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pyre v0.0.27 #186

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Jul 2, 2019
Merged

pyre v0.0.27 #186

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8 changes: 4 additions & 4 deletions WDL/Lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -275,9 +275,9 @@ def expr(self, obj: Expr.Base) -> Any:
msg = "{} argument of {}() = :{}:".format(str(F_i), F.name, str(arg_i.type))
self.add(pt, msg, arg_i.pos)
elif obj.function_name == "size":
if not isinstance(obj.arguments[0].type, Type.File) and not (
isinstance(obj.arguments[0].type, Type.Array)
and isinstance(obj.arguments[0].type.item_type, Type.File)
arg0ty = obj.arguments[0].type
if not isinstance(arg0ty, Type.File) and not (
isinstance(arg0ty, Type.Array) and isinstance(arg0ty.item_type, Type.File)
):
self.add(
pt,
Expand Down Expand Up @@ -719,7 +719,7 @@ def decl(self, obj: Tree.Decl) -> Any:
while not isinstance(tw, (Tree.Task, Tree.Workflow)):
tw = getattr(tw, "parent")
assert isinstance(tw, (Tree.Task, Tree.Workflow))
if tw.inputs is not None and obj not in tw.inputs:
if isinstance(tw.inputs, list) and obj not in tw.inputs:
self.add(
obj,
"unnecessary optional quantifier (?) for non-input {} {}".format(
Expand Down
81 changes: 38 additions & 43 deletions WDL/StdLib.py
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Original file line number Diff line number Diff line change
Expand Up @@ -448,20 +448,15 @@ class _Size(EagerFunction):
def infer_type(self, expr: "Expr.Apply") -> Type.Base:
if not expr.arguments:
raise Error.WrongArity(expr, 1)
if not expr.arguments[0].type.coerces(Type.File(optional=True)):
if isinstance(expr.arguments[0].type, Type.Array):
if expr.arguments[0].type.optional or not expr.arguments[0].type.item_type.coerces(
Type.File(optional=True)
):
arg0ty = expr.arguments[0].type
if not arg0ty.coerces(Type.File(optional=True)):
if isinstance(arg0ty, Type.Array):
if arg0ty.optional or not arg0ty.item_type.coerces(Type.File(optional=True)):
raise Error.StaticTypeMismatch(
expr.arguments[0],
Type.Array(Type.File(optional=True)),
expr.arguments[0].type,
expr.arguments[0], Type.Array(Type.File(optional=True)), arg0ty
)
else:
raise Error.StaticTypeMismatch(
expr.arguments[0], Type.File(optional=True), expr.arguments[0].type
)
raise Error.StaticTypeMismatch(expr.arguments[0], Type.File(optional=True), arg0ty)
if len(expr.arguments) == 2:
if expr.arguments[1].type != Type.String():
raise Error.StaticTypeMismatch(
Expand Down Expand Up @@ -505,17 +500,14 @@ class _SelectFirst(EagerFunction):
def infer_type(self, expr: "Expr.Apply") -> Type.Base:
if len(expr.arguments) != 1:
raise Error.WrongArity(expr, 1)
if not isinstance(expr.arguments[0].type, Type.Array) or (
expr.arguments[0]._check_quant and expr.arguments[0].type.optional
arg0ty = expr.arguments[0].type
if not isinstance(arg0ty, Type.Array) or (
expr.arguments[0]._check_quant and arg0ty.optional
):
raise Error.StaticTypeMismatch(
expr.arguments[0], Type.Array(Type.Any()), expr.arguments[0].type
)
if isinstance(expr.arguments[0].type.item_type, Type.Any):
raise Error.StaticTypeMismatch(expr.arguments[0], Type.Array(Type.Any()), arg0ty)
if isinstance(arg0ty.item_type, Type.Any):
raise Error.IndeterminateType(expr.arguments[0], "can't infer item type of empty array")
ty = expr.arguments[0].type.item_type
assert isinstance(ty, Type.Base)
return ty.copy(optional=False)
return arg0ty.item_type.copy(optional=False)

