Remove remains of Travis. (DataBiosphere#3976)

.gitlab-ci.yml

@@ -76,9 +76,6 @@ wdl_dependency_is_stand_alone:
     - virtualenv -p ${MAIN_PYTHON_PKG} venv && . venv/bin/activate && make prepare && make develop extras=[wdl]
     - make test tests=src/toil/test/wdl/toilwdlTest.py::ToilWdlIntegrationTest::testMD5sum
 
-# Tests that used to be on Travis
-# The Makefile sets "TRAVIS=true", which is now a misnomer, but we don't need
-# to also do it here.
 quick_test_offline:
   stage: basic_tests
   script:

Makefile

@@ -118,25 +118,21 @@ clean_sdist:
 	- rm -rf dist
 	- rm src/toil/version.py
 
-# We always claim to be Travis, so that local test runs will not skip Travis tests.
 # Setting SET_OWNER_TAG will tag cloud resources so that UCSC's cloud murder bot won't kill them.
 test: check_venv check_build_reqs
-	TRAVIS=true TOIL_OWNER_TAG="shared" \
+	TOIL_OWNER_TAG="shared" \
 	    python -m pytest --durations=0 --log-level DEBUG --log-cli-level INFO -r s $(cov) $(tests)
 
 
 # This target will skip building docker and all docker based tests
-# these are our travis tests; rename?
 test_offline: check_venv check_build_reqs
 	@printf "$(cyan)All docker related tests will be skipped.$(normal)\n"
 	TOIL_SKIP_DOCKER=True \
-	TRAVIS=true \
 	    python -m pytest -vv --timeout=600 --log-level DEBUG --log-cli-level INFO $(cov) $(tests)
 
 ifdef TOIL_DOCKER_REGISTRY
 
 docker_image:=$(TOIL_DOCKER_REGISTRY)/$(TOIL_DOCKER_NAME)
-
 grafana_image:=$(TOIL_DOCKER_REGISTRY)/toil-grafana
 prometheus_image:=$(TOIL_DOCKER_REGISTRY)/toil-prometheus
 mtail_image:=$(TOIL_DOCKER_REGISTRY)/toil-mtail

common.mk

@@ -67,7 +67,6 @@ export TOIL_AWS_NODE_DEBUG?=False  # Don't shut down EC2 instances that fail so
 export TOIL_TEST_INTEGRATIVE?=False  # If ``True``, this allows the integration tests to run.
 export TOIL_TEST_QUICK?=False  # If ``True``, long running tests are skipped.
 export TOIL_SKIP_DOCKER?=False  # Skip docker dependent tests
-export TRAVIS?=True  # Run tests for travis (shorter unit tests)
 
 export TOIL_AWS_KEYNAME?=id_rsa  # SSH key to use for tests in AWS.
 export TOIL_GOOGLE_KEYNAME?=id_rsa  # SSH key to use for tests in google.

docs/contributing/contributing.rst

@@ -375,7 +375,7 @@ Pull Requests
 
   .. _Draft Changelog: https://github.com/DataBiosphere/toil/wiki/Draft-Changelog
 
-* Pull requests will not be merged unless Travis and Gitlab CI tests pass.
+* Pull requests will not be merged unless CI tests pass.
   Gitlab tests are only run on code in the main Toil repository on some branch,
   so it is the responsibility of the approving reviewer to make sure that pull
   requests from outside repositories are copied to branches in the main

src/toil/test/__init__.py

@@ -371,13 +371,6 @@ def needs_aws_ec2(test_item: MT) -> MT:
     return test_item
 
 
-def travis_test(test_item: MT) -> MT:
-    test_item = _mark_test('travis', test_item)
-    if os.environ.get('TRAVIS') != 'true':
-        return unittest.skip("Set TRAVIS='true' to include this test.")(test_item)
-    return test_item
-
-
 def needs_google(test_item: MT) -> MT:
     """Use as a decorator before test classes or methods to run only if Google is usable."""
     test_item = _mark_test('google', test_item)

src/toil/test/batchSystems/batchSystemTest.py

@@ -55,8 +55,7 @@
                        needs_slurm,
                        needs_tes,
                        needs_torque,
-                       slow,
-                       travis_test)
+                       slow)
 from toil.test.batchSystems.parasolTestSupport import ParasolTestSupport
 
 logger = logging.getLogger(__name__)
@@ -530,7 +529,6 @@ def write_temp_file(s: str, temp_dir: str) -> str:
         os.close(fd)
 
