Drop MS Windows support in favor of WSL 2

Author: mr-c

Makefile

@@ -25,20 +25,19 @@ MODULE=cwltool
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
 PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
-DEVPKGS=diff_cover black pylint coverage pep257 pydocstyle flake8 tox\
+DEVPKGS=diff_cover black pylint pep257 pydocstyle flake8 tox tox-pyenv \
 	isort wheel autoflake flake8-bugbear pyupgrade bandit \
 	-rtest-requirements.txt -rmypy_requirements.txt
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
 	   python-flake8 python-mock shellcheck
 
-VERSION=3.0.$(shell TZ=UTC git log --first-parent --max-count=1 \
+VERSION=3.1.$(shell TZ=UTC git log --first-parent --max-count=1 \
 	--format=format:%cd --date=format-local:%Y%m%d%H%M%S)
 mkfile_dir := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
 UNAME_S=$(shell uname -s)
 
 ## all         : default task
-all:
-	pip install -e .
+all: dev
 
 ## help        : print this help message and exit
 help: Makefile
@@ -47,7 +46,7 @@ help: Makefile
 ## install-dep : install most of the development dependencies via pip
 install-dep: install-dependencies
 
-install-dependencies:
+install-dependencies: FORCE
 	pip install --upgrade $(DEVPKGS)
 	pip install -r requirements.txt
 
@@ -112,7 +111,7 @@ pylint: $(PYSOURCES)
 	pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
                 $^ -j0|| true
 
-pylint_report.txt: ${PYSOURCES}
+pylint_report.txt: $(PYSOURCES)
 	pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
 		$^ -j0> $@ || true
 
@@ -143,26 +142,26 @@ diff-cover.html: coverage.xml
 	diff-cover $^ --html-report $@
 
 ## test        : run the ${MODULE} test suite
-test: $(pysources)
-	python setup.py test --addopts "-n auto --dist=loadfile"
+test: $(PYSOURCES)
+	python setup.py test
 
 ## testcov     : run the ${MODULE} test suite and collect coverage
-testcov: $(pysources)
-	python setup.py test --addopts "--cov cwltool -n auto --dist=loadfile"
+testcov: $(PYSOURCES)
+	python setup.py test --addopts "--cov --cov-config=.coveragerc --cov-report= -n auto --dist=loadfile"
 
-sloccount.sc: ${PYSOURCES} Makefile
+sloccount.sc: $(PYSOURCES) Makefile
 	sloccount --duplicates --wide --details $^ > $@
 
 ## sloccount   : count lines of code
-sloccount: ${PYSOURCES} Makefile
+sloccount: $(PYSOURCES) Makefile
 	sloccount $^
 
 list-author-emails:
 	@echo 'name, E-Mail Address'
 	@git log --format='%aN,%aE' | sort -u | grep -v 'root'
 
 mypy3: mypy
-mypy: $(filter-out setup.py gittagger.py,${PYSOURCES})
+mypy: $(filter-out setup.py gittagger.py,$(PYSOURCES))
 	if ! test -f $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))')/py.typed ; \
 	then \
 		rm -Rf typeshed/ruamel/yaml ; \
@@ -171,14 +170,14 @@ mypy: $(filter-out setup.py gittagger.py,${PYSOURCES})
 	fi  # if minimally required ruamel.yaml version is 0.15.99 or greater, than the above can be removed
 	MYPYPATH=$$MYPYPATH:typeshed mypy $^
 
-mypyc: ${PYSOURCES}
+mypyc: $(PYSOURCES)
 	MYPYPATH=typeshed CWLTOOL_USE_MYPYC=1 pip install --verbose -e . && pytest --ignore cwltool/schemas --basetemp ./tmp
 
 shellcheck: FORCE
 	shellcheck build-cwl-docker.sh cwl-docker.sh release-test.sh conformance-test.sh \
 		cwltool-in-docker.sh
 
-pyupgrade: ${PYSOURCES}
+pyupgrade: $(PYSOURCES)
 	pyupgrade --exit-zero-even-if-changed --py36-plus $^
 
 release-test: FORCE
@@ -192,7 +191,7 @@ release: release-test
 		twine upload testenv2/src/${MODULE}/dist/* && \
 		git tag ${VERSION} && git push --tags
 
