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@copier-update copier-update bot commented Nov 2, 2025 •
edited by liblaf bot
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Automated changes by Bot > Copier Update Workflow

@copier-update copier-update bot requested a review from liblaf November 2, 2025 01:48
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liblaf previously approved these changes Nov 2, 2025
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✅⚠️MegaLinter analysis: Success with warnings

Descriptor Linter Files Fixed Errors Warnings Elapsed time
✅ BASH shellcheck 1 0 0 0.29s
✅ BASH shfmt 1 0 0 0 0.6s
⚠️ COPYPASTE jscpd yes 198 no 6.49s
⚠️ JSON jsonlint 7 1 0 0.16s
✅ JSON prettier 7 0 0 0 1.04s
✅ JSON v8r 7 0 0 4.41s
⚠️ PYTHON ruff yes yes 1481 no 15.64s
✅ SPELL cspell 225 0 0 5.81s
✅ YAML prettier 4 0 0 0 0.82s
✅ YAML v8r 4 0 0 3.44s
✅ YAML yamllint 4 0 0 0.25s

Detailed Issues

⚠️ COPYPASTE / jscpd - 198 errors 
Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/phace/func.py [98:6 - 104:17] (6 lines, 85 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/phace/func.py [71:6 - 76:17]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/arap_active/_main.py [1:1 - 15:11] (14 lines, 119 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/phace/_main.py [1:1 - 15:6]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/arap_active/_main.py [15:11 - 39:3] (24 lines, 227 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/phace/_main.py [15:6 - 39:16]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/arap/func.py [43:5 - 54:5] (11 lines, 134 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/arap_active/func.py [49:6 - 60:6]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/arap/func.py [57:5 - 68:5] (11 lines, 137 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/arap_active/func.py [63:6 - 74:6]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/arap/_main.py [1:1 - 11:5] (10 lines, 100 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/phace/_main.py [1:1 - 9:2]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/arap/_main.py [23:5 - 40:2] (17 lines, 167 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/phace/_main.py [16:5 - 33:2]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [83:11 - 92:5] (9 lines, 99 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [58:11 - 67:7]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [92:5 - 103:4] (11 lines, 162 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [67:7 - 78:7]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [113:17 - 133:10] (20 lines, 262 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [58:11 - 78:7]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [154:2 - 169:3] (15 lines, 217 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [62:2 - 77:12]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [184:17 - 210:10] (26 lines, 359 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [149:17 - 175:10]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [220:19 - 229:4] (9 lines, 90 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [58:11 - 67:7]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [230:4 - 241:4] (11 lines, 171 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [92:7 - 78:7]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [252:25 - 261:4] (9 lines, 90 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [58:11 - 67:7]

Clone found (python):
 - src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [262:10 - 274:9] (12 lines, 188 tokens)
   src/liblaf/apple/warp/sim/energy/elastic/_elastic.py [92:7 - 104:4]

Clone found (python):
 - src/liblaf/apple/jax/sim/energy/elastic/_phace_active.py [6:1 - 13:5] (7 lines, 78 tokens)
   src/liblaf/apple/jax/sim/energy/elastic/_phace_static.py [3:1 - 12:6]

Clone found (python):
 - src/liblaf/apple/jax/sim/energy/elastic/_phace_active.py [40:9 - 45:2] (5 lines, 129 tokens)
   src/liblaf/apple/jax/sim/energy/elastic/_phace_static.py [29:9 - 34:2]

Clone found (python):
 - src/liblaf/apple/jax/sim/energy/elastic/_arap_active.py [1:1 - 19:11] (18 lines, 145 tokens)
   src/liblaf/apple/jax/sim/energy/elastic/_phace_active.py [1:1 - 19:12]

Clone found (python):
 - src/liblaf/apple/jax/sim/energy/elastic/_arap_active.py [27:13 - 37:3] (10 lines, 100 tokens)
   src/liblaf/apple/jax/sim/energy/elastic/_phace_active.py [30:9 - 40:8]

