How do I fix the problems in pytest when i try to install domainator_esmologs?

nebiolabs / domainator

A flexible and modular software suite for domain-based gene neighborhood and protein search, extraction, and clustering.

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How do I fix the problems in pytest when i try to install domainator_esmologs? #15

Open Xiewentao17 opened 2 weeks ago

Xiewentao17 commented 2 weeks ago

FAILED test/test_build_ssn.py::test_build_ssn_4 - FileNotFoundError: [Errno 2] No such file or directory: 'test_out/FeSOD_dist.tsv_out.xgmml' FAILED test/test_color_genbank.py::test_color_genbank_databases_1 - FileNotFoundError: [Errno 2] No such file or directory: 'test_out/tmp_colored_genbank.gb' FAILED test/test_select_by_cds.py::test_select_by_cds_domain_expr_config_file - SystemExit: 2 FAILED test/test_select_by_contig.py::test_select_by_conting_domain_expression_config_file - SystemExit: 2 14da4304c3046e0e99088ec2f220093

seanrjohnson commented 2 weeks ago

Hi @Xiewentao17, the first two were bugs. I fixed those and pushed the fix.

The second two, I'm not sure, I can't reproduce those. Maybe something to do with the jsonargparse library?

Do you have more detailed error messages for that?

In any case, neither of those failed tests should affect the program function, I think, unless you are using config files.