Fix test suite #796
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Fix test suite #796
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The `gilda` and `semsimian` modules are optional dependencies, but the tests that depend do not expect that they may not be present and error out if they cannot be imported. Since they are optional, their absence should not cause the test suite to fail, so this commit ensures that the corresponding tests are properly skipped if the optional modules are not found. closes INCATools#794
The `test_annotate_file` command may fail because the `annotate` command may emit some unexpected warnings on STDERR about invalid CURIEs, even if there are no errors and the expected output is normally produced on STDOUT. This commit amends the test so that it ignores any 'WARNING:' line in the STDERR stream produced by the `annotate` command. closes INCATools#795.
cmungall
approved these changes
Aug 17, 2024
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This PR fixes two issues with the test suite.
The first (#794) is that the test suite fails if
gildaand/orsemsimianare not installed in the environment, even though those modules are optional dependencies and as such not installed by a standardpoetry installcommand. This PR fixes that by detecting the absence of those modules and skipping the corresponding tests, instead of letting them fail.The second (#795) is that the
test_annotate_filefile may fail because of unexpected warnings emitted by theannotatecommand, even if the command runs normally and produces the expected output file. This PR fixes that by making the test ignore anyWARNINGline when checking the STDERR output of the command.(That second fix is based on the assumption that we don’t actually care about those warnings, as long as the command does what is expected of it. If that is not the case – if it is instead important to test that
annotatedoes not produce any warning, then obviously the proposed fix is wrong and we should instead figure out where those warnings are emitted to shut them off.)