scqubits · kochjens · May 20, 2026 · May 20, 2026 · May 21, 2026 · May 21, 2026
diff --git a/docs/source/acknowledgments.rst b/docs/source/acknowledgments.rst
@@ -8,9 +8,9 @@ Funding
 *******
 
 We gratefully acknowledge financial support for the continued development of the scqubits library by the Air Force
-Office for Scientific Research under grant no. FA9550-20-1-0271. The scqubits library was additionally supported
+Office of Scientific Research under grant no. FA9550-20-1-0271. The scqubits library was additionally supported
 by the Army Research Office under grant nos. W911NF-1510421, W911NF-1910016, by the DOE under grant
-nos. DE-SC0012704, DE-AC02-07CH113, and by the Northwestern-Fermilab Center for Applied Physics and Superconducting
+nos. DE-SC0012704, DE-AC02-07CH11359, and by the Northwestern-Fermilab Center for Applied Physics and Superconducting
 Technologies (CAPST).
 
 .. table::

diff --git a/docs/source/api-doc/for_developer.rst b/docs/source/api-doc/for_developer.rst
@@ -42,13 +42,17 @@ CentralDispatch and related classes
 CentralDispatch
 ---------------
 
+.. toctree::
+
    _autosummary/scqubits.core.central_dispatch.CentralDispatch.rst
 
 .. _classes-dispatchclient:
 
 DispatchClient
 ---------------
 
+.. toctree::
+
    _autosummary/scqubits.core.central_dispatch.DispatchClient.rst
 
 
@@ -61,11 +65,15 @@ Descriptor classes
 WatchedProperty
 ---------------
 
+.. toctree::
+
    _autosummary/scqubits.core.descriptors.WatchedProperty.rst
 
 .. _classes-readonly:
 
 ReadOnlyProperty
 ----------------
 
+.. toctree::
+
    _autosummary/scqubits.core.descriptors.ReadOnlyProperty.rst
diff --git a/docs/source/bibliography.rst b/docs/source/bibliography.rst
@@ -8,15 +8,15 @@ Refs
 ****
 
 .. [Brooks2013] Brooks et al., Phys. Rev. A 87, 052306 (2013), https://link.aps.org/doi/10.1103/PhysRevA.87.052306
-.. [Catelani2011] Catelani et al., Phys. Rev. B, 84, 064517 (2011), https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.064517
+.. [Catelani2011] Catelani et al., Phys. Rev. B 84, 064517 (2011), https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.064517
 .. [Dempster2014] Dempster et al., Phys. Rev. B 90, 094518 (2014), https://link.aps.org/doi/10.1103/PhysRevB.90.094518
 .. [Groszkowski2018] Groszkowski et al., New J. Phys. 20, 043053 (2018), https://doi.org/10.1088/1367-2630/aab7cd
 .. [Ithier2005] Ithier et al., Phys. Rev. B 72 134519 (2005), https://journals.aps.org/prb/abstract/10.1103/PhysRevB.72.134519
 .. [Koch2007] Koch et al., Phys. Rev. A 76, 042319 (2007), https://link.aps.org/doi/10.1103/PhysRevA.76.042319
 .. [Manucharyan2009] Manucharyan et al., Science 326, 113-116 (2009), https://doi.org/10.1126/science.1175552
-.. [Nguyen2019] Nguyen et al., Phys. Rev. X 041041 (2019), https://journals.aps.org/prx/abstract/10.1103/PhysRevX.9.041041
+.. [Nguyen2019] Nguyen et al., Phys. Rev. X 9, 041041 (2019), https://journals.aps.org/prx/abstract/10.1103/PhysRevX.9.041041
 .. [Orlando1999] Orlando et al., Phys. Rev. B 60, 15398 (1999), https://link.aps.org/doi/10.1103/PhysRevB.60.15398
-.. [Pop2014] Pop et al., Nature, 508 (7496) (2014), https://www.nature.com/articles/nature13017/
+.. [Pop2014] Pop et al., Nature 508 (7496) (2014), https://www.nature.com/articles/nature13017/
 .. [Schoelkopf2003] Schoelkopf et al., Quantum noise in mesoscopic physics, pp. 175-203. (2003), https://link.springer.com/chapter/10.1007/978-94-010-0089-5_9
 .. [Smith2020] Smith et al., npj Quantum Information 6.1 (2020), https://www.nature.com/articles/s41534-019-0231-2
 .. [Zhu2013] Zhu et al., PRB 87, 024510 (2013), https://link.aps.org/doi/10.1103/PhysRevB.87.024510

diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
@@ -192,7 +192,7 @@ Version 4.3
       make sure this is secure. 
     - Fix parameter functions for parametric driving in the Circuit module.
     - Fix configure method in `SymbolicCircuit`, now does not reset the instance when run with no arguments.
-    - Fix bugs #193 and #209 related to`ParameterSweep`.
+    - Fix bugs #193 and #209 related to `ParameterSweep`.
     - Fix compatibility of `Circuit` module with `HilbertSpace`, bugs #253 and #254.
     - Fix #211, a bug that could occur when `op_in_dressed_eigenbasis` was called without prior lookup generation.
     - `SymbolicCircuit` instances now do not need to be re-initiated when their `configure` method fails (e.g., because of incorrect parameters).
@@ -218,7 +218,7 @@ Version 4.2
 
 **BUG FIXES**
 
-    - Fix prefactor for evaluations noise spectral density for quasiparticle noise - adds an additional factor of :math:`\hbar/e^2`.
+    - Fix prefactor for evaluation of noise spectral density for quasiparticle noise - adds an additional factor of :math:`\hbar/e^2`.
     - Fix error in symbolic Hamiltonian for multi-harmonic junctions.
 
 **UNDER THE HOOD**
@@ -393,7 +393,7 @@ Version 3.0.3
 
 **Under the hood**
 
-    - Initialization of a circuit instance now does not globally switch to latex output (avoids unnecessary slowdowns with regular, non-sympy, output.
+    - Initialization of a circuit instance now does not globally switch to latex output (avoids unnecessary slowdowns with regular, non-sympy, output).
 
 
 Version 3.0.2
@@ -415,7 +415,7 @@ Version 3.0.2
 **Under the hood**
 
     - All numerical diagonalization is now delayed until explicitly required. Changing circuit parameters thus does not incur a repeated runtime cost anymore.
-    - When hierarchical diagonalization is used, the bare eigensystems for each subsystems are now stored and reused for calculations, and only replaced by a new set when necessary. This dramatically improves the performance of wavefunction plotting, identity wrapping, etc.
+    - When hierarchical diagonalization is used, the bare eigensystems for each subsystem are now stored and reused for calculations, and only replaced by a new set when necessary. This dramatically improves the performance of wavefunction plotting, identity wrapping, etc.
     - If the circuit parameters are not updated, successive diagonalizations are skipped for all subsystems.
     - Implemented `eigsh_safe` (wrapper for scipy.sparse.linalg.eigsh) that orthogonalizes the eigenvectors when degenerate eigenvalues are detected. In rare cases of actual degeneracies in the spectrum, sparse matrix methods could have given incorrect results because `scipy.sparse.linalg.eigsh` does not guarantee orthogonality of eigenvectors in degenerate subspaces.
 
@@ -498,8 +498,8 @@ Version 2.2.2
       overlap)^2 instead of (state overlap) for thresholding.
 
 **Under the Hood**
-    typing_extensions is new dependency (used for enhanced typing annotations such as
-    `@overload` and `Literal`
+    typing_extensions is a new dependency (used for enhanced typing annotations such as
+    `@overload` and `Literal`)
 
