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fix(notebooks): illustrate 05 and 12 - #64
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…te 05 and 12 Three tutorial notebooks carried a RuntimeWarning in their outputs, and a warning names the file that raised it — the absolute path of the venv on the machine that executed them. The warning itself is expected: every optimizer wrapper scores an unbuildable candidate as +inf on purpose, and scipy's finite differences and pymoo's crowding distance then compute inf - inf. The wrappers now run the third-party optimizer under numpy.errstate(invalid="ignore"), and a new test refuses any notebook whose outputs name a home directory. Notebooks 05 and 12 had never been executed: their figures are now stored. Executing 05 showed that eliminate_theta() returned an expression still in theta (it rewrote cos as sin before substituting cos). It now substitutes directly, turns each square root into an unknown with a polynomial constraint, and reads floats as exact rationals; the four-bar rocker tip gives its circle in under a second. The notebook explains why that curve has degree 2 and not 6. Notebooks 02, 10 and 11 are re-executed against the current code.
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HugoFara
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Summary
RuntimeWarning: invalid value encountered in subtractin their stored outputs, and a warning names the file that raised it. Root cause: every optimizer wrapper scores an unbuildable candidate as+infon purpose, so scipy's finite differences (dual_annealing, DE's polish, gradient methods inminimize_linkage) and pymoo's crowding distance (multi_objective_optimization,co_optimize) computeinf - inf. The wrappers now run the third-party optimizer undernumpy.errstate(invalid="ignore").eliminate_theta()rewrotecosassin(theta + pi/2)before substitutingcos(theta), so nothing was substituted and it returned an expression still intheta(the notebook printed a "degree 0" curve). Rewritten: direct substitution, each square root becomes an unknownrwithr**2 = R, floats are read as exact rationals,cos(2θ)and the like are expanded. The four-bar rocker tip gives(x-4)² + y² = 9in ~0.4 s; the soft "skip if it fails" test is replaced by exact ones. Symbolic lengths and a joint built on a second dyad (nested roots) are still slow — documented.main.Test plan
uv run pytest— 2671 passed