chore(release): v0.8.0 by liblaf-release-please[bot] · Pull Request #104 · liblaf/apple

liblaf-release-please · 2026-05-18T13:20:02Z

v0.8.0 - 2026-05-18

💥 BREAKING CHANGES

Refactored warp elastic energy module structure - 100c251 by @liblaf
remove the previous model, inverse, optim, scene, utils, consts, jax.model, and warp.energies APIs; use the new forward, collision, common, and warp.fem modules instead - b7c4348 by @liblaf

✨ Features

(apple) improve inverse simulation with coarse-to-fine transfer and enhanced solvers - 61d530e by @liblaf
(apple) implement hybrid JAX/Warp model framework and WarpPhaceV2 - 315b58e by @liblaf
(apple) add SMAS support and volume fraction for elastic energies - 0710f9c by @liblaf
(exp) update inverse-toy simulation and add Newton solver - cee4852 by @liblaf
(exp) add SMAS forward simulation experiments - e27c9da by @liblaf
(inverse) enhance inverse solver with constraint support and improved adjoint solver - 892dbfd by @liblaf
(smas) add stable neo-hookean simulation experiments - 22accae by @liblaf
add inverse toy experiments for forward simulation and muscle activation - 19c2c46 by @liblaf
[breaking] refactor elastic energies and add inverse physics module - 100c251 by @liblaf
add Neo-Hookean Warp energies and line-search PNCG - 0dbe70c by @liblaf
add staged PNCG continuation for forward solves - 6362af3 by @liblaf

🐛 Bug Fixes

(warp) correct ARAP muscle energy implementation and kernel function names - d734e9b by @liblaf

📝 Documentation

(smas) update inverse-unreachable clipped figures - ed3b81a by @liblaf

🎨 Styles

collapse multi-line return expressions to single line - 0603f83 by @liblaf

♻️ Code Refactoring

[breaking] replace model stack with forward simulation API - b7c4348 by @liblaf

❤️ Contributors

@liblaf

for more information, see https://pre-commit.ci

liblaf-mega-linter · 2026-05-18T13:21:17Z

✅⚠️MegaLinter analysis: Success with warnings

Descriptor	Linter	Files	Fixed	Errors	Warnings	Elapsed time
✅ BASH	shellcheck	2		0	0	0.02s
✅ BASH	shfmt	2	0	0	0	1.32s
⚠️ COPYPASTE	jscpd	yes		406	no	8.33s
✅ JSON	prettier	8	4	0	0	1.62s
✅ JSON	v8r	8		0	0	3.45s
✅ MARKDOWN	rumdl	19	0	0	0	1.35s
⚠️ PYTHON	ruff	yes	yes	47	no	1.15s
✅ PYTHON	ruff-format	yes	yes	no	no	0.16s
✅ REPOSITORY	git_diff	yes		no	no	1.33s
⚠️ SPELL	cspell	yes		6	no	5.79s

Detailed Issues

⚠️ SPELL / cspell - 6 errors

.vscode/settings.json:8:10      - Unknown word (grimp)      -- "**/.grimp_cache/": true,
	 Suggestions: [gimp, grim, grip, gramp, grime]
src/liblaf/apple/jax/fem/region/_region.py:23:5      - Unknown word (dhdr)       -- dhdr: Float[Array, "q a J
	 Suggestions: [ddr, xhdr, DDR, hdd, dada]
src/liblaf/apple/jax/fem/region/_region.py:88:9      - Unknown word (dhdr)       -- dhdr: Float[Array, "q a J
	 Suggestions: [ddr, xhdr, DDR, hdd, dada]
src/liblaf/apple/jax/fem/region/_region.py:92:44     - Unknown word (dhdr)       -- points[self.cells_local], dhdr, "c a I, q a J -> c
	 Suggestions: [ddr, xhdr, DDR, hdd, dada]
src/liblaf/apple/jax/fem/region/_region.py:101:13    - Unknown word (dhdr)       -- dhdr, drdX, "q a I, c q I
	 Suggestions: [ddr, xhdr, DDR, hdd, dada]
src/liblaf/apple/jax/fem/region/_region.py:104:14    - Unknown word (dhdr)       -- self.dhdr = dhdr
	 Suggestions: [ddr, xhdr, DDR, hdd, dada]
CSpell: Files checked: 260, skipped: 2, Issues found: 6 in 2 files.


