pass (out of 56 total)
CI will catch regressions automatically
Good foundation for further consolidation work

Notes

The fact that package loads and 5 tests pass is actually very good news - it means the core architecture is sound. These are just API compatibility issues that accumulated over 6 years of Julia evolution.

Most fixes are mechanical (update signatures) rather than requiring deep understanding of the algorithms.

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