relax subprocess dependency (#757)

* bump cwltest version
* consolidate subprocess usage

Author: mr-c

cwltool/docker.py

@@ -18,11 +18,7 @@
 from .job import ContainerCommandLineJob
 from .pathmapper import PathMapper, ensure_writable
 from .secrets import SecretStore
-from .utils import docker_windows_path_adjust, onWindows
-if os.name == 'posix' and sys.version_info[0] < 3:
-    import subprocess32 as subprocess  # type: ignore
-else:
-    import subprocess  # type: ignore
+from .utils import docker_windows_path_adjust, onWindows, subprocess
 
 _logger = logging.getLogger("cwltool")
 

cwltool/docker_id.py

@@ -3,11 +3,7 @@
 import os
 import sys
 from typing import List, Text, Tuple
-if os.name == 'posix' and sys.version_info[0] < 3:
-    import subprocess32 as subprocess  # type: ignore
-else:
-    import subprocess  # type: ignore
-
+from .utils import subprocess
 
 def docker_vm_id():  # type: () -> Tuple[int, int]
     """

cwltool/job.py

@@ -25,13 +25,8 @@
 from .process import (UnsupportedRequirement, get_feature,
                       stageFiles)
 from .secrets import SecretStore
-from .utils import bytes2str_in_dicts
-from .utils import copytree_with_merge, onWindows
-if os.name == 'posix' and sys.version_info[0] < 3:
-    import subprocess32 as subprocess  # type: ignore
-else:
-    import subprocess  # type: ignore
-
+from .utils import (bytes2str_in_dicts, copytree_with_merge, onWindows,
+                    subprocess)
 
 _logger = logging.getLogger("cwltool")
 
@@ -49,7 +44,13 @@
 import json
 import os
 import sys
-import subprocess
+if os.name == 'posix':
+    try:
+        import subprocess32 as subprocess  # type: ignore
+    except Exception:
+        import subprocess
+else:
+    import subprocess  # type: ignore
 
 with open(sys.argv[1], "r") as f:
     popen_description = json.load(f)

cwltool/sandboxjs.py

@@ -11,16 +11,12 @@
 from typing import Any, Dict, List, Mapping, Text, Tuple, Union
 import six
 from pkg_resources import resource_stream
-from .utils import onWindows
+from .utils import onWindows, subprocess
 
 try:
     import queue  # type: ignore
 except ImportError:
     import Queue as queue  # type: ignore
-if os.name == 'posix' and sys.version_info[0] < 3:
-    import subprocess32 as subprocess  # type: ignore
-else:
-    import subprocess  # type: ignore
 
 
 class JavascriptException(Exception):

cwltool/singularity.py

@@ -13,14 +13,10 @@
 from .process import (UnsupportedRequirement)
 from .utils import docker_windows_path_adjust
 from schema_salad.sourceline import SourceLine
-if os.name == 'posix' and sys.version_info[0] < 3:
+if os.name == 'posix':
     from subprocess32 import (check_call, check_output,  # pylint: disable=import-error
                               CalledProcessError, DEVNULL, PIPE, Popen,
                               TimeoutExpired)
-elif os.name == 'posix':
-    from subprocess import (check_call, check_output,  # type: ignore
-                            CalledProcessError, DEVNULL, PIPE, Popen,
-                            TimeoutExpired)
 else:  # we're not on Unix, so none of this matters
     pass
 

cwltool/utils.py

@@ -7,6 +7,10 @@
 import shutil
 import stat
 from typing import Any, Callable, Dict, List, Text, Tuple, Union
+if os.name == 'posix':
+    import subprocess32 as subprocess  # type: ignore # pylint: disable=import-error,unused-import
+else:
+    import subprocess  # type: ignore # pylint: disable=unused-import
 
 import six
 from pkg_resources import (Requirement, ResolutionError,  # type: ignore

jenkins.bash

@@ -39,7 +39,7 @@ do
 	pip${PYTHON_VERSION} install -U setuptools wheel pip
 	pip${PYTHON_VERSION} uninstall -y cwltool
 	pip${PYTHON_VERSION} install .
-	pip${PYTHON_VERSION} install -U "cwltest>=1.0.20180130081614"
+	pip${PYTHON_VERSION} install -U "cwltest>=1.0.20180518074130"
 	pushd common-workflow-language
 	# shellcheck disable=SC2154
 	if [[ "$version" = *dev* ]]

requirements.txt

@@ -1,8 +1,9 @@
 requests>=2.4.3
 ruamel.yaml>=0.12.4,<0.15
-rdflib==4.2.2
-rdflib-jsonld==0.4.0
-shellescape==3.4.1
-schema-salad>=2.6,<3
-typing==3.5.3
+rdflib>=4.2.2,<4.3
+shellescape>=3.4.1,<3.5
+schema-salad>=2.6.20170927145003,<3
+typing>=3.5.3
 pathlib2==2.3.2; python_version<"3"
+subprocess32 >= 3.5.0; platform_system=="Linux"
+

setup.py

@@ -58,8 +58,7 @@
           'six >= 1.8.0',
       ],
       extras_require={
-          ':python_version<"3" and platform_system=="Linux"':
-          ['subprocess32 == 3.5.0rc1'],
+          ':platform_system=="Linux"': ['subprocess32 >= 3.5.0'],
           ':python_version<"3"': ['pathlib2 == 2.3.2'],
           'deps': ["galaxy-lib >= 17.09.3"]
       },

tests/test_examples.py

@@ -1,21 +1,19 @@
 from __future__ import absolute_import
 import unittest
-import pytest
-import subprocess
 from os import path
 import sys
 import json
 import logging
 import tempfile
 import shutil
-
 from io import StringIO, BytesIO
+import schema_salad.validate
 
 from cwltool.errors import WorkflowException
 
 try:
     reload
-except:
+except:  # pylint: disable=bare-except
     try:
         from imp import reload
     except:
@@ -26,13 +24,13 @@
 import cwltool.pathmapper
 import cwltool.process
 import cwltool.workflow
-import schema_salad.validate
 from cwltool.main import main
-from cwltool.utils import onWindows
+from cwltool.utils import onWindows, subprocess
 
 from .util import (get_data, needs_docker, get_windows_safe_factory,
         windows_needs_docker)
 
+
 sys.argv = ['']
 
 class TestParamMatching(unittest.TestCase):