Fatal crash in ipynb file #20789
Description
Summary
panic: Panicked at crates/ruff_notebook/src/notebook.rs:281:21 when checking `/workspaces/thesis_calculations/scripts/local_basis/alpha_dynamics.ipynb`: `Transformed content out of bounds (2610..2609) for cell at 1`
--> scripts/local_basis/alpha_dynamics.ipynb:1:1
info: This indicates a bug in Ruff.
info: If you could open an issue at https://github.com/astral-sh/ruff/issues/new?title=%5Bpanic%5D, we'd be very appreciative!
info: Backtrace:
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20: <unknown>
21: start_thread
22: clone
Found 1 error.
error: Panic during linting indicates a bug in Ruff. If you could open an issue at:
https://github.com/astral-sh/ruff/issues/new?title=%5BLinter%20panic%5D
...with the relevant file contents, the `pyproject.toml` settings, and the stack trace above, we'd be very appreciative!
The file
{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"id": "775be936",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Alpha Derivative\n"
]
},
{
"data": {
"text/latex": [
"$\\displaystyle - \\lambda \\left(\\alpha - \\overline{\\alpha}\\right)$"
],
"text/plain": [
"<IPython.core.display.Math object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/latex": [
"$\\displaystyle - \\frac{i \\left(\\alpha \\text{hbar}^{2} - \\overline{\\alpha} \\text{hbar}^{2} + \\omega^{2} \\alpha m^{2} + \\omega^{2} m^{2} \\overline{\\alpha}\\right)}{2 m \\text{hbar}}$"
],
"text/plain": [
"<IPython.core.display.Math object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/latex": [
"$\\displaystyle - \\frac{\\sqrt{2} \\sqrt{\\lambda} \\left(\\xi(t) \\beta \\text{hbar}^{2} - \\xi(t) \\text{hbar}^{2} + \\beta \\overline{\\xi(t)} \\overline{\\beta} \\text{hbar}^{2} - \\beta \\overline{\\xi(t)} \\text{hbar}^{2} + 4 K_{B} T \\xi(t) \\beta m + 4 K_{B} T \\xi(t) m + 4 K_{B} T \\beta m \\overline{\\xi(t)} \\overline{\\beta} + 4 K_{B} T \\beta m \\overline{\\xi(t)}\\right)}{4 \\sqrt{K_{B} T} \\sqrt{m} \\left(\\beta \\overline{\\beta} - 1\\right) \\text{hbar}}$"
],
"text/plain": [
"<IPython.core.display.Math object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/latex": [
"$\\displaystyle \\frac{\\sqrt{2} \\left(\\alpha + \\overline{\\alpha}\\right)}{2}$"
],
"text/plain": [
"<IPython.core.display.Math object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/latex": [
"$\\displaystyle \\frac{\\sqrt{2} i \\left(- \\alpha + \\overline{\\alpha}\\right) \\text{hbar}}{2}$"
],
"text/plain": [
"<IPython.core.display.Math object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"{alpha: sqrt(2)*\\langle x \\rangle/2 + sqrt(2)*I*\\langle p \\rangle/(2*hbar), conjugate(alpha): sqrt(2)*\\langle x \\rangle/2 - sqrt(2)*I*\\langle p \\rangle/(2*hbar)}\n"
]
},
{
"data": {
"text/latex": [
"$\\displaystyle \\frac{\\langle p \\rangle}{m} - \\frac{\\sqrt{\\lambda} \\left(\\xi(t) \\beta \\overline{\\beta} \\text{hbar}^{2} + \\xi(t) \\beta \\text{hbar}^{2} - \\xi(t) \\overline{\\beta} \\text{hbar}^{2} - \\xi(t) \\text{hbar}^{2} + \\beta \\overline{\\xi(t)} \\overline{\\beta} \\text{hbar}^{2} - \\beta \\overline{\\xi(t)} \\text{hbar}^{2} + \\overline{\\xi(t)} \\overline{\\beta} \\text{hbar}^{2} - \\overline{\\xi(t)} \\text{hbar}^{2} + 4 K_{B} T \\xi(t) \\beta m \\overline{\\beta} + 4 K_{B} T \\xi(t) \\beta m + 4 K_{B} T \\xi(t) m \\overline{\\beta} + 4 K_{B} T \\xi(t) m + 4 K_{B} T \\beta m \\overline{\\xi(t)} \\overline{\\beta} + 4 K_{B} T \\beta m \\overline{\\xi(t)} + 4 K_{B} T m \\overline{\\xi(t)} \\overline{\\beta} + 4 K_{B} T m \\overline{\\xi(t)}\\right)}{4 \\sqrt{K_{B} T} \\sqrt{m} \\left(\\beta \\overline{\\beta} - 1\\right) \\text{hbar}}$"
