toil 8.1.0b1__py3-none-any.whl → 9.0.0__py3-none-any.whl

toil/test/batchSystems/batch_system_plugin_test.py

@@ -26,6 +26,7 @@ from toil.batchSystems.registry import add_batch_system_factory
 from toil.common import Toil, addOptions
 from toil.job import JobDescription
 from toil.test import ToilTest
+from toil.lib.plugins import remove_plugin
 
 logger = logging.getLogger(__name__)
 
@@ -68,6 +69,11 @@ class FakeBatchSystem(BatchSystemCleanupSupport):
 
 
 class BatchSystemPluginTest(ToilTest):
+    def tearDown(self) -> None:
+        # Restore plugin state
+        remove_plugin("batch_system", "fake")
+        super().tearDown()
+
     def test_batchsystem_plugin_installable(self):
         """
         Test that installing a batch system plugin works.
@@ -76,6 +82,7 @@ class BatchSystemPluginTest(ToilTest):
 
         def fake_batch_system_factory() -> type[AbstractBatchSystem]:
             return FakeBatchSystem
+        
 
         add_batch_system_factory("fake", fake_batch_system_factory)
 

toil/test/batchSystems/test_slurm.py

@@ -619,3 +619,30 @@ class SlurmTest(ToilTest):
         command = self.worker.prepareSbatch(1, 100, 5, "job5", None, None)
         assert "--export=ALL" not in command
 
+    def test_option_detector(self):
+        detector = toil.batchSystems.slurm.option_detector("foobar", "f")
+
+        self.assertTrue(detector("--foobar"))
+        self.assertTrue(detector("--foobar=1"))
+        self.assertTrue(detector("-f"))
+        self.assertFalse(detector("-F"))
+        self.assertFalse(detector("--foo-bar"))
+        self.assertFalse(detector("foobar"))
+        self.assertFalse(detector("-foobar"))
+        self.assertFalse(detector("f"))
+
+    def test_any_option_detector(self):
+        detector = toil.batchSystems.slurm.any_option_detector([])
+        self.assertFalse(detector("--anything"))
+
+        detector = toil.batchSystems.slurm.any_option_detector([("foobar", "f"), "many-bothans", ("bazz-only", "B")])
+
+        self.assertTrue(detector("--foobar"))
+        self.assertTrue(detector("-f"))
+        self.assertTrue(detector("--many-bothans=False"))
+        self.assertTrue(detector("--bazz-only"))
+        self.assertTrue(detector("-B"))
+        self.assertFalse(detector("--no-bazz"))
+        self.assertFalse(detector("--foo-bar=--bazz-only"))
+       
+

toil/test/conftest.py

@@ -0,0 +1,7 @@
+import pytest
+
+
+@pytest.fixture(scope="class")
+def rootpath(request: pytest.FixtureRequest) -> None:
+    """Records the rootpath at the class level, for use on a unittest.TestCase."""
+    request.cls._rootpath = request.config._rootpath

toil/test/cwl/2.fasta

@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt
+tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac
+cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg
+aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg
+gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt
+tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac
+ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt
+ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt
+tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa
+aacaattcta atggtcaaaa a

toil/test/cwl/2.fastq

@@ -0,0 +1,12 @@
+@EAS54_6_R1_2_1_413_324
+CCCTTCTTGTCTTCAGCGTTTCTCC
++
+;;3;;;;;;;;;;;;7;;;;;;;88
+@EAS54_6_R1_2_1_540_792
+TTGGCAGGCCAAGGCCGATGGATCA
++
+;;;;;;;;;;;7;;;;;-;;;3;83
+@EAS54_6_R1_2_1_443_348
+GTTGCTTCTGGCGTGGGTGGGGGGG
++EAS54_6_R1_2_1_443_348
+;;;;;;;;;;;9;7;;.7;393333

toil/test/cwl/conftest.py

@@ -34,7 +34,7 @@ def pytest_cwl_execute_test(
         processfile: str,
         jobfile: Optional[str]
 ) -> Tuple[int, Optional[Dict[str, Any]]]:
-    """Use the CWL reference runner (cwltool) to execute tests."""
+    """Use Toil to execute CWL tests (equivalent to running toil-cwl-runner)."""
     from toil.cwl.cwltoil import main
 
     stdout = StringIO()