use importlib instead of the deprecated pkg_resources (#1844)

Author: mr-c

Makefile

@@ -177,7 +177,7 @@ list-author-emails:
 	@git log --format='%aN,%aE' | sort -u | grep -v 'root'
 
 mypy3: mypy
-mypy: $(filter-out setup.py gittagger.py,$(PYSOURCES))
+mypy: $(PYSOURCES)
 	if ! test -f $(shell python -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))')/py.typed ; \
 	then \
 		rm -Rf mypy-stubs/ruamel/yaml ; \

cwltool/builder.py

@@ -22,16 +22,15 @@
 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 ruamel.yaml.representer import RoundTripRepresenter
+from ruamel.yaml.scalarfloat import ScalarFloat
 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 ruamel.yaml.representer import RoundTripRepresenter
-from ruamel.yaml.scalarfloat import ScalarFloat
-
 from .errors import WorkflowException
 from .loghandler import _logger
 from .mutation import MutationManager

cwltool/command_line_tool.py

@@ -33,15 +33,14 @@
 
 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

@@ -18,13 +18,12 @@
     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

@@ -4,11 +4,10 @@
 
 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

@@ -21,6 +21,7 @@
 )
 
 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
@@ -34,8 +35,6 @@
     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

@@ -33,7 +33,10 @@
 
 import argcomplete
 import coloredlogs
-import pkg_resources  # part of setuptools
+import ruamel.yaml
+from importlib_resources import files
+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
@@ -45,10 +48,6 @@
     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
@@ -646,12 +645,12 @@ def setup_schema(
     if custom_schema_callback is not None:
         custom_schema_callback()
     elif args.enable_ext:
-        with pkg_resources.resource_stream(__name__, "extensions.yml") as res:
-            ext10 = res.read().decode("utf-8")
-        with pkg_resources.resource_stream(__name__, "extensions-v1.1.yml") as res:
-            ext11 = res.read().decode("utf-8")
-        with pkg_resources.resource_stream(__name__, "extensions-v1.2.yml") as res:
-            ext12 = res.read().decode("utf-8")
+        with files("cwltool").joinpath("extensions.yml") as res:
+            ext10 = res.read_text("utf-8")
+        with files("cwltool").joinpath("extensions-v1.1.yml") as res:
+            ext11 = res.read_text("utf-8")
+        with files("cwltool").joinpath("extensions-v1.2.yml") as res:
+            ext12 = res.read_text("utf-8")
         use_custom_schema("v1.0", "http://commonwl.org/cwltool", ext10)
         use_custom_schema("v1.1", "http://commonwl.org/cwltool", ext11)
         use_custom_schema("v1.2", "http://commonwl.org/cwltool", ext12)

cwltool/pack.py

@@ -14,11 +14,10 @@
     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

@@ -33,9 +33,10 @@
 )
 
 from cwl_utils import expression
+from importlib_resources import files
 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,
@@ -49,8 +50,6 @@
 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
@@ -195,22 +194,19 @@ def get_schema(
         version = ".".join(version.split(".")[:-1])
     for f in cwl_files:
         try:
-            res = resource_stream(__name__, f"schemas/{version}/{f}")
-            cache["https://w3id.org/cwl/" + f] = res.read().decode("UTF-8")
-            res.close()
+            with files("cwltool").joinpath(f"schemas/{version}/{f}") as res:
+                cache["https://w3id.org/cwl/" + f] = res.read_text("UTF-8")
         except OSError:
             pass
 
     for f in salad_files:
         try:
-            res = resource_stream(
-                __name__,
+            with files("cwltool").joinpath(
                 f"schemas/{version}/salad/schema_salad/metaschema/{f}",
-            )
-            cache["https://w3id.org/cwl/salad/schema_salad/metaschema/" + f] = res.read().decode(
-                "UTF-8"
-            )
-            res.close()
+            ) as res:
+                cache["https://w3id.org/cwl/salad/schema_salad/metaschema/" + f] = res.read_text(
+                    "UTF-8"
+                )
         except OSError:
             pass
 

cwltool/procgenerator.py

@@ -1,11 +1,10 @@
 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