Clone found (python):
 - src/liblaf/apple/jax/sim/energy/elastic/_arap_active.py [42:5 - 56:7] (14 lines, 200 tokens)
   src/liblaf/apple/jax/sim/energy/elastic/_phace_active.py [50:5 - 64:7]

Clone found (python):
 - src/liblaf/apple/jax/sim/energy/elastic/_arap.py [3:1 - 13:5] (10 lines, 86 tokens)
   src/liblaf/apple/jax/sim/energy/elastic/_phace_static.py [3:1 - 13:12]

Clone found (python):
 - exp/2025/07/30/dynamics/collision/collision-bunny-bunny/main.py [1:1 - 14:5] (13 lines, 115 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny-sphere/main.py [1:1 - 14:4]

Clone found (python):
 - exp/2025/07/30/dynamics/collision/collision-bunny-bunny/main.py [22:5 - 84:78] (62 lines, 768 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny-sphere/main.py [22:5 - 84:8]

Clone found (python):
 - exp/2025/07/30/dynamics/collision/collision-bunny-bunny/main.py [87:5 - 114:2] (27 lines, 319 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny-sphere/main.py [84:4 - 111:2]

Clone found (python):
 - exp/2025/07/30/dynamics/collision/collision-bunny/main.py [21:5 - 35:7] (14 lines, 116 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny-bunny/main.py [17:5 - 31:4]

Clone found (python):
 - exp/2025/07/30/dynamics/collision/collision-bunny/main.py [58:1 - 67:4] (9 lines, 151 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny-sphere/main.py [31:1 - 40:3]

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 - exp/2025/07/30/dynamics/collision/collision-bunny/main.py [67:3 - 77:9] (10 lines, 124 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny-sphere/main.py [40:3 - 49:6]

Clone found (python):
 - exp/2025/07/30/dynamics/collision/collision-bunny/main.py [81:9 - 88:5] (7 lines, 101 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny-sphere/main.py [52:9 - 59:7]

Clone found (python):
 - exp/2025/07/30/dynamics/collision/collision-bunny/main.py [90:4 - 100:5] (10 lines, 128 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny-sphere/main.py [58:2 - 68:4]

Clone found (python):
 - exp/2025/07/30/dynamics/collision/collision-bunny/main.py [100:2 - 116:4] (16 lines, 181 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny-sphere/main.py [68:2 - 84:10]

Clone found (python):
 - exp/2025/07/30/dynamics/collision/collision-bunny/main.py [116:6 - 132:5] (16 lines, 200 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny-sphere/main.py [87:5 - 103:13]

Clone found (python):
 - exp/2025/07/30/dynamics/collision/collision-box/main.py [1:1 - 50:5] (49 lines, 490 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny/main.py [1:1 - 50:3]

Clone found (python):
 - exp/2025/07/30/dynamics/collision/collision-box/main.py [52:9 - 79:28] (27 lines, 359 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny/main.py [54:2 - 81:3]

Clone found (python):
 - exp/2025/07/30/dynamics/collision/collision-box/main.py [78:9 - 96:75] (18 lines, 224 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny-sphere/main.py [49:10 - 96:8]

Clone found (python):
 - exp/2025/07/30/dynamics/collision/collision-box/main.py [104:5 - 142:10] (38 lines, 481 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny/main.py [97:8 - 105:12]

Clone found (python):
 - tests/warp/sim/energy/elastic/utils/test_hess_diag.py [9:10 - 30:15] (21 lines, 241 tokens)
   tests/warp/sim/energy/elastic/utils/test_hess_quad.py [10:6 - 31:11]

Clone found (python):
 - tests/warp/sim/energy/elastic/utils/test_hess_diag.py [87:5 - 93:13] (6 lines, 71 tokens)
   tests/warp/sim/energy/elastic/utils/test_hess_quad.py [97:5 - 103:13]

Clone found (python):
 - tests/warp/sim/energy/elastic/utils/test_hess_diag.py [94:5 - 106:11] (12 lines, 239 tokens)
   tests/warp/sim/energy/elastic/utils/test_hess_quad.py [105:5 - 117:11]

