Versioning with latest python libs

cwltool/argparser.py

@@ -7,7 +7,7 @@
                     Optional, Sequence, Union, cast)
 
 from schema_salad.ref_resolver import file_uri
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from .loghandler import _logger

cwltool/builder.py

@@ -13,7 +13,7 @@
 from schema_salad.avro.schema import make_avsc_object, Schema
 from schema_salad.sourceline import SourceLine
 from six import iteritems, string_types
-from typing_extensions import (TYPE_CHECKING,  # pylint: disable=unused-import
+from typing import (TYPE_CHECKING,  # pylint: disable=unused-import
                                Text, Type)
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 

cwltool/checker.py

@@ -5,7 +5,7 @@
 import six
 from schema_salad import validate
 from schema_salad.sourceline import SourceLine, bullets, strip_dup_lineno
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from .errors import WorkflowException

cwltool/command_line_tool.py

@@ -23,7 +23,7 @@
 from six import string_types
 
 from six.moves import map, urllib
-from typing_extensions import (TYPE_CHECKING,  # pylint: disable=unused-import
+from typing import (TYPE_CHECKING,  # pylint: disable=unused-import
                                Text, Type)
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 

cwltool/context.py

@@ -7,7 +7,7 @@
 from schema_salad import schema
 from schema_salad.ref_resolver import (ContextType,  # pylint: disable=unused-import
                                        Fetcher, Loader)
-from typing_extensions import (TYPE_CHECKING,  # pylint: disable=unused-import
+from typing import (TYPE_CHECKING,  # pylint: disable=unused-import
                                Text)
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 from .builder import Builder, HasReqsHints

cwltool/cwlrdf.py

@@ -6,7 +6,7 @@
 from schema_salad.jsonld_context import makerdf
 from schema_salad.ref_resolver import ContextType
 from six.moves import urllib
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from .process import Process

cwltool/docker.py

@@ -13,7 +13,7 @@
 from typing import Dict, List, MutableMapping, Optional, Set, Tuple
 
 import requests
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from .context import RuntimeContext  # pylint: disable=unused-import

cwltool/docker_id.py

@@ -3,7 +3,7 @@
 
 from typing import List, Optional, Tuple  # pylint: disable=unused-import
 
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from .utils import subprocess

cwltool/executors.py

@@ -9,7 +9,7 @@
 
 import psutil
 from six import string_types, with_metaclass
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 from schema_salad.validate import ValidationException
 
 from .builder import Builder  # pylint: disable=unused-import

cwltool/expression.py

@@ -8,7 +8,7 @@
 
 import six
 from six import string_types, u
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from .sandboxjs import default_timeout, execjs, JavascriptException

cwltool/factory.py

@@ -4,7 +4,7 @@
 from typing import Callable as tCallable  # pylint: disable=unused-import
 from typing import Any, Dict, Tuple, Union
 
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from . import load_tool

cwltool/job.py

@@ -23,7 +23,7 @@
 from prov.model import PROV
 from schema_salad.sourceline import SourceLine
 from six import PY2, with_metaclass
-from typing_extensions import (TYPE_CHECKING,  # pylint: disable=unused-import
+from typing import (TYPE_CHECKING,  # pylint: disable=unused-import
                                Text)
 
 from .builder import Builder, HasReqsHints  # pylint: disable=unused-import

cwltool/load_tool.py

@@ -18,7 +18,7 @@
 from schema_salad.validate import ValidationException
 from six import itervalues, string_types
 from six.moves import urllib
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from . import process, update

cwltool/main.py

@@ -25,7 +25,7 @@
 from schema_salad.ref_resolver import Loader, file_uri, uri_file_path
 from schema_salad.sourceline import strip_dup_lineno, cmap
 from six import string_types, iteritems, PY3
-from typing_extensions import Text
+from typing import Text
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from . import command_line_tool, workflow

cwltool/mutation.py

@@ -3,7 +3,7 @@
 from collections import namedtuple
 from typing import Any, Dict
 
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from .errors import WorkflowException

cwltool/pack.py

@@ -10,7 +10,7 @@
 from schema_salad.ref_resolver import SubLoader
 from six import iteritems, string_types
 from six.moves import urllib
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from .process import shortname, uniquename

cwltool/pathmapper.py

@@ -17,7 +17,7 @@
 from schema_salad.ref_resolver import uri_file_path
 from schema_salad.sourceline import SourceLine
 from six.moves import urllib
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from .loghandler import _logger

cwltool/process.py

@@ -24,7 +24,7 @@
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from six import PY3, iteritems, itervalues, string_types, with_metaclass
 from six.moves import urllib
-from typing_extensions import (TYPE_CHECKING,  # pylint: disable=unused-import
+from typing import (TYPE_CHECKING,  # pylint: disable=unused-import
                                Text)
 from schema_salad import schema, validate
 from schema_salad.ref_resolver import Loader, file_uri

