guard import pwd for windows (#1822)

Co-authored-by: Jake Fennick <[email protected]>
Co-authored-by: Michael R. Crusoe <[email protected]>

Author: jfennick

cwltool/builder.py

@@ -21,13 +21,14 @@
 from cwl_utils.file_formats import check_format
 from mypy_extensions import mypyc_attr
 from rdflib import Graph
-from ruamel.yaml.comments import CommentedMap
 from schema_salad.avro.schema import Names, Schema, make_avsc_object
 from schema_salad.exceptions import ValidationException
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import convert_to_dict, json_dumps
 from schema_salad.validate import validate
 
+from ruamel.yaml.comments import CommentedMap
+
 from .errors import WorkflowException
 from .loghandler import _logger
 from .mutation import MutationManager

cwltool/command_line_tool.py

@@ -33,14 +33,15 @@
 
 import shellescape
 from mypy_extensions import mypyc_attr
-from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.avro.schema import Schema
 from schema_salad.exceptions import ValidationException
 from schema_salad.ref_resolver import file_uri, uri_file_path
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dumps
 from schema_salad.validate import validate_ex
 
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
+
 from .builder import (
     INPUT_OBJ_VOCAB,
     Builder,

cwltool/context.py

@@ -18,12 +18,13 @@
     Union,
 )
 
-from ruamel.yaml.comments import CommentedMap
 from schema_salad.avro.schema import Names
 from schema_salad.ref_resolver import Loader
 from schema_salad.utils import FetcherCallableType
 from typing_extensions import Literal
 
+from ruamel.yaml.comments import CommentedMap
+
 from .mpi import MpiConfig
 from .pathmapper import PathMapper
 from .stdfsaccess import StdFsAccess

cwltool/cwlrdf.py

@@ -4,10 +4,11 @@
 
 from rdflib import Graph
 from rdflib.query import ResultRow
-from ruamel.yaml.comments import CommentedMap
 from schema_salad.jsonld_context import makerdf
 from schema_salad.utils import ContextType
 
+from ruamel.yaml.comments import CommentedMap
+
 from .cwlviewer import CWLViewer
 from .process import Process
 

cwltool/load_tool.py

@@ -21,7 +21,6 @@
 )
 
 from cwl_utils.parser import cwl_v1_2, cwl_v1_2_utils
-from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.exceptions import ValidationException
 from schema_salad.fetcher import Fetcher
 from schema_salad.ref_resolver import Loader, file_uri
@@ -35,6 +34,8 @@
     json_dumps,
 )
 
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
+
 from . import CWL_CONTENT_TYPES, process, update
 from .context import LoadingContext
 from .errors import GraphTargetMissingException

cwltool/main.py

@@ -34,9 +34,6 @@
 import argcomplete
 import coloredlogs
 import pkg_resources  # part of setuptools
-import ruamel.yaml
-from ruamel.yaml.comments import CommentedMap, CommentedSeq
-from ruamel.yaml.main import YAML
 from schema_salad.exceptions import ValidationException
 from schema_salad.ref_resolver import Loader, file_uri, uri_file_path
 from schema_salad.sourceline import cmap, strip_dup_lineno
@@ -48,6 +45,10 @@
     yaml_no_ts,
 )
 
+import ruamel.yaml
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
+from ruamel.yaml.main import YAML
+
 from . import CWL_CONTENT_TYPES, workflow
 from .argparser import arg_parser, generate_parser, get_default_args
 from .context import LoadingContext, RuntimeContext, getdefault

cwltool/pack.py

@@ -14,10 +14,11 @@
     cast,
 )
 
-from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.ref_resolver import Loader, SubLoader
 from schema_salad.utils import ResolveType
 
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
+
 from .context import LoadingContext
 from .load_tool import fetch_document, resolve_and_validate_document
 from .process import shortname, uniquename

cwltool/process.py

@@ -36,7 +36,6 @@
 from mypy_extensions import mypyc_attr
 from pkg_resources import resource_stream
 from rdflib import Graph
-from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.avro.schema import (
     Names,
     Schema,
@@ -50,6 +49,8 @@
 from schema_salad.utils import convert_to_dict
 from schema_salad.validate import avro_type_name, validate_ex
 
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
+
 from .builder import INPUT_OBJ_VOCAB, Builder
 from .context import LoadingContext, RuntimeContext, getdefault
 from .errors import UnsupportedRequirement, WorkflowException

cwltool/procgenerator.py

@@ -1,10 +1,11 @@
 import copy
 from typing import Dict, Optional, Tuple, cast
 
-from ruamel.yaml.comments import CommentedMap
 from schema_salad.exceptions import ValidationException
 from schema_salad.sourceline import indent
 
+from ruamel.yaml.comments import CommentedMap
+
 from .context import LoadingContext, RuntimeContext
 from .errors import WorkflowException
 from .load_tool import load_tool

cwltool/provenance.py

@@ -8,7 +8,13 @@
 import datetime
 import hashlib
 import os
-import pwd
+
+try:
+    import pwd
+except ImportError:
+    # Guard against `from .provenance import ...` on windows.
+    # See windows_check() in main.py
+    pass
 import re
 import shutil
 import tempfile

cwltool/update.py

@@ -11,11 +11,12 @@
     cast,
 )
 
