model.fit generates error in Example 2

[Malarius1999]

When I execute either Example 1 or 2 of the git repo i get an error while fitting the model. Not sure if i did something wrong on installation, but i tried several hours to get it running.

Error message:

---

ValueError Traceback (most recent call last)
Cell In[28], line 1
----> 1 model.fit(X, t=t)

File /usr/local/lib/python3.10/site-packages/pysindy/pysindy.py:246, in SINDy.fit(self, x, t, x_dot, u)
240 u = validate_control_variables(
241 x,
242 u,
243 trim_last_point=(self.discrete_time and x_dot is None),
244 )
245 self.n_control_features_ = u[0].shape[u[0].ax_coord]
--> 246 x, x_dot = self._process_trajectories(x, t, x_dot)
248 # Append control variables
249 if u is not None:

File /usr/local/lib/python3.10/site-packages/pysindy/pysindy.py:491, in SINDy._process_trajectories(self, x, t, x_dot)
488 x = [xi[:-1] for xi in x]
489 else:
490 x, x_dot = zip(
--> 491 *[
492 self.feature_library.calc_trajectory(
493 self.differentiation_method, xi, ti
494 )
495 for xi, ti in _zip_like_sequence(x, t)
496 ]
497 )
498 return x, x_dot

File /usr/local/lib/python3.10/site-packages/pysindy/pysindy.py:492, in (.0)
488 x = [xi[:-1] for xi in x]
489 else:
490 x, x_dot = zip(
491 *[
--> 492 self.feature_library.calc_trajectory(
493 self.differentiation_method, xi, ti
494 )
495 for xi, ti in _zip_like_sequence(x, t)
496 ]
497 )
498 return x, x_dot

File /usr/local/lib/python3.10/site-packages/pysindy/feature_library/base.py:66, in BaseFeatureLibrary.calc_trajectory(self, diff_method, x, t)
65 def calc_trajectory(self, diff_method, x, t):
---> 66 x_dot = diff_method(x, t=t)
67 x = AxesArray(diff_method.smoothed_x_, x.axes)
68 return x, AxesArray(x_dot, x.axes)

File /usr/local/lib/python3.10/site-packages/pysindy/differentiation/base.py:53, in BaseDifferentiation.call(self, x, t)
52 def call(self, x, t=1):
---> 53 return self._differentiate(x, t)

File /usr/local/lib/python3.10/site-packages/pysindy/differentiation/finite_difference.py:269, in FiniteDifference._differentiate(self, x, t)
267 else:
268 t = AxesArray(np.array(t), axes={"ax_time": 0})
--> 269 coeffs = self._coefficients(t)
270 interior = self._accumulate(coeffs, x)
271 s[self.axis] = slice((self.n_stencil - 1) // 2, -(self.n_stencil - 1) // 2)

File /usr/local/lib/python3.10/site-packages/pysindy/differentiation/finite_difference.py:112, in FiniteDifference._coefficients(self, t)
110 b = AxesArray(np.zeros((1, self.n_stencil)), {"ax_time": 0, "ax_power": 1})
111 b[0, self.d] = factorial(self.d)
--> 112 return np.linalg.solve(matrices, b)

File /usr/local/lib/python3.10/site-packages/pysindy/utils/axes.py:420, in AxesArray.array_function(self, func, types, args, kwargs)
418 if not all(issubclass(t, AxesArray) for t in types):
419 return NotImplemented
--> 420 return HANDLED_FUNCTIONS[func](*args, **kwargs)

File /usr/local/lib/python3.10/site-packages/pysindy/utils/axes.py:631, in linalg_solve(a, b)
629 @_implements(np.linalg.solve)
630 def linalg_solve(a: AxesArray, b: AxesArray) -> AxesArray:
--> 631 result = np.linalg.solve(np.asarray(a), np.asarray(b))
632 a_rev = a._ax_map.reverse_map
633 a_names = [a_rev[k] for k in sorted(a_rev)]

File /usr/local/lib/python3.10/site-packages/numpy/linalg/_linalg.py:413, in solve(a, b)
410 signature = 'DD->D' if isComplexType(t) else 'dd->d'
411 with errstate(call=_raise_linalgerror_singular, invalid='call',
412 over='ignore', divide='ignore', under='ignore'):
--> 413 r = gufunc(a, b, signature=signature)
415 return wrap(r.astype(result_t, copy=False))

ValueError: solve: Input operand 1 has a mismatch in its core dimension 0, with gufunc signature (m,m),(m,n)->(m,n) (size 1 is different from 3)

PySINDy/Python version information:

Python 3.10.12
1.7.6.dev485+g23da590.d20241007 3.10.12 (main, Jun 7 2023, 19:32:10) [GCC 10.2.1 20210110]

[Malarius1999]

update: I got it working again with

Python 3.10.15
numpy==1.21.6
pysindy==1.7.3

[michaelkalz]

I tried example 1 (without modification) and got:

Traceback (most recent call last):
File "/home/mkalz/fit_lorenz.py", line 8, in
x = solve_ivp(lorenz, [-8,8,27], t)
File "/home/mkalz/.conda/envs/photon_systems/lib/python3.10/site-packages/scipy/integrate/_ivp/ivp.py", line 577, in solve_ivp
t0, tf = map(float, t_span)
ValueError: too many values to unpack (expected 2)

Did you change anything? @Malarius1999