 
 Version 2.2
@@ -508,7 +508,7 @@ Version 2.2
 **Bug Fixes**
     - Use of `<ParameterSweep>.plot_transitions` could previously lead to a spurious
       switch of `<ParameterSweep>["evals"]` to transition energies.
-    - Include the :math:`/frac{1}{1}hbar` omega term when diagonalizing fluxonium in the harmonic
+    - Include the :math:`\frac{1}{2}\hbar\omega` term when diagonalizing fluxonium in the harmonic
       osc. basis. The omission of this only affected absolute energies, not the energy
       differences which are the relevant quantities in most cases. However, wavefunction
       plots for fluxonium were previously incorrectly positioned relative to the potential energy.
@@ -534,7 +534,7 @@ Version 2.2
     - `supported_noise_channels` and `effective_noise_channels` are now `@classmethods`
       and can be called either directly through a class, or through a class instance.
     - `t1_charge_impedance` is no longer returned by `effective_noise_channels` in the
-      case of a `TunableTransmon` and `Transmon` qubits
+      case of `TunableTransmon` and `Transmon` qubits
     - Added about function that shows basic information about scqubits as well as
       versions of some of the most important libraries that scqubits relies on.
     - Extended `pytests` for enhanced coverage.
@@ -684,7 +684,7 @@ Version 1.1.0
 +++++++++++++
 
    - new class ``InteractionTerm`` works in tandem with ``HilbertSpace`` to ease setup of composite systems with pairwise interactions
-   - new ``ParameterSweep`` class efficiently generates spectral data for performing a scan of a ``HilbertSpace`` object over an external parameters
+   - new ``ParameterSweep`` class efficiently generates spectral data for performing a scan of a ``HilbertSpace`` object over external parameters
    - new ``Explorer`` class introduces interactive plots (see docs and demo ipynb)
    - cleaned up implementation of file Serializable operations
 

diff --git a/docs/source/contents.rst b/docs/source/contents.rst
@@ -2,7 +2,7 @@
    Copyright (C) 2019, Jens Koch & Peter Groszkowski
 
 
-scQubits documentation
+scqubits documentation
 ======================
 
 scqubits is an open-source Python library for simulating superconducting qubits.

diff --git a/docs/source/example-notebooks.rst b/docs/source/example-notebooks.rst
@@ -14,7 +14,7 @@ Users can easily clone it to their local file system by executing::
 
     git clone https://github.com/scqubits/scqubits-examples
 
-The full contents of `scqubits-examples` can also be explored in a live jupyter
+The full contents of `scqubits-examples` can also be explored in a live Jupyter
 notebook via Binder:
 
