Remove duplicate functions due to libraries merging

src/blue_cwl/core/parser.py

@@ -11,8 +11,8 @@
 from blue_cwl.core.exceptions import CWLError
 from blue_cwl.core.executor import LocalExecutor, SallocExecutor
 from blue_cwl.core.types import PathLike
-from blue_cwl.core.utils import load_yaml, resolve_path
 from blue_cwl.core.validate import validate_workflow
+from blue_cwl.utils import load_yaml, resolve_path
 
 L = logging.getLogger(__name__)
 

src/blue_cwl/utils.py

@@ -626,3 +626,11 @@ def get_obj(
  if isinstance(obj, str):
  return get_entity(resource_id=obj, cls=cls, base=base, org=org, proj=proj, token=token)
  return obj
+
+
+def resolve_path(path: StrOrPath, base_dir: StrOrPath | None = None) -> Path:
+ """Resolve path if it's relative wrt base_dir if given."""
+ if base_dir is not None:
+ return Path(base_dir, path).resolve()
+
+ return Path(path).resolve()

tests/unit/core/test_cwl.py

@@ -13,7 +13,7 @@
 from blue_cwl.core.cwl_types import File, Directory, CWLType
 from blue_cwl.core.exceptions import CWLError
 
-from blue_cwl.core import utils
+from blue_cwl import utils
 from blue_cwl.core import parse_cwl_file
 
 DATA_DIR = Path(__file__).parent / "data"

tests/unit/core/test_parser.py

@@ -7,7 +7,7 @@
 from blue_cwl.core import cwl
 from blue_cwl.core.exceptions import CWLError, CWLValidationError
 from blue_cwl.core.executor import LocalExecutor, SallocExecutor
-from blue_cwl.core import utils
+from blue_cwl import utils
 
 
 TESTS_DIR = Path(__file__).parent

tests/unit/core/test_use_cases.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 from blue_cwl.core import parse_cwl_file
 from blue_cwl.core.cwl_types import Directory, CWLType, File, NexusResource
-from blue_cwl.core.utils import cwd
+from blue_cwl.utils import cwd
 from blue_cwl.core import cwl
 
 import pytest
@@ -62,7 +62,10 @@ def test_essential_parameters():
  "example_float": 3.2,
  }
  res = tool.make(input_values=input_values)
- assert res.build_command() == "echo -f -i42 -d3.2 --file=whale.txt --example-string hello"
+ assert (
+ res.build_command()
+ == "echo -f -i42 -d3.2 --file=whale.txt --example-string hello"
+ )
 
 
 def test_array_types_tool():
@@ -214,7 +217,9 @@ def test_copy_file_workflow(tmp_path, cwl_file):
  )
  s3.run()
 
- assert Path(process.outputs["output_file"].path).read_text() == input_file.read_text()
+ assert (
+ Path(process.outputs["output_file"].path).read_text() == input_file.read_text()
+ )
 
 
 def test_generator_tool():
@@ -317,15 +322,20 @@ def test_generator_workflow():
  "cell_composition": NexusResource(id="my-composition-id"),
  "output_dir": Directory(path="my-output-dir"),
  }
- assert s1.outputs == {"staged_resource": File(path="my-output-dir/staged_resource.json")}
+ assert s1.outputs == {
+ "staged_resource": File(path="my-output-dir/staged_resource.json")
+ }
  assert s1.base_command == [
  "blue-cwl",
  "stage",
  "cell-composition",
  "my-composition-id",
  "my-output-dir",
  ]
- assert s1.environment == {"env_type": "MODULE", "modules": ["unstable", "py-blue-cwl"]}
+ assert s1.environment == {
+ "env_type": "MODULE",
+ "modules": ["unstable", "py-blue-cwl"],
+ }
  assert s1.executor.to_dict() == {
  "env_vars": {"FOO": "foo"},
  "remote_config": {"host": "bbpv1.epfl.ch"},
@@ -361,8 +371,13 @@ def test_generator_workflow():
  "variant_config": NexusResource(id="my-config-id"),
  "output_dir": Directory(path="my-output-dir"),
  }
- assert s2.outputs == {"staged_resource": File(path="my-output-dir/staged_resource.json")}
- assert s2.environment == {"env_type": "MODULE", "modules": ["unstable", "py-blue-cwl"]}
+ assert s2.outputs == {
+ "staged_resource": File(path="my-output-dir/staged_resource.json")
+ }
+ assert s2.environment == {
+ "env_type": "MODULE",
+ "modules": ["unstable", "py-blue-cwl"],
+ }
  assert s2.base_command == [
  "blue-cwl",
  "stage",
@@ -408,7 +423,10 @@ def test_generator_workflow():
  }
 
  assert s3.outputs == {"partial_circuit": File(path="my-output-dir/circuit.json")}
- assert s3.environment == {"env_type": "MODULE", "modules": ["unstable", "py-blue-cwl"]}
+ assert s3.environment == {
+ "env_type": "MODULE",
+ "modules": ["unstable", "py-blue-cwl"],
+ }
  assert s3.base_command == [
  "blue-cwl",
  "execute",

tests/unit/test_registering.py

@@ -58,9 +58,7 @@ def test_brain_location(monkeypatch):
  mock_region.get_id.return_value = "foo"
  mock_region.label = "bar"
 
- monkeypatch.setattr(
- AtlasBrainRegion, "from_id", lambda *args, **kwargs: mock_region
- )
+ monkeypatch.setattr(AtlasBrainRegion, "from_id", lambda *args, **kwargs: mock_region)
 
  payload = {
  "@id": "foo",
@@ -424,17 +422,13 @@ def upload_file(name, data, *args, **kwargs):
  "@id": "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/Foo",
  "label": "Foo",
  "about": ["https://neuroshapes.org/EType"],
- "hasPart": [
- {"@type": "METypeDensity", "@id": "foo-id", "_rev": 2}
- ],
+ "hasPart": [{"@type": "METypeDensity", "@id": "foo-id", "_rev": 2}],
  },
  {
  "@id": "http://bbp.epfl.ch/neurosciencegraph/ontologies/etypes/Bar",
  "label": "Bar",
  "about": ["https://neuroshapes.org/EType"],
- "hasPart": [
- {"@id": "bar-id", "_rev": 1, "@type": "METypeDensity"}
- ],
+ "hasPart": [{"@id": "bar-id", "_rev": 1, "@type": "METypeDensity"}],
  },
  ],
  }