-from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.exceptions import ValidationException
 from schema_salad.ref_resolver import Loader
 from schema_salad.sourceline import SourceLine
 
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
+
 from .loghandler import _logger
 from .utils import CWLObjectType, CWLOutputType, aslist, visit_class, visit_field
 

cwltool/validate_js.py

@@ -19,7 +19,6 @@
 from cwl_utils.expression import scanner as scan_expression
 from cwl_utils.sandboxjs import code_fragment_to_js, exec_js_process
 from pkg_resources import resource_stream
-from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.avro.schema import (
     ArraySchema,
     EnumSchema,
@@ -31,6 +30,8 @@
 from schema_salad.utils import json_dumps
 from schema_salad.validate import validate_ex
 
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
+
 from .errors import WorkflowException
 from .loghandler import _logger
 

cwltool/workflow.py

@@ -17,10 +17,11 @@
 )
 from uuid import UUID
 
-from ruamel.yaml.comments import CommentedMap
 from schema_salad.exceptions import ValidationException
 from schema_salad.sourceline import SourceLine, indent
 
+from ruamel.yaml.comments import CommentedMap
+
 from . import command_line_tool, context, procgenerator
 from .checker import circular_dependency_checker, loop_checker, static_checker
 from .context import LoadingContext, RuntimeContext, getdefault

tests/test_anon_types.py

@@ -1,11 +1,11 @@
 from typing import cast
 
 import pytest
-from ruamel.yaml.comments import CommentedMap
 from schema_salad.sourceline import cmap
 
 from cwltool.command_line_tool import CommandLineTool
 from cwltool.context import LoadingContext
+from ruamel.yaml.comments import CommentedMap
 
 snippet = cast(
     CommentedMap,

tests/test_examples.py

@@ -15,7 +15,6 @@
 import pytest
 from cwl_utils.errors import JavascriptException
 from cwl_utils.sandboxjs import param_re
-from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.exceptions import ValidationException
 
 import cwltool.checker
@@ -29,6 +28,7 @@
 from cwltool.main import main
 from cwltool.process import CWL_IANA
 from cwltool.utils import CWLObjectType, dedup
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
 
 from .util import get_data, get_main_output, needs_docker, working_directory
 

tests/test_mpi.py

@@ -8,7 +8,6 @@
 
 import pkg_resources
 import pytest
-from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.avro.schema import Names
 from schema_salad.utils import yaml_no_ts
 
@@ -19,6 +18,7 @@
 from cwltool.context import LoadingContext, RuntimeContext
 from cwltool.main import main
 from cwltool.mpi import MpiConfig, MPIRequirementName
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
 
 from .util import get_data, working_directory
 

tests/test_path_checks.py

@@ -4,7 +4,6 @@
 from typing import IO, Any, List, cast
 
 import pytest
-from ruamel.yaml.comments import CommentedMap
 from schema_salad.sourceline import cmap
 
 from cwltool.command_line_tool import CommandLineTool
@@ -13,6 +12,7 @@
 from cwltool.stdfsaccess import StdFsAccess
 from cwltool.update import INTERNAL_VERSION
 from cwltool.utils import CWLObjectType
+from ruamel.yaml.comments import CommentedMap
 
 from .util import needs_docker
 

tests/test_streaming.py

@@ -4,7 +4,6 @@
 from typing import cast
 
 import pytest
-from ruamel.yaml.comments import CommentedMap
 from schema_salad.sourceline import cmap
 
 from cwltool.command_line_tool import CommandLineTool
@@ -13,6 +12,7 @@
 from cwltool.job import JobBase
 from cwltool.update import INTERNAL_VERSION, ORIGINAL_CWLVERSION
 from cwltool.utils import CWLObjectType
+from ruamel.yaml.comments import CommentedMap
 
 from .util import get_data
 

tests/test_subclass_mypyc.py

@@ -7,14 +7,14 @@
 import pickle
 
 import pytest
-from ruamel.yaml.comments import CommentedMap
 from schema_salad.avro import schema
 
 from cwltool.builder import Builder
 from cwltool.command_line_tool import CommandLineTool, ExpressionTool
 from cwltool.context import LoadingContext, RuntimeContext
 from cwltool.stdfsaccess import StdFsAccess
 from cwltool.update import INTERNAL_VERSION
+from ruamel.yaml.comments import CommentedMap
 
 from .test_anon_types import snippet
 

tests/test_tmpdir.py

@@ -5,7 +5,6 @@
 from typing import List, cast
 
 import pytest
-from ruamel.yaml.comments import CommentedMap
 from schema_salad.avro import schema
 from schema_salad.sourceline import cmap
 
@@ -19,6 +18,7 @@
 from cwltool.stdfsaccess import StdFsAccess
 from cwltool.update import INTERNAL_VERSION, ORIGINAL_CWLVERSION
 from cwltool.utils import create_tmp_dir
+from ruamel.yaml.comments import CommentedMap
 
 from .util import get_data, needs_docker