[Debian-med-packaging] Bug#1074745: python-skbio: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.11 3.12" returned exit code 13
Lucas Nussbaum
lucas at debian.org
Tue Jul 2 14:20:41 BST 2024
Source: python-skbio
Version: 0.6.1-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20240702 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> echo No testing for the -doc package
> No testing for the -doc package
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_auto_test -O--buildsystem=pybuild -Npython-skbio-doc
> I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build; python3.11 -m pytest
> ============================= test session starts ==============================
> platform linux -- Python 3.11.9, pytest-8.2.2, pluggy-1.5.0
> rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build
> configfile: pyproject.toml
> collected 2761 items
>
> skbio/alignment/tests/test_pairwise.py ......................... [ 0%]
> skbio/alignment/tests/test_path.py ................. [ 1%]
> skbio/alignment/tests/test_ssw.py ........................... [ 2%]
> skbio/alignment/tests/test_tabular_msa.py .............................. [ 3%]
> ........................................................................ [ 6%]
> ........................................................................ [ 8%]
> ........................................................................ [ 11%]
> ........................................................................ [ 14%]
> ........................................................................ [ 16%]
> ........... [ 17%]
> skbio/diversity/alpha/tests/test_ace.py .. [ 17%]
> skbio/diversity/alpha/tests/test_base.py .....................F...... [ 18%]
> skbio/diversity/alpha/tests/test_chao1.py ... [ 18%]
> skbio/diversity/alpha/tests/test_gini.py .... [ 18%]
> skbio/diversity/alpha/tests/test_lladser.py ............ [ 18%]
> skbio/diversity/alpha/tests/test_pd.py ................ [ 19%]
> skbio/diversity/beta/tests/test_unifrac.py ............................ [ 20%]
> skbio/diversity/tests/test_block.py ........... [ 20%]
> skbio/diversity/tests/test_driver.py ................................... [ 22%]
> .. [ 22%]
> skbio/diversity/tests/test_util.py ................ [ 22%]
> skbio/embedding/tests/test_embedding.py ................... [ 23%]
> skbio/embedding/tests/test_protein.py .............. [ 23%]
> skbio/io/format/tests/test_base.py ................................ [ 25%]
> skbio/io/format/tests/test_binary_dm.py ......... [ 25%]
> skbio/io/format/tests/test_biom.py ... [ 25%]
> skbio/io/format/tests/test_blast6.py ........... [ 25%]
> skbio/io/format/tests/test_blast7.py .............. [ 26%]
> skbio/io/format/tests/test_clustal.py ............. [ 26%]
> skbio/io/format/tests/test_embed.py ........ [ 27%]
> skbio/io/format/tests/test_embl.py ............................... [ 28%]
> skbio/io/format/tests/test_emptyfile.py .. [ 28%]
> skbio/io/format/tests/test_fasta.py ................ [ 28%]
> skbio/io/format/tests/test_fastq.py ............... [ 29%]
> skbio/io/format/tests/test_genbank.py ..................... [ 30%]
> skbio/io/format/tests/test_gff3.py ........................ [ 31%]
> skbio/io/format/tests/test_lsmat.py ....... [ 31%]
> skbio/io/format/tests/test_newick.py ....... [ 31%]
> skbio/io/format/tests/test_ordination.py ..... [ 31%]
> skbio/io/format/tests/test_phylip.py ....... [ 32%]
> skbio/io/format/tests/test_qseq.py ...... [ 32%]
> skbio/io/format/tests/test_sample_metadata.py .... [ 32%]
> skbio/io/format/tests/test_sequence_feature_vocabulary.py .... [ 32%]
> skbio/io/format/tests/test_stockholm.py ................................ [ 33%]
> ........................................... [ 35%]
> skbio/io/format/tests/test_taxdump.py ...... [ 35%]
> skbio/io/tests/test_iosources.py .......... [ 35%]
> skbio/io/tests/test_registry.py ........................................ [ 37%]
> ...................................................... [ 39%]
> skbio/io/tests/test_util.py .......................................XXsss [ 40%]
> sssssssssssssssssssssssssss..................................XX......... [ 43%]
> .........................XX..................................XX......... [ 46%]
> .........................XX..... [ 47%]