 .. image:: https://mybinder.org/badge_logo.svg

diff --git a/docs/source/guide/basics/basics-spectra.ipynb b/docs/source/guide/basics/basics-spectra.ipynb
@@ -1249,12 +1249,7 @@
      "name": "#%% md\n"
     }
    },
-   "source": [
-    "### Plotting energy dispersion\n",
-    "The sensitivity of energy levels (or, more specifically, transition energies) to changes in an external parameter like the offset charge are important for qubit's dephasing time. Plots of the energy dispersion, can be obtained easily:\n",
-    "\n",
-    "* either for individual energy levels:"
-   ]
+   "source": "### Plotting energy dispersion\nThe sensitivity of energy levels (or, more specifically, transition energies) to changes in an external parameter like the offset charge is important for the qubit's dephasing time. Plots of the energy dispersion can be obtained easily:\n\n* either for individual energy levels:"
   },
   {
    "cell_type": "code",
@@ -4979,4 +4974,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/docs/source/guide/basics/basics-wavefunctions.ipynb b/docs/source/guide/basics/basics-wavefunctions.ipynb
@@ -43,9 +43,7 @@
      "name": "#%% md\n"
     }
    },
-   "source": [
-    "For a qubit as simple as the transmon, wavefunctions are one-dimensional and can be plotted easily. The first option, is to employ the discrete charge basis (`n`):"
-   ]
+   "source": "For a qubit as simple as the transmon, wavefunctions are one-dimensional and can be plotted easily. The first option is to employ the discrete charge basis (`n`):"
   },
   {
    "cell_type": "code",
@@ -4977,4 +4975,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/docs/source/guide/circuit/ipynb/custom_circuit_bases.ipynb b/docs/source/guide/circuit/ipynb/custom_circuit_bases.ipynb
@@ -48,19 +48,7 @@
      "name": "#%% md\n"
     }
    },
-   "source": [
-    "### Basis choices\n",
-    "\n",
-    "For **periodic degrees of freedom** scqubits employs the discrete charge basis.\n",
-    "\n",
-    "For **extended degrees of freedom** two choices are available:\n",
-    "- `ext_basis = \"discretized\"` (default)<br> Discretizes the variables for extended degrees of freedom.\n",
-    "- `ext_basis = \"harmonic\"`<br>Employs the harmonic-oscillator basis for th extended degrees of freedom (taking the potential to be the one arising from the geometric inductance).\n",
-    "\n",
-    "For instance, the following would switch the treatment of the extended degrees of freedom to using harmonic-oscillator basis:\n",
-    "\n",
-    "`zero_pi = scq.Circuit.from_yaml_string(zp_yaml, ext_basis=\"harmonic\")`"
-   ]
+   "source": "### Basis choices\n\nFor **periodic degrees of freedom** scqubits employs the discrete charge basis.\n\nFor **extended degrees of freedom** two choices are available:\n- `ext_basis = \"discretized\"` (default)<br> Discretizes the variables for extended degrees of freedom.\n- `ext_basis = \"harmonic\"`<br>Employs the harmonic-oscillator basis for the extended degrees of freedom (taking the potential to be the one arising from the geometric inductance).\n\nFor instance, the following would switch the treatment of the extended degrees of freedom to using harmonic-oscillator basis:\n\n`zero_pi = scq.Circuit.from_yaml_string(zp_yaml, ext_basis=\"harmonic\")`"
   },
   {
    "cell_type": "markdown",
@@ -110,18 +98,7 @@
      "name": "#%% md\n"
     }
    },
-   "source": [
-    "These cutoffs must be varied by the user to ensure convergence. \n",
-    "We distinguish two cutoff types:\n",
-    "\n",
-    "#### Cutoffs for periodic degrees of freedom:\n",
-    "- `cutoff_n_<i>` - use all the integer charge states in the range `[-cutoff_n_<i>, cutoff_n_<i>]` for the periodic degree of freedom $i$.\n",
-    "\n",
-    "#### Cutoffs for extended degrees of freedom:\n",
-    "- `cutoff_ext_<i>` - the meaning of this cutoff differs according to the choice of  basis, specified via `ext_basis` upon initialization of the `Circuit` instance.\n",
-    "    - `ext_basis = \"discretized\"`: <br>For discretization of $\\theta_i$, `cutoff_ext_<i>` sets the number of points used to in the \"spatial\" range given by the attribute `discretized_phi_range`.\n",
-    "    - `ext_basis = \"harmonic\"`: <br>When using the harmonic oscillator basis, `cutoff_ext_<i>` sets the number of harmonic oscillator states admitted to the basis set for the extended degree of freedom $i$."
-   ]
+   "source": "These cutoffs must be varied by the user to ensure convergence. \nWe distinguish two cutoff types:\n\n#### Cutoffs for periodic degrees of freedom:\n- `cutoff_n_<i>` - use all the integer charge states in the range `[-cutoff_n_<i>, cutoff_n_<i>]` for the periodic degree of freedom $i$.\n\n#### Cutoffs for extended degrees of freedom:\n- `cutoff_ext_<i>` - the meaning of this cutoff differs according to the choice of  basis, specified via `ext_basis` upon initialization of the `Circuit` instance.\n    - `ext_basis = \"discretized\"`: <br>For discretization of $\\theta_i$, `cutoff_ext_<i>` sets the number of points used in the \"spatial\" range given by the attribute `discretized_phi_range`.\n    - `ext_basis = \"harmonic\"`: <br>When using the harmonic oscillator basis, `cutoff_ext_<i>` sets the number of harmonic oscillator states admitted to the basis set for the extended degree of freedom $i$."