You can skip this misspellings by defining the following .cspell.json file at the root of your repository
Of course, please correct real typos before :)

{
    "version": "0.2",
    "language": "en",
    "ignorePaths": [
        "**/node_modules/**",
        "**/vscode-extension/**",
        "**/.git/**",
        "**/.pnpm-lock.json",
        ".vscode",
        "package-lock.json",
        "megalinter-reports"
    ],
    "words": [
        "dhdr",
        "grimp"
    ]
}


You can also copy-paste megalinter-reports/LINTER_DEFAULT at the root of your repository

⚠️ COPYPASTE / jscpd - 406 errors

e found (python):
 - exp/2025/08/27/inverse/src/30-inverse.py [72:5 - 87:7] (15 lines, 221 tokens)
   exp/2025/08/27/inverse-segement/src/30-inverse.py [77:5 - 92:4]

Clone found (python):
 - exp/2025/08/27/inverse/src/30-inverse.py [85:9 - 92:3] (7 lines, 78 tokens)
   exp/2025/09/10/inverse-mixed/src/30-inverse.py [130:13 - 137:67]

Clone found (python):
 - exp/2025/08/27/inverse/src/30-inverse.py [87:2 - 102:13] (15 lines, 211 tokens)
   exp/2025/08/27/inverse-segement/src/30-inverse.py [92:2 - 107:15]

Clone found (python):
 - exp/2025/08/27/inverse/src/30-inverse.py [98:9 - 104:11] (6 lines, 94 tokens)
   exp/2025/09/10/inverse/src/30-inverse.py [133:9 - 157:15]

Clone found (python):
 - exp/2025/08/27/inverse/src/30-inverse.py [113:1 - 128:8] (15 lines, 166 tokens)
   exp/2025/09/24/inverse-grin/src/30-inverse.py [229:1 - 140:8]

Clone found (python):
 - exp/2025/08/27/inverse/src/30-inverse.py [122:12 - 130:11] (8 lines, 102 tokens)
   exp/2025/09/10/inverse-mixed/src/30-inverse.py [261:6 - 267:12]

Clone found (python):
 - exp/2025/08/27/inverse/src/30-inverse.py [131:8 - 173:2] (42 lines, 472 tokens)
   exp/2025/08/27/inverse-segement/src/30-inverse.py [138:2 - 242:2]

Clone found (python):
 - exp/2025/08/27/inverse/src/20-forward.py [1:1 - 29:11] (28 lines, 244 tokens)
   exp/2025/08/27/inverse-segement/src/20-forward.py [1:1 - 29:12]

Clone found (python):
 - exp/2025/08/27/inverse/src/20-forward.py [33:2 - 51:2] (18 lines, 191 tokens)
   exp/2025/08/27/inverse-segement/src/20-forward.py [33:15 - 51:2]

Clone found (python):
 - exp/2025/08/27/inverse/src/10-gen.py [32:5 - 39:2] (7 lines, 85 tokens)
   exp/2025/08/27/inverse-segement/src/10-gen.py [46:5 - 53:2]

Clone found (python):
 - exp/2025/07/30/phace/wind/main.py [126:5 - 136:6] (10 lines, 141 tokens)
   exp/2025/07/30/dynamics/collision/inter-collision/main.py [132:2 - 142:7]

Clone found (python):
 - exp/2025/07/30/phace/wind/main.py [139:9 - 152:2] (13 lines, 156 tokens)
   exp/2025/07/30/dynamics/collision/inter-collision/main.py [142:9 - 155:2]

Clone found (python):
 - exp/2025/07/30/phace/open-mouth/main.py [9:1 - 19:9] (10 lines, 102 tokens)
   exp/2025/07/30/phace/wind/main.py [8:1 - 18:8]

Clone found (python):
 - exp/2025/07/30/phace/open-mouth/main.py [24:5 - 36:10] (12 lines, 96 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny-bunny/main.py [19:5 - 31:5]

Clone found (python):
 - exp/2025/07/30/phace/open-mouth/main.py [25:2 - 55:8] (30 lines, 317 tokens)
   exp/2025/07/30/phace/wind/main.py [30:2 - 60:11]

Clone found (python):
 - exp/2025/07/30/phace/open-mouth/main.py [95:2 - 105:17] (10 lines, 145 tokens)
   exp/2025/07/30/dynamics/collision/inter-collision/main.py [132:2 - 136:22]