> skbio/metadata/tests/test_enan.py ... [ 47%]
> skbio/metadata/tests/test_intersection.py ............... [ 47%]
> skbio/metadata/tests/test_interval.py .................................. [ 49%]
> ..................................... [ 50%]
> skbio/metadata/tests/test_io.py ........................................ [ 51%]
> .................................................................. [ 54%]
> skbio/metadata/tests/test_metadata.py .................................. [ 55%]
> .......................... [ 56%]
> skbio/metadata/tests/test_metadata_column.py ........................... [ 57%]
> .............................................. [ 59%]
> skbio/metadata/tests/test_missing.py ................ [ 59%]
> skbio/metadata/tests/test_mixin.py ..................................... [ 61%]
> ............................................................. [ 63%]
> skbio/sequence/tests/test_alphabet.py ..... [ 63%]
> skbio/sequence/tests/test_distance.py .......................... [ 64%]
> skbio/sequence/tests/test_dna.py ... [ 64%]
> skbio/sequence/tests/test_genetic_code.py .......................... [ 65%]
> skbio/sequence/tests/test_grammared_sequence.py ........................ [ 66%]
> ......................... [ 67%]
> skbio/sequence/tests/test_nucleotide_sequences.py ...................... [ 67%]
> ....... [ 68%]
> skbio/sequence/tests/test_protein.py ........... [ 68%]
> skbio/sequence/tests/test_rna.py ... [ 68%]
> skbio/sequence/tests/test_sequence.py .................................. [ 69%]
> ........................................................................ [ 72%]
> ........................................................................ [ 75%]
> ........................................................................ [ 77%]
> ............. [ 78%]
> skbio/sequence/tests/test_substitution.py ........ [ 78%]
> skbio/stats/distance/tests/test_anosim.py .... [ 78%]
> skbio/stats/distance/tests/test_base.py ................................ [ 79%]
> ............................................................... [ 82%]
> skbio/stats/distance/tests/test_bioenv.py ................. [ 82%]
> skbio/stats/distance/tests/test_mantel.py .............................. [ 83%]
> .............. [ 84%]
> skbio/stats/distance/tests/test_permanova.py ..... [ 84%]
> skbio/stats/distance/tests/test_permdisp.py .............. [ 85%]
> skbio/stats/evolve/tests/test_hommola.py ............ [ 85%]
> skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py . [ 85%]
> ..... [ 85%]
> skbio/stats/ordination/tests/test_correspondence_analysis.py ........ [ 85%]
> skbio/stats/ordination/tests/test_ordination_results.py ............ [ 86%]
> skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [ 86%]
> ....... [ 86%]
> skbio/stats/ordination/tests/test_redundancy_analysis.py .... [ 86%]
> skbio/stats/ordination/tests/test_util.py .......... [ 87%]
> skbio/stats/tests/test_composition.py .................................. [ 88%]
> ................................................. [ 90%]
> skbio/stats/tests/test_gradient.py .......................... [ 91%]
> skbio/stats/tests/test_misc.py ... [ 91%]
> skbio/stats/tests/test_power.py ........................................ [ 92%]
> ... [ 92%]
> skbio/stats/tests/test_subsample.py ............ [ 93%]
> skbio/table/tests/test_base.py . [ 93%]
> skbio/tests/test_base.py ..... [ 93%]
> skbio/tests/test_workflow.py ................. [ 94%]
> skbio/tree/tests/test_majority_rule.py ...... [ 94%]
> skbio/tree/tests/test_nj.py ........... [ 94%]
> skbio/tree/tests/test_tree.py .......................................... [ 96%]
> ................................................... [ 98%]
> skbio/util/tests/test_decorator.py ........ [ 98%]
> skbio/util/tests/test_misc.py .................... [ 99%]
> skbio/util/tests/test_plotting.py ...... [ 99%]
> skbio/util/tests/test_testing.py ............... [100%]
>
> =================================== FAILURES ===================================
> ____________________________ BaseTests.test_shannon ____________________________
>
> self = <skbio.diversity.alpha.tests.test_base.BaseTests testMethod=test_shannon>
>
> def test_shannon(self):
> self.assertAlmostEqual(shannon([5, 5]), 0.693147181)
> self.assertEqual(shannon([5, 5], base=2), 1)