 
-@travis_test
 class SingleMachineBatchSystemTest(hidden.AbstractBatchSystemTest):
     """
     Tests against the single-machine batch system
@@ -989,7 +987,6 @@ def tearDown(self):
         super().tearDown()
 
 
-@travis_test
 class SingleMachineBatchSystemJobTest(hidden.AbstractBatchSystemJobTest):
     """
     Tests Toil workflow against the SingleMachine batch system

src/toil/test/docs/scriptsTest.py

@@ -8,7 +8,7 @@
 pkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))  # noqa
 sys.path.insert(0, pkg_root)  # noqa
 
-from toil.test import ToilTest, needs_cwl, needs_docker, travis_test
+from toil.test import ToilTest, needs_cwl, needs_docker
 from toil.version import python
 
 
@@ -69,100 +69,80 @@ def checkExpectedPattern(self, script, expectedPattern):
     def testCwlexample(self):
         self.checkExitCode("tutorial_cwlexample.py")
 
-    @travis_test
     def testDiscoverfiles(self):
         self.checkExitCode("tutorial_discoverfiles.py")
 
-    @travis_test
     def testDynamic(self):
         self.checkExitCode("tutorial_dynamic.py")
 
-    @travis_test
     def testEncapsulation(self):
         self.checkExitCode("tutorial_encapsulation.py")
 
-    @travis_test
     def testEncapsulation2(self):
         self.checkExitCode("tutorial_encapsulation2.py")
 
-    @travis_test
     def testHelloworld(self):
         self.checkExpectedOut("tutorial_helloworld.py", "Hello, world!, here's a message: You did it!\n")
 
-    @travis_test
     def testInvokeworkflow(self):
         self.checkExpectedOut("tutorial_invokeworkflow.py", "Hello, world!, here's a message: Woot\n")
 
-    @travis_test
     def testInvokeworkflow2(self):
         self.checkExpectedOut("tutorial_invokeworkflow2.py", "Hello, world!, I have a message: Woot!\n")
 
-    @travis_test
     def testJobFunctions(self):
         self.checkExpectedOut("tutorial_jobfunctions.py", "Hello world, I have a message: Woot!\n")
 
-    @travis_test
     def testManaging(self):
         self.checkExitCode("tutorial_managing.py")
 
-    @travis_test
     def testManaging2(self):
         self.checkExitCode("tutorial_managing2.py")
 
-    @travis_test
     def testMultiplejobs(self):
         self.checkExpectedPattern("tutorial_multiplejobs.py",
                                   "Hello world, I have a message: first.*Hello world, I have a message: "
                                   "second or third.*Hello world, I have a message: second or third.*Hello world,"
                                   " I have a message: last")
 
-    @travis_test
     def testMultiplejobs2(self):
         self.checkExpectedPattern("tutorial_multiplejobs2.py",
                                   "Hello world, I have a message: first.*Hello world, I have a message: "
                                   "second or third.*Hello world, I have a message: second or third.*Hello world,"
                                   " I have a message: last")
 
-    @travis_test
     def testMultiplejobs3(self):
         self.checkExpectedPattern("tutorial_multiplejobs3.py",
                                   "Hello world, I have a message: first.*Hello world, I have a message: "
                                   "second or third.*Hello world, I have a message: second or third.*Hello world,"
                                   " I have a message: last")
 
-    @travis_test
     def testPromises2(self):
         self.checkExpectedOut("tutorial_promises2.py",
                               "['00000', '00001', '00010', '00011', '00100', '00101', '00110', '00111',"
                               " '01000', '01001', '01010', '01011', '01100', '01101', '01110', '01111',"
                               " '10000', '10001', '10010', '10011', '10100', '10101', '10110', '10111',"
                               " '11000', '11001', '11010', '11011', '11100', '11101', '11110', '11111']")
 
-    @travis_test
     def testQuickstart(self):
         self.checkExpectedOut("tutorial_quickstart.py", "Hello, world!, here's a message: Woot\n")
 