Clone found (python):
 - exp/2025/07/30/phace/open-mouth/main.py [105:2 - 119:7] (14 lines, 153 tokens)
   exp/2025/07/30/phace/wind/main.py [138:9 - 155:5]

Clone found (python):
 - exp/2025/07/30/phace/grin/main.py [1:1 - 12:6] (11 lines, 103 tokens)
   exp/2025/07/30/phace/wind/main.py [1:1 - 12:7]

Clone found (python):
 - exp/2025/07/30/phace/grin/main.py [19:5 - 36:8] (17 lines, 144 tokens)
   exp/2025/07/30/phace/open-mouth/main.py [20:5 - 42:8]

Clone found (python):
 - exp/2025/07/30/phace/dynamics/main.py [1:1 - 14:29] (13 lines, 106 tokens)
   exp/2025/07/30/phace/wind/main.py [1:1 - 15:6]

Clone found (python):
 - exp/2025/07/30/phace/dynamics/main.py [35:5 - 53:14] (18 lines, 166 tokens)
   exp/2025/07/30/phace/wind/main.py [32:5 - 44:21]

Clone found (python):
 - exp/2025/07/30/phace/dynamics/main.py [53:14 - 66:2] (13 lines, 146 tokens)
   exp/2025/07/30/phace/grin/main.py [44:21 - 56:2]

Clone found (python):
 - exp/2025/07/30/phace/dynamics/main.py [90:10 - 97:2] (7 lines, 79 tokens)
   exp/2025/07/30/phace/grin/main.py [90:6 - 97:2]

Clone found (python):
 - exp/2025/07/30/phace/dynamics/main.py [107:5 - 117:5] (10 lines, 139 tokens)
   exp/2025/07/30/phace/grin/main.py [101:5 - 111:18]

Clone found (python):
 - exp/2025/07/30/phace/dynamics/main.py [118:5 - 126:15] (8 lines, 101 tokens)
   exp/2025/07/30/phace/grin/main.py [112:18 - 120:13]

Clone found (python):
 - exp/2025/07/30/phace/collide-ball/main.py [9:1 - 18:4] (9 lines, 95 tokens)
   exp/2025/07/30/phace/wind/main.py [9:1 - 19:4]

Clone found (python):
 - exp/2025/07/30/phace/collide-ball/main.py [12:7 - 35:6] (23 lines, 197 tokens)
   exp/2025/07/30/phace/grin/main.py [12:4 - 41:13]

Clone found (python):
 - exp/2025/07/30/phace/collide-ball/main.py [35:6 - 42:13] (7 lines, 122 tokens)
   exp/2025/07/30/phace/wind/main.py [41:13 - 48:11]

Clone found (python):
 - exp/2025/07/30/phace/close-mouth/main.py [1:1 - 22:8] (21 lines, 180 tokens)
   exp/2025/07/30/phace/open-mouth/main.py [1:1 - 21:6]

Clone found (python):
 - exp/2025/07/30/phace/close-mouth/main.py [29:5 - 57:8] (28 lines, 313 tokens)
   exp/2025/07/30/phace/wind/main.py [32:5 - 60:11]

Clone found (python):
 - exp/2025/07/30/phace/close-mouth/main.py [101:5 - 140:17] (39 lines, 452 tokens)
   exp/2025/07/30/phace/open-mouth/main.py [55:5 - 124:5]

Clone found (python):
 - exp/2025/07/30/phace/close-mouth/main.py [140:5 - 165:2] (25 lines, 353 tokens)
   exp/2025/07/30/phace/open-mouth/main.py [94:5 - 155:2]

Clone found (python):
 - exp/2025/07/30/dynamics/free-falling/main.py [25:2 - 58:4] (33 lines, 360 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny/main.py [24:2 - 57:7]

Clone found (python):
 - exp/2025/07/30/dynamics/free-falling/main.py [78:5 - 84:3] (6 lines, 86 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny/main.py [75:5 - 81:3]

Clone found (python):
 - exp/2025/07/30/dynamics/free-falling/main.py [137:5 - 151:10] (14 lines, 138 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny-sphere/main.py [69:5 - 83:10]

Clone found (python):
 - exp/2025/04/30/fat-muscle/src/20-simulate.py [17:5 - 30:6] (13 lines, 138 tokens)
   exp/2025/04/30/human-head/src/10-simulate.py [18:5 - 31:8]