> self.assertAlmostEqual(shannon([5, 5], base=10), 0.301029996)
>
> # taxa with 0 counts are excluded from calculation
> self.assertAlmostEqual(shannon([1, 2, 3, 4]), 1.279854226)
> self.assertAlmostEqual(shannon([0, 1, 2, 3, 4]), 1.279854226)
>
> # Shannon index of a single-taxon community is always 0
> self.assertEqual(shannon(np.array([5])), 0)
>
> # Shannon index cannot be calculated for an empty community
> self.assertTrue(np.isnan(shannon([0, 0])))
>
> # NaN still holds if input is empty (instead of 0's), this behavior is
> # different from scipy.stats.entropy, which would return 0.0.
> self.assertTrue(np.isnan(shannon([])))
>
> # Exponential of Shannon index
> self.assertAlmostEqual(shannon([1, 2, 3, 4], exp=True), 3.596115467)
>
> # Equally abundant taxa, exp(H) = # taxa
> > self.assertEqual(shannon([5, 5, 5], exp=True), 3.0)
> E AssertionError: 3.000000000000001 != 3.0
>
> skbio/diversity/alpha/tests/test_base.py:319: AssertionError
> =============================== warnings summary ===============================
> skbio/alignment/tests/test_pairwise.py::PairwiseAlignmentTests::test_compute_score_and_traceback_matrices
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_warning.py:56: DeprecationWarning: make_identity_substitution_matrix is deprecated as of 0.4.0. It has been replaced by the SubstitutionMatrix class. Additional details at https://github.com/scikit-bio/scikit-bio/pull/1913.
> warn(
>
> skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_warning.py:56: DeprecationWarning: local_pairwise_align_ssw is deprecated as of 0.5.8. It will be removed in favor of more general purpose and performant aligners. Additional details at https://github.com/scikit-bio/scikit-bio/issues/1814.
> warn(
>
> skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/alignment/_tabular_msa.py:1648: RuntimeWarning: invalid value encountered in divide
> gap_freqs /= length
>
> skbio/diversity/tests/test_block.py::ParallelBetaDiversity::test_block_beta_diversity
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_warning.py:56: DeprecationWarning: partial_beta_diversity is deprecated as of 0.5.0. The return type is unstable. Developer caution is advised. The resulting DistanceMatrix object will include zeros when distance has not been calculated, and therefore can be misleading.
> warn(
>
> skbio/metadata/tests/test_io.py::TestSave::test_numeric_metadata_column_insdc_missing
> skbio/metadata/tests/test_metadata_column.py::TestToSeries::test_encode_missing_true
> skbio/metadata/tests/test_metadata_column.py::TestToDataframe::test_encode_missing_true
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/metadata/_metadata.py:1102: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['missing']' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
> series[missing.index] = missing
>
> skbio/metadata/tests/test_missing.py::TestISNDC::test_roundtrip_all_missing_object
> skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_all_missing_object
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/metadata/tests/test_missing.py:53: FutureWarning: Mismatched null-like values nan and None found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
> pdt.assert_series_equal(missing, series.astype(object))
>
> skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_bool
> skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_string
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/metadata/tests/test_missing.py:31: FutureWarning: Mismatched null-like values nan and None found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
> pdt.assert_series_equal(missing, series[1:].astype(object))
>
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/_grammared_sequence.py:639: DeprecationWarning: has_nondegenerates is deprecated as of 0.5.0
> warn("has_nondegenerates is deprecated as of 0.5.0", DeprecationWarning)
>
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars
> skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/_grammared_sequence.py:313: DeprecationWarning: nondegenerate_chars is deprecated as of 0.5.0
> warn("nondegenerate_chars is deprecated as of 0.5.0", DeprecationWarning)
>
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/_grammared_sequence.py:572: DeprecationWarning: nondenengerates is deprecated as of 0.5.0.
