Merge branch 'master' into unicode_literal_usage

Author: mr-c

Makefile

@@ -26,8 +26,8 @@ MODULE=cwltool
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
 PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
-DEVPKGS=pep8 diff_cover autopep8 pylint coverage pep257 flake8 pytest isort mock
-DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pep257 sloccount python-flake8 python-mock
+DEVPKGS=pep8 diff_cover autopep8 pylint coverage pydocstyle flake8 pytest isort mock
+DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount python-flake8 python-mock
 VERSION=1.0.$(shell date +%Y%m%d%H%M%S --date=`git log --first-parent \
 	--max-count=1 --format=format:%cI`)
 mkfile_dir := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
@@ -80,15 +80,16 @@ pep8_report.txt: $(PYSOURCES)
 diff_pep8_report: pep8_report.txt
 	diff-quality --violations=pep8 pep8_report.txt
 
-## pep257      : check Python code style
-pep257: $(PYSOURCES)
-	pep257 --ignore=D100,D101,D102,D103 $^ || true
+pep257: pydocstyle
+## pydocstyle      : check Python code style
+pydocstyle: $(PYSOURCES)
+	pydocstyle --ignore=D100,D101,D102,D103 $^ || true
 
-pep257_report.txt: $(PYSOURCES)
-	pep257 setup.py $^ > pep257_report.txt 2>&1 || true
+pydocstyle_report.txt: $(PYSOURCES)
+	pydocstyle setup.py $^ > pydocstyle_report.txt 2>&1 || true
 
-diff_pep257_report: pep257_report.txt
-	diff-quality --violations=pep8 pep257_report.txt
+diff_pydocstyle_report: pydocstyle_report.txt
+	diff-quality --violations=pep8 $^
 
 ## autopep8    : fix most Python code indentation and formatting
 autopep8: $(PYSOURCES)

README.rst

@@ -413,43 +413,67 @@ Extension points
 The following functions can be provided to main(), to load_tool(), or to the
 executor to override or augment the listed behaviors.
 
-executor(tool, job_order_object, **kwargs)
-  (Process, Dict[Text, Any], **Any) -> Tuple[Dict[Text, Any], Text]
+executor
+  ::
+
+    executor(tool, job_order_object, **kwargs)
+      (Process, Dict[Text, Any], **Any) -> Tuple[Dict[Text, Any], Text]
 
   A toplevel workflow execution loop, should synchronously execute a process
   object and return an output object.
 
-makeTool(toolpath_object, **kwargs)
-  (Dict[Text, Any], **Any) -> Process
+makeTool
+  ::
+
+    makeTool(toolpath_object, **kwargs)
+      (Dict[Text, Any], **Any) -> Process
 
   Construct a Process object from a document.
 
-selectResources(request)
-  (Dict[Text, int]) -> Dict[Text, int]
+selectResources
+  ::
+
+    selectResources(request)
+      (Dict[Text, int]) -> Dict[Text, int]
 
   Take a resource request and turn it into a concrete resource assignment.
 
-versionfunc()
-  () -> Text
+versionfunc
+  ::
+
+    ()
+      () -> Text
 
   Return version string.
 
-make_fs_access(basedir)
-  (Text) -> StdFsAccess
+make_fs_access
+  ::
+
+    make_fs_access(basedir)
+      (Text) -> StdFsAccess
 
   Return a file system access object.
 
-fetcher_constructor(cache, session)
-  (Dict[unicode, unicode], requests.sessions.Session) -> Fetcher
+fetcher_constructor
+  ::
+
+    fetcher_constructor(cache, session)
+      (Dict[unicode, unicode], requests.sessions.Session) -> Fetcher
 
   Construct a Fetcher object with the supplied cache and HTTP session.
 
-resolver(document_loader, document)
-  (Loader, Union[Text, dict[Text, Any]]) -> Text
+resolver
+  ::
+
+    resolver(document_loader, document)
+      (Loader, Union[Text, dict[Text, Any]]) -> Text
 
   Resolve a relative document identifier to an absolute one which can be fetched.
 
 logger_handler
-  logging.Handler
+  ::
+
+    logger_handler
+      logging.Handler
 
   Handler object for logging.

cwltool/draft2tool.py

@@ -391,9 +391,9 @@ def rm_pending_output_callback(output_callbacks, jobcachepending,
                             "writable": t.get("writable")
                         }
                     else:
-                        if t["entryname"] or t["writable"]:
+                        if t.get("entryname") or t.get("writable"):
                             t = copy.deepcopy(t)
-                            if t["entryname"]:
+                            if t.get("entryname"):
                                 t["entry"]["basename"] = t["entryname"]
                             t["entry"]["writable"] = t.get("writable")
                         ls[i] = t["entry"]

tox.ini

@@ -3,7 +3,9 @@ envlist =
   py{27,33,34,35,36}-lint,
   py{27,33,34,35,36}-unit,
   py35-mypy{2,3},
-  py27-pipconflictchecker
+  py27-pipconflictchecker,
+  py27-lint-readme,
+  py27-pydocstyle
 
 skipsdist = True
 skip_missing_interpreters = True
@@ -44,4 +46,18 @@ deps =
 [testenv:py27-pipconflictchecker]
 commands = pipconflictchecker
 whitelist_externals = pipconflictchecker
-deps = pip-conflict-checker
+deps = pip-conflict-checker
+
+[testenv:py27-unit]
+commands = python setup.py test
+
+[testenv:py27-lint-readme]
+commands = python setup.py check -r -s
+deps =
+    readme
+
+[testenv:py27-pydocstyle]
+commands = make diff_pydocstyle_report
+deps =
+    pydocstyle
+    diff-cover