Clone found (python):
 - src/liblaf/apple/jax/sim/model/_model.py [40:10 - 48:10] (8 lines, 102 tokens)
   src/liblaf/apple/jax/sim/model/_model.py [22:4 - 30:4]

Clone found (python):
 - src/liblaf/apple/jax/sim/model/_model.py [58:2 - 66:10] (8 lines, 97 tokens)
   src/liblaf/apple/jax/sim/model/_model.py [22:2 - 30:4]

Clone found (python):
 - src/liblaf/apple/jax/optim/_minimize/_minimizer.py [77:5 - 85:2] (8 lines, 91 tokens)
   src/liblaf/apple/jax/optim/_minimize/_scipy.py [21:5 - 30:8]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [416:18 - 422:9] (6 lines, 109 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [360:16 - 366:16]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [429:15 - 434:12] (5 lines, 88 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [360:16 - 365:14]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/38-inverse-cbrt.py [1:1 - 37:7] (36 lines, 317 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [1:1 - 37:10]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/38-inverse-cbrt.py [37:29 - 123:9] (86 lines, 799 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [37:31 - 123:8]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/38-inverse-cbrt.py [124:10 - 138:16] (14 lines, 101 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [126:11 - 140:8]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/38-inverse-cbrt.py [141:5 - 211:7] (70 lines, 741 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [145:5 - 215:6]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/38-inverse-cbrt.py [212:10 - 322:9] (110 lines, 968 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [218:11 - 328:8]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/38-inverse-cbrt.py [333:10 - 353:2] (20 lines, 292 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [349:11 - 369:4]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/38-inverse-cbrt.py [353:2 - 368:11] (15 lines, 193 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [369:2 - 384:4]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/38-inverse-cbrt.py [368:2 - 385:71] (17 lines, 189 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [384:2 - 401:6]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/38-inverse-cbrt.py [396:9 - 457:2] (61 lines, 662 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [464:13 - 525:2]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/38-inverse-cbrt.py [457:2 - 488:2] (31 lines, 134 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [525:2 - 556:2]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/37-inverse-quadratic.py [1:1 - 37:34] (36 lines, 319 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [1:1 - 37:29]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/37-inverse-quadratic.py [37:34 - 401:5] (364 lines, 3645 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [37:31 - 416:18]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/37-inverse-quadratic.py [396:13 - 458:2] (62 lines, 677 tokens)
   exp/2025/09/24/inverse-grin/src/38-inverse-cbrt.py [395:13 - 525:2]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/37-inverse-quadratic.py [458:2 - 489:2] (31 lines, 134 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [525:2 - 556:2]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/36-inverse-abs.py [1:1 - 37:28] (36 lines, 319 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [1:1 - 37:29]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/36-inverse-abs.py [37:28 - 382:9] (345 lines, 3480 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [37:31 - 398:42]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/36-inverse-abs.py [392:13 - 488:2] (96 lines, 821 tokens)
   exp/2025/09/24/inverse-grin/src/37-inverse-quadratic.py [393:13 - 556:2]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/35-inverse-small-reg.py [1:1 - 37:24] (36 lines, 319 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [1:1 - 37:29]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/35-inverse-small-reg.py [37:24 - 138:4] (101 lines, 914 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [37:31 - 138:4]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/35-inverse-small-reg.py [141:5 - 265:47] (124 lines, 1184 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [145:5 - 271:44]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/35-inverse-small-reg.py [269:17 - 282:25] (13 lines, 126 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [279:17 - 292:22]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/35-inverse-small-reg.py [284:35 - 378:15] (94 lines, 1138 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [294:32 - 398:42]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/35-inverse-small-reg.py [385:5 - 439:46] (54 lines, 595 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [469:5 - 523:56]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/35-inverse-small-reg.py [443:5 - 451:8] (8 lines, 96 tokens)
   exp/2025/09/24/inverse-grin/src/38-inverse-cbrt.py [456:5 - 464:32]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/34-inverse-no-reg.py [1:1 - 37:24] (36 lines, 319 tokens)
   exp/2025/09/24/inverse-grin/src/39-inverse-sparse.py [1:1 - 37:29]