Clone found (python):
 - exp/2025/04/30/fat-muscle/src/20-simulate.py [48:2 - 58:6] (10 lines, 136 tokens)
   exp/2025/04/30/human-head/src/10-simulate.py [47:2 - 57:8]

Clone found (python):
 - exp/2025/04/30/fat-muscle/src/20-simulate.py [59:6 - 72:3] (13 lines, 109 tokens)
   exp/2025/04/30/human-head/src/10-simulate.py [58:8 - 71:4]

Clone found (python):
 - exp/2025/04/30/cubic/src/10-gen.py [21:4 - 44:4] (23 lines, 196 tokens)
   exp/2025/04/30/human-head/src/10-simulate.py [24:7 - 46:9]

Clone found (python):
 - exp/2025/04/30/cubic/src/10-gen.py [44:2 - 71:2] (27 lines, 305 tokens)
   exp/2025/04/30/fat-muscle/src/20-simulate.py [46:3 - 73:2]

Clone found (python):
 - src/liblaf/apple/warp/model/_adapter.py [83:19 - 88:10] (5 lines, 74 tokens)
   src/liblaf/apple/warp/model/_adapter.py [66:14 - 69:5]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean_muscle.py [55:1 - 61:27] (6 lines, 83 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean_muscle.py [34:4 - 40:9]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean_muscle.py [78:6 - 90:8] (12 lines, 171 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean_muscle.py [34:6 - 67:44]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean_muscle.py [98:6 - 104:2] (6 lines, 82 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean_muscle.py [19:6 - 24:3]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean_muscle.py [99:9 - 111:8] (12 lines, 153 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean_muscle.py [55:6 - 67:44]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean.py [6:1 - 19:3] (13 lines, 93 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean_muscle.py [7:1 - 20:2]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean.py [22:2 - 32:3] (10 lines, 126 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean_muscle.py [25:2 - 35:2]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean.py [71:4 - 81:8] (10 lines, 127 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean.py [50:1 - 60:44]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean.py [90:9 - 100:8] (10 lines, 121 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean.py [50:6 - 60:44]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean.py [115:2 - 152:8] (37 lines, 339 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean_muscle.py [131:13 - 168:11]

Clone found (python):
 - src/liblaf/apple/warp/fem/_base.py [231:6 - 238:2] (7 lines, 88 tokens)
   src/liblaf/apple/warp/fem/_base.py [207:9 - 214:7]

Clone found (python):
 - src/liblaf/apple/warp/fem/_base.py [277:5 - 284:2] (7 lines, 92 tokens)
   src/liblaf/apple/warp/fem/_base.py [253:9 - 260:4]

Clone found (python):
 - src/liblaf/apple/warp/fem/_base.py [308:9 - 314:7] (6 lines, 88 tokens)
   src/liblaf/apple/warp/fem/_base.py [254:9 - 260:4]

Clone found (python):
 - src/liblaf/apple/warp/fem/_base.py [334:2 - 342:7] (8 lines, 95 tokens)
   src/liblaf/apple/warp/fem/_base.py [304:2 - 312:10]

Clone found (python):
 - src/liblaf/apple/warp/fem/_base.py [369:9 - 376:7] (7 lines, 105 tokens)
   src/liblaf/apple/warp/fem/_base.py [338:9 - 345:7]

Clone found (python):
 - src/liblaf/apple/warp/fem/_arap.py [1:1 - 19:3] (18 lines, 128 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean.py [1:1 - 20:2]

Clone found (python):
 - src/liblaf/apple/warp/fem/_arap.py [87:2 - 124:3] (37 lines, 350 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean.py [115:2 - 168:11]

Clone found (python):
 - exp/2025/07/30/static/stretch.py [12:5 - 19:2] (7 lines, 107 tokens)
   exp/2025/07/30/static/random/main.py [19:5 - 25:3]

Clone found (python):
 - exp/2025/07/30/static/stretch.py [28:9 - 39:3] (11 lines, 124 tokens)
   exp/2025/07/30/static/random/main.py [40:9 - 51:8]

Clone found (python):
 - exp/2025/07/30/static/stretch.py [49:1 - 54:6] (5 lines, 83 tokens)
   exp/2025/07/30/static/random/main.py [60:17 - 65:6]

