release v0.12

mr-c · mr-c · commit cae534912c19 · 2021-11-07T10:23:05.000+01:00
diff --git a/Makefile b/Makefile
@@ -26,7 +26,7 @@ EXTRAS=
 
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
-PYSOURCES=$(filter-out parser/cwl_v%,$(shell find $(MODULE) -name "*.py")) $(wildcard tests/*.py) *.py
+PYSOURCES=$(filter-out $(MODULE)/parser/cwl_v%,$(shell find $(MODULE) -name "*.py")) $(wildcard tests/*.py) $(wildcard *.py)
 DEVPKGS=diff_cover black pylint pep257 pydocstyle flake8 tox tox-pyenv \
 	isort wheel autoflake flake8-bugbear pyupgrade bandit \
 	-rtest-requirements.txt -rmypy-requirements.txt
diff --git a/create_cwl_from_objects.py b/create_cwl_from_objects.py
@@ -1,9 +1,9 @@
 #!/usr/bin/env python3
 # SPDX-License-Identifier: Apache-2.0
-from cwl_utils.parser import cwl_v1_2 as cwl
-
 from ruamel import yaml
 
+from cwl_utils.parser import cwl_v1_2 as cwl
+
 
 def main() -> None:
     """Generate a CWL object to match "cat-tool.cwl"."""
diff --git a/cwl_utils/__meta__.py b/cwl_utils/__meta__.py
@@ -1,2 +1,2 @@
 """Global version number for the cwl_utils package."""
-__version__ = "0.11"
+__version__ = "0.12"
diff --git a/cwl_utils/cwl_expression_refactor.py b/cwl_utils/cwl_expression_refactor.py
@@ -8,6 +8,7 @@
 import sys
 from pathlib import Path
 from typing import (
+    TYPE_CHECKING,
     Any,
     Callable,
     Dict,
@@ -16,7 +17,6 @@
     Optional,
     Tuple,
     Union,
-    TYPE_CHECKING,
 )
 
 from cwltool.loghandler import _logger as _cwltoollogger
@@ -38,12 +38,7 @@
     cwl_v1_1_expression_refactor,
     cwl_v1_2_expression_refactor,
 )
-
-from cwl_utils.parser import (
-    cwl_v1_0,
-    cwl_v1_1,
-    cwl_v1_2,
-)
+from cwl_utils.parser import cwl_v1_0, cwl_v1_1, cwl_v1_2
 
 save_type = Union[Dict[str, str], List[Union[Dict[str, str], List[Any], None]], None]
 
@@ -109,7 +104,7 @@ def run(args: argparse.Namespace) -> int:
     """Primary processing loop."""
     for document in args.inputs:
         _logger.info("Processing %s.", document)
-        with open(document, "r") as doc_handle:
+        with open(document) as doc_handle:
             result = yaml.main.round_trip_load(doc_handle, preserve_quotes=True)
         version = result["cwlVersion"]
         uri = Path(document).resolve().as_uri()
diff --git a/cwl_utils/cwl_normalizer.py b/cwl_utils/cwl_normalizer.py
@@ -7,12 +7,7 @@
 import sys
 import tempfile
 from pathlib import Path
-from typing import (
-    List,
-    MutableSequence,
-    Optional,
-    Set,
-)
+from typing import List, MutableSequence, Optional, Set
 
 from cwltool.context import LoadingContext, RuntimeContext
 from cwltool.load_tool import (
@@ -89,7 +84,7 @@ def run(args: argparse.Namespace) -> int:
     imports: Set[str] = set()
     for document in args.inputs:
         _logger.info("Processing %s.", document)
-        with open(document, "r") as doc_handle:
+        with open(document) as doc_handle:
             result = yaml.main.round_trip_load(doc_handle, preserve_quotes=True)
         add_lc_filename(result, document)
         version = result.get("cwlVersion", None)
diff --git a/cwl_utils/cwl_v1_0_expression_refactor.py b/cwl_utils/cwl_v1_0_expression_refactor.py
diff --git a/cwl_utils/cwl_v1_1_expression_refactor.py b/cwl_utils/cwl_v1_1_expression_refactor.py
diff --git a/cwl_utils/cwl_v1_2_expression_refactor.py b/cwl_utils/cwl_v1_2_expression_refactor.py
diff --git a/cwl_utils/docker_extract.py b/cwl_utils/docker_extract.py
@@ -98,8 +98,7 @@ def get_process_from_step(step: cwl.WorkflowStep) -> ProcessType:
 def traverse_workflow(workflow: cwl.Workflow) -> Iterator[cwl.DockerRequirement]:
     """Iterate over the steps of this workflow, yielding the docker reqs."""
     for step in workflow.steps:
-        for req in extract_docker_reqs(step):
-            yield req
+        yield from extract_docker_reqs(step)
         yield from traverse(get_process_from_step(step))
 
 
diff --git a/cwl_utils/graph_split.py b/cwl_utils/graph_split.py
@@ -58,7 +58,7 @@ def main() -> None:
     """Split the packed CWL at the path of the first argument."""
     options = arg_parser().parse_args()
 
