eliminate restriction on pytest

add Sybil

docs/conftest.py

@@ -0,0 +1,23 @@
+import numpy as np
+import qutip
+import scqubits
+from sybil import Sybil
+from sybil.parsers.doctest import DocTestParser
+from sybil.parsers.markdown import PythonCodeBlockParser, SkipParser
+
+import floquet
+
+
+def sybil_setup(namespace):  # noqa ARG001
+    namespace["np"] = np
+    namespace["scq"] = scqubits
+    namespace["ft"] = floquet
+    namespace["qt"] = qutip
+
+
+# sybil configuration
+pytest_collect_file = Sybil(
+    parsers=[DocTestParser(), PythonCodeBlockParser(), SkipParser()],
+    patterns=["*.md"],
+    setup=sybil_setup,
+).pytest()

docs/floquet.md

@@ -37,4 +37,3 @@ The **floquet** Python API consists largely of the **floquet_analysis** function
 ::: floquet.utils.file_io
     options:
         show_source: false
-

docs/index.md

@@ -15,10 +15,6 @@ Requires Python 3.10+
 
 Before jumping straight into the Floquet analysis, we first need to define our system Hamiltonian and the drive parameters. Here we take the example of a transmon and utilize the scubits library to help define the system Hamiltonian. Note however that the code accepts QuTiP `Qobj` as input for the Hamiltonian. 
 ```python
-import numpy as np
-import qutip as qt
-import scqubits as scq
-
 num_states = 20
 qubit_params = {"EJ": 20.0, "EC": 0.2, "ng": 0.25, "ncut": 41}
 tmon = scq.Transmon(**qubit_params, truncated_dim=num_states)
@@ -32,15 +28,15 @@ H1 = hilbert_space.op_in_dressed_eigenbasis(tmon.n_operator)
 ```
 We then also need to specify the drive frequencies we plan to drive at, which correspond to the cavity frequencies
 ```python
-omega_d_linspace = 2.0 * np.pi * np.linspace(7.5, 10.0, 120)
+omega_d_values = 2.0 * np.pi * np.linspace(7.5, 10.0, 120)
 ```
 Finally, we specify the induced ac-stark shift that we want the qubit to experience. The dispersive coupling of a qubit to the cavity differs as a function of the cavity frequency. Thus we provide helper functions for normalizing the drive amplitudes so that we scan over the same induced ac-Stark shifts for all given frequencies. 
 ```python
 import floquet as ft
 
 state_indices = [0, 1]  # get data for ground and first excited states
 chi_ac_linspace = 2.0 * np.pi * np.linspace(0.0, 0.1, 59) # 100 MHz ac-Stark shift
-chi_to_amp = ft.ChiacToAmp(H0, H1, state_indices, omega_d_linspace)
+chi_to_amp = ft.ChiacToAmp(H0, H1, state_indices, omega_d_values)
 drive_amplitudes = chi_to_amp.amplitudes_for_omega_d(chi_ac_linspace)
 ```
 We can now pass these derived quantities to `Model` which specifies the model system
@@ -51,7 +47,8 @@ model = ft.Model(
 ```
 We are now ready to create an instance of the `FloquetAnalysis` class, and run the full Floquet simulation
 ```python
-floquet_analysis = ft.FloquetAnalysis(model, state_indices=state_indices)
+options = ft.Options(num_cpus=6)
+floquet_analysis = ft.FloquetAnalysis(model, state_indices=state_indices, options=options)
 data_vals = floquet_analysis.run()
 ```
 `data_vals` is a dictionary containing all quantities computed during the call to `run()`. This includes the overlap with the "ideal" displaced state, which can be plotted to reveal "scars" in the drive frequency and amplitude space where resonances occur. Additionally we compute the [Blais branch crossing analysis](https://arxiv.org/abs/2402.06615) to understand which states are responsible for ionization. See the tutorial notebook under Examples on the left to see how to plot and visualize these quantities.  

floquet/model.py

@@ -46,9 +46,8 @@ def __init__(
             drive_amplitudes = np.array(drive_amplitudes)
         if len(drive_amplitudes.shape) == 1:
             drive_amplitudes = np.tile(drive_amplitudes, (len(omega_d_values), 1)).T
-        else:
-            assert len(drive_amplitudes.shape) == 2
-            assert drive_amplitudes.shape[1] == len(omega_d_values)
+        assert len(drive_amplitudes.shape) == 2
+        assert drive_amplitudes.shape[1] == len(omega_d_values)
 
         self.H0 = H0
         self.H1 = H1

pyproject.toml

@@ -25,7 +25,7 @@ dev = [
     "ruff",
     "codespell",
     "pygments",
-    "pytest>=7.0,<8.0",
+    "pytest",
     "pytest-xdist",
     "pymdown-extensions",
     "mkdocs",
@@ -39,7 +39,7 @@ dev = [
     "mkdocs-exclude",
     "mknotebooks",
     "nbconvert==6.5.0",
-    "sybil>=6",
+    "sybil[pytest]",
     "black",  # needed by mkdocstrings to format function signatures
 ]
 
@@ -57,9 +57,13 @@ select = ["F", "E", "W", "C90", "I", "D", "UP", "YTT", "ANN", "BLE", "B", "A", "
     "INP", "NPY201", "PIE", "T20", "PYI", "PT", "RSE", "RET", "SLF", "SIM", "INT",
     "ARG", "PTH", "PL", "TRY", "FLY", "NPY", "RUF",
 ]
+extend-select = ["D204", "D400", "D404", "D406", "D410"]
 ignore = [
     "ANN101",
+    "C901",
     "D100", "D101", "D102", "D103", "D104", "D105", "D106", "D107", "D417",
+    "E741",
+    "INP001",
     "PLC0414",
     "PLR0913", "PLR2004",
     "T201",
@@ -105,6 +109,10 @@ help = "clean the code (ruff + codespell)"
 cmd = 'echo "\n>>> pytest -n=auto tests" && pytest -n=auto tests'
 help = "run the unit tests suite (pytest)"
 
+[tool.taskipy.tasks.doctest]
+cmd = 'echo "\n>>> pytest docs" && pytest docs'
+help = "check documentation examples (doctest)"
+
 [tool.taskipy.tasks.docbuild]
 cmd = 'mkdocs build'
 help = "build the documentation website"
@@ -114,13 +122,14 @@ cmd = 'mkdocs serve'
 help = "preview documentation website with hot-reloading"
 
 [tool.taskipy.tasks.all]
-cmd = 'task clean && task test'
+cmd = 'task clean && task test && task doctest'
 help = "run all tasks before a commit (ruff + codespell + pytest + doctest)"
 
 [tool.taskipy.tasks.ci]
 cmd = '''echo "\n>>> ruff check" && ruff check &&
          echo "\n>>> ruff format --check" && ruff format --check &&
          task codespell &&
          task test &&
+         task doctest &&
          task docbuild'''
 help = "run all the CI checks"