Clone found (python):
 - exp/2025/09/24/inverse-grin/src/34-i

(Truncated to 13333 characters out of 36839)
⚠️ JSON / jsonlint - 1 error 
File: .vscode/settings.json
Parse error on line 27, column 5:
....customTags": [    // ref: <https://squ...
----------------------^
Unexpected token "/"
⚠️ PYTHON / ruff - 1481 errors 
F722 Syntax error in forward annotation: Expected an expression
  --> exp/2025/04/30/cubic/src/10-gen.py:54:29
   |
53 |     def callback(intermediate_result: apple.OptimizeResult) -> None:
54 |         u: Float[jax.Array, " F"] = intermediate_result["x"]
   |                             ^^^^
55 |         u: Float[jax.Array, " T"] = physics.fill_dirichlet(u, q)
56 |         u: Float[jax.Array, "P 3"] = u[physics.objects["box"].dof_id]
   |

F722 Syntax error in forward annotation: Expected an expression
  --> exp/2025/04/30/cubic/src/10-gen.py:55:29
   |
53 |     def callback(intermediate_result: apple.OptimizeResult) -> None:
54 |         u: Float[jax.Array, " F"] = intermediate_result["x"]
55 |         u: Float[jax.Array, " T"] = physics.fill_dirichlet(u, q)
   |                             ^^^^
56 |         u: Float[jax.Array, "P 3"] = u[physics.objects["box"].dof_id]
57 |         result: pv.UnstructuredGrid = physics.objects["box"].geometry
   |

F722 Syntax error in forward annotation: Unexpected token at the end of an expression
  --> exp/2025/04/30/cubic/src/10-gen.py:56:29
   |
54 |         u: Float[jax.Array, " F"] = intermediate_result["x"]
55 |         u: Float[jax.Array, " T"] = physics.fill_dirichlet(u, q)
56 |         u: Float[jax.Array, "P 3"] = u[physics.objects["box"].dof_id]
   |                             ^^^^^
57 |         result: pv.UnstructuredGrid = physics.objects["box"].geometry
58 |         result.point_data["solution"] = np.asarray(u)
   |

F722 Syntax error in forward annotation: Unexpected token at the end of an expression
  --> exp/2025/04/30/fat-muscle/src/10-gen.py:32:40
   |
30 |     ):
31 |         cell: pv.Cell
32 |         barycentric: Float[np.ndarray, "N 3"] = melon.sample_barycentric_coords(
   |                                        ^^^^^
33 |             (cfg.n_samples, 4)
34 |         )
   |

F722 Syntax error in forward annotation: Unexpected token at the end of an expression
  --> exp/2025/04/30/fat-muscle/src/10-gen.py:35:36
   |
33 |             (cfg.n_samples, 4)
34 |         )
35 |         samples: Float[np.ndarray, "N 3"] = melon.barycentric_to_points(
   |                                    ^^^^^
36 |             einops.repeat(cell.points, "B D -> N B D", N=cfg.n_samples), barycentric
37 |         )
   |

F722 Syntax error in forward annotation: Expected an expression
  --> exp/2025/04/30/fat-muscle/src/10-gen.py:38:33
   |
36 |             einops.repeat(cell.points, "B D -> N B D", N=cfg.n_samples), barycentric
37 |         )
38 |         is_in: Bool[np.ndarray, " N"] = melon.triangle.contains(muscle, samples)
   |                                 ^^^^
39 |         tetmesh.cell_data["muscle-fraction"][cid] = (
40 |             np.count_nonzero(is_in) / cfg.n_samples
   |

F722 Syntax error in forward annotation: Expected an expression
  --> exp/2025/04/30/fat-muscle/src/11-inspect-volume.py:24:40
   |
23 |     tetmesh = tetmesh.compute_cell_sizes()
24 |     muscle_fraction: Float[np.ndarray, " C"] = tetmesh.cell_data["muscle-fraction"]
   |                                        ^^^^
25 |     volume: Float[np.ndarray, " C"] = tetmesh.cell_data["Volume"]
26 |     occupied_volume: Float[np.ndarray, " C"] = np.sum(volume[muscle_fraction > 1e-9])
   |

F722 Syntax error in forward annotation: Expected an expression
  --> exp/2025/04/30/fat-muscle/src/11-inspect-volume.py:25:31
   |
23 |     tetmesh = tetmesh.compute_cell_sizes()
24 |     muscle_fraction: Float[np.ndarray, " C"] = tetmesh.cell_data["muscle-fraction"]
25 |     volume: Float[np.ndarray, " C"] = tetmesh.cell_data["Volume"]
   |                               ^^^^
26 |     occupied_volume: Float[np.ndarray, " C"] = np.sum(volume[muscle_fraction > 1e-9])
27 |     ic(occupied_volume / tetmesh.volume)
   |

F722 Syntax error in forward annotation: Expected an expression
  --> exp/2025/04/30/fat-muscle/src/11-inspect-volume.py:26:40
   |
24 |     muscle_fraction: Float[np.ndarray, " C"] = tetmesh.cell_data["muscle-fraction"]
25 |     volume: Float[np.ndarray, " C"] = tetmesh.cell_data["Volume"]
26 |     occupied_volume: Float[np.ndarray, " C"] = np.sum(volume[muscle_fraction > 1e-9])
   |                                        ^^^^
27 |     ic(occupied_volume / tetmesh.volume)
   |

F722 Syntax error in forward annotation: Expected an expression
  --> exp/2025/04/30/fat-muscle/src/20-simulate.py:56:29
   |
55 |     def callback(intermediate_result: apple.OptimizeResult) -> None:
56 |         u: Float[jax.Array, " F"] = intermediate_result["x"]
   |                             ^^^^
57 |         u: Float[jax.Array, " T"] = physics.fill_dirichlet(u, q)
58 |         u: Float[jax.Array, "P 3"] = u[physics.objects["box"].dof_id]
   |

F722 Syntax error in forward annotation: Expected an expression
  --> exp/2025/04/30/fat-muscle/src/20-simulate.py:57:29
   |
55 |     def callback(intermediate_result: apple.OptimizeResult) -> None:
56 |         u: Float[jax.Array, " F"] = intermediate_result["x"]
57 |         u: Float[jax.Array, " T"] = physics.fill_dirichlet(u, q)
   |                             ^^^^
58 |         u: Float[jax.Array, "P 3"] = u[physics.objects["box"].dof_id]
59 |         result: pv.UnstructuredGrid = physics.objects["box"].geometry
   |

F722 Syntax error in forward annotation: Unexpected token at the end of an expression
  --> exp/2025/04/30/fat-muscle/src/20-simulate.py:58:29
   |
56 |         u: Float[jax.Array, " F"] = intermediate_result["x"]
57 |         u: Float[jax.Array, " T"] = physics.fill_dirichlet(u, q)
58 |         u: Float[jax.Array, "P 3"] = u[physics.objects["box"].dof_id]
   |                             ^^^^^
59 |         result: pv.UnstructuredGrid = physics.objects["box"].geometry
60 |         result.point_data["solution"] = np.asarray(u)
   |

F722 Syntax error in forward annotation: Unexpected token at the end of an expression
  --> exp/2025/04/30/human-head/src/10-simulate.py:32:34
   |
30 |     )
31 |     physics.add(apple.Object("flesh", apple.jax.energy.tetra.Phace(), geometry))
32 |     activation: Float[jax.Array, "C 3 3"] = activations(
   |                                  ^^^^^^^
33 |         geometry,
34 |         np.asarray(
   |

F722 Syntax error in forward annotation: Expected an expression
  --> exp/2025/04/30/human-head/src/10-simulate.py:55:29
   |
54 |     def callback(intermediate_result: apple.OptimizeResult) -> None:
55 |         u: Float[jax.Array, " F"] = intermediate_result["x"]
   |                             ^^^^
56 |         u: Float[jax.Array, " T"] = physics.fill_dirichlet(u, q)
57 |         u: Float[jax.Array, "P 3"] = u[physics.objects["flesh"].dof_id]
   |

