chore(copier): update from template

[liblaf-copier]

Automated changes by Shared / Copier Update Workflow

[liblaf-mega-linter]

✅⚠️MegaLinter analysis: Success with warnings

Descriptor	Linter	Files	Fixed	Errors	Warnings	Elapsed time
✅ BASH	shellcheck	2		0	0	0.49s
✅ BASH	shfmt	2	0	0	0	1.8s
⚠️ COPYPASTE	jscpd	yes		464	no	9.69s
✅ JSON	prettier	19	15	0	0	2.76s
✅ JSON	v8r	19		0	0	5.38s
✅ MARKDOWN	rumdl	28	0	0	0	1.81s
⚠️ PYTHON	ruff	yes	yes	47	no	1.18s
✅ PYTHON	ruff-format	yes	yes	no	no	0.17s
✅ REPOSITORY	git_diff	yes		no	no	2.23s
⚠️ SPELL	cspell	yes		15	no	7.2s

Detailed Issues

⚠️ SPELL / cspell - 15 errors

.github/workflows/release-pr.yaml:72:15     - Unknown word (orhun)      -- uses: orhun/git-cliff-action@f5
	 Suggestions: [oahu, oran, ordn, oren, orin]
.github/workflows/release-pr.yaml:80:15     - Unknown word (orhun)      -- uses: orhun/git-cliff-action@f5
	 Suggestions: [oahu, oran, ordn, oren, orin]
exp/2026/05/13/toy/data/30-inverse-activation-diff-forward-no-collision-summary.json:13:4      - Unknown word (bbox)       -- "bbox_diagonal": 1.732050
	 Suggestions: [box, mbox, vbox, xbox, Xbox]
exp/2026/05/13/toy/data/40-inverse-activation-diff-forward-collision-summary.json:17:12     - Unknown word (atol)       -- "forward_atol": 0.001,
	 Suggestions: [atob, atom, aton, atop, awol]
exp/2026/05/13/toy/data/40-inverse-activation-diff-forward-collision-summary.json:19:4      - Unknown word (bbox)       -- "bbox_diagonal": 2.872281
	 Suggestions: [box, mbox, vbox, xbox, Xbox]
exp/2026/05/13/toy/data/41-inverse-active-tet-activation-diff-forward-collision-summary.json:23:12     - Unknown word (atol)       -- "forward_atol": 0.001,
	 Suggestions: [atob, atom, aton, atop, awol]
exp/2026/05/13/toy/data/41-inverse-active-tet-activation-diff-forward-collision-summary.json:29:4      - Unknown word (bbox)       -- "bbox_diagonal": 2.872281
	 Suggestions: [box, mbox, vbox, xbox, Xbox]
exp/2026/05/13/toy/src/20-smas-layer-bottom-force-collision.py:151:22    - Unknown word (Efat)       -- mesh.field_data["Efat"] = np.asarray([cfg
	 Suggestions: [Efta, Feat, Erat, Eat, Eft]
exp/2026/05/13/toy/src/20-smas-layer-bottom-force-collision.py:152:22    - Unknown word (Esmas)      -- mesh.field_data["Esmas"] = np.asarray([cfg
	 Suggestions: [Smas, Seams, Seas, edams, Edams]
exp/2026/05/20/inverse-face/docs/20-inverse-face.md:42:38     - Unknown word (atol)       -- tolerance: `rtol=0.0005`, `atol=0`
	 Suggestions: [atob, atom, aton, atop, awol]
exp/2026/05/20/inverse-face/docs/20-inverse-face.md:43:38     - Unknown word (atol)       -- tolerance: `rtol=0.0005`, `atol=0`
	 Suggestions: [atob, atom, aton, atop, awol]
exp/2026/05/20/inverse-face/docs/30-transfer-activation-3152k.md:75:11     - Unknown word (atol)       -- forward_atol: 0.0
	 Suggestions: [atob, atom, aton, atop, awol]
exp/2026/05/20/inverse-face/docs/31-transfer-activation-3152k-smas1.md:72:11     - Unknown word (atol)       -- forward_atol: 0.0
	 Suggestions: [atob, atom, aton, atop, awol]
src/liblaf/apple/inverse/_diff_forward.py:92:9      - Unknown word (rprecondition) -- def rprecondition(self, p_free: Free)
	 Suggestions: [precondition, preCondition, PRECONDITION, recondition, rpreconditioner]
src/liblaf/apple/inverse/_diff_forward.py:99:21     - Unknown word (rprecondition) -- return self.rprecondition(p_free)
	 Suggestions: [precondition, preCondition, PRECONDITION, recondition, rpreconditioner]
CSpell: Files checked: 320, skipped: 5, Issues found: 15 in 9 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": [
        "Efat",
        "Esmas",
        "atol",
        "bbox",
        "orhun",
        "rprecondition"
    ]
}


