[BUG] problem running Multiple Trajectories in the `1_feature_overview/example.ipynb`

[georgemilosh]

The issue with running the notebook ./pysindy/examples/1_feature_overview/example.ipynb when getting to Multiple Trajectories with pysindy=1.7.5

Note that as explained in README I tried installing with pip install pysindy[dev] which gave me WARNING: pysindy 1.7.5 does not provide the extra 'dev'

Reproducing code example:

import pysindy
import warnings
from contextlib import contextmanager
from copy import copy
from pathlib import Path

import matplotlib.pyplot as plt
import numpy as np
from scipy.integrate import solve_ivp
from scipy.linalg import LinAlgWarning
from sklearn.exceptions import ConvergenceWarning
from sklearn.linear_model import Lasso

import pysindy as ps
from pysindy.utils import enzyme
from pysindy.utils import lorenz
from pysindy.utils import lorenz_control

if __name__ != "testing":
    t_end_train = 10
    t_end_test = 15
else:
    t_end_train = 0.04
    t_end_test = 0.04

data = (Path() / "../data").resolve()

@contextmanager
def ignore_specific_warnings():
    filters = copy(warnings.filters)
    warnings.filterwarnings("ignore", category=ConvergenceWarning)
    warnings.filterwarnings("ignore", category=LinAlgWarning)
    warnings.filterwarnings("ignore", category=UserWarning)
    yield
    warnings.filters = filters

if __name__ == "testing":
    import sys
    import os

    sys.stdout = open(os.devnull, "w")
# %%
# Seed the random number generators for reproducibility
np.random.seed(100)

integrator_keywords = {}
integrator_keywords["rtol"] = 1e-12
integrator_keywords["method"] = "LSODA"
integrator_keywords["atol"] = 1e-12

dt = 0.002

t_train = np.arange(0, t_end_train, dt)
x0_train = [-8, 8, 27]
t_train_span = (t_train[0], t_train[-1])
x_train = solve_ivp(
    lorenz, t_train_span, x0_train, t_eval=t_train, **integrator_keywords
).y.T

# %% [markdown]
# ### Multiple trajectories
# We use the Lorenz equations to evolve multiple different initial conditions forward in time, passing all the trajectories into a single `SINDy` object. Note that `x_train_multi` is a list of 2D numpy arrays.

# %%
if __name__ != "testing":
    n_trajectories = 20
    sample_range = (500, 1500)
else:
    n_trajectories = 2
    sample_range = (10, 15)
x0s = np.array([36, 48, 41]) * (np.random.rand(n_trajectories, 3) - 0.5) + np.array(
    [0, 0, 25]
)
x_train_multi = []
for i in range(n_trajectories):
    x_train_multi.append(
        solve_ivp(
            lorenz, t_train_span, x0s[i], t_eval=t_train, **integrator_keywords
        ).y.T
    )

model = ps.SINDy()
model.fit(x_train_multi, t=dt)
model.print()

Error message:

Traceback (most recent call last):
  File "/net/nfs/ssd1/gmiloshe/pysindy/examples/1_feature_overview/test.py", line 85, in <module>
    model.fit(x_train_multi, t=dt)
  File "/net/nfs/ssd1/miniconda3/envs/pysindy/lib/python3.10/site-packages/pysindy/pysindy.py", line 314, in fit
    x, t, x_dot, u = _adapt_to_multiple_trajectories(x, t, x_dot, u)
  File "/net/nfs/ssd1/miniconda3/envs/pysindy/lib/python3.10/site-packages/pysindy/pysindy.py", line 934, in _adapt_to_multiple_trajectories
    raise ValueError(
ValueError: x is a Sequence, but multiple_trajectories not set.  Did you mean to set multiple trajectories?

PySINDy/Python version information:

1.7.5 3.10.12 | packaged by conda-forge | (main, Jun 23 2023, 22:40:32) [GCC 12.3.0]

[Jacob-Stevens-Haas]

The README, as well as certain example notebooks (1, 2, 5) are kept up to date with the master branch. That branch is backwards incompatible, as we prepare for a 2.0 release. It has removed the multiple_trajectories kwarg to SINDy.fit() and added the dev extras.

If you're on a 1.x release, you need to specify that x is a sequence of trajectories. You also will not have pysindy[dev].