-    with open(options.cwlfile, "r") as source_handle:
+    with open(options.cwlfile) as source_handle:
         run(
             source_handle,
             options.outdir,
@@ -95,10 +95,10 @@ def my_represent_none(
         imports = rewrite(entry, entry_id)
         if imports:
             for import_name in imports:
-                rewrite_types(entry, "#{}".format(import_name), False)
+                rewrite_types(entry, f"#{import_name}", False)
         if entry_id == "main":
             if mainfile is None:
-                entry_id = "unpacked_{}".format(os.path.basename(sourceIO.name))
+                entry_id = f"unpacked_{os.path.basename(sourceIO.name)}"
             else:
                 entry_id = mainfile
 
@@ -112,7 +112,7 @@ def my_represent_none(
 def rewrite(document: Any, doc_id: str) -> Set[str]:
     """Rewrite the given element from the CWL $graph."""
     imports = set()
-    if isinstance(document, list) and not isinstance(document, Text):
+    if isinstance(document, list) and not isinstance(document, str):
         for entry in document:
             imports.update(rewrite(entry, doc_id))
     elif isinstance(document, dict):
@@ -133,22 +133,20 @@ def rewrite_id(entry: Any) -> Union[MutableMapping[Any, Any], str]:
                         elif isinstance(entry, str):
                             if entry.startswith(this_id):
                                 return entry[len(this_id) + 1 :]
-                        raise Exception(
-                            "{} is neither a dictionary nor string.".format(entry)
-                        )
+                        raise Exception(f"{entry} is neither a dictionary nor string.")
 
                     document[key][:] = [rewrite_id(entry) for entry in value]
                 elif key in ("source", "scatter", "items", "format"):
                     if (
-                        isinstance(value, Text)
+                        isinstance(value, str)
                         and value.startswith("#")
                         and "/" in value
                     ):
                         referrant_file, sub = value[1:].split("/", 1)
                         if referrant_file == doc_id:
                             document[key] = sub
                         else:
-                            document[key] = "{}#{}".format(referrant_file, sub)
+                            document[key] = f"{referrant_file}#{sub}"
                     elif isinstance(value, list):
                         new_sources = list()
                         for entry in value:
@@ -174,15 +172,15 @@ def rewrite_import(document: MutableMapping[str, Any]) -> None:
 
 def rewrite_types(field: Any, entry_file: str, sameself: bool) -> None:
     """Clean up the names of the types."""
-    if isinstance(field, list) and not isinstance(field, Text):
+    if isinstance(field, list) and not isinstance(field, str):
         for entry in field:
             rewrite_types(entry, entry_file, sameself)
         return
     if isinstance(field, dict):
         for key, value in field.items():
             for name in ("type", "items"):
                 if key == name:
-                    if isinstance(value, Text) and value.startswith(entry_file):
+                    if isinstance(value, str) and value.startswith(entry_file):
                         if sameself:
                             field[key] = value[len(entry_file) + 1 :]
                         else:
@@ -191,7 +189,7 @@ def rewrite_types(field: Any, entry_file: str, sameself: bool) -> None:
                             )
             if isinstance(value, dict):
                 rewrite_types(value, entry_file, sameself)
-            if isinstance(value, list) and not isinstance(value, Text):
+            if isinstance(value, list) and not isinstance(value, str):
                 for entry in value:
                     rewrite_types(entry, entry_file, sameself)
 
diff --git a/cwl_utils/image_puller.py b/cwl_utils/image_puller.py
@@ -78,7 +78,7 @@ class SingularityImagePuller(ImagePuller):
 
     def __init__(self, req: str, save_directory: str) -> None:
         """Create a Singularity-based software container image downloader."""
-        super(SingularityImagePuller, self).__init__(req, save_directory)
+        super().__init__(req, save_directory)
         version = subprocess.check_output(  # nosec
             ["singularity", "--version"], universal_newlines=True
         )
diff --git a/cwl_utils/parser/__init__.py b/cwl_utils/parser/__init__.py
@@ -1,24 +1,25 @@
 # SPDX-License-Identifier: Apache-2.0
 
-from schema_salad.exceptions import ValidationException
-from schema_salad.utils import yaml_no_ts
-from . import cwl_v1_0 as cwl_v1_0
-from . import cwl_v1_1 as cwl_v1_1
-from . import cwl_v1_2 as cwl_v1_2
-
 import os
 from pathlib import Path
-from urllib.parse import unquote_plus, urlparse
 from typing import (
-    cast,
     Any,
     Dict,
     MutableMapping,
     MutableSequence,
+    Optional,
     Tuple,
     Union,
-    Optional,
+    cast,
 )
+from urllib.parse import unquote_plus, urlparse
+
+from schema_salad.exceptions import ValidationException
+from schema_salad.utils import yaml_no_ts
+
+from . import cwl_v1_0 as cwl_v1_0
+from . import cwl_v1_1 as cwl_v1_1
+from . import cwl_v1_2 as cwl_v1_2
 