def _call_eager(self, expr: "Expr.Apply", arguments: List[Value.Base]) -> Value.Base:
arr = arguments[0].coerce(Type.Array(Type.Any()))
Expand All @@ -530,17 +522,14 @@ class _SelectAll(EagerFunction):
def infer_type(self, expr: "Expr.Apply") -> Type.Base:
if len(expr.arguments) != 1:
raise Error.WrongArity(expr, 1)
if not isinstance(expr.arguments[0].type, Type.Array) or (
expr.arguments[0]._check_quant and expr.arguments[0].type.optional
arg0ty = expr.arguments[0].type
if not isinstance(arg0ty, Type.Array) or (
expr.arguments[0]._check_quant and arg0ty.optional
):
raise Error.StaticTypeMismatch(
expr.arguments[0], Type.Array(Type.Any()), expr.arguments[0].type
)
if isinstance(expr.arguments[0].type.item_type, Type.Any):
raise Error.StaticTypeMismatch(expr.arguments[0], Type.Array(Type.Any()), arg0ty)
if isinstance(arg0ty.item_type, Type.Any):
raise Error.IndeterminateType(expr.arguments[0], "can't infer item type of empty array")
ty = expr.arguments[0].type.item_type
assert isinstance(ty, Type.Base)
return Type.Array(ty.copy(optional=False))
return Type.Array(arg0ty.item_type.copy(optional=False))

def _call_eager(self, expr: "Expr.Apply", arguments: List[Value.Base]) -> Value.Base:
arr = arguments[0].coerce(Type.Array(Type.Any()))
Expand Down Expand Up @@ -609,19 +598,23 @@ def _call_eager(self, expr: "Expr.Apply", arguments: List[Value.Base]) -> Value.

class _Flatten(EagerFunction):
# t array array -> t array
# TODO: if any of the input arrays are statically nonempty then so is output
def infer_type(self, expr: "Expr.Apply") -> Type.Base:
if len(expr.arguments) != 1:
raise Error.WrongArity(expr, 1)
expr.arguments[0].typecheck(Type.Array(Type.Any()))
# TODO: won't handle implicit coercion from T to Array[T]
assert isinstance(expr.arguments[0].type, Type.Array)
if expr.arguments[0].type.item_type is None:
arg0ty = expr.arguments[0].type
assert isinstance(arg0ty, Type.Array)
if isinstance(arg0ty.item_type, Type.Any):
return Type.Array(Type.Any())
if not isinstance(expr.arguments[0].type.item_type, Type.Array):
if not isinstance(arg0ty.item_type, Type.Array) or (
expr._check_quant and arg0ty.item_type.optional
):
raise Error.StaticTypeMismatch(
expr.arguments[0], Type.Array(Type.Array(Type.Any())), expr.arguments[0].type
expr.arguments[0], Type.Array(Type.Array(Type.Any())), arg0ty
)
return Type.Array(expr.arguments[0].type.item_type.item_type)
return Type.Array(arg0ty.item_type.item_type)

def _call_eager(self, expr: "Expr.Apply", arguments: List[Value.Base]) -> Value.Base:
ty = self.infer_type(expr)
Expand All @@ -634,19 +627,23 @@ def _call_eager(self, expr: "Expr.Apply", arguments: List[Value.Base]) -> Value.

class _Transpose(EagerFunction):
# t array array -> t array array
# TODO: if any of the input arrays are statically nonempty then so is output
def infer_type(self, expr: "Expr.Apply") -> Type.Base:
if len(expr.arguments) != 1:
raise Error.WrongArity(expr, 1)
expr.arguments[0].typecheck(Type.Array(Type.Any()))
# TODO: won't handle implicit coercion from T to Array[T]
assert isinstance(expr.arguments[0].type, Type.Array)
if expr.arguments[0].type.item_type is None:
arg0ty = expr.arguments[0].type
assert isinstance(arg0ty, Type.Array)
if isinstance(arg0ty.item_type, Type.Any):
return Type.Array(Type.Any())
if not isinstance(expr.arguments[0].type.item_type, Type.Array):
if not isinstance(arg0ty.item_type, Type.Array) or (
expr._check_quant and arg0ty.item_type.optional
):
raise Error.StaticTypeMismatch(
expr.arguments[0], Type.Array(Type.Array(Type.Any())), expr.arguments[0].type
expr.arguments[0], Type.Array(Type.Array(Type.Any())), arg0ty
)
return expr.arguments[0].type
return Type.Array(Type.Array(arg0ty.item_type.item_type))