Clone found (python):
 - exp/2025/07/30/static/stretch.py [67:5 - 77:10] (10 lines, 115 tokens)
   exp/2025/07/30/static/random/main.py [73:5 - 83:6]

Clone found (python):
 - src/liblaf/apple/collision/_collision.py [161:5 - 178:29] (17 lines, 100 tokens)
   src/liblaf/apple/collision/_collision.py [138:7 - 155:23]

Clone found (python):
 - src/liblaf/apple/collision/_collision.py [188:2 - 204:29] (16 lines, 88 tokens)
   src/liblaf/apple/collision/_collision.py [139:9 - 155:23]

Clone found (python):
 - src/liblaf/apple/collision/_collision.py [211:2 - 227:24] (16 lines, 95 tokens)
   src/liblaf/apple/collision/_collision.py [139:2 - 155:23]

Clone found (python):
 - src/liblaf/apple/collision/_collision.py [235:2 - 251:29] (16 lines, 88 tokens)
   src/liblaf/apple/collision/_collision.py [139:9 - 155:23]

Clone found (python):
 - tests/forward/test_static_simulation.py [77:5 - 85:7] (8 lines, 80 tokens)
   exp/2026/05/06/toy/src/10-stretched-cylinder.py [84:17 - 92:13]

Clone found (python):
 - benches/test_aggregation.py [115:9 - 129:7] (14 lines, 161 tokens)
   benches/test_aggregation.py [68:2 - 80:38]

Clone found (python):
 - benches/bench_pncg_branching_backends.py [180:16 - 192:4] (12 lines, 87 tokens)
   benches/bench_pncg_branching_backends.py [141:10 - 153:5]

Clone found (python):
 - benches/bench_pncg_branching_backends.py [347:9 - 357:3] (10 lines, 94 tokens)
   benches/bench_pncg_branching_backends.py [279:9 - 289:5]

Clone found (python):
 - benches/bench_pncg_branching_backends.py [459:36 - 481:2] (22 lines, 172 tokens)
   benches/bench_pncg_branching_backends.py [413:30 - 435:14]

Clone found (python):
 - benches/bench_pncg_branching_backends.py [649:6 - 663:18] (14 lines, 159 tokens)
   benches/bench_pncg_branching_backends.py [475:4 - 489:21]

┌────────┬────────────────┬─────────────┬──────────────┬──────────────┬──────────────────┬───────────────────┐
│ Format │ Files analyzed │ Total lines │ Total tokens │ Clones found │ Duplicated lines │ Duplicated tokens │
├────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ python │ 175            │ 24390       │ 246126       │ 406          │ 10813 (44.33%)   │ 113316 (46.04%)   │
├────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ bash   │ 2              │ 45          │ 136          │ 0            │ 0 (0%)           │ 0 (0%)            │
├────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ Total: │ 177            │ 24435       │ 246262       │ 406          │ 10813 (44.25%)   │ 113316 (46.01%)   │
└────────┴────────────────┴─────────────┴──────────────┴──────────────┴──────────────────┴───────────────────┘
Found 406 clones.
HTML report saved to megalinter-reports/copy-paste/html/
ERROR: jscpd found too many duplicates (44.25%) over threshold (0%)
Error: ERROR: jscpd found too many duplicates (44.25%) over threshold (0%)
    at ThresholdReporter.report (/node-deps/node_modules/@jscpd/finder/dist/index.js:615:13)
    at /node-deps/node_modules/@jscpd/finder/dist/index.js:109:18
    at Array.forEach (<anonymous>)
    at /node-deps/node_modules/@jscpd/finder/dist/index.js:108:22
    at async /node-deps/node_modules/jscpd/dist/bin/jscpd.js:9:5

(Truncated to last 13333 characters out of 78347)

⚠️ PYTHON / ruff - 47 errors

able first
   --> exp/2026/01/28/smas/src/20-forward-ext-force-stable-neo-hookean-ramped.py:206:21
    |
204 |               if not stage_result.solver_result.success:
205 |                   raise RuntimeError(
206 | /                     "forward stage failed at "
207 | |                     f"force scale {force_scale:g} with status "
208 | |                     f"{stage_result.solver_result.status}"
    | |__________________________________________________________^
209 |                   )
210 |               cherries.set_step(stage_index)
    |
help: Assign to variable; remove f-string literal

RUF046 Value being cast to `int` is already an integer
  --> exp/2026/01/28/smas/src/20-forward-ext-force-stable-neo-hookean-smas-only.py:48:20
   |
46 | def format_lambda_value(lambda_value: float) -> str:
47 |     if np.isclose(lambda_value, round(lambda_value)):
48 |         return str(int(round(lambda_value)))
   |                    ^^^^^^^^^^^^^^^^^^^^^^^^
49 |     mantissa, exponent = f"{lambda_value:.0e}".split("e")
50 |     return f"{mantissa}e{int(exponent)}"
   |
help: Remove unnecessary `int` call

TRY003 Avoid specifying long messages outside the exception class
  --> exp/2026/01/28/smas/src/20-forward-ext-force-stable-neo-hookean-smas-only.py:57:15
   |
55 |   ) -> pv.UnstructuredGrid:
56 |       if "Force" not in mesh.point_data:
57 |           raise KeyError(
   |  _______________^
58 | |             "mesh is missing point_data['Force']; run 11-smas-bottom-force.py first"
59 | |         )
   | |_________^
60 |       mesh.point_data["Force"] = force_scale * np.asarray(mesh.point_data["Force"])
61 |       return mesh
   |

EM101 Exception must not use a string literal, assign to variable first
  --> exp/2026/01/28/smas/src/20-forward-ext-force-stable-neo-hookean-smas-only.py:58:13
   |
56 |     if "Force" not in mesh.point_data:
57 |         raise KeyError(
58 |             "mesh is missing point_data['Force']; run 11-smas-bottom-force.py first"
   |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
59 |         )
60 |     mesh.point_data["Force"] = force_scale * np.asarray(mesh.point_data["Force"])
   |
help: Assign to variable; remove string literal

RUF046 Value being cast to `int` is already an integer
  --> exp/2026/01/28/smas/src/20-forward-ext-force-stable-neo-hookean.py:49:20
   |
47 | def format_lambda_value(lambda_value: float) -> str:
48 |     if np.isclose(lambda_value, round(lambda_value)):
49 |         return str(int(round(lambda_value)))
   |                    ^^^^^^^^^^^^^^^^^^^^^^^^
50 |     mantissa, exponent = f"{lambda_value:.0e}".split("e")
51 |     return f"{mantissa}e{int(exponent)}"
   |
help: Remove unnecessary `int` call

RUF046 Value being cast to `int` is already an integer
  --> exp/2026/01/28/smas/src/20-forward-ext-force.py:49:20
   |
47 | def format_lambda_value(lambda_value: float) -> str:
48 |     if np.isclose(lambda_value, round(lambda_value)):
49 |         return str(int(round(lambda_value)))
   |                    ^^^^^^^^^^^^^^^^^^^^^^^^
50 |     mantissa, exponent = f"{lambda_value:.0e}".split("e")
51 |     return f"{mantissa}e{int(exponent)}"
   |
help: Remove unnecessary `int` call

ARG001 Unused function argument: `failure_dir`
   --> exp/2026/01/28/smas/src/30-inverse-unreachable-stable-neo-hookean.py:286:5
    |
284 |     target: pv.UnstructuredGrid,
285 |     forward: Forward,
286 |     failure_dir: Path,
    |     ^^^^^^^^^^^
287 | ) -> MyInverse:
288 |     surface_indices: Integer[Array, " surface_points"] = mesh.surface_indices()
    |

D205 1 blank line required between summary line and description
  --> exp/2026/04/18/2d-demo/src/10-simulation.py:1:1
   |
 1 | / """2D Muscle-Fascia Neohookean FEM Simulation
 2 | | ==========================================
 3 | |
 4 | | Simulates a flat meat slab (100x11 elements) with a stiff fascia middle layer.
 5 | | Uses analytical First Piola-Kirchhoff stress with NumPy vectorized computation.
 6 | | Real-time visualization with Pygame.
 7 | |
 8 | | Material: Neohookean hyperelastic
 9 | |   Psi(F) = mu/2 * (tr(F^T F) - 2) - mu * ln(J) + lam/2 * (ln J)^2
10 | |   P      = mu * (F - F^{-T}) + lam * ln(J) * F^{-T}
11 | |
12 | | Controls:
13 | |     Up/Down    Increase/decrease wind force
14 | |     R          Reset simulation
15 | |     SPACE      Pause/resume
16 | |     W          Toggle wireframe overlay
17 | |     ESC        Quit
18 | | """
   | |___^
19 |
20 |   import sys
   |
help: Insert single blank line

