Test problems using python -m nose -s hdbscan

[xavgit]

Hi,
I have installed hdbscan with pip without any errors:
...........................................................................................
Installing collected packages: hdbscan
Attempting uninstall: hdbscan
Found existing installation: hdbscan 0.8.37
Uninstalling hdbscan-0.8.37:
Successfully uninstalled hdbscan-0.8.37
Successfully installed hdbscan-0.8.38.post1

When I run the following I receive errors.

python3 -m nose -s hdbscan
Exception ignored on calling ctypes callback function: <function _ThreadpoolInfo._find_modules_with_dl_iterate_phdr..match_module_callback at 0x7fa138d46f70>
Traceback (most recent call last):
File "/home/xxxx/.local/lib/python3.8/site-packages/threadpoolctl.py", line 400, in match_module_callback
self._make_module_from_path(filepath)
File "/home/xxxx/.local/lib/python3.8/site-packages/threadpoolctl.py", line 515, in _make_module_from_path
module = module_class(filepath, prefix, user_api, internal_api)
File "/home/xxxx/.local/lib/python3.8/site-packages/threadpoolctl.py", line 606, in init
self.version = self.get_version()
File "/home/xxxx/.local/lib/python3.8/site-packages/threadpoolctl.py", line 646, in get_version
config = get_config().split()
AttributeError: 'NoneType' object has no attribute 'split'
..E..................E............................../home/xxxx/.local/lib/python3.8/site-packages/hdbscan/tests/test_hdbscan.py:80: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (matplotlib.pyplot.figure) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam figure.max_open_warning). Consider using matplotlib.pyplot.close().
plt.figure()
Exception ignored on calling ctypes callback function: <function _ThreadpoolInfo._find_modules_with_dl_iterate_phdr..match_module_callback at 0x7fa114b849d0>
Traceback (most recent call last):
File "/home/xxxx/.local/lib/python3.8/site-packages/threadpoolctl.py", line 400, in match_module_callback
self._make_module_from_path(filepath)
File "/home/xxxx/.local/lib/python3.8/site-packages/threadpoolctl.py", line 515, in _make_module_from_path
module = module_class(filepath, prefix, user_api, internal_api)
File "/home/xxxx/.local/lib/python3.8/site-packages/threadpoolctl.py", line 606, in init
self.version = self.get_version()
File "/home/xxxx/.local/lib/python3.8/site-packages/threadpoolctl.py", line 646, in get_version
config = get_config().split()
AttributeError: 'NoneType' object has no attribute 'split'
Exception ignored on calling ctypes callback function: <function _ThreadpoolInfo._find_modules_with_dl_iterate_phdr..match_module_callback at 0x7fa11435daf0>
Traceback (most recent call last):
File "/home/xxxx/.local/lib/python3.8/site-packages/threadpoolctl.py", line 400, in match_module_callback
self._make_module_from_path(filepath)
File "/home/xxxx/.local/lib/python3.8/site-packages/threadpoolctl.py", line 515, in _make_module_from_path
module = module_class(filepath, prefix, user_api, internal_api)
File "/home/xxxx/.local/lib/python3.8/site-packages/threadpoolctl.py", line 606, in init
self.version = self.get_version()
File "/home/xxxx/.local/lib/python3.8/site-packages/threadpoolctl.py", line 646, in get_version
config = get_config().split()
AttributeError: 'NoneType' object has no attribute 'split'
..............EE..........E

ERROR: Check warning on unsupported metric.

Traceback (most recent call last):
File "sklearn/metrics/_dist_metrics.pyx", line 420, in sklearn.metrics._dist_metrics.DistanceMetric64.get_metric
KeyError: 'cosine'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/xxxx/.local/lib/python3.8/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/home/xxxx/.local/lib/python3.8/site-packages/hdbscan/tests/test_branches.py", line 147, in test_branch_detection_data_with_non_tree_metric
c = HDBSCAN(
File "/home/xxxx/.local/lib/python3.8/site-packages/hdbscan/hdbscan_.py", line 1221, in fit
) = hdbscan(clean_data, **kwargs)
File "/home/xxxx/.local/lib/python3.8/site-packages/hdbscan/hdbscan_.py", line 869, in hdbscan
(single_linkage_tree, result_min_span_tree) = memory.cache(
File "/home/xxxx/.local/lib/python3.8/site-packages/joblib/memory.py", line 349, in call
return self.func(*args, **kwargs)
File "/home/xxxx/.local/lib/python3.8/site-packages/hdbscan/hdbscan_.py", line 384, in _hdbscan_boruvka_balltree
tree = BallTree(X, metric=metric, leaf_size=leaf_size, **kwargs)
File "sklearn/neighbors/_binary_tree.pxi", line 837, in sklearn.neighbors._ball_tree.BinaryTree.init
File "sklearn/metrics/_dist_metrics.pyx", line 211, in sklearn.metrics._dist_metrics.DistanceMetric.get_metric
File "sklearn/metrics/_dist_metrics.pyx", line 422, in sklearn.metrics._dist_metrics.DistanceMetric64.get_metric
ValueError: Unrecognized metric 'cosine'

======================================================================
ERROR: hdbscan.tests.test_branches.test_branch_detector_is_sklearn_estimator

Traceback (most recent call last):
File "/home/xxxx/.local/lib/python3.8/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/home/xxxx/.local/lib/python3.8/site-packages/hdbscan/tests/test_branches.py", line 473, in test_branch_detector_is_sklearn_estimator
check_estimator(BranchDetector)
File "/home/xxxx/.local/lib/python3.8/site-packages/sklearn/utils/estimator_checks.py", line 616, in check_estimator
raise TypeError(msg)
TypeError: Passing a class was deprecated in version 0.23 and isn't supported anymore from 0.24.Please pass an instance instead.

