Merge branch 'master' of github.com:common-workflow-language/schema_salad

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

Author: Peter Amstutz

Makefile

@@ -65,7 +65,7 @@ pep8: $(PYSOURCES)
 	pep8 --exclude=_version.py  --show-source --show-pep8 $^ || true
 
 pep8_report.txt: $(PYSOURCES)
-	pep8 --exclude=_version.py $^ > pep8_report.txt || true
+	pep8 --exclude=_version.py $^ > $@ || true
 
 diff_pep8_report: pep8_report.txt
 	diff-quality --violations=pep8 pep8_report.txt
@@ -75,7 +75,7 @@ pep257: $(PYSOURCES)
 	pep257 --ignore=D100,D101,D102,D103 $^ || true
 
 pep257_report.txt: $(PYSOURCES)
-	pep257 setup.py $^ > pep257_report.txt 2>&1 || true
+	pep257 setup.py $^ > $@ 2>&1 || true
 
 diff_pep257_report: pep257_report.txt
 	diff-quality --violations=pep8 pep257_report.txt
@@ -96,7 +96,7 @@ pylint: $(PYSOURCES)
 
 pylint_report.txt: ${PYSOURCES}
 	pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
-		$^ > pylint_report.txt || true
+		$^ > $@ || true
 
 diff_pylint_report: pylint_report.txt
 	diff-quality --violations=pylint pylint_report.txt
@@ -147,19 +147,18 @@ htmlcov/index.html: .coverage
 coverage-report: .coverage
 	coverage report
 
-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 $@
 
 ## test        : run the ${MODULE} test suite
 test: FORCE
-	python tests/test_examples.py 
+	python setup.py test
 
 sloccount.sc: ${PYSOURCES} Makefile
-	sloccount --duplicates --wide --details $^ > sloccount.sc
+	sloccount --duplicates --wide --details $^ > $@
 
 ## sloccount   : count lines of code
 sloccount: ${PYSOURCES} Makefile
@@ -170,13 +169,15 @@ list-author-emails:
 	@git log --format='%aN,%aE' | sort -u | grep -v 'root'
 
 mypy: ${PYSOURCES}
-	MYPYPATH=typeshed/2.7 mypy --py2 schema_salad
-	#MYPYPATH=typeshed/2.7 mypy --py2  --disallow-untyped-calls schema_salad
+	MYPYPATH=typeshed/2.7 mypy --py2 --disallow-untyped-calls schema_salad
 
 jenkins:
 	if ! test -d env ; then virtualenv env ; fi
 	. env/bin/activate ; \
-	${MAKE} install-dep coverage.html coverage.xml mypy pep257_report.txt \
+	${MAKE} install-dep coverage.html coverage.xml pep257_report.txt \
 		sloccount.sc pep8_report.txt pylint_report.txt
+	if ! test -d env3 ; then virtualenv -p python3 env3 ; fi
+	. env3/bin/activate ; \
+	pip install mypy-lang; ${MAKE} mypy
 
 FORCE:

schema_salad/ref_resolver.py

@@ -17,6 +17,7 @@
 from .aslist import aslist
 import rdflib
 from rdflib.namespace import RDF, RDFS, OWL
+from rdflib.plugins.parsers.notation3 import BadSyntax
 import xml.sax
 from typing import cast, Union, Tuple, Dict, Any, Callable, Iterable
 
@@ -160,6 +161,10 @@ def add_schemas(self, ns, base_url):
                     break
                 except xml.sax.SAXParseException:  # type: ignore
                     pass
+                except TypeError:
+                    pass
+                except BadSyntax:
+                    pass
 
         for s, _, _ in self.graph.triples((None, RDF.type, RDF.Property)):
             self._add_properties(s)
@@ -268,9 +273,7 @@ def resolve_ref(self, ref, base_url=None):
         if not isinstance(ref, (str, unicode)):
             raise ValueError("Must be string: `%s`" % str(ref))
 
-        url = self.expand_url(cast(  # bug in mypy 0.3.1, fixed in 0.4-dev
-            Union[str, unicode], ref), base_url,
-            scoped=(obj is not None))
+        url = self.expand_url(ref, base_url, scoped=(obj is not None))
 