> warn("nondenengerates is deprecated as of 0.5.0.", DeprecationWarning)
>
> skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/_sequence.py:1824: RuntimeWarning: invalid value encountered in divide
> obs_counts = obs_counts / len(self)
>
> skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/_mantel.py:364: ConstantInputWarning: All values in data are exactly equal; results may not be reliable.
> warnings.warn(ConstantInputWarning())
>
> skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/_mantel.py:483: ConstantInputWarning: All values in data are exactly equal; results may not be reliable.
> warnings.warn(ConstantInputWarning())
>
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.006573677549550485 and the largest is 0.17668321589384078.
> warn(
>
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -13.54184654426961 and the largest is 16.5872013747859.
> warn(
>
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -15.629533932395208 and the largest is 20.90315427793891.
> warn(
>
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:190: RuntimeWarning: invalid value encountered in divide
> proportion_explained = eigvals / sum_eigenvalues
>
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/_permdisp.py:304: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite
> stat, _ = f_oneway(*groups)
>
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.007758325147780521 and the largest is 2.7077929489469237.
> warn(
>
> skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape
> /usr/lib/python3.11/unittest/case.py:678: DeprecationWarning: It is deprecated to return a value that is not None from a test case (<bound method TestRDAErrors.test_shape of <skbio.stats.ordination.tests.test_redundancy_analysis.TestRDAErrors testMethod=test_shape>>)
> return self.run(*args, **kwds)
>
> skbio/stats/tests/test_composition.py::CompositionTests::test_multiplicative_replacement
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_warning.py:60: UserWarning: multiplicative_replacement is deprecated as of 0.6.0.
> warn(f"{func.__name__} is deprecated as of {ver}.")
>
> skbio/stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test
> /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:531: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable.
> res = hypotest_fun_out(*samples, **kwds)
>
> skbio/stats/tests/test_composition.py::AncomTests::test_ancom_multiple_comparisons_deprecated
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_warning.py:60: UserWarning: ancom is deprecated as of 0.6.0.
> warn(f"{func.__name__} is deprecated as of {ver}.")
>
> skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/composition.py:1654: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite
> return test(*[x[cats == k] for k in cs])
>
> skbio/stats/tests/test_composition.py::VLRTests::test_pairwise_vlr
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/composition.py:945: RuntimeWarning: divide by zero encountered in log
> X_log = np.log(mat)
>
> skbio/stats/tests/test_composition.py::VLRTests::test_pairwise_vlr
> /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2742: RuntimeWarning: invalid value encountered in subtract
> X -= avg[:, None]
>
> skbio/stats/tests/test_composition.py::VLRTests::test_vlr
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/composition.py:829: RuntimeWarning: divide by zero encountered in log
> x = np.log(x)
>
> skbio/stats/tests/test_composition.py::VLRTests::test_vlr
> /usr/lib/python3/dist-packages/numpy/core/_methods.py:173: RuntimeWarning: invalid value encountered in subtract
> x = asanyarray(arr - arrmean)
>
> skbio/stats/tests/test_gradient.py::GradientTests::test_weight_by_vector
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/gradient.py:167: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '6.357142857142857' has dtype incompatible with int64, please explicitly cast to a compatible dtype first.
> trajectories.loc[idx] = (
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> FAILED skbio/diversity/alpha/tests/test_base.py::BaseTests::test_shannon - As...
