Typed CWL parsers

.github/workflows/ci-tests.yml

@@ -74,7 +74,7 @@ jobs:
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
-          fail_ci_if_error: true
+          fail_ci_if_error: false
 
   tox-style:
     name: CI linters via Tox

Makefile

@@ -194,21 +194,25 @@ flake8: FORCE
 src/cwl_utils/parser/cwl_v1_0.py: FORCE
 	schema-salad-tool --codegen python \
 		--codegen-parser-info "org.w3id.cwl.v1_0" \
-		https://github.com/common-workflow-language/common-workflow-language/raw/codegen/v1.0/extensions.yml \
+		--codegen-parent "https://w3id.org/cwl/salad=schema_salad.metaschema" \
+		https://github.com/common-workflow-language/common-workflow-language/raw/codegen/v1.0/CommonWorkflowLanguage.yml \
 		> $@
 
 src/cwl_utils/parser/cwl_v1_1.py: FORCE
 	schema-salad-tool --codegen python \
 		--codegen-parser-info "org.w3id.cwl.v1_1" \
-		https://github.com/common-workflow-language/cwl-v1.1/raw/codegen/extensions.yml \
+		--codegen-parent "https://w3id.org/cwl/salad=schema_salad.metaschema" \
+		https://github.com/common-workflow-language/cwl-v1.1/raw/codegen/CommonWorkflowLanguage.yml \
 		> $@
 
 src/cwl_utils/parser/cwl_v1_2.py: FORCE
 	schema-salad-tool --codegen python \
 		--codegen-parser-info "org.w3id.cwl.v1_2" \
-		https://github.com/common-workflow-language/cwl-v1.2/raw/codegen/extensions.yml \
+		--codegen-parent "https://w3id.org/cwl/salad=schema_salad.metaschema" \
+		https://github.com/common-workflow-language/cwl-v1.2/raw/codegen/CommonWorkflowLanguage.yml \
 		> $@
 
+
 regen_parsers: src/cwl_utils/parser/cwl_v1_*.py
 
 FORCE:

README.rst

@@ -173,13 +173,13 @@ Regenerate parsers
 To regenerate install the ``schema_salad`` package and run:
 
 ``cwl_utils/parser/cwl_v1_0.py`` was created via
-``schema-salad-tool --codegen python https://github.com/common-workflow-language/common-workflow-language/raw/codegen/v1.0/extensions.yml --codegen-parser-info "org.w3id.cwl.v1_0" > cwl_utils/parser/cwl_v1_0.py``
+``schema-salad-tool --codegen python https://github.com/common-workflow-language/common-workflow-language/raw/codegen/v1.0/CommonWorkflowLanguage.yml --codegen-parent "https://w3id.org/cwl/salad=schema_salad.metaschema" --codegen-parser-info "org.w3id.cwl.v1_0" > src/cwl_utils/parser/cwl_v1_0.py``
 
 ``cwl_utils/parser/cwl_v1_1.py`` was created via
-``schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.1/raw/codegen/extensions.yml --codegen-parser-info "org.w3id.cwl.v1_1" > cwl_utils/parser/cwl_v1_1.py``
+``schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.1/raw/codegen/CommonWorkflowLanguage.yml --codegen-parent "https://w3id.org/cwl/salad=schema_salad.metaschema" --codegen-parser-info "org.w3id.cwl.v1_1" > src/cwl_utils/parser/cwl_v1_1.py``
 
 ``cwl_utils/parser/cwl_v1_2.py`` was created via
-``schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.2/raw/codegen/extensions.yml --codegen-parser-info "org.w3id.cwl.v1_2" > cwl_utils/parser/cwl_v1_2.py``
+``schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.2/raw/codegen/CommonWorkflowLanguage.yml --codegen-parent "https://w3id.org/cwl/salad=schema_salad.metaschema" --codegen-parser-info "org.w3id.cwl.v1_2" > src/cwl_utils/parser/cwl_v1_2.py``
 
 Release
 ~~~~~~~

pyproject.toml

@@ -36,7 +36,7 @@ dependencies = [
     "packaging",
     "rdflib",
     "requests",
-    "schema-salad >= 8.8.20250205075315,<9",
+    "schema-salad @ git+https://github.com/common-workflow-language/schema_salad.git@refs/pull/993/head",
     "ruamel.yaml >= 0.17.6, < 0.20",
     "typing_extensions >= 4.10.0",
 ]
@@ -71,6 +71,9 @@ cwl-pack = "cwl_utils.pack_cli:main"
 cwl-normalizer = "cwl_utils.normalizer:main"
 cwl-inputs-schema-gen = "cwl_utils.inputs_schema_gen:main"
 
+[tool.hatch.metadata]
+allow-direct-references = true
+
 [tool.pytest.ini_options]
 addopts = "-rsx -n auto --pyargs cwl_utils.tests"
 
@@ -135,3 +138,4 @@ ignore = [
 
 [tool.bandit]
 exclude_dirs = ["src/cwl_utils/tests"]
+skips = ["B101"]

src/cwl_utils/cite_extract.py

@@ -33,7 +33,7 @@ def main() -> int:
 
 
 def extract_software_reqs(
-    process: cwl.Process,
+    process: cwl.Process | cwl.WorkflowStep,
 ) -> Iterator[cwl.SoftwareRequirement]:
     """Return an iterator over any SoftwareRequirements found in the given process."""
     if process.requirements:
@@ -67,7 +67,7 @@ def get_process_from_step(step: cwl.WorkflowStep) -> cwl.Process:
     """Return the process for this step, loading it if needed."""
     if isinstance(step.run, str):
         return cast(cwl.Process, cwl.load_document_by_uri(step.run))
-    return cast(cwl.Process, step.run)
+    return step.run
 
 
 def traverse_workflow(workflow: cwl.Workflow) -> Iterator[cwl.SoftwareRequirement]: