remove usage of ancient shellescape backport of Stdlib's shlex (#2041)

Author: a-detiste

cwltool/command_line_tool.py

@@ -7,6 +7,7 @@
 import logging
 import os
 import re
+import shlex
 import shutil
 import threading
 import urllib
@@ -31,7 +32,6 @@
     cast,
 )
 
-import shellescape
 from mypy_extensions import mypyc_attr
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.avro.schema import Schema
@@ -1164,7 +1164,7 @@ def register_reader(f: CWLObjectType) -> None:
             for b in builder.bindings:
                 arg = builder.generate_arg(b)
                 if b.get("shellQuote", True):
-                    arg = [shellescape.quote(a) for a in aslist(arg)]
+                    arg = [shlex.quote(a) for a in aslist(arg)]
                 cmd.extend(aslist(arg))
             j.command_line = ["/bin/sh", "-c", " ".join(cmd)]
         else:

cwltool/job.py

@@ -5,6 +5,7 @@
 import math
 import os
 import re
+import shlex
 import shutil
 import signal
 import stat
@@ -35,7 +36,6 @@
 )
 
 import psutil
-import shellescape
 from prov.model import PROV
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dump, json_dumps
@@ -271,7 +271,7 @@ def _execute(
             self.outdir,
             " \\\n    ".join(
                 [
-                    shellescape.quote(str(arg)) if shouldquote(str(arg)) else str(arg)
+                    shlex.quote(str(arg)) if shouldquote(str(arg)) else str(arg)
                     for arg in (runtime + self.command_line)
                 ]
             ),

mypy-stubs/shellescape/__init__.pyi

@@ -1,7 +1,6 @@
 requests>=2.6.1
 ruamel.yaml>=0.16.0,<0.19
 rdflib>=4.2.2,<7.1
-shellescape>=3.4.1,<3.9
 schema-salad>=8.7,<9
 prov==1.5.1
 mypy-extensions

mypy-stubs/shellescape/main.pyi

@@ -126,7 +126,6 @@
         # https://github.com/ionrock/cachecontrol/issues/137
         "ruamel.yaml >= 0.16, < 0.19",
         "rdflib >= 4.2.2, < 7.1.0",
-        "shellescape >= 3.4.1, < 3.9",
         "schema-salad >= 8.7, < 9",
         "prov == 1.5.1",
         "mypy-extensions",