def _call_eager(self, expr: "Expr.Apply", arguments: List[Value.Base]) -> Value.Base:
ty = self.infer_type(expr)
Expand Down Expand Up @@ -703,11 +700,9 @@ def infer_type(self, expr: "Expr.Apply") -> Type.Base:
raise Error.WrongArity(expr, 2)
expr.arguments[0].typecheck(Type.String())
expr.arguments[1].typecheck(Type.Array(Type.String()))
arg1ty = expr.arguments[1].type
return Type.Array(
Type.String(),
nonempty=(
isinstance(expr.arguments[1].type, Type.Array) and expr.arguments[1].type.nonempty
),
Type.String(), nonempty=(isinstance(arg1ty, Type.Array) and arg1ty.nonempty)
)

def _call_eager(self, expr: "Expr.Apply", arguments: List[Value.Base]) -> Value.Base:
Expand Down
14 changes: 7 additions & 7 deletions WDL/Tree.py
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Original file line number Diff line number Diff line change
Expand Up @@ -379,12 +379,11 @@ def resolve(self, doc: TVDocument, call_names: Optional[Set[str]] = None) -> Non
callee_doc = imp.doc
if callee_doc:
assert isinstance(callee_doc, Document)
if callee_doc.workflow and callee_doc.workflow.name == self.callee_id[-1]:
if not callee_doc.workflow.complete_calls or (
callee_doc.workflow.outputs is None and callee_doc.workflow.effective_outputs
):
wf = callee_doc.workflow
if isinstance(wf, Workflow) and wf.name == self.callee_id[-1]:
if not wf.complete_calls or (wf.outputs is None and wf.effective_outputs):
raise Error.UncallableWorkflow(self, ".".join(self.callee_id))
self.callee = callee_doc.workflow
self.callee = wf
else:
for task in callee_doc.tasks:
if task.name == self.callee_id[-1]:
Expand Down Expand Up @@ -555,7 +554,7 @@ def add_to_type_env(
# seen as Array[T] outside)
inner_type_env: Env.Types = []
for elt in self.elements:
inner_type_env = elt.add_to_type_env(struct_typedefs, inner_type_env)
inner_type_env = elt.add_to_type_env(struct_typedefs, inner_type_env) # pyre-ignore
# Subtlety: if the scatter array is statically nonempty, then so too
# are the arrayized values.
nonempty = isinstance(self.expr._type, Type.Array) and self.expr._type.nonempty
Expand Down Expand Up @@ -1183,6 +1182,7 @@ def _build_workflow_type_env(
child_outer_type_env = type_env
for sibling in self.elements:
if sibling is not child:
# pyre-ignore
child_outer_type_env = sibling.add_to_type_env(
doc.struct_typedefs, child_outer_type_env
)
Expand All @@ -1197,7 +1197,7 @@ def _build_workflow_type_env(

# finally, populate self._type_env with all our children
for child in self.elements:
type_env = child.add_to_type_env(doc.struct_typedefs, type_env)
type_env = child.add_to_type_env(doc.struct_typedefs, type_env) # pyre-ignore
self._type_env = type_env


Expand Down
8 changes: 4 additions & 4 deletions WDL/runtime/task.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
from types import FrameType
from requests.exceptions import ReadTimeout
import docker
from .. import Error, Type, Env, Expr, Value, StdLib, Task, Tree, _util
from .. import Error, Type, Env, Expr, Value, StdLib, Tree, _util
from .error import *


Expand Down Expand Up @@ -287,7 +287,7 @@ def _run(self, logger: logging.Logger, command: str) -> int:


def run_local_task(
task: Task,
task: Tree.Task,
posix_inputs: Env.Values,
task_id: Optional[str] = None,
parent_dir: Optional[str] = None,
Expand Down Expand Up @@ -360,7 +360,7 @@ def run_local_task(


def _eval_task_inputs(
logger: logging.Logger, task: Task, posix_inputs: Env.Values, container: TaskContainer
logger: logging.Logger, task: Tree.Task, posix_inputs: Env.Values, container: TaskContainer
) -> Env.Values:
# Map all the provided input Files to in-container paths
# First make a pass to collect all the host paths and pass them to the
Expand Down Expand Up @@ -434,7 +434,7 @@ def map_files(v: Value.Base) -> Value.Base:


def _eval_task_outputs(
logger: logging.Logger, task: Task, env: Env.Values, container: TaskContainer
logger: logging.Logger, task: Tree.Task, env: Env.Values, container: TaskContainer
) -> Env.Values:

outputs = []
Expand Down
2 changes: 1 addition & 1 deletion requirements.dev.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# Packages needed for miniwdl development, in addition to those in
# requirements.txt which are needed for miniwdl to run in common use.
pyre-check==0.0.22
pyre-check==0.0.27
black==19.3b0
pylint
sphinx
Expand Down