Lint and deprecation fixes

gxformat2/normalize.py

@@ -184,7 +184,7 @@ def register_output_source(output_source):
 
     for step in steps_as_list(workflow_dict, mutate=False):
         step_in = step.get("in", {})
-        for step_in_name, step_in_def in step_in.items():
+        for step_in_def in step_in.values():
             register_output_source(step_in_def)
 
     for step in steps_as_list(workflow_dict, add_ids=True, inputs_offset=len(workflow_dict["inputs"]), mutate=True):

tests/test_basic.py

@@ -1,8 +1,8 @@
 import os
 
-from gxformat2._yaml import ordered_load
 from gxformat2.converter import ImportOptions
 from gxformat2.export import from_galaxy_native
+from gxformat2.yaml import ordered_load
 from ._helpers import (
     assert_valid_native,
     copy_without_workflow_output_labels,
@@ -263,7 +263,7 @@ def test_export_native_no_labels():
     # Ensure outputs don't get mapped to 'null' key and ensure
     native_unicycler = ordered_load(open(os.path.join(TEST_PATH, "unicycler.ga")).read())
     before_output_count = 0
-    for workflow_output in native_workflow_outputs(native_unicycler):
+    for _ in native_workflow_outputs(native_unicycler):
         before_output_count += 1
     before_step_count = len(native_unicycler["steps"])
 
@@ -273,7 +273,7 @@ def test_export_native_no_labels():
     round_trip_unicycler = to_native(as_format2)
 
     after_output_count = 0
-    for workflow_output in native_workflow_outputs(round_trip_unicycler):
+    for _ in native_workflow_outputs(round_trip_unicycler):
         after_output_count += 1
     after_step_count = len(round_trip_unicycler["steps"])
 

tests/test_export_abstract.py

@@ -12,8 +12,8 @@
     tool_resolver,
 )
 
-from gxformat2._yaml import ordered_dump, ordered_load
 from gxformat2.abstract import CWL_VERSION, from_dict
+from gxformat2.yaml import ordered_dump, ordered_load
 from ._helpers import TEST_PATH, to_example_path
 from .example_wfs import (
     BASIC_WORKFLOW,

tests/test_lint.py

@@ -1,8 +1,8 @@
 import copy
 import os
 
-from gxformat2._yaml import ordered_dump, ordered_load
 from gxformat2.lint import main
+from gxformat2.yaml import ordered_dump, ordered_load
 from ._helpers import (
     assert_valid_native,
     copy_without_workflow_output_labels,
@@ -93,7 +93,7 @@ def setup_module(module):
     _dump_with_exit_code(green_native, 0, "basic_native")
 
     green_explicit_errors_null = _deep_copy(green_native)
-    for step, step_def in green_explicit_errors_null["steps"].items():
+    for step_def in green_explicit_errors_null["steps"].values():
         step_def["errors"] = None
     _dump_with_exit_code(green_explicit_errors_null, 0, "basic_native_explicit_no_errors")
 

tests/test_normalize.py

@@ -1,5 +1,5 @@
-from gxformat2._yaml import ordered_load
 from gxformat2.normalize import Inputs, inputs_normalized, NormalizedWorkflow, outputs_normalized
+from gxformat2.yaml import ordered_load
 from ._helpers import (
     to_native,
 )
@@ -55,7 +55,7 @@ def test_normalized_workflow():
     # same workflow with slightly different input definitions, make sure normalize
     # unifies these
     for wf in [INTEGER_INPUT, INT_INPUT]:
-        int_input_normalized = NormalizedWorkflow(ordered_load(INT_INPUT)).normalized_workflow_dict
+        int_input_normalized = NormalizedWorkflow(ordered_load(wf)).normalized_workflow_dict
         inputs = int_input_normalized["inputs"]
         assert isinstance(inputs, list)
         assert isinstance(inputs[0], dict)  # str converted to dictionary

tests/test_to_native.py

@@ -2,10 +2,10 @@
 import os
 
 from gxformat2._scripts import ensure_format2_from_path
-from gxformat2._yaml import ordered_dump
 from gxformat2.converter import main
 from gxformat2.lint import lint_ga_path
 from gxformat2.linting import LintContext
+from gxformat2.yaml import ordered_dump
 from ._helpers import TEST_PATH, to_example_path
 from .example_wfs import (
     BASIC_WORKFLOW,

tox.ini

@@ -21,6 +21,7 @@ commands =
     mypy: mypy gxformat2 {posargs}
 deps =
     lint: flake8-import-order
+    lint: flake8-bugbear
     lint,lintdocstrings: flake8
     lintdocstrings: flake8_docstrings
     mypy: mypy