F722 Syntax error in forward annotation: Expected an expression
  --> exp/2025/04/30/human-head/src/10-simulate.py:56:29
   |
54 |     def callback(intermediate_result: apple.OptimizeResult) -> None:
55 |         u: Float[jax.Array, " F"] = intermediate_result["x"]
56 |         u: Float[jax.Array, " T"] = physics.fill_dirichlet(u, q)
   |                             ^^^^
57 |         u: Float[jax.Array, "P 3"] = u[physics.objects["flesh"].dof_id]
58 |         result: pv.UnstructuredGrid = physics.objects["flesh"].geometry
   |

F722 Syntax error in forward annotation: Unexpected token at the end of an expression
  --> exp/2025/04/30/human-head/src/10-simulate.py:57:29
   |
55 |         u: Float[jax.Array, " F"] = intermediate_result["x"]
56 |         u: Float[jax.Array, " T"] = physics.fill_dirichlet(u, q)
57 |         u: Float[jax.Array, "P 3"] = u[physics.objects["flesh"].dof_id]
   |                             ^^^^^
58 |         result: pv.UnstructuredGrid = physics.objects["flesh"].geometry
59 |         result.point_data["solution"] = np.asarray(u)
   |

F722 Syntax error in forward annotation: Expected an expression
  --> exp/2025/04/30/human-head/src/10-simulate.py:72:61
   |
71 | def activations(
72 |     tetmesh: pv.UnstructuredGrid, stretch: Float[ArrayLike, " 3"]
   |                                                             ^^^^
73 | ) -> Float[jax.Array, "C 3 3"]:
74 |     muscle_direction: Float[np.ndarray, "C 3"] = tetmesh.cell_data["muscle-direction"]
   |

F722 Syntax error in forward annotation: Unexpected token at the end of an expression
  --> exp/2025/04/30/human-head/src/10-simulate.py:73:23
   |
71 | def activations(
72 |     tetmesh: pv.UnstructuredGrid, stretch: Float[ArrayLike, " 3"]
73 | ) -> Float[jax.Array, "C 3 3"]:
   |                       ^^^^^^^
74 |     muscle_direction: Float[np.ndarray, "C 3"] = tetmesh.cell_data["muscle-direction"]
75 |     muscle_fraction: Float[np.ndarray, " C"] = tetmesh.cell_data["muscle-fraction"]
   |

F722 Syntax error in forward annotation: Unexpected token at the end of an expression
  --> exp/2025/04/30/human-head/src/10-simulate.py:74:41
   |
72 |     tetmesh: pv.UnstructuredGrid, stretch: Float[ArrayLike, " 3"]
73 | ) -> Float[jax.Array, "C 3 3"]:
74 |     muscle_direction: Float[np.ndarray, "C 3"] = tetmesh.cell_data["muscle-direction"]
   |                                         ^^^^^
75 |     muscle_fraction: Float[np.ndarray, " C"] = tetmesh.cell_data["muscle-fraction"]
76 |     stretch: Float[jax.Array, " 3"] = jnp.asarray(stretch)
   |

F722 Syntax error in forward annotation: Expected an expression
  --> exp/2025/04/30/human-head/src/10-simulate.py:75:40
   |
73 | ) -> Float[jax.Array, "C 3 3"]:
74 |     muscle_direction: Float[np.ndarray, "C 3"] = tetmesh.cell_data["muscle-direction"]
75 |     muscle_fraction: Float[np.ndarray, " C"] = tetmesh.cell_data["muscle-fraction"]
   |                                        ^^^^
76 |     stretch: Float[jax.Array, " 3"] = jnp.asarray(stretch)
77 |     orientation: Float[jax.Array, "C 3 3"] = apple.jax.math.orientation_matrix(
   |

