Error on Import #1
Comments
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It looks as if numba is balking at some type issues, but it is not clear to
me what those could be from the error. This has worked acceptably on a few
different machines and configurations I tried, so it isn't the default
state of things.
What version of numba are you using?
…On Wed, Mar 15, 2023 at 7:21 PM zilch42 ***@***.***> wrote:
Hi there, I'm getting an error trying to import HDBSCAN from fast_hdbscan
from fast_hdbscan import HDBSCAN
---------------------------------------------------------------------------
TypingError Traceback (most recent call last)
Cell In[1], line 10
8 from sklearn.feature_extraction.text import CountVectorizer
9 from umap import UMAP
---> 10 from fast_hdbscan import HDBSCAN
11 import pickle
12 import sys
File [c:\Users\abb064\AppData\Local\miniconda3\envs\csiro-horizon-scanning39\lib\site-packages\fast_hdbscan\__init__.py:7](file:///C:/Users/abb064/AppData/Local/miniconda3/envs/csiro-horizon-scanning39/lib/site-packages/fast_hdbscan/__init__.py:7)
5 random_state = np.random.RandomState(42)
6 random_data = random_state.random(size=(100, 3))
----> 7 HDBSCAN(allow_single_cluster=True).fit(random_data)
8 HDBSCAN(cluster_selection_method="leaf").fit(random_data)
10 __all__ = ["HDBSCAN", "fast_hdbscan"]
File [c:\Users\abb064\AppData\Local\miniconda3\envs\csiro-horizon-scanning39\lib\site-packages\fast_hdbscan\hdbscan.py:217](file:///C:/Users/abb064/AppData/Local/miniconda3/envs/csiro-horizon-scanning39/lib/site-packages/fast_hdbscan/hdbscan.py:217), in HDBSCAN.fit(self, X, y, **fit_params)
207 clean_data = X
209 kwargs = self.get_params()
211 (
212 self.labels_,
213 self.probabilities_,
214 self._single_linkage_tree,
215 self._condensed_tree,
216 self._min_spanning_tree,
--> 217 ) = fast_hdbscan(clean_data, return_trees=True, **kwargs)
219 self._condensed_tree = to_numpy_rec_array(self._condensed_tree)
221 if not self._all_finite:
222 # remap indices to align with original data in the case of non-finite entries.
File [c:\Users\abb064\AppData\Local\miniconda3\envs\csiro-horizon-scanning39\lib\site-packages\fast_hdbscan\hdbscan.py:149](file:///C:/Users/abb064/AppData/Local/miniconda3/envs/csiro-horizon-scanning39/lib/site-packages/fast_hdbscan/hdbscan.py:149), in fast_hdbscan(data, min_samples, min_cluster_size, cluster_selection_method, allow_single_cluster, return_trees)
147 sklearn_tree = KDTree(data)
148 numba_tree = kdtree_to_numba(sklearn_tree)
--> 149 edges = parallel_boruvka(
150 numba_tree, min_samples=min_cluster_size if min_samples is None else min_samples
151 )
152 sorted_mst = edges[np.argsort(edges.T[2])]
153 linkage_tree = mst_to_linkage_tree(sorted_mst)
File [c:\Users\abb064\AppData\Local\miniconda3\envs\csiro-horizon-scanning39\lib\site-packages\fast_hdbscan\boruvka.py:270](file:///C:/Users/abb064/AppData/Local/miniconda3/envs/csiro-horizon-scanning39/lib/site-packages/fast_hdbscan/boruvka.py:270), in parallel_boruvka(tree, min_samples)
267 while n_components > 1:
268 candidate_distances, candidate_indices = boruvka_tree_query(tree, node_components, point_components,
269 core_distances)
--> 270 new_edges = merge_components(components_disjoint_set, candidate_indices, candidate_distances, point_components)
271 update_component_vectors(tree, components_disjoint_set, node_components, point_components)
273 edges = np.vstack((edges, new_edges))
File [c:\Users\abb064\AppData\Local\miniconda3\envs\csiro-horizon-scanning39\lib\site-packages\numba\core\dispatcher.py:468](file:///C:/Users/abb064/AppData/Local/miniconda3/envs/csiro-horizon-scanning39/lib/site-packages/numba/core/dispatcher.py:468), in _DispatcherBase._compile_for_args(self, *args, **kws)
464 msg = (f"{str(e).rstrip()} \n\nThis error may have been caused "
465 f"by the following argument(s):\n{args_str}\n")
466 e.patch_message(msg)
--> 468 error_rewrite(e, 'typing')
469 except errors.UnsupportedError as e:
470 # Something unsupported is present in the user code, add help info
471 error_rewrite(e, 'unsupported_error')
...