],
"text/plain": [
"<IPython.core.display.Math object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/latex": [
"$\\displaystyle - 2 \\lambda \\langle p \\rangle - \\langle x \\rangle \\omega^{2} m - \\frac{i \\sqrt{\\lambda} \\left(\\xi(t) \\beta \\overline{\\beta} \\text{hbar}^{2} - \\xi(t) \\beta \\text{hbar}^{2} - \\xi(t) \\overline{\\beta} \\text{hbar}^{2} + \\xi(t) \\text{hbar}^{2} - \\beta \\overline{\\xi(t)} \\overline{\\beta} \\text{hbar}^{2} + \\beta \\overline{\\xi(t)} \\text{hbar}^{2} + \\overline{\\xi(t)} \\overline{\\beta} \\text{hbar}^{2} - \\overline{\\xi(t)} \\text{hbar}^{2} + 4 K_{B} T \\xi(t) \\beta m \\overline{\\beta} - 4 K_{B} T \\xi(t) \\beta m + 4 K_{B} T \\xi(t) m \\overline{\\beta} - 4 K_{B} T \\xi(t) m - 4 K_{B} T \\beta m \\overline{\\xi(t)} \\overline{\\beta} - 4 K_{B} T \\beta m \\overline{\\xi(t)} + 4 K_{B} T m \\overline{\\xi(t)} \\overline{\\beta} + 4 K_{B} T m \\overline{\\xi(t)}\\right)}{4 \\sqrt{K_{B} T} \\sqrt{m} \\left(\\beta \\overline{\\beta} - 1\\right)}$"
],
"text/plain": [
"<IPython.core.display.Math object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/latex": [
"$\\displaystyle - \\frac{\\sqrt{2} i \\lambda \\langle p \\rangle}{\\text{hbar}} + \\frac{\\sqrt{2} \\left(\\langle p \\rangle \\text{hbar} - i \\langle x \\rangle \\omega^{2} m^{2}\\right)}{2 m \\text{hbar}} + \\frac{\\sqrt{2} \\sqrt{\\lambda} \\left(- \\frac{\\xi(t) \\beta \\text{hbar}^{2}}{4} + \\frac{\\xi(t) \\text{hbar}^{2}}{4} - \\frac{\\beta \\overline{\\xi(t)} \\overline{\\beta} \\text{hbar}^{2}}{4} + \\frac{\\beta \\overline{\\xi(t)} \\text{hbar}^{2}}{4} - K_{B} T \\xi(t) \\beta m - K_{B} T \\xi(t) m - K_{B} T \\beta m \\overline{\\xi(t)} \\overline{\\beta} - K_{B} T \\beta m \\overline{\\xi(t)}\\right)}{\\sqrt{K_{B} T} \\sqrt{m} \\left(\\beta \\overline{\\beta} - 1\\right) \\text{hbar}}$"
],
"text/plain": [
"<IPython.core.display.Math object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"import sympy as sp\n",
"\n",
"from thesis_calculations.open_harmonic import (\n",
" get_closed_operator,\n",
" get_noise_operator,\n",
" get_open_operator,\n",
" noise,\n",
")\n",
"from thesis_calculations.squeezed_states import (\n",
" alpha,\n",
" as_b_expr,\n",
" beta,\n",
" display_latex,\n",
" eval_groundstate,\n",
" get_alpha_derivative,\n",
" mu,\n",
" nu,\n",
" p_expr,\n",
" x_expr,\n",
")\n",
"\n",
"\n",
"def _simplify_squeeze_params(expr: sp.Expr) -> sp.Expr:\n",
" expr = sp.simplify(expr)\n",
" expr = sp.simplify(expr.subs({nu: beta * mu}))\n",
" expr = expr.subs({mu**2: 1 / (1 - beta * sp.conjugate(beta))})\n",
" return sp.factor(sp.simplify(expr))\n",
"\n",
"\n",
"print(\"Alpha Derivative\") # noqa: T201\n",
"open_operator = get_open_operator()\n",
"open_derivative = get_alpha_derivative(get_open_operator())\n",
"open_derivative = _simplify_squeeze_params(open_derivative)\n",
"display_latex(open_derivative)\n",
"\n",
"\n",
"closed_derivative = get_alpha_derivative(get_closed_operator())\n",
"closed_derivative = _simplify_squeeze_params(closed_derivative)\n",
"display_latex(closed_derivative)\n",
"\n",
"\n",
"noise_derivative = get_alpha_derivative(get_noise_operator())\n",
