simplify IO

Author: mr-c

Makefile

@@ -133,11 +133,11 @@ diff-cover.html: coverage.xml
 
 ## test        : run the ${MODULE} test suite
 test: FORCE
-	python setup.py test # --addopts "-n auto --dist=loadfile"
+	python setup.py test --addopts "tests"  #-n auto --dist=loadfile"
 
 ## testcov     : run the ${MODULE} test suite and collect coverage
 testcov: $(pysources)
-	python setup.py test --addopts "--cov ${MODULE}" # -n auto --dist=loadfile"
+	python setup.py test --addopts "tests --cov ${MODULE}" # -n auto --dist=loadfile"
 
 sloccount.sc: ${PYSOURCES} Makefile
 	sloccount --duplicates --wide --details $^ > $@

cwl_utils/graph_split.py

@@ -7,9 +7,8 @@
 
 import os
 import sys
-from io import StringIO
 from pathlib import Path
-from typing import Any, Dict, List, MutableMapping, Set, Text, Union, cast
+from typing import IO, Any, Dict, List, MutableMapping, Set, Text, Union, cast
 
 from ruamel import yaml
 from schema_salad.sourceline import SourceLine, add_lc_filename
@@ -18,16 +17,13 @@
 def main(args: List[str]) -> None:
     """Split the packed CWL at the path of the first argument."""
     with open(args[0], "r") as source_handle:
-        sourceStr = str(source_handle.read())
-    run(sourceStr, (Path.cwd() / args[0]).as_uri())
+        run(source_handle)
 
 
-def run(sourceStr: str, source_uri: str) -> None:
+def run(sourceIO: IO[str]) -> None:
     """Loop over the provided packed CWL document and split it up."""
-    sourceIO = StringIO(sourceStr)
-    sourceIO.name = source_uri
     source = yaml.main.round_trip_load(sourceIO, preserve_quotes=True)
-    add_lc_filename(source, source_uri)
+    add_lc_filename(source, sourceIO.name)
 
     if "$graph" not in source:
         print("No $graph, so not for us.")
@@ -51,8 +47,8 @@ def my_represent_none(
             for import_name in imports:
                 rewrite_types(entry, "#{}".format(import_name), False)
         if entry_id == "main":
-            entry_id = "unpacked_{}".format(os.path.basename(source_uri))
-        with open(entry_id, "w") as result_handle:
+            entry_id = "unpacked_{}".format(os.path.basename(sourceIO.name))
+        with open(entry_id, "w", encoding="utf-8") as result_handle:
             yaml.main.round_trip_dump(
                 entry,
                 result_handle,
@@ -159,7 +155,7 @@ def rewrite_schemadef(document: MutableMapping[str, Any]) -> Set[str]:
             for field in entry["fields"]:
                 field["name"] = field["name"].split("/")[2]
                 rewrite_types(field, entry_file, True)
-            with open(entry_file[1:], "a") as entry_handle:
+            with open(entry_file[1:], "a", encoding="utf-8") as entry_handle:
                 yaml.dump([entry], entry_handle, Dumper=yaml.RoundTripDumper)
             entry["$import"] = entry_file[1:]
             del entry["name"]

requirements.txt

@@ -1,2 +1,2 @@
 ruamel.yaml<=0.16.5,>=0.12.4
-schema_salad
+schema-salad

setup.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
 import sys
-import os
 
 from setuptools import find_packages, setup
 

tests/test_etools_to_clt.py

@@ -1,5 +1,4 @@
 """Test the CWL Expression refactoring tool."""
-from os import environ
 from pathlib import Path
 
 from cwltool.errors import WorkflowException

tests/test_graph_split.py

@@ -1,5 +1,6 @@
 """Test the CWL $graph document splitter tool."""
 import os
+from io import StringIO
 from pathlib import Path
 from unittest import TestCase
 
@@ -13,4 +14,6 @@
 def test_graph_split(tmp_path: Path):
     """Confirm that a user provided example produces no exception."""
     os.chdir(tmp_path)
-    run(requests.get(URI).text, URI)
+    sourceIO = StringIO(requests.get(URI).text)
+    sourceIO.name = URI
+    run(sourceIO)

tox.ini

@@ -46,7 +46,7 @@ setenv =
 commands =
   py{36,37,38,39}-unit: python -m pip install -U pip setuptools wheel
   py{36,37,38,39}-unit: python -m pip install -e .
-  py{36,37,38,39}-unit: coverage run --parallel-mode -m pytest --strict {posargs}
+  py{36,37,38,39}-unit: coverage run --parallel-mode -m pytest --strict tests {posargs}
   py{36,37,38,39}-unit: coverage combine
   py{36,37,38,39}-unit: coverage report
   py{36,37,38,39}-unit: coverage xml
@@ -55,7 +55,7 @@ commands =
   py{36,37,38,39}-lint: flake8 setup.py cwl_utils
   py{36,37,38,39}-lint: black --diff --check --exclude 'parser_v.*' setup.py cwl_utils
   py{36,37,38,39}-mypy: make mypy
-  py{36,37,38,39}-mypy: make mypyc
+# py{36,37,38,39}-mypy: make mypyc
 
 whitelist_externals =
   py{36,37,38,39}-lint: flake8