-    @travis_test
     def testRequirements(self):
         self.checkExitCode("tutorial_requirements.py")
 
-    @travis_test
     def testArguments(self):
         self.checkExpectedOut("tutorial_arguments.py", "Hello, world!, here's a message: Woot")
 
     @needs_docker
     def testDocker(self):
         self.checkExitCode("tutorial_docker.py")
 
-    @travis_test
     def testPromises(self):
         self.checkExpectedPattern("tutorial_promises.py", "i is: 1.*i is: 2.*i is: 3")
 
-    @travis_test
     def testServices(self):
         self.checkExitCode("tutorial_services.py")
 
-    @travis_test
     def testStaging(self):
         self.checkExitCode("tutorial_staging.py")
 

src/toil/test/jobStores/jobStoreTest.py

@@ -48,8 +48,7 @@
                        needs_aws_s3,
                        needs_encryption,
                        needs_google,
-                       slow,
-                       travis_test)
+                       slow)
 
 # noinspection PyPackageRequirements
 # (installed by `make prepare`)
@@ -142,13 +141,11 @@ def tearDown(self):
             self.jobstore_resumed_noconfig.destroy()
             super(AbstractJobStoreTest.Test, self).tearDown()
 
-        @travis_test
         def testInitialState(self):
             """Ensure proper handling of nonexistant files."""
             self.assertFalse(self.jobstore_initialized.job_exists('nonexistantFile'))
             self.assertRaises(NoSuchJobException, self.jobstore_initialized.load_job, 'nonexistantFile')
 
-        @travis_test
         def testJobCreation(self):
             """
             Test creation of a job.
@@ -179,7 +176,6 @@ def testJobCreation(self):
             self.assertEqual(job.jobName, 'test1')
             self.assertEqual(job.unitName, 'onParent')
 
-        @travis_test
         def testConfigEquality(self):
             """
             Ensure that the command line configurations are successfully loaded and stored.
@@ -193,7 +189,6 @@ def testConfigEquality(self):
             self.assertEqual(newJobStore.config, self.config)
             self.assertIsNot(newJobStore.config, self.config)
 
-        @travis_test
         def testJobLoadEquality(self):
             """Tests that a job created via one JobStore instance can be loaded from another."""
 
@@ -209,7 +204,6 @@ def testJobLoadEquality(self):
 
             self.assertEqual(jobDesc1.command, jobDesc2.command)
 
-        @travis_test
         def testChildLoadingEquality(self):
             """Test that loading a child job operates as expected."""
             job = JobDescription(command='parent1',
@@ -228,7 +222,6 @@ def testChildLoadingEquality(self):
 
             self.assertEqual(self.jobstore_initialized.load_job(list(job.allSuccessors())[0]).command, childJob.command)
 
-        @travis_test
         def testPersistantFilesToDelete(self):
             """
             Make sure that updating a job carries over filesToDelete.
@@ -249,7 +242,6 @@ def testPersistantFilesToDelete(self):
             self.jobstore_initialized.update_job(job)
             self.assertEqual(self.jobstore_initialized.load_job(job.jobStoreID).filesToDelete, ['1', '2'])
 
-        @travis_test
         def testUpdateBehavior(self):
             """Tests the proper behavior during updating jobs."""
             jobstore1 = self.jobstore_initialized
@@ -297,7 +289,6 @@ def testUpdateBehavior(self):
             self.assertNotEqual(jobstore1.load_job(childJob1.jobStoreID), childJob1)
             self.assertNotEqual(jobstore1.load_job(childJob2.jobStoreID), childJob2)
 
-        @travis_test
         def testJobDeletions(self):
             """Tests the consequences of deleting jobs."""
             # A local jobstore object for testing.
@@ -361,7 +352,6 @@ def testJobDeletions(self):
             except NoSuchFileException:
                 pass
 
-        @travis_test
         def testSharedFiles(self):
             """Tests the sharing of files."""
             jobstore1 = self.jobstore_initialized
@@ -421,7 +411,6 @@ def testReadWriteFileStreamTextMode(self):
             with jobstore.read_file_stream(fileID, encoding='utf-8') as f:
                 self.assertEqual(bar, f.read())
 
-        @travis_test
         def testPerJobFiles(self):
             """Tests the behavior of files on jobs."""
             jobstore1 = self.jobstore_initialized
@@ -495,7 +484,6 @@ def testPerJobFiles(self):
                 except NoSuchFileException:
                     pass
 
-        @travis_test
         def testStatsAndLogging(self):
             """Tests behavior of reading and writting stats and logging."""
             jobstore1 = self.jobstore_initialized
@@ -550,7 +538,6 @@ def callback(f2):
             self.assertFalse(jobstore1.job_exists(jobOnJobStore1.jobStoreID))
             # TODO: Who deletes the shared files?
 