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

⚠️ COPYPASTE / jscpd - 464 errors

inverse-segement/src/30-inverse.py [138:39 - 242:24]

Clone found (python):
 - exp/2025/08/27/inverse/src/20-forward.py [1:1 - 29:42] (28 lines, 244 tokens)
   exp/2025/08/27/inverse-segement/src/20-forward.py [1:1 - 29:43]

Clone found (python):
 - exp/2025/08/27/inverse/src/20-forward.py [33:40 - 51:24] (18 lines, 191 tokens)
   exp/2025/08/27/inverse-segement/src/20-forward.py [33:30 - 51:24]

Clone found (python):
 - exp/2025/08/27/inverse/src/10-gen.py [32:5 - 39:24] (7 lines, 85 tokens)
   exp/2025/08/27/inverse-segement/src/10-gen.py [46:5 - 53:24]

Clone found (python):
 - exp/2025/07/30/phace/wind/main.py [126:5 - 136:14] (10 lines, 144 tokens)
   exp/2025/07/30/dynamics/collision/inter-collision/main.py [132:84 - 142:15]

Clone found (python):
 - exp/2025/07/30/phace/wind/main.py [139:9 - 152:46] (13 lines, 156 tokens)
   exp/2025/07/30/dynamics/collision/inter-collision/main.py [142:9 - 155:46]

Clone found (python):
 - exp/2025/07/30/phace/open-mouth/main.py [9:1 - 19:13] (10 lines, 102 tokens)
   exp/2025/07/30/phace/wind/main.py [8:1 - 18:12]

Clone found (python):
 - exp/2025/07/30/phace/open-mouth/main.py [24:5 - 36:14] (12 lines, 94 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny-bunny/main.py [19:5 - 31:9]

Clone found (python):
 - exp/2025/07/30/phace/open-mouth/main.py [25:21 - 55:12] (30 lines, 315 tokens)
   exp/2025/07/30/phace/wind/main.py [30:19 - 60:15]

Clone found (python):
 - exp/2025/07/30/phace/open-mouth/main.py [95:85 - 105:33] (10 lines, 148 tokens)
   exp/2025/07/30/dynamics/collision/inter-collision/main.py [132:84 - 136:38]

Clone found (python):
 - exp/2025/07/30/phace/open-mouth/main.py [105:88 - 119:25] (14 lines, 153 tokens)
   exp/2025/07/30/phace/wind/main.py [138:9 - 155:23]

Clone found (python):
 - exp/2025/07/30/phace/grin/main.py [1:1 - 12:59] (11 lines, 103 tokens)
   exp/2025/07/30/phace/wind/main.py [1:1 - 12:60]

Clone found (python):
 - exp/2025/07/30/phace/grin/main.py [19:5 - 36:12] (17 lines, 142 tokens)
   exp/2025/07/30/phace/open-mouth/main.py [20:5 - 42:12]

Clone found (python):
 - exp/2025/07/30/phace/grin/main.py [101:5 - 107:45] (6 lines, 74 tokens)
   exp/2025/07/30/dynamics/collision/inter-collision/main.py [132:84 - 138:36]

