Remove .config references on the Toil object and isolate options tests

DataBiosphere · Feb 5, 2025 · 0905e03 · 0905e03
1 parent 9824495
commit 0905e03
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Showing 3 changed files with 12 additions and 7 deletions.
diff --git a/src/toil/test/options/options.py b/src/toil/test/options/options.py
@@ -1,3 +1,5 @@
+import os
+
 from configargparse import ArgParser
 
 from toil.common import Toil, addOptions
@@ -14,29 +16,32 @@ def test_default_caching_slurm(self):
         Test to ensure that caching will be set to false when running on Slurm
         :return:
         """
+        job_store = os.path.join(self._createTempDir(), "tree")
         parser = ArgParser()
         addOptions(parser, jobstore_as_flag=True, wdl=False, cwl=False)
-        test_args = ["--jobstore=example-jobstore", "--batchSystem=slurm"]
+        test_args = ["--jobstore", job_store, "--batchSystem=slurm"]
         options = parser.parse_args(test_args)
         with Toil(options) as toil:
-            caching_value = toil.config.caching
+            caching_value = toil._config.caching
         self.assertEqual(caching_value, False)
 
     def test_caching_option_priority(self):
         """
         Test to ensure that the --caching option takes priority over the default_caching() return value
         :return:
         """
+        job_store = os.path.join(self._createTempDir(), "tree")
         parser = ArgParser()
         addOptions(parser, jobstore_as_flag=True, wdl=False, cwl=False)
         # the kubernetes batchsystem (and I think all batchsystems including singlemachine) return False
         # for default_caching
         test_args = [
-            "--jobstore=example-jobstore",
+            "--jobstore",
+            job_store,
             "--batchSystem=kubernetes",
             "--caching=True",
         ]
         options = parser.parse_args(test_args)
         with Toil(options) as toil:
-            caching_value = toil.config.caching
+            caching_value = toil._config.caching
         self.assertEqual(caching_value, True)
diff --git a/src/toil/test/provisioners/aws/awsProvisionerTest.py b/src/toil/test/provisioners/aws/awsProvisionerTest.py
@@ -661,7 +661,7 @@ def job(job, disk="10M", cores=1, memory="10M", preemptible=True):
             if __name__ == "__main__":
                 options = Job.Runner.getDefaultArgumentParser().parse_args()
                 with Toil(options) as toil:
-                    if toil.config.restart:
+                    if options.restart:
                         toil.restart()
                     else:
                         toil.start(Job.wrapJobFn(job))

diff --git a/src/toil/test/src/autoDeploymentTest.py b/src/toil/test/src/autoDeploymentTest.py
@@ -66,7 +66,7 @@ def job(job, disk="10M", cores=1, memory="10M"):
                 if __name__ == "__main__":
                     options = Job.Runner.getDefaultArgumentParser().parse_args()
                     with Toil(options) as toil:
-                        if toil.config.restart:
+                        if options.restart:
                             toil.restart()
                         else:
                             toil.start(Job.wrapJobFn(job))
@@ -139,7 +139,7 @@ def job(job, disk="10M", cores=1, memory="10M"):
                 if __name__ == "__main__":
                     options = Job.Runner.getDefaultArgumentParser().parse_args()
                     with Toil(options) as toil:
-                        if toil.config.restart:
+                        if options.restart:
                             toil.restart()
                         else:
                             toil.start(Job.wrapJobFn(job))