Merge branch 'master' into fix-823

Author: mr-c

.travis.yml

@@ -1,5 +1,5 @@
 dist: trusty
-sudo: true
+sudo: required
 services:
   - docker
 
@@ -17,18 +17,26 @@ cache:
   pip: true
   directories:
     - .mypy_cache
-python:
-  - 2.7
-  - 3.4
-  - 3.5
-  - 3.6
+
 os:
   - linux
 install:
   - pip install tox-travis
 jobs:
   include:
+    - stage: test
+      python: "2.7"
+    - stage: test
+      python: "3.4"
+    - stage: test
+      python: "3.5"
+    - stage: test
+      python: "3.6"
+    - stage: test
+      python: "3.7"
+      dist: xenial
     - stage: release-test
+      python: "2.7"
       script: RELEASE_SKIP=head ${TRAVIS_BUILD_DIR}/release-test.sh
 script: tox
 branches:

Makefile

@@ -26,7 +26,7 @@ MODULE=cwltool
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
 PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
-DEVPKGS=pycodestyle diff_cover autopep8 pylint coverage pydocstyle flake8 pytest isort mock
+DEVPKGS=pycodestyle diff_cover autopep8 pylint coverage pydocstyle flake8 pytest isort 
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
 	   python-flake8 python-mock shellcheck
 VERSION=1.0.$(shell date +%Y%m%d%H%M%S --utc --date=`git log --first-parent \
@@ -50,7 +50,7 @@ help: Makefile
 
 ## install-dep : install most of the development dependencies via pip
 install-dep:
-	pip install --upgrade $(DEVPKGS)
+	pip install --upgrade $(DEVPKGS) -rtest-requirements.txt
 
 ## install-deb-dep: install most of the dev dependencies via apt-get
 install-deb-dep:
@@ -134,12 +134,11 @@ coverage.html: htmlcov/index.html
 htmlcov/index.html: .coverage
 	coverage html
 
-diff-cover: coverage-gcovr.xml coverage.xml
-	diff-cover coverage-gcovr.xml coverage.xml
+diff-cover: coverage.xml
+	diff-cover $^
 
-diff-cover.html: coverage-gcovr.xml coverage.xml
-	diff-cover coverage-gcovr.xml coverage.xml \
-		--html-report diff-cover.html
+diff-cover.html:  coverage.xml
+	diff-cover $^ --html-report diff-cover.html
 
 ## test        : run the ${MODULE} test suite
 test: $(pysources)

README.rst

@@ -76,7 +76,7 @@ To run the basis tests after installing `cwltool` execute the following:
 
 .. code:: bash
 
-  pip install pytest mock
+  pip install -rtest-requirements.txt
   py.test --ignore cwltool/schemas/ --pyarg cwltool
 
 To run various tests in all supported Python environments we use `tox <https://github.com/common-workflow-language/cwltool/tree/master/tox.ini>`_. To run the test suite in all supported Python environments

appveyor.yml

@@ -24,20 +24,30 @@ environment:
       PYTHON_VERSION: "3.6.x"
       PYTHON_ARCH: "64"
 
+    - PYTHON: "C:\\Python37-x64"
+      PYTHON_VERSION: "3.7.x"
+      PYTHON_ARCH: "64"
+
 install:
   - ps: 'Install-Product node 0.12 x64'
-  - "%PYTHON%\\python.exe -m pip install -U wheel pytest mock"
-  - "%PYTHON%\\python.exe -m pip show setuptools"
-  - "%PYTHON%\\python.exe -m pip install -U setuptools^>=20.3"
+  - "set PATH=%PYTHON%\\Scripts;%PATH%"
+  - "%PYTHON%\\python.exe -m pip install -U pip setuptools^>=20.3 wheel"
+  - "%PYTHON%\\python.exe -m pip install -U codecov pytest-xdist pytest-cov galaxy-lib -rtest-requirements.txt"
     # Note the use of a `^` to escape the `>`
-    #- "%PYTHON%\\python.exe -m pip install -U wheel pytest pytest-xdist mock"
+
+for:
+  - matrix:
+      only: [ { PYTHON_VERSION: "3.7.x" } ]
+    before_build:
+      - "%PYTHON%\\python.exe -m pip install https://download.lfd.uci.edu/pythonlibs/l8ulg3xw/lxml-4.2.3-cp37-cp37m-win_amd64.whl"
 
