A few issues running example notebooks in documetation

[nikolasibalic]

As part of a review, I attempted to run the example notebooks in your documentation. Without making any changes, I encountered three issues. I outlined them below

Discrepancies

• Analytical Doppler Demo

https://rydiqule.readthedocs.io/en/stable/examples/Analytical%20Doppler%20Demo.html#d-doppler-free-configuration

Here I get the following three plots

Neither of which matches the plots in example notebook.

• Calculate SNR

1D Optimum first cell fails with

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[4], line 4
      2 basis_size = 4
      3 Rb_sensor = rq.Sensor(basis_size)
----> 4 Rb_sensor.set_experiment_values(probe_freq = probe_freq,probe_tuple = (0,1),
      5                               kappa = kappa, eta = eta, cell_length = .000001)
      7 red_rabi = np.linspace(0.1,6,100)
      8 blue_rabi = np.linspace(0.1,4,101)

TypeError: Sensor.set_experiment_values() got an unexpected keyword argument 'probe_tuple'

• RF heterodyne with Doppler Example

Notebook at start imports numba but numba is not dependancy of the package. Please clarify relation.

My environment

❯ uv run python --version
Python 3.13.11

❯ uv pip list
Package                       Version
----------------------------- -----------
anyio                         4.12.1
arc-alkali-rydberg-calculator 3.9.0
argon2-cffi                   25.1.0
argon2-cffi-bindings          25.1.0
arrow                         1.4.0
asteval                       1.0.8
asttokens                     3.0.1
async-lru                     2.1.0
attrs                         25.4.0
babel                         2.17.0
beautifulsoup4                4.14.3
bleach                        6.3.0
certifi                       2026.1.4
cffi                          2.0.0
charset-normalizer            3.4.4
comm                          0.2.3
contourpy                     1.3.3
cycler                        0.12.1
debugpy                       1.8.19
decorator                     5.2.1
defusedxml                    0.7.1
dill                          0.4.0
executing                     2.2.1
fastjsonschema                2.21.2
fonttools                     4.61.1
fqdn                          1.5.1
h11                           0.16.0
h5py                          3.15.1
httpcore                      1.0.9
httpx                         0.28.1
idna                          3.11
ipykernel                     7.1.0
ipython                       9.9.0
ipython-pygments-lexers       1.1.1
ipywidgets                    8.1.8
isoduration                   20.11.0
jedi                          0.19.2
jinja2                        3.1.6
json5                         0.13.0
jsonpointer                   3.0.0
jsonschema                    4.26.0
jsonschema-specifications     2025.9.1
jupyter                       1.1.1
jupyter-client                8.8.0
jupyter-console               6.6.3
jupyter-core                  5.9.1
jupyter-events                0.12.0
jupyter-lsp                   2.3.0
jupyter-server                2.17.0
jupyter-server-terminals      0.5.4
jupyterlab                    4.5.2
jupyterlab-pygments           0.3.0
jupyterlab-server             2.28.0
jupyterlab-widgets            3.0.16
kiwisolver                    1.4.9
lark                          1.3.1
leveldiagram                  0.3.2
lmfit                         1.3.4
markdown-it-py                4.0.0
markupsafe                    3.0.3
matplotlib                    3.10.8
matplotlib-inline             0.2.1
mdurl                         0.1.2
mistune                       3.2.0
mpmath                        1.3.0
nbclient                      0.10.4
nbconvert                     7.16.6
nbformat                      5.10.4
nest-asyncio                  1.6.0
networkx                      3.6.1
notebook                      7.5.2
notebook-shim                 0.2.4
numpy                         2.4.1
packaging                     25.0
pandocfilters                 1.5.1
parso                         0.8.5
pexpect                       4.9.0
pillow                        12.1.0
platformdirs                  4.5.1
prometheus-client             0.24.1
prompt-toolkit                3.0.52
psutil                        7.2.1
ptyprocess                    0.7.0
pure-eval                     0.2.3
pycparser                     2.23
pygments                      2.19.2
pyparsing                     3.3.1
python-dateutil               2.9.0.post0
python-json-logger            4.0.0
pyyaml                        6.0.3
pyzmq                         27.1.0
referencing                   0.37.0
requests                      2.32.5
rfc3339-validator             0.1.4
rfc3986-validator             0.1.1
rfc3987-syntax                1.1.0
rich                          14.2.0
rpds-py                       0.30.0
rydiqule                      2.1.1
scipy                         1.15.3
send2trash                    2.1.0
setuptools                    80.9.0
six                           1.17.0
soupsieve                     2.8.1
stack-data                    0.6.3
sympy                         1.14.0
terminado                     0.18.1
tinycss2                      1.4.0
tornado                       6.5.4
traitlets                     5.14.3
typing-extensions             4.15.0
tzdata                        2025.3
uncertainties                 3.2.4
uri-template                  1.3.0
urllib3                       2.6.3
wcwidth                       0.2.14
webcolors                     25.10.0
webencodings                  0.5.1
websocket-client              1.9.0
widgetsnbextension            4.0.15

[dihm]

@nikolasibalic Thanks for finding these! We've struggled to find a good way to incorporate the example notebooks into our usual test suite, meaning they don't get re-run regularly and have a tendency to go stale. I've made the necessary fixes in #59, but I'll describe them here so the issue and resolution are in one place. Going in reverse order:

• RF heterodyne with Doppler example: numba comes in with our optional dependency group backends which we often install for dev work. It's use here dates way back to early v1 days trying to speed up the time-solver. Obviously it isn't actually needed so I've deleted it.
• Calculate SNR: This calling convention was deprecated with v2.0.0 as probe_tuple is now automatically inferred as the first coupling added to the system. Honestly not sure how it has persisted this long. Regardless, deleting the argument is the correct modification.
• Analytic Doppler Demo: This one is more subtle. v2.0.0 introduced a number of regressions in how Cell handles dephasings. Most notably, transit broadening was not included. These issues were fixed by Cell fixes #38. The calculations of this notebook in particular are quite susceptible to these errors since they involve a number of fine-tuned values and absolute value comparisons. I've re-tuned the hard-coded values and re-ran the entire notebook.