> = 1 failed, 2720 passed, 30 skipped, 10 xpassed, 56 warnings in 96.32s (0:01:36) =
> E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build; python3.11 -m pytest
> I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build; python3.12 -m pytest
> ============================= test session starts ==============================
> platform linux -- Python 3.12.4, pytest-8.2.2, pluggy-1.5.0
> rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build
> configfile: pyproject.toml
> collected 2761 items
>
> skbio/alignment/tests/test_pairwise.py ......................... [ 0%]
> skbio/alignment/tests/test_path.py ................. [ 1%]
> skbio/alignment/tests/test_ssw.py ........................... [ 2%]
> skbio/alignment/tests/test_tabular_msa.py .............................. [ 3%]
> ........................................................................ [ 6%]
> ........................................................................ [ 8%]
> ........................................................................ [ 11%]
> ........................................................................ [ 14%]
> ........................................................................ [ 16%]
> ........... [ 17%]
> skbio/diversity/alpha/tests/test_ace.py .. [ 17%]
> skbio/diversity/alpha/tests/test_base.py .....................F...... [ 18%]
> skbio/diversity/alpha/tests/test_chao1.py ... [ 18%]
> skbio/diversity/alpha/tests/test_gini.py .... [ 18%]
> skbio/diversity/alpha/tests/test_lladser.py ............ [ 18%]
> skbio/diversity/alpha/tests/test_pd.py ................ [ 19%]
> skbio/diversity/beta/tests/test_unifrac.py ............................ [ 20%]
> skbio/diversity/tests/test_block.py ........... [ 20%]
> skbio/diversity/tests/test_driver.py ................................... [ 22%]
> .. [ 22%]
> skbio/diversity/tests/test_util.py ................ [ 22%]
> skbio/embedding/tests/test_embedding.py ................... [ 23%]
> skbio/embedding/tests/test_protein.py .............. [ 23%]
> skbio/io/format/tests/test_base.py ................................ [ 25%]
> skbio/io/format/tests/test_binary_dm.py ......... [ 25%]
> skbio/io/format/tests/test_biom.py ... [ 25%]
> skbio/io/format/tests/test_blast6.py ........... [ 25%]
> skbio/io/format/tests/test_blast7.py .............. [ 26%]
> skbio/io/format/tests/test_clustal.py ............. [ 26%]
> skbio/io/format/tests/test_embed.py ........ [ 27%]
> skbio/io/format/tests/test_embl.py ............................... [ 28%]
> skbio/io/format/tests/test_emptyfile.py .. [ 28%]
> skbio/io/format/tests/test_fasta.py ................ [ 28%]
> skbio/io/format/tests/test_fastq.py ............... [ 29%]
> skbio/io/format/tests/test_genbank.py ..................... [ 30%]
> skbio/io/format/tests/test_gff3.py ........................ [ 31%]
> skbio/io/format/tests/test_lsmat.py ....... [ 31%]
> skbio/io/format/tests/test_newick.py ....... [ 31%]
> skbio/io/format/tests/test_ordination.py ..... [ 31%]
> skbio/io/format/tests/test_phylip.py ....... [ 32%]
> skbio/io/format/tests/test_qseq.py ...... [ 32%]
> skbio/io/format/tests/test_sample_metadata.py .... [ 32%]
> skbio/io/format/tests/test_sequence_feature_vocabulary.py .... [ 32%]
> skbio/io/format/tests/test_stockholm.py ................................ [ 33%]
> ........................................... [ 35%]
> skbio/io/format/tests/test_taxdump.py ...... [ 35%]
> skbio/io/tests/test_iosources.py .......... [ 35%]
> skbio/io/tests/test_registry.py ........................................ [ 37%]
> ...................................................... [ 39%]
> skbio/io/tests/test_util.py .......................................XXsss [ 40%]
> sssssssssssssssssssssssssss..................................XX......... [ 43%]
> .........................XX..................................XX......... [ 46%]
> .........................XX..... [ 47%]
> skbio/metadata/tests/test_enan.py ... [ 47%]
> skbio/metadata/tests/test_intersection.py ............... [ 47%]
> skbio/metadata/tests/test_interval.py .................................. [ 49%]
> ..................................... [ 50%]
> skbio/metadata/tests/test_io.py ........................................ [ 51%]
> .................................................................. [ 54%]
> skbio/metadata/tests/test_metadata.py .................................. [ 55%]