 build_script:
-  - "%PYTHON%\\python.exe -m pip install ."
+  - "%PYTHON%\\python.exe -m pip install -rrequirements.txt"
 
 test_script:
-  - "%PYTHON%\\python.exe -m pytest --verbose -p no:cacheprovider --junit-xml=tests.xml"
-    #- "%PYTHON%\\python.exe -m pytest --verbose -p no:cacheprovider --junit-xml=tests.xml -n2"
+  - |
+    %PYTHON%\\python.exe setup.py test --addopts "--cov-report xml --cov cwltool -p no:cacheprovider --junit-xml=tests.xml"
+  - "%PYTHON%\\python.exe -m codecov"
 
 on_finish:
   - ps: |

cwltool.py

@@ -11,4 +11,4 @@
 from cwltool import main
 
 if __name__ == "__main__":
-    sys.exit(main.main(sys.argv[1:]))
+    main.run(sys.argv[1:])

cwltool/__main__.py

@@ -4,4 +4,4 @@
 
 from . import main
 
-sys.exit(main.main())
+main.run()

cwltool/argparser.py

@@ -179,6 +179,12 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     exgroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.")
     exgroup.add_argument("--debug", action="store_true", help="Print even more logging")
 
+    parser.add_argument(
+        "--strict-memory-limit", action="store_true", help="When running with "
+        "software containers and the Docker engine, pass either the "
+        "calculated memory allocation from ResourceRequirements or the "
+        "default of 1 gigabyte to Docker's --memory option.")
+
     parser.add_argument("--timestamps", action="store_true", help="Add "
                         "timestamps to the errors, warnings, and "
                         "notifications.")

cwltool/context.py

@@ -33,6 +33,7 @@ def make_tool_notimpl(toolpath_object,      # type: Dict[Text, Any]
                      ):  # type: (...) -> Process
     raise NotImplementedError()
 
+
 default_make_tool = make_tool_notimpl  # type: Callable[[Dict[Text, Any], LoadingContext], Process]
 
 class LoadingContext(ContextBase):
@@ -46,7 +47,7 @@ def __init__(self, kwargs=None):
         self.overrides_list = []           # type: List[Dict[Text, Any]]
         self.loader = None                 # type: Optional[Loader]
         self.avsc_names = None             # type: Optional[schema.Names]
-        self.disable_js_validation = False # type: bool
+        self.disable_js_validation = False  # type: bool
         self.js_hint_options_file = None
         self.do_validate = True            # type: bool
         self.enable_dev = False            # type: bool
@@ -72,7 +73,7 @@ def __init__(self, kwargs=None):
         # type: (Optional[Dict[str, Any]]) -> None
         select_resources_callable = Callable[  # pylint: disable=unused-variable
             [Dict[str, int], RuntimeContext], Dict[str, int]]
-        self.user_space_docker_cmd = "" # type: Text
+        self.user_space_docker_cmd = ""  # type: Text
         self.secret_store = None        # type: Optional[SecretStore]
         self.no_read_only = False       # type: bool
         self.custom_net = ""            # type: Text
@@ -115,6 +116,7 @@ def __init__(self, kwargs=None):
         self.eval_timeout = 20          # type: float
         self.postScatterEval = None     # type: Optional[Callable[[Dict[Text, Any]], Dict[Text, Any]]]
         self.on_error = "stop"          # type: Text
+        self.strict_memory_limit = False  # type: bool
 
         self.record_container_id = None
         self.cidfile_dir = None