-flake8: ${PYSOURCES}
+flake8: $(PYSOURCES)
 	flake8 $^
 
 FORCE:

README.rst

@@ -2,7 +2,7 @@
 Common Workflow Language tool description reference implementation
 ==================================================================
 
-|Linux Status| |Debian Stable package| |Debian Testing package| |Windows Status| |Coverage Status| |Downloads|
+|Linux Status| |Debian Stable package| |Debian Testing package| |Coverage Status| |Downloads|
 
 .. |Linux Status| image:: https://github.com/common-workflow-language/cwltool/actions/workflows/ci-tests.yml/badge.svg?branch=main
    :target: https://github.com/common-workflow-language/cwltool/actions/workflows/ci-tests.yml
@@ -13,9 +13,6 @@ Common Workflow Language tool description reference implementation
 .. |Debian Testing package| image:: https://badges.debian.net/badges/debian/testing/cwltool/version.svg
    :target: https://packages.debian.org/testing/cwltool
 
-.. |Windows Status| image:: https://img.shields.io/appveyor/ci/mr-c/cwltool/main.svg?label=Windows%20builds
-   :target: https://ci.appveyor.com/project/mr-c/cwltool
-
 .. |Coverage Status| image:: https://img.shields.io/codecov/c/github/common-workflow-language/cwltool.svg
    :target: https://codecov.io/gh/common-workflow-language/cwltool
 

appveyor.yml

@@ -21,7 +21,7 @@
 from .process import Process, shortname
 from .resolver import ga4gh_tool_registries
 from .software_requirements import SOFTWARE_REQUIREMENTS_ENABLED
-from .utils import DEFAULT_TMP_PREFIX, onWindows
+from .utils import DEFAULT_TMP_PREFIX
 
 
 def arg_parser() -> argparse.ArgumentParser:
@@ -516,14 +516,13 @@ def arg_parser() -> argparse.ArgumentParser:
         "--enable-color",
         action="store_true",
         help="Enable logging color (default enabled)",
-        default=not onWindows(),
+        default=True,
     )
     colorgroup.add_argument(
         "--disable-color",
         action="store_false",
         dest="enable_color",
         help="Disable colored logging (default false)",
-        default=onWindows(),
     )
 
     parser.add_argument(

cwltool/argparser.py

@@ -37,10 +37,8 @@
     CWLObjectType,
     CWLOutputType,
     aslist,
-    docker_windows_path_adjust,
     get_listing,
     normalizeFilesDirs,
-    onWindows,
     visit_class,
 )
 
@@ -551,14 +549,6 @@ def tostr(self, value: Union[MutableMapping[str, str], Any]) -> str:
                 raise WorkflowException(
                     '{} object missing "path": {}'.format(value["class"], value)
                 )
-
-            # Path adjust for windows file path when passing to docker, docker accepts unix like path only
-            (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
-            if onWindows() and docker_req is not None:
-                # docker_req is none only when there is no dockerRequirement
-                # mentioned in hints and Requirement
-                path = docker_windows_path_adjust(value["path"])
-                return path
             return value["path"]
         else:
             return str(value)

cwltool/builder.py

@@ -1,7 +1,6 @@
 """Implementation of CommandLineTool."""
 
 import copy
-from enum import Enum
 import hashlib
 import json
 import locale
@@ -12,6 +11,7 @@
 import threading
 import urllib
 import urllib.parse
+from enum import Enum
 from functools import cmp_to_key, partial
 from typing import (
     Any,
@@ -70,17 +70,13 @@
     adjustDirObjs,
     adjustFileObjs,
     aslist,
-    convert_pathsep_to_unix,
-    docker_windows_path_adjust,
     get_listing,
     normalizeFilesDirs,
-    onWindows,
     random_outdir,
     shared_file_lock,
     trim_listing,
     upgrade_lock,
     visit_class,
-    windows_default_container_id,
 )
 
 if TYPE_CHECKING:
@@ -99,21 +95,6 @@ class PathCheckingMode(Enum):
     RELAXED = re.compile(r".*")  # Accept anything
 
 
-DEFAULT_CONTAINER_MSG = """
-We are on Microsoft Windows and not all components of this CWL description have a
-container specified. This means that these steps will be executed in the default container,
-which is %s.
-
-Note, this could affect portability if this CWL description relies on non-POSIX features
-or commands in this container. For best results add the following to your CWL
-description's hints section:
-
-hints:
-  DockerRequirement:
-    dockerPull: %s
-"""
-
-
 class ExpressionJob:
     """Job for ExpressionTools."""
 