File ".[.\..\..\..\..\AppData\Local\miniconda3\envs\csiro-horizon-scanning39\lib\site-packages\fast_hdbscan\boruvka.py](https://file+.vscode-resource.vscode-cdn.net/c%3A/Users/abb064/OneDrive%20-%20CSIRO/AppData/Local/miniconda3/envs/csiro-horizon-scanning39/lib/site-packages/fast_hdbscan/boruvka.py)", line 9:
def merge_components(disjoint_set, candidate_neighbors, candidate_neighbor_distances, point_components):
component_edges = {0: (0, np.int32(1), np.float32(0.0)) for i in range(0)}
Python 3.9.16
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Numba 0.56.4 Here is my whole environment |
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Running into the same error. I have this additional error message: Python 3.9.0 Seems like a int32 vs int64 in a dict key problem. EDIT: found it. Will create a PR |
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Getting a kinda different import error: TypingError Traceback (most recent call last)
Cell In[1], line 20
18 import optuna
19 import multiprocessing
---> 20 import fast_hdbscan
File [c:\Users\.venv\Lib\site-packages\fast_hdbscan\__init__.py:7](file:///C:/Users/.venv/Lib/site-packages/fast_hdbscan/__init__.py:7)
5 random_state = np.random.RandomState(42)
6 random_data = random_state.random(size=(100, 3))
----> 7 HDBSCAN(allow_single_cluster=True).fit(random_data)
8 HDBSCAN(cluster_selection_method="leaf").fit(random_data)
10 __all__ = ["HDBSCAN", "fast_hdbscan"]
File [c:\Users\.venv\Lib\site-packages\fast_hdbscan\hdbscan.py:217](file:///C:/Users/.venv/Lib/site-packages/fast_hdbscan/hdbscan.py:217), in HDBSCAN.fit(self, X, y, **fit_params)
207 clean_data = X
209 kwargs = self.get_params()
211 (
212 self.labels_,
213 self.probabilities_,
214 self._single_linkage_tree,
215 self._condensed_tree,
216 self._min_spanning_tree,
--> 217 ) = fast_hdbscan(clean_data, return_trees=True, **kwargs)
219 self._condensed_tree = to_numpy_rec_array(self._condensed_tree)
...
File "..\.venv\Lib\site-packages\fast_hdbscan\boruvka.py", line 9:
def merge_components(disjoint_set, candidate_neighbors, candidate_neighbor_distances, point_components):
component_edges = {0: (0, np.int32(1), np.float32(0.0)) for i in range(0)}
My environment: |
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I had to downgrade numpy 2.0.2 to1.23.X to get rid of a numpy error on import. (Something about np.boool8 not existing). |
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I'm hoping that as numpy and numba settle down with reagrd to the new APIs etc. that some of this will magically resolve itself ( I don't think this package does anything weird, or uses anything particularly specific/internal). For now I'll keep it as a "wait and see". |
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Hi there, I'm getting an error trying to import HDBSCAN from fast_hdbscan
from fast_hdbscan import HDBSCANPython 3.9.16
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