task runtime skeleton (#134)

Initial skeleton of the local task runtime, with proofs of concept for docker container management, file path mapping, and I/O stdlib functions like `stdout()` and `write_lines()`.

.travis.yml

@@ -7,5 +7,4 @@ script:
   - |
       set -ex -o pipefail
       make docker
-      docker run --env TRAVIS_JOB_ID=${TRAVIS_JOB_ID} --env TRAVIS_BRANCH=${TRAVIS_BRANCH} miniwdl coveralls
-      docker run --env TRAVIS_JOB_ID=${TRAVIS_JOB_ID} --env TRAVIS_BRANCH=${TRAVIS_BRANCH} miniwdl make sopretty
+      docker run --env TRAVIS_JOB_ID=${TRAVIS_JOB_ID} --env TRAVIS_BRANCH=${TRAVIS_BRANCH} -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp miniwdl bash -c "make sopretty && make && coveralls && make doc"

Dockerfile

@@ -11,8 +11,7 @@ RUN bash -o pipefail -c "pip3 install --user -r <(cat /miniwdl/requirements.txt
 # minor source change.
 ADD . /miniwdl
 WORKDIR /miniwdl
-# Run the default make rule, which will trigger typechecking and tests.
 ENV PYTHONPATH $PYTHONPATH:/root/.local/lib/python3.6
 ENV PATH $PATH:/root/.local/bin
-RUN make && make doc
+# will trigger typechecking & tests:
 CMD make

Makefile

@@ -35,7 +35,8 @@ sopretty:
 	$(MAKE) pretty
 	@git diff --quiet || (echo "ERROR: source files were modified by black; please fix up this commit with 'make pretty'"; exit 1)
 
-# run tests in a docker image
+# build docker image with current source tree, poised to run tests e.g.:
+#   docker run --rm -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp miniwdl
 docker:
 	docker build -t miniwdl .
 

WDL/Lint.py

@@ -754,7 +754,7 @@ def task(self, obj: WDL.Task) -> Any:
             else:
                 assert isinstance(part, str)
                 command.append(part)
-        col_offset, command = _strip_leading_whitespace("".join(command))
+        col_offset, command = WDL._util.strip_leading_whitespace("".join(command))
 
         # write out a temp file with this fake script
         tfn = os.path.join(self._tmpdir, obj.name)
@@ -830,29 +830,6 @@ def _shellcheck_dummy_value(ty, pos):
     return "x" * desired_length
 
 
-def _strip_leading_whitespace(txt):
-    lines = txt.split("\n")
-
-    to_strip = None
-    for line in lines:
-        lsl = len(line.lstrip())
-        if lsl:
-            c = len(line) - lsl
-            assert c >= 0
-            if to_strip is None or to_strip > c:
-                to_strip = c
-            # TODO: do something about mixed tabs & spaces
-
-    if not to_strip:
-        return (0, txt)
-
-    for i, line_i in enumerate(lines):
-        if line_i.lstrip():
-            lines[i] = line_i[to_strip:]
-
-    return (to_strip, "\n".join(lines))
-
-
 @a_linter
 class MixedIndentation(Linter):
     # Line of task command mixes tab and space indentation

WDL/__init__.py

@@ -3,8 +3,9 @@
 import errno
 import inspect
 from typing import List, Optional, Callable
-from WDL import _parser, Error, Type, Value, Env, Expr, Tree, Walker, StdLib
+from WDL import _util, _parser, Error, Type, Value, Env, Expr, Tree, Walker, StdLib
 from WDL.Tree import Decl, StructTypeDef, Task, Call, Scatter, Conditional, Workflow, Document
+import WDL.runtime
 
 SourcePosition = Error.SourcePosition
 SourceNode = Error.SourceNode

WDL/_util.py

@@ -0,0 +1,30 @@
+# pyre-strict
+# misc utility functions...
+
+from typing import Tuple
+
+
+def strip_leading_whitespace(txt: str) -> Tuple[int, str]:
+    # Given a multi-line string, determine the largest w such that each line
+    # begins with at least w whitespace characters. Return w and the string
+    # with w characters removed from the beginning of each line.
+    lines = txt.split("\n")
+
+    to_strip = None
+    for line in lines:
+        lsl = len(line.lstrip())
+        if lsl:
+            c = len(line) - lsl
+            assert c >= 0
+            if to_strip is None or to_strip > c:
+                to_strip = c
+            # TODO: do something about mixed tabs & spaces
+
+    if not to_strip:
+        return (0, txt)
+
+    for i, line_i in enumerate(lines):
+        if line_i.lstrip():
+            lines[i] = line_i[to_strip:]
+
+    return (to_strip, "\n".join(lines))

WDL/runtime/__init__.py

@@ -0,0 +1,3 @@
+# pyre-strict
+import WDL.runtime.task
+from WDL.runtime.task import run_local_task