> .......................... [ 56%]
> skbio/metadata/tests/test_metadata_column.py ........................... [ 57%]
> .............................................. [ 59%]
> skbio/metadata/tests/test_missing.py ................ [ 59%]
> skbio/metadata/tests/test_mixin.py ..................................... [ 61%]
> ............................................................. [ 63%]
> skbio/sequence/tests/test_alphabet.py ..... [ 63%]
> skbio/sequence/tests/test_distance.py .......................... [ 64%]
> skbio/sequence/tests/test_dna.py ... [ 64%]
> skbio/sequence/tests/test_genetic_code.py .......................... [ 65%]
> skbio/sequence/tests/test_grammared_sequence.py ........................ [ 66%]
> ......................... [ 67%]
> skbio/sequence/tests/test_nucleotide_sequences.py ...................... [ 67%]
> ....... [ 68%]
> skbio/sequence/tests/test_protein.py ........... [ 68%]
> skbio/sequence/tests/test_rna.py ... [ 68%]
> skbio/sequence/tests/test_sequence.py .................................. [ 69%]
> ........................................................................ [ 72%]
> ........................................................................ [ 75%]
> ........................................................................ [ 77%]
> ............. [ 78%]
> skbio/sequence/tests/test_substitution.py ........ [ 78%]
> skbio/stats/distance/tests/test_anosim.py .... [ 78%]
> skbio/stats/distance/tests/test_base.py ................................ [ 79%]
> ............................................................... [ 82%]
> skbio/stats/distance/tests/test_bioenv.py ................. [ 82%]
> skbio/stats/distance/tests/test_mantel.py .............................. [ 83%]
> .............. [ 84%]
> skbio/stats/distance/tests/test_permanova.py ..... [ 84%]
> skbio/stats/distance/tests/test_permdisp.py .............. [ 85%]
> skbio/stats/evolve/tests/test_hommola.py ............ [ 85%]
> skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py . [ 85%]
> ..... [ 85%]
> skbio/stats/ordination/tests/test_correspondence_analysis.py ........ [ 85%]
> skbio/stats/ordination/tests/test_ordination_results.py ............ [ 86%]
> skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [ 86%]
> ....... [ 86%]
> skbio/stats/ordination/tests/test_redundancy_analysis.py .... [ 86%]
> skbio/stats/ordination/tests/test_util.py .......... [ 87%]
> skbio/stats/tests/test_composition.py .................................. [ 88%]
> ................................................. [ 90%]
> skbio/stats/tests/test_gradient.py .......................... [ 91%]
> skbio/stats/tests/test_misc.py ... [ 91%]
> skbio/stats/tests/test_power.py ........................................ [ 92%]
> ... [ 92%]
> skbio/stats/tests/test_subsample.py ............ [ 93%]
> skbio/table/tests/test_base.py . [ 93%]
> skbio/tests/test_base.py ..... [ 93%]
> skbio/tests/test_workflow.py ................. [ 94%]
> skbio/tree/tests/test_majority_rule.py ...... [ 94%]
> skbio/tree/tests/test_nj.py ........... [ 94%]
> skbio/tree/tests/test_tree.py .......................................... [ 96%]
> ................................................... [ 98%]
> skbio/util/tests/test_decorator.py ........ [ 98%]
> skbio/util/tests/test_misc.py .................... [ 99%]
> skbio/util/tests/test_plotting.py ...... [ 99%]
> skbio/util/tests/test_testing.py ............... [100%]
>
> =================================== FAILURES ===================================
> ____________________________ BaseTests.test_shannon ____________________________
>
> self = <skbio.diversity.alpha.tests.test_base.BaseTests testMethod=test_shannon>
>
> def test_shannon(self):
> self.assertAlmostEqual(shannon([5, 5]), 0.693147181)
> self.assertEqual(shannon([5, 5], base=2), 1)
> self.assertAlmostEqual(shannon([5, 5], base=10), 0.301029996)
>
> # taxa with 0 counts are excluded from calculation
> self.assertAlmostEqual(shannon([1, 2, 3, 4]), 1.279854226)
> self.assertAlmostEqual(shannon([0, 1, 2, 3, 4]), 1.279854226)
>
> # Shannon index of a single-taxon community is always 0
> self.assertEqual(shannon(np.array([5])), 0)
>
> # Shannon index cannot be calculated for an empty community
> self.assertTrue(np.isnan(shannon([0, 0])))
>
> # NaN still holds if input is empty (instead of 0's), this behavior is
> # different from scipy.stats.entropy, which would return 0.0.