D415 First line should end with a period, question mark, or exclamation point
  --> exp/2026/04/18/2d-demo/src/10-simulation.py:1:1
   |
 1 | / """2D Muscle-Fascia Neohookean FEM Simulation
 2 | | ==========================================
 3 | |
 4 | | Simulates a flat meat slab (100x11 elements) with a stiff fascia middle layer.
 5 | | Uses analytical First Piola-Kirchhoff stress with NumPy vectorized computation.
 6 | | Real-time visualization with Pygame.
 7 | |
 8 | | Material: Neohookean hyperelastic
 9 | |   Psi(F) = mu/2 * (tr(F^T F) - 2) - mu * ln(J) + lam/2 * (ln J)^2
10 | |   P      = mu * (F - F^{-T}) + lam * ln(J) * F^{-T}
11 | |
12 | | Controls:
13 | |     Up/Down    Increase/decrease wind force
14 | |     R          Reset simulation
15 | |     SPACE      Pause/resume
16 | |     W          Toggle wireframe overlay
17 | |     ESC        Quit
18 | | """
   | |___^
19 |
20 |   import sys
   |
help: Add closing punctuation

ANN001 Missing type annotation for function argument `f2v`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:126:16
    |
126 | def init_state(f2v):
    |                ^^^
127 |     """Initialize node positions and precompute reference configuration.
    |

ANN001 Missing type annotation for function argument `pos`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:185:28
    |
185 | def compute_elastic_forces(pos, f2v, Dm_inv, Dm_inv_T, W, elem_mu, elem_lam):
    |                            ^^^
186 |     """Compute internal elastic forces using the analytical Neohookean stress.
    |

ANN001 Missing type annotation for function argument `f2v`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:185:33
    |
185 | def compute_elastic_forces(pos, f2v, Dm_inv, Dm_inv_T, W, elem_mu, elem_lam):
    |                                 ^^^
186 |     """Compute internal elastic forces using the analytical Neohookean stress.
    |

ANN001 Missing type annotation for function argument `Dm_inv`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:185:38
    |
185 | def compute_elastic_forces(pos, f2v, Dm_inv, Dm_inv_T, W, elem_mu, elem_lam):
    |                                      ^^^^^^
186 |     """Compute internal elastic forces using the analytical Neohookean stress.
    |

ANN001 Missing type annotation for function argument `Dm_inv_T`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:185:46
    |
185 | def compute_elastic_forces(pos, f2v, Dm_inv, Dm_inv_T, W, elem_mu, elem_lam):
    |                                              ^^^^^^^^
186 |     """Compute internal elastic forces using the analytical Neohookean stress.
    |

ANN001 Missing type annotation for function argument `W`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:185:56
    |
185 | def compute_elastic_forces(pos, f2v, Dm_inv, Dm_inv_T, W, elem_mu, elem_lam):
    |                                                        ^
186 |     """Compute internal elastic forces using the analytical Neohookean stress.
    |

ANN001 Missing type annotation for function argument `elem_mu`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:185:59
    |
185 | def compute_elastic_forces(pos, f2v, Dm_inv, Dm_inv_T, W, elem_mu, elem_lam):
    |                                                           ^^^^^^^
186 |     """Compute internal elastic forces using the analytical Neohookean stress.
    |

ANN001 Missing type annotation for function argument `elem_lam`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:185:68
    |
185 | def compute_elastic_forces(pos, f2v, Dm_inv, Dm_inv_T, W, elem_mu, elem_lam):
    |                                                                    ^^^^^^^^
186 |     """Compute internal elastic forces using the analytical Neohookean stress.
    |

ANN001 Missing type annotation for function argument `pos`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:256:5
    |
255 | def substep(
256 |     pos,
    |     ^^^
257 |     vel,
258 |     rest_pos,
    |

ANN001 Missing type annotation for function argument `vel`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:257:5
    |
255 | def substep(
256 |     pos,
257 |     vel,
    |     ^^^
258 |     rest_pos,
259 |     f2v,
    |

ANN001 Missing type annotation for function argument `rest_pos`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:258:5
    |
256 |     pos,
257 |     vel,
258 |     rest_pos,
    |     ^^^^^^^^
259 |     f2v,
260 |     Dm_inv,
    |