 LoadingOptions = Union[
     cwl_v1_0.LoadingOptions, cwl_v1_1.LoadingOptions, cwl_v1_2.LoadingOptions
@@ -131,7 +132,7 @@ def load_document_by_yaml(
         raise ValidationException("could not get the cwlVersion")
     else:
         raise ValidationException(
-            "Version error. Did not recognise {} as a CWL version".format(version)
+            f"Version error. Did not recognise {version} as a CWL version"
         )
 
     if isinstance(result, MutableSequence):
@@ -162,7 +163,7 @@ def save(
             save(v, top=top, base_url=base_url, relative_uris=relative_uris)
             for v in val
         ]
-        if top and all((is_process(v) for v in val)):
+        if top and all(is_process(v) for v in val):
             vers = [
                 e.get("cwlVersion") for i, e in enumerate(lst) if is_process(val[i])
             ]
diff --git a/tests/load_cwl_by_path.py b/tests/load_cwl_by_path.py
@@ -1,8 +1,9 @@
 """This is the example from README.md, please synchronize all changes between the two."""
 # SPDX-License-Identifier: Apache-2.0
+import sys
 from pathlib import Path
+
 from ruamel import yaml
-import sys
 
 from cwl_utils.parser import load_document_by_uri, save
 
diff --git a/tests/test_docker_extract.py b/tests/test_docker_extract.py
@@ -1,8 +1,9 @@
 from pathlib import Path
-from pytest import mark
 from shutil import which
 from tempfile import TemporaryDirectory
 
+from pytest import mark
+
 import cwl_utils.parser.cwl_v1_0 as parser
 from cwl_utils.docker_extract import traverse
 from cwl_utils.image_puller import DockerImagePuller, SingularityImagePuller
diff --git a/tests/test_meta.py b/tests/test_meta.py
@@ -0,0 +1,9 @@
+"""Test __meta__ properties."""
+
+from cwl_utils.__meta__ import __version__
+
+
+def test_graph_split() -> None:
+    """Confirm that __version__ exists and is a string."""
+    assert __version__
+    assert isinstance(__version__, str)
diff --git a/tests/test_parser.py b/tests/test_parser.py
@@ -1,8 +1,10 @@
 """Test the load and save functions for CWL."""
-from cwl_utils.parser import cwl_version, load_document, load_document_by_uri, save
 from pathlib import Path
+
 from ruamel import yaml
 
+from cwl_utils.parser import cwl_version, load_document, load_document_by_uri, save
+
 HERE = Path(__file__).resolve().parent
 TEST_v1_0_CWL = HERE / "../testdata/md5sum.cwl"
 TEST_v1_0_CWL_REMOTE = "https://raw.githubusercontent.com/common-workflow-language/cwl-utils/main/testdata/md5sum.cwl"
@@ -11,15 +13,15 @@
 
 def test_cwl_version() -> None:
     """Test cwl_version for a CommandLineTool."""
-    with open(TEST_v1_0_CWL, "r") as cwl_h:
+    with open(TEST_v1_0_CWL) as cwl_h:
         yaml_obj = yaml.main.round_trip_load(cwl_h, preserve_quotes=True)
     ver = cwl_version(yaml_obj)
     assert ver == "v1.0"
 
 
 def test_load_document() -> None:
     """Test load_document for a CommandLineTool."""
-    with open(TEST_v1_0_CWL, "r") as cwl_h:
+    with open(TEST_v1_0_CWL) as cwl_h:
         yaml_obj = yaml.main.round_trip_load(cwl_h, preserve_quotes=True)
     cwl_obj = load_document(yaml_obj)
     assert cwl_obj.cwlVersion == "v1.0"
@@ -44,12 +46,12 @@ def test_load_document_with_remote_uri() -> None:
 
 def test_save() -> None:
     """Test save for a list of Process objects with different cwlVersions."""
-    with open(TEST_v1_0_CWL, "r") as cwl_h:
+    with open(TEST_v1_0_CWL) as cwl_h:
         yaml_obj10 = yaml.main.round_trip_load(cwl_h, preserve_quotes=True)
     cwl_obj10 = load_document(yaml_obj10)
     assert cwl_obj10.cwlVersion == "v1.0"
 
-    with open(TEST_v1_2_CWL, "r") as cwl_h:
+    with open(TEST_v1_2_CWL) as cwl_h:
         yaml_obj12 = yaml.main.round_trip_load(cwl_h, preserve_quotes=True)
     cwl_obj12 = load_document(yaml_obj12)
     assert cwl_obj12.cwlVersion == "v1.2"

Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`"""Global version number for the cwl_utils package."""`
`2`		`-__version__ = "0.11"`
	`2`	`+__version__ = "0.12"`