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 - 53:37] (18 lines, 164 tokens)
   exp/2025/07/30/phace/wind/main.py [32:5 - 44:44]

Clone found (python):
 - exp/2025/07/30/phace/dynamics/main.py [53:37 - 66:12] (13 lines, 146 tokens)
   exp/2025/07/30/phace/grin/main.py [44:44 - 56:11]

Clone found (python):
 - exp/2025/07/30/phace/dynamics/main.py [90:54 - 97:67] (7 lines, 77 tokens)
   exp/2025/07/30/phace/grin/main.py [90:27 - 97:67]

Clone found (python):
 - exp/2025/07/30/phace/dynamics/main.py [107:5 - 117:13] (10 lines, 142 tokens)
   exp/2025/07/30/dynamics/collision/inter-collision/main.py [132:84 - 111:26]

Clone found (python):
 - exp/2025/07/30/phace/dynamics/main.py [118:81 - 126:43] (8 lines, 101 tokens)
   exp/2025/07/30/phace/grin/main.py [112:77 - 120:41]

Clone found (python):
 - exp/2025/07/30/phace/collide-ball/main.py [9:1 - 18:26] (9 lines, 95 tokens)
   exp/2025/07/30/phace/wind/main.py [9:1 - 19:26]

Clone found (python):
 - exp/2025/07/30/phace/collide-ball/main.py [12:60 - 35:40] (23 lines, 195 tokens)
   exp/2025/07/30/phace/grin/main.py [12:52 - 36:47]

Clone found (python):
 - exp/2025/07/30/phace/collide-ball/main.py [35:40 - 42:66] (7 lines, 122 tokens)
   exp/2025/07/30/phace/wind/main.py [41:47 - 48:64]

Clone found (python):
 - exp/2025/07/30/phace/close-mouth/main.py [1:1 - 22:12] (21 lines, 180 tokens)
   exp/2025/07/30/phace/open-mouth/main.py [1:1 - 21:10]

Clone found (python):
 - exp/2025/07/30/phace/close-mouth/main.py [29:5 - 57:12] (28 lines, 311 tokens)
   exp/2025/07/30/phace/wind/main.py [32:5 - 60:15]

Clone found (python):
 - exp/2025/07/30/phace/close-mouth/main.py [101:5 - 140:21] (39 lines, 450 tokens)
   exp/2025/07/30/phace/open-mouth/main.py [55:5 - 124:9]

Clone found (python):
 - exp/2025/07/30/phace/close-mouth/main.py [140:47 - 165:46] (25 lines, 356 tokens)
   exp/2025/07/30/phace/open-mouth/main.py [94:46 - 155:46]

Clone found (python):
 - exp/2025/07/30/dynamics/free-falling/main.py [25:21 - 58:8] (33 lines, 358 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny/main.py [24:19 - 57:11]

Clone found (python):
 - exp/2025/07/30/dynamics/free-falling/main.py [78:5 - 84:11] (6 lines, 86 tokens)
   exp/2025/07/30/dynamics/collision/collision-bunny/main.py [75:5 - 81:11]

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

Clone found (python):
 - exp/2025/04/30/fat-muscle/src/20-simulate.py [17:5 - 30:35] (13 lines, 138 tokens)
   exp/2025/04/30/human-head/src/10-simulate.py [18:5 - 31:37]

Clone found (python):
 - exp/2025/04/30/fat-muscle/src/20-simulate.py [48:43 - 58:61] (10 lines, 136 tokens)
   exp/2025/04/30/human-head/src/10-simulate.py [47:56 - 57:63]

Clone found (python):
 - exp/2025/04/30/fat-muscle/src/20-simulate.py [59:60 - 72:3] (13 lines, 107 tokens)
   exp/2025/04/30/human-head/src/10-simulate.py [58:62 - 71:4]

