Update how-to guide notebook - #478
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Ports notebooks/tmol_how_to_guide.ipynb from the stale tmol_how_to_notebook branch onto current master and brings it up to date with the file-naming refactor: fixes moved imports, the 4-column FoldForest edge format, the fast_relax unification of kin/cartesian relax, and several real bugs (non-contiguous jump indices, frozen-dataclass evolve, off-by-one chi expansion, per-block-type connection indices). Fills in 20 of 23 "TO DO" placeholder cells with working examples; the 3 idealization cells are left as notes since no such routine currently exists in tmol. Verified end to end: all 72 code cells execute with zero errors.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #478 +/- ##
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+ Coverage 92.09% 92.41% +0.31%
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Files 450 455 +5
Lines 38243 40061 +1818
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+ Hits 35220 37021 +1801
- Misses 3023 3040 +17
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Ports notebooks/tmol_how_to_guide.ipynb from the stale tmol_how_to_notebook branch onto current master and brings it up to date with the file-naming refactor: fixes moved imports, the 4-column FoldForest edge format, the fast_relax unification of kin/cartesian relax, and several real bugs (non-contiguous jump indices, frozen-dataclass evolve, off-by-one chi expansion, per-block-type connection indices). Fills in 20 of 23 "TO DO" placeholder cells with working examples; the 3 idealization cells are left as notes since no such routine currently exists in tmol. Verified end to end: all 72 code cells execute with zero errors.