F722 Syntax error in forward annotation: Expected an expression
  --> exp/2025/04/30/human-head/src/10-simulate.py:76:31
   |
74 |     muscle_direction: Float[np.ndarray, "C 3"] = tetmesh.cell_data["muscle-direction"]
75 |     muscle_fraction: Float[np.ndarray, " C"] = tetmesh.cell_data["muscle-fraction"]
76 |     stretch: Float[jax.Array, " 3"] = jnp.asarray(stretch)
   |                               ^^^^
77 |     orientation: Float[jax.Array, "C 3 3"] = apple.jax.math.orientation_matrix(
78 |         muscle_direction,
   |

F722 Syntax error in forward annotation: Unexpected token at the end of an expression
  --> exp/2025/04/30/human-head/src/10-simulate.py:77:35
   |
75 |     muscle_fraction: Float[np.ndarray, " C"] = tetmesh.cell_data["muscle-fraction"]
76 |     stretch: Float[jax.Array, " 3"] = jnp.asarray(stretch)
77 |     orientation: Float[jax.Array, "C 3 3"] = apple.jax.math.orientation_matrix(
   |                                   ^^^^^^^
78 |         muscle_direction,
79 |         einops.repeat(np.asarray([1.0, 0.0, 0.0]), "i -> C i", C=tetmesh.n_cells),
   |

F722 Syntax error in forward annotation: Unexpected token at the end of an expression
  --> exp/2025/04/30/human-head/src/10-simulate.py:81:34
   |
79 |         einops.repeat(np.asarray([1.0, 0.0, 0.0]), "i -> C i", C=tetmesh.n_cells),
80 |     )
81 |     activation: Float[jax.Array, "C 3 3"] = einops.einsum(
   |                                  ^^^^^^^
82 |         orientation,
83 |         jnp.asarray(stretch),
   |

F722 Syntax error in forward annotation: Unexpected token at the end of an expression
  --> exp/2025/04/30/human-head/src/11-muscle-deformation.py:23:40
   |
21 |     tetmesh: pv.UnstructuredGrid = melon.load_unstructured_grid(cfg.tetmesh)
22 |
23 |     muscle_direction: Float[jax.Array, "C 3"] = jnp.asarray(
   |                                        ^^^^^
24 |         tetmesh.cell_data["muscle-direction"]
25 |     )
   |

F722 Syntax error in forward annotation: Expected an expression
  --> exp/2025/04/30/human-head/src/11-muscle-deformation.py:26:39
   |
24 |         tetmesh.cell_data["muscle-direction"]
25 |     )
26 |     muscle_fraction: Float[jax.Array, " C"] = jnp.asarray(
   |                                       ^^^^
27 |         tetmesh.cell_data["muscle-fraction"]
28 |     )
   |

F722 Syntax error in forward annotation: Unexpected token at the end of an expression
  --> exp/2025/04/30/human-head/src/11-muscle-deformation.py:29:35
   |
27 |         tetmesh.cell_data["muscle-fraction"]
28 |     )
29 |     orientation: Float[jax.Array, "C 3 3"] = apple.jax.math.orientation_matrix(
   |                                   ^^^^^^^
30 |         muscle_direction,
31 |         einops.repeat(jnp.asarray([1.0, 0.0, 0.0]), "i -> C i", C=tetmesh.n_cells),
   |

F722 Syntax error in forward annotation: Unexpected token at the end of an expression
  --> exp/2025/04/30/human-head/src/11-muscle-deformation.py:34:30
   |
32 |     )
33 |
34 |     points: Float[jax.Array, "P 3"] = jnp.asarray(tetmesh.points)
   |                              ^^^^^
35 |     cells: Float[jax.Array, "C 4"] = jnp.asarray(tetmesh.cells_dict[pv.CellType.TETRA])
36 |     dh_dX: Float[jax.Array, "C 4 3"] = apple.jax.elem.tetra.dh_dX(points[cells])
   |

F722 Syntax error in forward annotation: Unexpected token at the end of an expression
  --> exp/2025/04/30/human-head/src/11-muscle-deformation.py:35:29
   |
34 |     points: Float[jax.Array, "P 3"] = jnp.asarray(tetmesh.points)
35 |     cells: Float[jax.Array, "C 4"] = jnp.asarray(tetmesh.cells_dict[pv.C

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