Clone found (python):
 - exp/2025/04/30/cubic/src/10-gen.py [21:54 - 44:35] (23 lines, 196 tokens)
   exp/2025/04/30/human-head/src/10-simulate.py [24:76 - 46:40]

Clone found (python):
 - exp/2025/04/30/cubic/src/10-gen.py [44:66 - 71:24] (27 lines, 303 tokens)
   exp/2025/04/30/fat-muscle/src/20-simulate.py [46:74 - 73:24]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean_active.py [57:1 - 63:31] (6 lines, 83 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean_active.py [36:67 - 42:13]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean_active.py [81:46 - 93:11] (12 lines, 171 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean_active.py [36:35 - 69:48]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean_active.py [102:36 - 108:6] (6 lines, 82 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean_active.py [21:28 - 26:7]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean_active.py [103:14 - 116:12] (13 lines, 166 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean_active.py [57:11 - 94:12]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean.py [25:18 - 35:7] (10 lines, 126 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean_active.py [27:18 - 37:10]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean.py [74:78 - 84:12] (10 lines, 127 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean.py [53:1 - 63:48]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean.py [93:14 - 103:12] (10 lines, 121 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean.py [53:11 - 63:48]

Clone found (python):
 - src/liblaf/apple/warp/fem/_stable_neo_hookean.py [116:43 - 150:6] (34 lines, 323 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean_active.py [135:10 - 169:6]

Clone found (python):
 - src/liblaf/apple/warp/fem/_neo_hookean.py [1:1 - 28:18] (27 lines, 251 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean.py [1:1 - 28:17]

Clone found (python):
 - src/liblaf/apple/warp/fem/_neo_hookean.py [29:51 - 39:17] (10 lines, 105 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean.py [29:58 - 39:17]

Clone found (python):
 - src/liblaf/apple/warp/fem/_neo_hookean.py [39:44 - 60:17] (21 lines, 193 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean.py [39:47 - 60:17]

Clone found (python):
 - src/liblaf/apple/warp/fem/_neo_hookean.py [62:63 - 84:12] (22 lines, 280 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean.py [62:22 - 63:48]

Clone found (python):
 - src/liblaf/apple/warp/fem/_neo_hookean.py [83:63 - 103:12] (20 lines, 280 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean.py [83:22 - 63:48]

Clone found (python):
 - src/liblaf/apple/warp/fem/_neo_hookean.py [102:63 - 110:17] (8 lines, 92 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean.py [102:22 - 110:23]

Clone found (python):
 - src/liblaf/apple/warp/fem/_neo_hookean.py [110:17 - 150:6] (40 lines, 380 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean.py [110:23 - 169:6]

Clone found (python):
 - src/liblaf/apple/warp/fem/_base.py [189:37 - 196:14] (7 lines, 90 tokens)
   src/liblaf/apple/warp/fem/_base.py [166:40 - 173:19]

Clone found (python):
 - src/liblaf/apple/warp/fem/_base.py [211:31 - 218:16] (7 lines, 92 tokens)
   src/liblaf/apple/warp/fem/_base.py [166:31 - 173:19]

Clone found (python):
 - src/liblaf/apple/warp/fem/_base.py [235:36 - 243:22] (8 lines, 108 tokens)
   src/liblaf/apple/warp/fem/_base.py [166:40 - 197:19]

Clone found (python):
 - src/liblaf/apple/warp/fem/_base.py [266:9 - 272:19] (6 lines, 86 tokens)
   src/liblaf/apple/warp/fem/_base.py [167:9 - 173:19]

Clone found (python):
 - src/liblaf/apple/warp/fem/_base.py [292:14 - 300:19] (8 lines, 102 tokens)
   src/liblaf/apple/warp/fem/_base.py [262:14 - 270:22]