-        @travis_test
         def testWriteLogFiles(self):
             """Test writing log files."""
             jobNames = ['testStatsAndLogging_writeLogFiles']
@@ -565,7 +552,6 @@ def testWriteLogFiles(self):
                 self.assertEqual(f.read(), 'string\nbytes\n\nnewline\n')
             os.remove(jobLogFile)
 
-        @travis_test
         def testBatchCreate(self):
             """Test creation of many jobs."""
             jobstore = self.jobstore_initialized
@@ -582,7 +568,6 @@ def testBatchCreate(self):
             for job in jobs:
                 self.assertTrue(jobstore.job_exists(job.jobStoreID))
 
-        @travis_test
         def testGrowingAndShrinkingJob(self):
             """Make sure jobs update correctly if they grow/shrink."""
             # Make some very large data, large enough to trigger
@@ -750,7 +735,6 @@ def testImportSharedFile(self, otherCls):
                        cls,
                        otherCls=activeTestClassesByName)
 
-        @travis_test
         def testImportHttpFile(self):
             '''Test importing a file over HTTP.'''
             http = socketserver.TCPServer(('', 0), StubHttpRequestHandler)
@@ -775,7 +759,6 @@ def testImportHttpFile(self):
             finally:
                 http.server_close()
 
-        @travis_test
         def testImportFtpFile(self):
             '''Test importing a file over FTP'''
             ftpfile = {'name': 'foo', 'content': 'foo bar baz qux'}
@@ -896,7 +879,6 @@ def checksumThreadFn():
                 self.assertEqual(before, after)
             self.jobstore_initialized.delete_job(job.jobStoreID)
 
-        @travis_test
         def testZeroLengthFiles(self):
             '''Test reading and writing of empty files.'''
             job = self.arbitraryJob()
@@ -1003,7 +985,6 @@ def testCleanCache(self):
         # NB: the 'thread' method seems to be needed here to actually
         # ensure the timeout is raised, probably because the only
         # "live" thread doesn't hold the GIL.
-        @travis_test
         @pytest.mark.timeout(45, method='thread')
         def testPartialReadFromStream(self):
             """Test whether readFileStream will deadlock on a partial read."""
@@ -1038,7 +1019,6 @@ def testDestructionOfCorruptedJobStore(self):
             jobstore.destroy()
             # Note that self.jobstore_initialized.destroy() is done as part of shutdown
 
-        @travis_test
         def testDestructionIdempotence(self):
             # Jobstore is fully initialized
             self.jobstore_initialized.destroy()
@@ -1051,7 +1031,6 @@ def testDestructionIdempotence(self):
             cleaner = self._createJobStore()
             cleaner.destroy()
 
-        @travis_test
         def testEmptyFileStoreIDIsReadable(self):
             """Simply creates an empty fileStoreID and attempts to read from it."""
             id = self.jobstore_initialized.get_empty_file_store_id()
@@ -1157,7 +1136,6 @@ def _createExternalStore(self):
     def _cleanUpExternalStore(self, dirPath):
         shutil.rmtree(dirPath)
 
-    @travis_test
     def testPreserveFileName(self):
         """Check that the fileID ends with the given file name."""
         fh, path = tempfile.mkstemp()
@@ -1187,7 +1165,6 @@ def test_jobstore_init_preserves_symlink_path(self):
             if original_filestore and os.path.exists(original_filestore):
                 shutil.rmtree(original_filestore)
 
-    @travis_test
     def test_jobstore_does_not_leak_symlinks(self):
         """Test that if we link imports into the FileJobStore, we can't get hardlinks to symlinks."""