cwltool/provenance.py

@@ -27,7 +27,7 @@
 from ruamel import yaml
 from schema_salad.sourceline import SourceLine
 from six.moves import urllib
-from typing_extensions import (TYPE_CHECKING,  # pylint: disable=unused-import
+from typing import (TYPE_CHECKING,  # pylint: disable=unused-import
                                Text)
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 

cwltool/sandboxjs.py

@@ -13,7 +13,7 @@
 
 import six
 from pkg_resources import resource_stream
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from .loghandler import _logger

cwltool/secrets.py

@@ -3,7 +3,7 @@
 from typing import Any, Dict, List, MutableMapping, MutableSequence
 
 from six import string_types
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 

cwltool/singularity.py

@@ -12,7 +12,7 @@
 from typing import Dict, List, MutableMapping, Optional, Tuple
 
 from schema_salad.sourceline import SourceLine
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from .context import RuntimeContext  # pylint: disable=unused-import

cwltool/software_requirements.py

@@ -13,7 +13,7 @@
 import string
 from typing import Dict, List, MutableSequence, Optional
 
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from .builder import Builder, HasReqsHints

cwltool/stdfsaccess.py

@@ -8,7 +8,7 @@
 
 from schema_salad.ref_resolver import file_uri, uri_file_path
 from six.moves import urllib
-from typing_extensions import Text
+from typing import Text
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from .utils import onWindows

cwltool/update.py

@@ -10,7 +10,7 @@
 from schema_salad.ref_resolver import Loader  # pylint: disable=unused-import
 from six import string_types
 from six.moves import urllib
-from typing_extensions import Text
+from typing import Text
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from .utils import visit_class

cwltool/utils.py

@@ -18,7 +18,7 @@
 from mypy_extensions import TypedDict
 from schema_salad.utils import json_dump, json_dumps  # pylint: disable=unused-import
 from six.moves import urllib, zip_longest
-from typing_extensions import Deque, Text  # pylint: disable=unused-import
+from typing import Deque, Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 # no imports from cwltool allowed

cwltool/validate_js.py

@@ -9,7 +9,7 @@
 from pkg_resources import resource_stream
 from ruamel.yaml.comments import CommentedMap  # pylint: disable=unused-import
 from six import string_types
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 from schema_salad import avro
 from schema_salad.sourceline import SourceLine
 from schema_salad.validate import Schema  # pylint: disable=unused-import

cwltool/workflow.py

@@ -17,7 +17,7 @@
 from schema_salad.sourceline import SourceLine
 from six import string_types, iteritems
 from six.moves import range
-from typing_extensions import Text  # pylint: disable=unused-import
+from typing import Text  # pylint: disable=unused-import
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 
 from . import command_line_tool, context, expression

gittaggers.py

@@ -6,10 +6,12 @@
 SETUPTOOLS_VER = pkg_resources.get_distribution(
     "setuptools").version.split('.')
 
-RECENT_SETUPTOOLS = int(SETUPTOOLS_VER[0]) > 40 or (
-    int(SETUPTOOLS_VER[0]) == 40 and int(SETUPTOOLS_VER[1]) > 0) or (
-        int(SETUPTOOLS_VER[0]) == 40 and int(SETUPTOOLS_VER[1]) == 0 and
-        int(SETUPTOOLS_VER[2]) > 0)
+[major,minor,sub] = [ int(item) for item in SETUPTOOLS_VER ]
+
+RECENT_SETUPTOOLS = major > 40 or (major == 40 and minor or (major == 40 and minor==0 and sub > 0))
+# 40.6.3 does not have vtags
+if major == 40 and minor == 6 and sub == 3:
+    RECENT_SETUPTOOLS=False
 
 class EggInfoFromGit(egg_info):
     """Tag the build with git commit timestamp.

requirements.txt

@@ -3,12 +3,10 @@ ruamel.yaml>=0.12.4,<=0.15.77
 rdflib>=4.2.2,<4.3
 shellescape>=3.4.1,<3.5
 schema-salad>=3.0,<3.1
-typing>=3.5.3; python_version<"3.6"
 pathlib2==2.3.2; python_version<"3"
-prov==1.5.1
+prov>=1.5.1,!=1.5.2
 bagit==1.6.4
 mypy-extensions
 psutil
 scandir
 subprocess32 >= 3.5.0; os.name=="posix" and python_version<"3.5"
-typing-extensions

setup.py

@@ -58,9 +58,9 @@
           'six >= 1.9.0',  # >= 1.9.0 required by prov
           'psutil',
           'scandir',
-          'prov == 1.5.1',
+          'prov >=1.5.1, !=1.5.2',
           'bagit >= 1.6.4',
-          'typing-extensions',
+          # 'typing-extensions',
       ],
       extras_require={
           ':os.name=="posix" and python_version<"3.5"': ['subprocess32 >= 3.5.0'],
@@ -109,6 +109,6 @@
           'Topic :: Scientific/Engineering :: Information Analysis',
           'Topic :: Scientific/Engineering :: Medical Science Apps.',
           'Topic :: System :: Distributed Computing',
-          'Topic :: Utilities',
+          'Topic :: Utilities'
       ]
      )