> self.assertTrue(np.isnan(shannon([])))
>
> # Exponential of Shannon index
> self.assertAlmostEqual(shannon([1, 2, 3, 4], exp=True), 3.596115467)
>
> # Equally abundant taxa, exp(H) = # taxa
> > self.assertEqual(shannon([5, 5, 5], exp=True), 3.0)
> E AssertionError: 3.000000000000001 != 3.0
>
> skbio/diversity/alpha/tests/test_base.py:319: AssertionError
> =============================== warnings summary ===============================
> skbio/alignment/tests/test_pairwise.py::PairwiseAlignmentTests::test_compute_score_and_traceback_matrices
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/util/_warning.py:56: DeprecationWarning: make_identity_substitution_matrix is deprecated as of 0.4.0. It has been replaced by the SubstitutionMatrix class. Additional details at https://github.com/scikit-bio/scikit-bio/pull/1913.
> warn(
>
> skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/util/_warning.py:56: DeprecationWarning: local_pairwise_align_ssw is deprecated as of 0.5.8. It will be removed in favor of more general purpose and performant aligners. Additional details at https://github.com/scikit-bio/scikit-bio/issues/1814.
> warn(
>
> skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/alignment/_tabular_msa.py:1648: RuntimeWarning: invalid value encountered in divide
> gap_freqs /= length
>
> skbio/diversity/tests/test_block.py::ParallelBetaDiversity::test_block_beta_diversity
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/util/_warning.py:56: DeprecationWarning: partial_beta_diversity is deprecated as of 0.5.0. The return type is unstable. Developer caution is advised. The resulting DistanceMatrix object will include zeros when distance has not been calculated, and therefore can be misleading.
> warn(
>
> skbio/metadata/tests/test_io.py::TestSave::test_numeric_metadata_column_insdc_missing
> skbio/metadata/tests/test_metadata_column.py::TestToSeries::test_encode_missing_true
> skbio/metadata/tests/test_metadata_column.py::TestToDataframe::test_encode_missing_true
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/metadata/_metadata.py:1102: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['missing']' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
> series[missing.index] = missing
>
> skbio/metadata/tests/test_missing.py::TestISNDC::test_roundtrip_all_missing_object
> skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_all_missing_object
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/metadata/tests/test_missing.py:53: FutureWarning: Mismatched null-like values nan and None found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
> pdt.assert_series_equal(missing, series.astype(object))
>
> skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_bool
> skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_string
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/metadata/tests/test_missing.py:31: FutureWarning: Mismatched null-like values nan and None found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
> pdt.assert_series_equal(missing, series[1:].astype(object))
>
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/sequence/_grammared_sequence.py:639: DeprecationWarning: has_nondegenerates is deprecated as of 0.5.0
> warn("has_nondegenerates is deprecated as of 0.5.0", DeprecationWarning)
>
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars
> skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/sequence/_grammared_sequence.py:313: DeprecationWarning: nondegenerate_chars is deprecated as of 0.5.0
> warn("nondegenerate_chars is deprecated as of 0.5.0", DeprecationWarning)
>
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/sequence/_grammared_sequence.py:572: DeprecationWarning: nondenengerates is deprecated as of 0.5.0.