@@ -224,7 +205,7 @@ def revmap_file(
     if "location" in f and "path" not in f:
         location = cast(str, f["location"])
         if location.startswith("file://"):
-            f["path"] = convert_pathsep_to_unix(uri_file_path(location))
+            f["path"] = uri_file_path(location)
         else:
             return f
 
@@ -324,9 +305,7 @@ def check_adjust(
         raise ValueError(
             "Do not call check_adjust using a builder that doesn't have a pathmapper."
         )
-    file_o["path"] = path = docker_windows_path_adjust(
-        builder.pathmapper.mapper(cast(str, file_o["location"]))[1]
-    )
+    file_o["path"] = path = builder.pathmapper.mapper(cast(str, file_o["location"]))[1]
     basename = cast(str, file_o.get("basename"))
     dn, bn = os.path.split(path)
     if file_o.get("dirname") != dn:
@@ -405,17 +384,6 @@ def make_job_runner(self, runtimeContext: RuntimeContext) -> Type[JobBase]:
                         self.requirements.insert(0, dockerReq)
                         dockerRequired = True
 
-                    if (
-                        default_container == windows_default_container_id
-                        and runtimeContext.use_container
-                        and onWindows()
-                    ):
-                        _logger.warning(
-                            DEFAULT_CONTAINER_MSG,
-                            windows_default_container_id,
-                            windows_default_container_id,
-                        )
-
         if dockerReq is not None and runtimeContext.use_container:
             if mpiReq is not None:
                 _logger.warning("MPIRequirement with containers is a beta feature")

cwltool/command_line_tool.py

@@ -20,13 +20,7 @@
 from .job import ContainerCommandLineJob
 from .loghandler import _logger
 from .pathmapper import MapperEnt, PathMapper
-from .utils import (
-    CWLObjectType,
-    create_tmp_dir,
-    docker_windows_path_adjust,
-    ensure_writable,
-    onWindows,
-)
+from .utils import CWLObjectType, create_tmp_dir, ensure_writable
 
 _IMAGES = set()  # type: Set[str]
 _IMAGES_LOCK = threading.Lock()
@@ -61,14 +55,10 @@ def _get_docker_machine_mounts() -> List[str]:
 def _check_docker_machine_path(path: Optional[str]) -> None:
     if path is None:
         return
-    if onWindows():
-        path = path.lower()
     mounts = _get_docker_machine_mounts()
 
     found = False
     for mount in mounts:
-        if onWindows():
-            mount = mount.lower()
         if path.startswith(mount):
             found = True
             break
@@ -268,7 +258,7 @@ def add_file_or_directory_volume(
     ) -> None:
         """Append volume a file/dir mapping to the runtime option list."""
         if not volume.resolved.startswith("_:"):
-            _check_docker_machine_path(docker_windows_path_adjust(volume.resolved))
+            _check_docker_machine_path(volume.resolved)
             self.append_volume(runtime, volume.resolved, volume.target)
 
     def add_writable_file_volume(
@@ -369,9 +359,7 @@ def create_runtime(
             runtime = [x.replace(":ro", "") for x in runtime]
             runtime = [x.replace(":rw", "") for x in runtime]
 
-        runtime.append(
-            "--workdir=%s" % (docker_windows_path_adjust(self.builder.outdir))
-        )
+        runtime.append("--workdir=%s" % (self.builder.outdir))
         if not user_space_docker_cmd:
 
             if not runtimeContext.no_read_only:
@@ -387,9 +375,7 @@ def create_runtime(
                 runtime.append("--log-driver=none")
 
             euid, egid = docker_vm_id()
-            if not onWindows():
-                # MS Windows does not have getuid() or geteuid() functions
-                euid, egid = euid or os.geteuid(), egid or os.getgid()
+            euid, egid = euid or os.geteuid(), egid or os.getgid()
 
             if runtimeContext.no_match_user is False and (
                 euid is not None and egid is not None