Merge pull request #113 from common-workflow-language/formal_py3.6_support

Formal py3.6 support + fixes for toil

Author: mr-c

cwl_flask.py

@@ -16,7 +16,7 @@
 
 class Job(threading.Thread):
     def __init__(self, jobid, path, inputobj):
-        super(Job, self).__init__()
+        super().__init__()
         self.jobid = jobid
         self.path = path
         self.inputobj = inputobj
@@ -108,7 +108,7 @@ def jobcontrol(jobid):
 
 
 def logspooler(job):
-    with open(job.logname, "r") as f:
+    with open(job.logname) as f:
         while True:
             r = f.read(4096)
             if r:

setup.py

@@ -20,7 +20,7 @@
     url="https://github.com/common-workflow-language/cwltool-service",
     download_url="https://github.com/common-workflow-language/cwltool-service",
     license="Apache 2.0",
-    python_requires="~=3.5",
+    python_requires="~=3.6",
     setup_requires=["pytest-runner"],
     tests_require=["pytest"],
     packages=["wes_service", "wes_client"],
@@ -53,6 +53,7 @@
         "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
         "Topic :: Software Development :: Libraries :: Python Modules",
     ],
 )

test/test_client_util.py

@@ -4,7 +4,7 @@
 import subprocess
 import sys
 
-pkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))  # noqa
+pkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))  # noqa
 sys.path.insert(0, pkg_root)  # noqa
 
 from wes_client.util import expand_globs, wf_info
@@ -15,42 +15,47 @@
 class IntegrationTest(unittest.TestCase):
     def setUp(self):
         dirname, filename = os.path.split(os.path.abspath(__file__))
-        self.testdata_dir = dirname + 'data'
-        self.local = {'cwl': 'file://' + os.path.join(os.getcwd() + '/testdata/md5sum.cwl'),
-                 'wdl': 'file://' + os.path.join(os.getcwd() + '/testdata/md5sum.wdl'),
-                 'py': 'file://' + os.path.join(os.getcwd() + '/test/test_integration.py'),
-                 'unsupported': 'fake.txt'}
+        self.testdata_dir = dirname + "data"
+        self.local = {
+            "cwl": "file://" + os.path.join(os.getcwd() + "/testdata/md5sum.cwl"),
+            "wdl": "file://" + os.path.join(os.getcwd() + "/testdata/md5sum.wdl"),
+            "py": "file://" + os.path.join(os.getcwd() + "/test/test_integration.py"),
+            "unsupported": "fake.txt",
+        }
 
         self.remote = {
-            'cwl': 'https://raw.githubusercontent.com/common-workflow-language/workflow-service/master/testdata/md5sum.cwl',
-            'wdl': 'https://raw.githubusercontent.com/common-workflow-language/workflow-service/master/testdata/md5sum.wdl',
-            'py': 'https://raw.githubusercontent.com/common-workflow-language/workflow-service/master/test/test_integration.py',
-            'unsupported': 'gs://topmed_workflow_testing/topmed_aligner/small_test_files_sbg/example_human_known_snp.py',
-            'unreachable': 'https://fake.py'}
-
-        self.expected = {'cwl': ('v1.0', 'CWL'),
-                    'wdl': ('draft-2', 'WDL'),
-                    'py': ('2.7', 'PY'),
-                    'pyWithPrefix': ('2.7', 'PY')}
+            "cwl": "https://raw.githubusercontent.com/common-workflow-language/workflow-service/master/testdata/md5sum.cwl",
+            "wdl": "https://raw.githubusercontent.com/common-workflow-language/workflow-service/master/testdata/md5sum.wdl",
+            "py": "https://raw.githubusercontent.com/common-workflow-language/workflow-service/master/test/test_integration.py",
+            "unsupported": "gs://topmed_workflow_testing/topmed_aligner/small_test_files_sbg/example_human_known_snp.py",
+            "unreachable": "https://fake.py",
+        }
+
+        self.expected = {
+            "cwl": ("v1.0", "CWL"),
+            "wdl": ("draft-2", "WDL"),
+            "py": ("2.7", "PY"),
+            "pyWithPrefix": ("2.7", "PY"),
+        }
 
     def tearDown(self):
         unittest.TestCase.tearDown(self)
 
     def test_expand_globs(self):
         """Asserts that wes_client.expand_globs() sees the same files in the cwd as 'ls'."""
-        files = subprocess.check_output(['ls', '-1', '.'])
+        files = subprocess.check_output(["ls", "-1", "."])
 
         # python 2/3 bytestring/utf-8 compatibility
         if isinstance(files, str):
-            files = files.split('\n')
+            files = files.split("\n")
         else:
-            files = files.decode('utf-8').split('\n')
+            files = files.decode("utf-8").split("\n")
 
-        if '' in files:
-            files.remove('')
-        files = ['file://' + os.path.abspath(f) for f in files]
-        glob_files = expand_globs('*')
-        assert set(files) == glob_files, '\n' + str(set(files)) + '\n' + str(glob_files)
+        if "" in files:
+            files.remove("")
+        files = ["file://" + os.path.abspath(f) for f in files]
+        glob_files = expand_globs("*")
+        assert set(files) == glob_files, "\n" + str(set(files)) + "\n" + str(glob_files)
 
     def testSupportedFormatChecking(self):
         """
@@ -60,7 +65,7 @@ def testSupportedFormatChecking(self):
         """
 
         for file_format, location in self.local.items():
-            if file_format != 'unsupported':
+            if file_format != "unsupported":
                 # Tests the behavior after receiving supported file types with and without the 'file://' prefix
                 self.assertEqual(wf_info(location), self.expected[file_format])
                 self.assertEqual(wf_info(location[7:]), self.expected[file_format])
@@ -78,20 +83,24 @@ def testFileLocationChecking(self):
         """
 
         for file_format, location in self.remote.items():
-            if file_format == 'unsupported':
+            if file_format == "unsupported":
                 # Tests behavior after receiving a file hosted at an unsupported location.
                 with self.assertRaises(NotImplementedError):
                     wf_info(location)
 
-            elif file_format == 'unreachable':
+            elif file_format == "unreachable":
                 # Tests behavior after receiving a non-existent file.
                 with self.assertRaises(IOError):
                     wf_info(location)
 
             else:
                 self.assertEqual(wf_info(location), self.expected[file_format])
-                self.assertFalse(os.path.isfile(os.path.join(os.getcwd(), 'fetchedFromRemote.' + file_format)))
+                self.assertFalse(
+                    os.path.isfile(
+                        os.path.join(os.getcwd(), "fetchedFromRemote." + file_format)
+                    )
+                )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     unittest.main()  # run all tests