"noise_derivative = _simplify_squeeze_params(noise_derivative)\n",
"display_latex(noise_derivative)\n",
"\n",
"derivative_alpha = open_derivative + closed_derivative + noise_derivative\n",
"\n",
"\n",
"expect_x_expr = eval_groundstate(as_b_expr(x_expr))\n",
"expect_p_expr = eval_groundstate(as_b_expr(p_expr))\n",
"expect_x = sp.Symbol(r\"\\langle x \\rangle\", real=True)\n",
"expect_p = sp.Symbol(r\"\\langle p \\rangle\", real=True)\n",
"\n",
"display_latex(expect_x_expr)\n",
"display_latex(expect_p_expr)\n",
"print(\n",
" sp.solve(\n",
" {\n",
" sp.Eq(expect_x, expect_x_expr),\n",
" sp.Eq(expect_p, expect_p_expr),\n",
" },\n",
" (alpha, sp.conjugate(alpha)),\n",
" )\n",
")\n",
"\n",
"\n",
"def _alpha_expr_as_xp(expr: sp.Expr) -> sp.Expr:\n",
" solutions = sp.solve(\n",
" {\n",
" sp.Eq(expect_x, expect_x_expr),\n",
" sp.Eq(expect_p, expect_p_expr),\n",
" },\n",
" (alpha, sp.conjugate(alpha)),\n",
" )\n",
" expr = expr.subs(\n",
" {\n",
" alpha: solutions[alpha],\n",
" sp.conjugate(alpha): solutions[sp.conjugate(alpha)],\n",
" }\n",
" )\n",
" return sp.simplify(sp.expand(expr))\n",
"\n",
"\n",
"derivative_as_xp = (\n",
" _alpha_expr_as_xp(open_derivative)\n",
" + _alpha_expr_as_xp(closed_derivative)\n",
" + _alpha_expr_as_xp(noise_derivative)\n",
")\n",
"\n",
"derivative_x = expect_x_expr.subs({alpha: derivative_as_xp})\n",
"a, b = sp.expand(sp.simplify(derivative_x)).as_independent(noise)\n",
"display_latex(sp.simplify(a) + sp.factor(sp.simplify(b)))\n",
"\n",
"\n",
"derivative_p = expect_p_expr.subs({alpha: derivative_as_xp})\n",
"a, b = sp.expand(sp.simplify(derivative_p)).as_independent(noise)\n",
"display_latex(sp.simplify(a) + sp.factor(sp.simplify(b)))\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "e4b7c166-1af3-4fc5-89eb-89b50c4e2b93",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "92ab2eeb-d419-4f73-9ab8-cee2d85108ac",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.14.0"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
The pyproject.toml
[project]
name = "thesis_calculations"
version = "0.0.1"
description = "A collection of scripts for my thesis"
readme = "README.md"
requires-python = ">=3.14,<3.15"
dependencies = ["matplotlib>=3.10.6", "sympy>=1.14.0"]
[dependency-groups]
dev = [
"ruff",
"pytest >=8.3.3,<9.0.0",
"sphinx >=8.1.3,<9.0.0",
"pydata-sphinx-theme >=0.16.0,<0.17.0",
"jupyter>=1.1.1",
"ty>=0.0.1a21",
"ipykernel>=6.30.1",
]
[tool.ruff]
unsafe-fixes = true
exclude = [".git", ".git-rewrite", ".vscode"]
[tool.ruff.lint]
select = ["ALL"]
preview = true
ignore = [
"COM812",
"E501",
"S101",
"PT009",
"D100",
"D105",
"CPY001",
"TD003",
"TD002",
"DOC201",
"DOC402",
"PD",
]
fixable = ["ALL"]
unfixable = ["T201"]
[tool.ruff.lint.extend-per-file-ignores]
"tests/**/*" = ["PLR6301", "INP001", "PLR0914", "D101", "D102", "D103", "D104"]
"scripts/**/*" = [
"PLR6301",
"INP001",
"PLR0914",
"D101",
"D102",
"D103",
"D104",
]
"examples/**/*" = ["INP001", "T201"]
"docs/**/*" = ["INP001", "I002"]
[tool.ruff.lint.pylint]
allow-dunder-method-names = [
"__as_fundamental__",
"__from_fundamental__",
"__into_fundamental__",
"__as_transformed__",
"__into_transformed__",
"__from_transformed__",
"__convert_vector_into__",
"__into_inner__",
"__from_inner__",
]
[tool.ruff.lint.pydocstyle]
convention = "numpy"
[tool.pytest.ini_options]
testpaths = ["tests"]
[build-system]
requires = ["setuptools"]
build-backend = "setuptools.build_meta"
Version
ruff 0.14.0