pre-release CI fails

[Zethson]

Please make sure these conditions are met

• [x] I have checked that this issue has not already been reported.
• [x] I have confirmed this bug exists on the latest version of pertpy.
• [x] (optional) I have confirmed this bug exists on the main branch.

Report

FAILED tests/tools/_coda/test_sccoda.py::test_load - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_coda/test_sccoda.py::test_prepare - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_coda/test_sccoda.py::test_run_nuts - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_coda/test_sccoda.py::test_credible_effects - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_coda/test_sccoda.py::test_make_arviz - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_differential_gene_expression/test_compare_groups.py::test_unified_api_single_group[array-pairing-PyDESeq2] - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_differential_gene_expression/test_compare_groups.py::test_unified_api_single_group[array-None-PyDESeq2] - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_differential_gene_expression/test_compare_groups.py::test_unified_api_single_group[csr_matrix-pairing-PyDESeq2] - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_differential_gene_expression/test_compare_groups.py::test_unified_api_single_group[csr_matrix-None-PyDESeq2] - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_differential_gene_expression/test_compare_groups.py::test_unified_api_single_group[csc_matrix-pairing-PyDESeq2] - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_differential_gene_expression/test_compare_groups.py::test_unified_api_single_group[csc_matrix-None-PyDESeq2] - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_differential_gene_expression/test_compare_groups.py::test_unified_api_multiple_groups[array-PyDESeq2] - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_differential_gene_expression/test_compare_groups.py::test_unified_api_multiple_groups[csr_matrix-PyDESeq2] - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_differential_gene_expression/test_compare_groups.py::test_unified_api_multiple_groups[csc_matrix-PyDESeq2] - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_differential_gene_expression/test_edger.py::test_edger_complex - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_differential_gene_expression/test_pydeseq2.py::test_pydeseq2_simple - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_differential_gene_expression/test_pydeseq2.py::test_pydeseq2_complex - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_differential_gene_expression/test_pydeseq2.py::test_pydeseq2_formula - IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
FAILED tests/tools/_perturbation_space/test_discriminator_classifiers.py::test_mlp_classifier_space - ValueError: `shape` is inconsistent with `obs` (40 rows instead of 20)

Versions

[Zethson]

It seems to be the anndata pre-release. mudata and pydeseq2 need the fixes and releases.