         # Has this reference been loaded already?
         if url in self.idx:
@@ -316,7 +319,7 @@ def resolve_ref(self, ref, base_url=None):
             return obj, metadata
 
     def resolve_all(self, document, base_url, file_base=None):
-        # type: (Any, Union[str, unicode], Union[str, unicode]) -> Tuple[Any, Dict[str, str]]
+        # type: (Any, Union[str, unicode], Union[str, unicode]) -> Tuple[Any, Dict[str, Any]]
         loader = self
         metadata = {}  # type: Dict[str, Any]
         if file_base is None:
@@ -526,13 +529,11 @@ def validate_link(self, field, link):
         if isinstance(link, (str, unicode)):
             if field in self.vocab_fields:
                 if link not in self.vocab and link not in self.idx and link not in self.rvocab:
-                    if not self.check_file(cast(  # bug in mypy 0.3.1
-                            Union[str, unicode], link)):  # fixed in mypy 0.4-dev
+                    if not self.check_file(link):
                         raise validate.ValidationException(
                             "Field `%s` contains undefined reference to `%s`" % (field, link))
             elif link not in self.idx and link not in self.rvocab:
-                if not self.check_file(cast(  # bug in mypy 0.3.1
-                        Union[str, unicode], link)):  # fixed in mypy 0.4-dev
+                if not self.check_file(link):
                     raise validate.ValidationException(
                         "Field `%s` contains undefined reference to `%s`" % (field, link))
         elif isinstance(link, list):

schema_salad/schema.py

@@ -159,7 +159,7 @@ def get_metaschema():
 
 
 def load_schema(schema_ref, cache=None):
-    # type: (Union[unicode, Dict[str, Any]], Dict) -> Tuple[ref_resolver.Loader, Union[avro.schema.Names, avro.schema.SchemaParseException], Dict[unicode, Any]]
+    # type: (Union[unicode, Dict[str, Any]], Dict) -> Tuple[ref_resolver.Loader, Union[avro.schema.Names, avro.schema.SchemaParseException], Dict[unicode, Any], ref_resolver.Loader]
     metaschema_names, metaschema_doc, metaschema_loader = get_metaschema()
     if cache is not None:
         metaschema_loader.cache = cache
@@ -330,12 +330,8 @@ def make_valid_avro(items, alltypes, found, union=False):
             ret.append(make_valid_avro(i, alltypes, found, union=union))
         return ret
     if union and isinstance(items, (str, unicode)):
-        if items in alltypes and avro_name(cast(  # bug in mypy 0.3.1, fixed in
-                Union[str, unicode], items)) not in found:  # 0.4-dev
-            return cast(Dict,
-                    make_valid_avro(alltypes[cast(  # bug in mypy 0.3.1, fixed
-                        # fixed in 0.4-dev
-                        Union[str, unicode], items)], alltypes, found,
+        if items in alltypes and avro_name(items) not in found:
+            return cast(Dict, make_valid_avro(alltypes[items], alltypes, found,
                         union=union))
         items = avro_name(items)  # type: ignore
         # bug in mypy 0.3.1, fixed in 0.4-dev

tox.ini

@@ -9,7 +9,7 @@ deps = -rrequirements.txt
 [testenv:py34-mypy]
 commands = make mypy
 whitelist_externals = make
-deps = mypy-lang
+deps = mypy-lang>=0.4
 
 [testenv:py35-lint]
 commands = flake8 schema_salad setup.py

typeshed/2.7/rdflib/graph.pyi

@@ -70,7 +70,10 @@ class Graph(Node):
     def namespaces(self): ...
     def absolutize(self, uri, defrag=1): ...
     def serialize(self, destination: Union[str, IO[Any]]=None, format: str='', base: str=None, encoding: str=None, **args) -> Union[bytes, None]: ...
-    def parse(self, source: str=None, publicID: str=None, format: str=None, location: str=None, file: IO[Any]=None, data: str=None, **args): ...
+    def parse(self, source: str = None, publicID: str = None,
+              format: Union[str, unicode] = None,
+              location: Union[str, unicode] = None, file: IO[Any] = None,
+              data: str = None, **args): ...
     def load(self, source, publicID=None, format=''): ...
     def query(self, query_object, processor: str = '', result: str = '', initNs: Dict = None, initBindings: Dict = None, use_store_provided: bool = True, **kwargs) -> Result: ...
     def update(self, update_object, processor='', initNs=..., initBindings=..., use_store_provided=True, **kwargs): ...

typeshed/2.7/rdflib/plugins/__init__.pyi

@@ -0,0 +1,4 @@
+# Stubs for rdflib.plugins (Python 3.5)
+#
+# NOTE: This dynamically typed stub was automatically generated by stubgen.
+

typeshed/2.7/rdflib/plugins/parsers/__init__.pyi

@@ -0,0 +1,4 @@
+# Stubs for rdflib.plugins.parsers (Python 3.5)
+#
+# NOTE: This dynamically typed stub was automatically generated by stubgen.
+

typeshed/2.7/rdflib/plugins/parsers/notation3.pyi

@@ -0,0 +1,12 @@
+# Stubs for rdflib.plugins.parsers.notation3 (Python 3.5)
+#
+# NOTE: This dynamically typed stub was automatically generated by stubgen.
+
+from typing import Any
+from rdflib.parser import Parser
+
+class BadSyntax(SyntaxError):
+    lines = ...  # type: Any
+    def __init__(self, uri, lines, argstr, i, why): ...
+    @property
+    def message(self): ...