> warn("nondenengerates is deprecated as of 0.5.0.", DeprecationWarning)
>
> skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/sequence/_sequence.py:1824: RuntimeWarning: invalid value encountered in divide
> obs_counts = obs_counts / len(self)
>
> skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/distance/_mantel.py:364: ConstantInputWarning: All values in data are exactly equal; results may not be reliable.
> warnings.warn(ConstantInputWarning())
>
> skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/distance/_mantel.py:483: ConstantInputWarning: All values in data are exactly equal; results may not be reliable.
> warnings.warn(ConstantInputWarning())
>
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.006573677549550485 and the largest is 0.17668321589384078.
> warn(
>
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -13.54184654426961 and the largest is 16.5872013747859.
> warn(
>
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -15.629533932395208 and the largest is 20.90315427793891.
> warn(
>
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:190: RuntimeWarning: invalid value encountered in divide
> proportion_explained = eigvals / sum_eigenvalues
>
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/distance/_permdisp.py:304: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite
> stat, _ = f_oneway(*groups)
>
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results
> skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.007758325147780521 and the largest is 2.7077929489469237.
> warn(
>
> skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape
> /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (<bound method TestRDAErrors.test_shape of <skbio.stats.ordination.tests.test_redundancy_analysis.TestRDAErrors testMethod=test_shape>>)
> return self.run(*args, **kwds)
>
> skbio/stats/tests/test_composition.py::CompositionTests::test_multiplicative_replacement
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/util/_warning.py:60: UserWarning: multiplicative_replacement is deprecated as of 0.6.0.
> warn(f"{func.__name__} is deprecated as of {ver}.")
>
> skbio/stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test
> /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:531: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable.
> res = hypotest_fun_out(*samples, **kwds)
>
> skbio/stats/tests/test_composition.py::AncomTests::test_ancom_multiple_comparisons_deprecated
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/util/_warning.py:60: UserWarning: ancom is deprecated as of 0.6.0.
> warn(f"{func.__name__} is deprecated as of {ver}.")
>
> skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/composition.py:1654: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite
> return test(*[x[cats == k] for k in cs])
>
> skbio/stats/tests/test_composition.py::VLRTests::test_pairwise_vlr
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/composition.py:945: RuntimeWarning: divide by zero encountered in log
> X_log = np.log(mat)
>
> skbio/stats/tests/test_composition.py::VLRTests::test_pairwise_vlr
> /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2742: RuntimeWarning: invalid value encountered in subtract
> X -= avg[:, None]
>
> skbio/stats/tests/test_composition.py::VLRTests::test_vlr
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/composition.py:829: RuntimeWarning: divide by zero encountered in log
> x = np.log(x)
>
> skbio/stats/tests/test_composition.py::VLRTests::test_vlr
> /usr/lib/python3/dist-packages/numpy/core/_methods.py:173: RuntimeWarning: invalid value encountered in subtract
> x = asanyarray(arr - arrmean)
>
> skbio/stats/tests/test_gradient.py::GradientTests::test_weight_by_vector
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/gradient.py:167: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '6.357142857142857' has dtype incompatible with int64, please explicitly cast to a compatible dtype first.
> trajectories.loc[idx] = (
>
> skbio/util/tests/test_plotting.py::TestPlottableMixin::test_figure_data
> skbio/util/tests/test_plotting.py::TestPlottableMixin::test_repr_svg
> skbio/util/tests/test_plotting.py::TestPlottableMixin::test_svg
> /usr/lib/python3/dist-packages/matplotlib/backends/backend_svg.py:413: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC).
> date = datetime.datetime.utcfromtimestamp(int(date))
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> FAILED skbio/diversity/alpha/tests/test_base.py::BaseTests::test_shannon - As...
> = 1 failed, 2720 passed, 30 skipped, 10 xpassed, 59 warnings in 90.16s (0:01:30) =
> E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build; python3.12 -m pytest
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.11 3.12" returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2024/07/02/python-skbio_0.6.1-2_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240702;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240702&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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