ANN001 Missing type annotation for function argument `f2v`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:259:5
    |
257 |     vel,
258 |     rest_pos,
259 |     f2v,
    |     ^^^
260 |     Dm_inv,
261 |     Dm_inv_T,
    |

ANN001 Missing type annotation for function argument `Dm_inv`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:260:5
    |
258 |     rest_pos,
259 |     f2v,
260 |     Dm_inv,
    |     ^^^^^^
261 |     Dm_inv_T,
262 |     W,
    |

ANN001 Missing type annotation for function argument `Dm_inv_T`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:261:5
    |
259 |     f2v,
260 |     Dm_inv,
261 |     Dm_inv_T,
    |     ^^^^^^^^
262 |     W,
263 |     elem_mu,
    |

ANN001 Missing type annotation for function argument `W`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:262:5
    |
260 |     Dm_inv,
261 |     Dm_inv_T,
262 |     W,
    |     ^
263 |     elem_mu,
264 |     elem_lam,
    |

ANN001 Missing type annotation for function argument `elem_mu`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:263:5
    |
261 |     Dm_inv_T,
262 |     W,
263 |     elem_mu,
    |     ^^^^^^^
264 |     elem_lam,
265 |     fixed_mask,
    |

ANN001 Missing type annotation for function argument `elem_lam`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:264:5
    |
262 |     W,
263 |     elem_mu,
264 |     elem_lam,
    |     ^^^^^^^^
265 |     fixed_mask,
266 |     bottom_mask,
    |

ANN001 Missing type annotation for function argument `fixed_mask`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:265:5
    |
263 |     elem_mu,
264 |     elem_lam,
265 |     fixed_mask,
    |     ^^^^^^^^^^
266 |     bottom_mask,
267 |     wind,
    |

ANN001 Missing type annotation for function argument `bottom_mask`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:266:5
    |
264 |     elem_lam,
265 |     fixed_mask,
266 |     bottom_mask,
    |     ^^^^^^^^^^^
267 |     wind,
268 |     mass,
    |

ANN001 Missing type annotation for function argument `wind`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:267:5
    |
265 |     fixed_mask,
266 |     bottom_mask,
267 |     wind,
    |     ^^^^
268 |     mass,
269 | ):
    |

ANN001 Missing type annotation for function argument `mass`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:268:5
    |
266 |     bottom_mask,
267 |     wind,
268 |     mass,
    |     ^^^^
269 | ):
270 |     """Single substep of Symplectic Euler integration.
    |

ANN001 Missing type annotation for function argument `sim_pos`
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:307:19
    |
307 | def sim_to_screen(sim_pos):
    |                   ^^^^^^^
308 |     """Convert simulation coordinates to screen pixel coordinates (y-flipped)."""
309 |     screen = np.empty_like(sim_pos)
    |

C901 `main` is too complex (18 > 10)
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:320:5
    |
320 | def main():
    |     ^^^^
321 |     # --- Build mesh & initialize state ---
322 |     f2v, is_fascia, elem_mu, elem_lam = build_mesh()
    |

PLR0912 Too many branches (17 > 12)
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:320:5
    |
320 | def main():
    |     ^^^^
321 |     # --- Build mesh & initialize state ---
322 |     f2v, is_fascia, elem_mu, elem_lam = build_mesh()
    |

PLR0915 Too many statements (57 > 50)
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:320:5
    |
320 | def main():
    |     ^^^^
321 |     # --- Build mesh & initialize state ---
322 |     f2v, is_fascia, elem_mu, elem_lam = build_mesh()
    |

FBT003 Boolean positional value in function call
   --> exp/2026/04/18/2d-demo/src/10-simulation.py:431:37
    |
429 |         y_pos = 12
430 |         for fnt, text, color in hud_lines:
431 |             surf = fnt.render(text, True, color)
    |                                     ^^^^
432 |             screen.blit(surf, (15, y_pos))
433 |             y_pos += 28
    |

B007 Loop control variable `step` not used within loop body
   --> exp/2026/04/18/2d-demo/src/30-simulation-stable-neo-hookean-self-collision.py:829:9
    |
827 |     contact_points = np.empty((0, 2), dtype=pos.dtype)
828 |
829 |     for step in range(SUBSTEPS):
    |         ^^^^
830 |         substep_contacts, substep_points = substep(
831 |             pos,
    |
help: Rename unused `step` to `_step`

Found 47 errors.
No fixes available (13 hidden fixes can be enabled with the `--unsafe-fixes` option).

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