   },
   {
    "cell_type": "code",
@@ -262,11 +239,7 @@
      "name": "#%% md\n"
     }
    },
-   "source": [
-    "## Choosing basis states for each of the subsystems\n",
-    "It is also possible to chose a basis states for each of the subsystems independently.\n",
-    "We start with defining a particular circuit"
-   ]
+   "source": "## Choosing basis states for each of the subsystems\nIt is also possible to choose basis states for each of the subsystems independently.\nWe start with defining a particular circuit"
   },
   {
    "cell_type": "code",
@@ -505,4 +478,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}
diff --git a/docs/source/guide/circuit/ipynb/custom_circuit_coherence_estimates.ipynb b/docs/source/guide/circuit/ipynb/custom_circuit_coherence_estimates.ipynb
@@ -62,28 +62,12 @@
   {
    "cell_type": "markdown",
    "metadata": {},
-   "source": [
-    "There two important arguments that are passed to `Circuit` constructor which determine if and how noise can calculated:\n",
-    "\n",
-    "`generate_noise_methods`: A boolean argument that determines whether methods for estimating coherences are generated for this object. \n",
-    "\n",
-    "`use_dynamic_flux_grouping`: A boolean argument that determines if a flux-grouping based on this [You at al. PRB(2019)](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.99.174512) (or [arXiv](https://arxiv.org/abs/1902.04734)) paper is generated. This grouping approach is recommended any time flux is assumed to have time-dependence (due to noise, or otherwise) as it aims to group flux among different branches in a way that would not require a term proportional to the flux-derivative. \n",
-    "\n",
-    "\n",
-    ".. warning::\n",
-    "If `generate_noise_methods` is not set to `True` when building a `Circuit` object, none of the coherence methods will be generated. Users can however, choose to generate them at a later time by executing `circ.configure(generate_noise_methods=True)`. \n",
-    "\n",
-    ".. warning::\n",
-    "If `use_dynamic_flux_grouping` is not set to `True` when estimating coherence times, to obtain results related to flux noise, `scqubits` will utilize a more arbitrary grouping, and not the one proposed by [You at al. PRB(2019)](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.99.174512). \n"
-   ]
+   "source": "There are two important arguments that are passed to the `Circuit` constructor, which determine whether and how noise can be calculated:\n\n`generate_noise_methods`: A boolean argument that determines whether methods for estimating coherences are generated for this object. \n\n`use_dynamic_flux_grouping`: A boolean argument that determines if a flux-grouping based on this [You et al. PRB(2019)](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.99.174512) (or [arXiv](https://arxiv.org/abs/1902.04734)) paper is generated. This grouping approach is recommended any time flux is assumed to have time-dependence (due to noise, or otherwise) as it aims to group flux among different branches in a way that would not require a term proportional to the flux-derivative. \n\n\n.. warning::\nIf `generate_noise_methods` is not set to `True` when building a `Circuit` object, none of the coherence methods will be generated. Users can however, choose to generate them at a later time by executing `circ.configure(generate_noise_methods=True)`. \n\n.. warning::\nIf `use_dynamic_flux_grouping` is not set to `True` when estimating coherence times, to obtain results related to flux noise, `scqubits` will utilize a more arbitrary grouping, and not the one proposed by [You et al. PRB(2019)](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.99.174512). "
   },
   {
    "cell_type": "markdown",
    "metadata": {},
-   "source": [
-    "### Auto-generated `supported channels`\n",
-    "The `circ` object now contains a variety of `supported_noise_methods` which can be explicitly listed with:"
-   ]
+   "source": "### Auto-generated `supported channels`\nThe `circ` object now contains a variety of `supported_noise_channels` which can be explicitly listed with:"
   },
   {
    "cell_type": "code",
@@ -180,9 +164,7 @@
   {
    "cell_type": "markdown",
    "metadata": {},
-   "source": [
-    "and look at the depolarization $T_1$ time, at temperature of 0.1 mK, due to the capacitor between nodes 0 and 3 (i.e., of branch 4), but only including contributions from the downward rate between levels 2 and 1:"
-   ]
+   "source": "and look at the depolarization $T_1$ time, at a temperature of 0.1 K, due to the capacitor between nodes 0 and 3 (i.e., of branch 4), but only including contributions from the downward rate between levels 2 and 1:"
   },
   {
    "cell_type": "code",
@@ -2986,4 +2968,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}