Clone found (python):
 - src/liblaf/apple/warp/fem/_base.py [327:9 - 334:19] (7 lines, 103 tokens)
   src/liblaf/apple/warp/fem/_base.py [296:9 - 303:19]

Clone found (python):
 - src/liblaf/apple/warp/fem/_arap.py [7:33 - 22:7] (15 lines, 106 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean.py [7:41 - 22:7]

Clone found (python):
 - src/liblaf/apple/warp/fem/_arap.py [89:53 - 121:6] (32 lines, 288 tokens)
   src/liblaf/apple/warp/fem/_stable_neo_hookean_active.py [137:55 - 169:6]

Clone found (python):
 - exp/2025/07/30/static/stretch.py [12:5 - 19:52] (7 lines, 105 tokens)
   exp/2025/07/30/static/random/main.py [19:5 - 25:53]

Clone found (python):
 - exp/2025/07/30/static/stretch.py [28:9 - 39:30] (11 lines, 124 tokens)
   exp/2025/07/30/static/random/main.py [40:9 - 51:35]

Clone found (python):
 - exp/2025/07/30/static/stretch.py [49:1 - 54:10] (5 lines, 83 tokens)
   exp/2025/07/30/static/random/main.py [60:44 - 65:10]

Clone found (python):
 - exp/2025/07/30/static/stretch.py [67:5 - 77:14] (10 lines, 115 tokens)
   exp/2025/07/30/static/random/main.py [73:5 - 83:10]

Clone found (python):
 - tests/forward/test_static_simulation.py [77:31 - 85:11] (8 lines, 80 tokens)
   exp/2026/05/06/toy/src/10-stretched-cylinder.py [84:43 - 92:17]

Clone found (python):
 - benches/test_aggregation.py [115:9 - 129:11] (14 lines, 161 tokens)
   benches/test_aggregation.py [68:88 - 80:92]

Clone found (python):
 - benches/bench_pncg_branching_backends.py [180:20 - 192:8] (12 lines, 87 tokens)
   benches/bench_pncg_branching_backends.py [141:14 - 153:9]

Clone found (python):
 - benches/bench_pncg_branching_backends.py [347:9 - 357:11] (10 lines, 94 tokens)
   benches/bench_pncg_branching_backends.py [279:9 - 289:13]

Clone found (python):
 - benches/bench_pncg_branching_backends.py [459:40 - 481:6] (22 lines, 172 tokens)
   benches/bench_pncg_branching_backends.py [413:34 - 435:18]

Clone found (python):
 - benches/bench_pncg_branching_backends.py [649:25 - 663:22] (14 lines, 159 tokens)
   benches/bench_pncg_branching_backends.py [475:23 - 489:25]

┌────────┬────────────────┬─────────────┬──────────────┬──────────────┬──────────────────┬───────────────────┐
│ Format │ Files analyzed │ Total lines │ Total tokens │ Clones found │ Duplicated lines │ Duplicated tokens │
├────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ python │ 190            │ 28966       │ 294565       │ 464          │ 11952 (41.26%)   │ 125342 (42.55%)   │
├────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ csv    │ 1              │ 15          │ 813          │ 0            │ 0 (0%)           │ 0 (0%)            │
├────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ bash   │ 2              │ 45          │ 136          │ 0            │ 0 (0%)           │ 0 (0%)            │
├────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ toml   │ 8              │ 933         │ 4016         │ 0            │ 0 (0%)           │ 0 (0%)            │
├────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ Total: │ 201            │ 29959       │ 299530       │ 464          │ 11952 (39.89%)   │ 125342 (41.85%)   │
└────────┴────────────────┴─────────────┴──────────────┴──────────────┴──────────────────┴───────────────────┘
Found 464 clones.
HTML report saved to megalinter-reports/copy-paste/html/
ERROR: jscpd found too many duplicates (39.89%) over threshold (0%)
Error: ERROR: jscpd found too many duplicates (39.89%) 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 92386)

⚠️ 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).

(Truncated to last 13333 characters out of 18919)

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