======================================================================
ERROR: hdbscan.tests.test_hdbscan.test_hdbscan_is_sklearn_estimator

Traceback (most recent call last):
File "/home/xxxx/.local/lib/python3.8/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/home/xxxx/.local/lib/python3.8/site-packages/hdbscan/tests/test_hdbscan.py", line 654, in test_hdbscan_is_sklearn_estimator
check_estimator(HDBSCAN)
File "/home/xxxx/.local/lib/python3.8/site-packages/sklearn/utils/estimator_checks.py", line 616, in check_estimator
raise TypeError(msg)
TypeError: Passing a class was deprecated in version 0.23 and isn't supported anymore from 0.24.Please pass an instance instead.

======================================================================
ERROR: hdbscan.tests.test_prediction_utils.test_safe_always_positive_division

Traceback (most recent call last):
File "/home/xxxx/.local/lib/python3.8/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
TypeError: test_safe_always_positive_division() missing 1 required positional argument: 'denominator'

======================================================================
ERROR: hdbscan.tests.test_rsl.test_rsl_is_sklearn_estimator

Traceback (most recent call last):
File "/home/xxxx/.local/lib/python3.8/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/home/xxxx/.local/lib/python3.8/site-packages/hdbscan/tests/test_rsl.py", line 197, in test_rsl_is_sklearn_estimator
check_estimator(RobustSingleLinkage)
File "/home/xxxx/.local/lib/python3.8/site-packages/sklearn/utils/estimator_checks.py", line 616, in check_estimator
raise TypeError(msg)
TypeError: Passing a class was deprecated in version 0.23 and isn't supported anymore from 0.24.Please pass an instance instead.

---

Ran 79 tests in 13.621s

FAILED (errors=5)

Thanks.
Saverio

[xavgit]

The previous errors with Ubuntu 20.04.

With Ubuntu 22.04 instead:

python3 -m nose -s hdbscan
Traceback (most recent call last):
File "/usr/lib/python3.10/runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/usr/lib/python3.10/runpy.py", line 86, in _run_code
exec(code, run_globals)
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/main.py", line 8, in
run_exit()
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/core.py", line 118, in init
unittest.TestProgram.init(
File "/usr/lib/python3.10/unittest/main.py", line 100, in init
self.parseArgs(argv)
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/core.py", line 179, in parseArgs
self.createTests()
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/core.py", line 193, in createTests
self.test = self.testLoader.loadTestsFromNames(self.testNames)
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/loader.py", line 481, in loadTestsFromNames
return unittest.TestLoader.loadTestsFromNames(self, names, module)
File "/usr/lib/python3.10/unittest/loader.py", line 220, in loadTestsFromNames
suites = [self.loadTestsFromName(name, module) for name in names]
File "/usr/lib/python3.10/unittest/loader.py", line 220, in
suites = [self.loadTestsFromName(name, module) for name in names]
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/loader.py", line 431, in loadTestsFromName
return self.loadTestsFromModule(
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/loader.py", line 354, in loadTestsFromModule
tests.extend(self.loadTestsFromDir(module_path))
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/loader.py", line 191, in loadTestsFromDir
yield self.loadTestsFromName(
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/loader.py", line 431, in loadTestsFromName
return self.loadTestsFromModule(
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/loader.py", line 354, in loadTestsFromModule
tests.extend(self.loadTestsFromDir(module_path))
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/loader.py", line 183, in loadTestsFromDir
yield self.loadTestsFromName(
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/loader.py", line 431, in loadTestsFromName
return self.loadTestsFromModule(
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/loader.py", line 359, in loadTestsFromModule
return self.suiteClass(ContextList(tests, context=module))
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/suite.py", line 428, in call
return self.makeSuite(tests, context, **kw)
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/suite.py", line 475, in makeSuite
suite = self.suiteClass(
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/suite.py", line 159, in init
super(ContextSuite, self).init(tests)
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/suite.py", line 53, in init
super(LazySuite, self).init()
File "/usr/lib/python3.10/unittest/suite.py", line 22, in init
self._tests = []
File "/home/xxxx/.local/lib/python3.10/site-packages/nose/suite.py", line 106, in _set_tests
if isinstance(tests, collections.Callable) and not is_suite:
AttributeError: module 'collections' has no attribute 'Callable'

Where I'm wrong?

Thanks.

Saverio