NumbaDeprecationWarning via shap

[davidpomerenke]

from econml.dr import LinearDRLearner

will print the long warning log given below.

I am using Python 3.10.10, econml 0.14.1.

Econml requires shap >=0.38.1,<0.42.0 according to Poetry, and I have shap 0.41.0.

It seems that the issue is solved in shap 0.42.0: shap/shap#2909

Thus upgrading the shap dependency would probably fix this.

Warning log:

.venv/lib/python3.10/site-packages/shap/utils/_clustering.py:35: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _pt_shuffle_rec(i, indexes, index_mask, partition_tree, M, pos):
.venv/lib/python3.10/site-packages/shap/utils/_clustering.py:54: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def delta_minimization_order(all_masks, max_swap_size=100, num_passes=2):
.venv/lib/python3.10/site-packages/shap/utils/_clustering.py:63: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _reverse_window(order, start, length):
.venv/lib/python3.10/site-packages/shap/utils/_clustering.py:69: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _reverse_window_score_gain(masks, order, start, length):
.venv/lib/python3.10/site-packages/shap/utils/_clustering.py:77: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _mask_delta_score(m1, m2):
.venv/lib/python3.10/site-packages/shap/links.py:5: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def identity(x):
.venv/lib/python3.10/site-packages/shap/links.py:10: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _identity_inverse(x):
.venv/lib/python3.10/site-packages/shap/links.py:15: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def logit(x):
.venv/lib/python3.10/site-packages/shap/links.py:20: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _logit_inverse(x):
.venv/lib/python3.10/site-packages/shap/utils/_masked_model.py:363: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _build_fixed_single_output(averaged_outs, last_outs, outputs, batch_positions, varying_rows, num_varying_rows, link, linearizing_weights):
.venv/lib/python3.10/site-packages/shap/utils/_masked_model.py:385: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _build_fixed_multi_output(averaged_outs, last_outs, outputs, batch_positions, varying_rows, num_varying_rows, link, linearizing_weights):
.venv/lib/python3.10/site-packages/shap/utils/_masked_model.py:428: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _init_masks(cluster_matrix, M, indices_row_pos, indptr):
.venv/lib/python3.10/site-packages/shap/utils/_masked_model.py:439: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _rec_fill_masks(cluster_matrix, indices_row_pos, indptr, indices, M, ind):
.venv/lib/python3.10/site-packages/shap/maskers/_tabular.py:186: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _single_delta_mask(dind, masked_inputs, last_mask, data, x, noop_code):
.venv/lib/python3.10/site-packages/shap/maskers/_tabular.py:197: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _delta_masking(masks, x, curr_delta_inds, varying_rows_out,
.venv/lib/python3.10/site-packages/shap/maskers/_image.py:175: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _jit_build_partition_tree(xmin, xmax, ymin, ymax, zmin, zmax, total_ywidth, total_zwidth, M, clustering, q):
.venv/lib/python3.10/site-packages/shap/explainers/_partition.py:676: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def lower_credit(i, value, M, values, clustering):
The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.

[davidpomerenke]

Temporary workaround (via https://numba.pydata.org/numba-doc/dev/reference/deprecation.html):

from numba.core.errors import NumbaDeprecationWarning
import warnings

warnings.simplefilter('ignore', category=NumbaDeprecationWarning)

from econml.dr import LinearDRLearner

The warning suppression code must come before the econml imports for it to work.