Fix test suite (#796)

* Skip tests requiring optional modules when they are absent.

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 #794

* Prevent spurious warnings from causing test failure.

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 #795.

tests/test_cli.py

@@ -1522,7 +1522,7 @@ def test_annotate_file(self):
             ],
         )
         print("STDERR", result.stdout)
-        err = result.stderr
+        err = "\n".join([line for line in result.stderr.split("\n") if not line.startswith("WARNING")])
         self.assertEqual("", err)
         self.assertEqual(0, result.exit_code)
         with open(outfile) as stream:

tests/test_implementations/test_semsimian_implementation.py

@@ -1,6 +1,7 @@
 import os
 import timeit
 import unittest
+from importlib.util import find_spec
 
 from linkml_runtime.dumpers import yaml_dumper
 
@@ -31,6 +32,7 @@
 
 
 @unittest.skipIf(os.name == "nt", "DB path loading inconsistent on Windows")
+@unittest.skipIf(find_spec("semsimian") is None, "Semsimian not available")
 class TestSemSimianImplementation(unittest.TestCase):
     """Implementation tests for Rust-based semantic similarity."""
 

tests/test_selector.py

@@ -6,8 +6,13 @@
 import unittest
 from pathlib import Path
 
-from gilda.grounder import Grounder
-from gilda.term import Term
+try:
+    from gilda.grounder import Grounder
+    from gilda.term import Term
+
+    have_gilda = True
+except ImportError:
+    have_gilda = False
 
 from oaklib.datamodels.text_annotator import TextAnnotationConfiguration
 from oaklib.implementations.gilda import GildaImplementation
@@ -23,6 +28,7 @@
 from tests import INPUT_DIR
 
 
+@unittest.skipIf(not have_gilda, "Gilda not available")
 class TestResource(unittest.TestCase):
     def test_from_descriptor(self):
         # no scheme