Add IWC integration tests for lint (structural, pydantic, best practices)

Runs lint_ga, lint_pydantic_validation, and lint_best_practices_ga on all
IWC .ga workflows when GXFORMAT2_TEST_IWC_DIRECTORY is set. Skips when unset.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: jmchilton

tests/_helpers.py

@@ -1,4 +1,5 @@
 import copy
+import glob
 import os
 
 from gxformat2.converter import python_to_workflow, yaml_to_workflow
@@ -9,6 +10,31 @@
 TEST_PATH = os.path.abspath(os.path.dirname(__file__))
 TEST_INTEROP_EXAMPLES = os.environ.get("GXFORMAT2_INTEROP_EXAMPLES", os.path.join(TEST_PATH, "examples"))
 
+IWC_DIR = os.environ.get("GXFORMAT2_TEST_IWC_DIRECTORY")
+
+# TODO: remove after https://github.com/galaxyproject/iwc/pull/1167 is merged
+IWC_SKIP = {
+    "hic-fastq-to-cool-hicup-cooler.ga",
+    "chic-fastq-to-cool-hicup-cooler.ga",
+}
+
+
+def find_iwc_ga_files(skip=None):
+    """Find .ga workflow files in the IWC checkout, optionally skipping some by basename."""
+    if not IWC_DIR:
+        return []
+    skip = skip or IWC_SKIP
+    return sorted(
+        p
+        for p in glob.glob(os.path.join(IWC_DIR, "workflows", "**", "*.ga"), recursive=True)
+        if os.path.basename(p) not in skip
+    )
+
+
+def iwc_fixture_ids(paths):
+    """Generate pytest fixture IDs relative to IWC_DIR."""
+    return [os.path.relpath(p, IWC_DIR) if IWC_DIR else p for p in paths]
+
 
 def to_native(has_yaml, **kwds):
     if isinstance(has_yaml, dict):

tests/test_lint.py

@@ -1,11 +1,23 @@
 import copy
+import json
 import os
 
-from gxformat2.lint import main
+import pytest
+
+from gxformat2.lint import (
+    lint_best_practices_ga,
+    lint_ga,
+    lint_pydantic_validation,
+    main,
+)
+from gxformat2.linting import LintContext
 from gxformat2.yaml import ordered_dump, ordered_load
 from ._helpers import (
     assert_valid_native,
     copy_without_workflow_output_labels,
+    find_iwc_ga_files,
+    IWC_DIR,
+    iwc_fixture_ids,
     round_trip,
     TEST_INTEROP_EXAMPLES,
     TEST_PATH,
@@ -306,3 +318,39 @@ def _dump_with_exit_code(as_dict, exit_code, description):
     with open(os.path.join(TEST_LINT_EXAMPLES, "%d_%s.yml" % (exit_code, description)), "w") as fd:
         ordered_dump(as_dict, fd)
         fd.flush()
+
+
+# --- IWC integration tests ---
+
+GA_FILES = find_iwc_ga_files()
+
+
+@pytest.mark.skipif(IWC_DIR is None, reason="GXFORMAT2_TEST_IWC_DIRECTORY not set")
+class TestIWCLint:
+
+    @pytest.fixture(
+        params=GA_FILES,
+        ids=iwc_fixture_ids(GA_FILES),
+    )
+    def ga_path_and_dict(self, request):
+        with open(request.param) as f:
+            return request.param, json.load(f)
+
+    def test_structural_lint(self, ga_path_and_dict):
+        path, workflow_dict = ga_path_and_dict
+        ctx = LintContext()
+        lint_ga(ctx, workflow_dict, path=path)
+        assert not ctx.error_messages, f"Structural lint errors in {os.path.basename(path)}: {ctx.error_messages}"
+
+    def test_pydantic_validation(self, ga_path_and_dict):
+        _, workflow_dict = ga_path_and_dict
+        ctx = LintContext()
+        lint_pydantic_validation(ctx, workflow_dict, format2=False)
+        assert not ctx.error_messages, f"Pydantic validation errors: {ctx.error_messages}"
+
+    def test_best_practices(self, ga_path_and_dict):
+        _, workflow_dict = ga_path_and_dict
+        ctx = LintContext()
+        lint_best_practices_ga(ctx, workflow_dict)
+        # Best practices produce warnings, not errors — just ensure no crash.
+        # Warnings are expected for many IWC workflows.

tests/test_native_schema.py

@@ -7,13 +7,13 @@
 found in that IWC checkout.
 """
 
-import glob
 import json
 import os
 import tempfile
 
 import pytest
 
+from ._helpers import find_iwc_ga_files, IWC_DIR, iwc_fixture_ids
 from gxformat2.schema.native_v0_1 import load_document
 
 
@@ -213,24 +213,15 @@ def test_with_creator_mixed(self):
 
 # --- IWC integration tests ---
 
-IWC_DIR = os.environ.get("GXFORMAT2_TEST_IWC_DIRECTORY")
-
-
-def _find_ga_files():
-    if not IWC_DIR:
-        return []
-    return sorted(glob.glob(os.path.join(IWC_DIR, "workflows", "**", "*.ga"), recursive=True))
-
-
-GA_FILES = _find_ga_files()
+GA_FILES = find_iwc_ga_files()
 
 
 @pytest.mark.skipif(IWC_DIR is None, reason="GXFORMAT2_TEST_IWC_DIRECTORY not set")
 class TestIWCWorkflows:
 
     @pytest.fixture(
         params=GA_FILES,
-        ids=[os.path.relpath(p, IWC_DIR) if IWC_DIR else p for p in GA_FILES],
+        ids=iwc_fixture_ids(GA_FILES),
     )
     def ga_workflow(self, request):
         with open(request.param) as f:

tests/test_pydantic_schema.py

@@ -4,12 +4,11 @@
 can load and validate both Format2 and native Galaxy workflow documents.
 """
 
-import glob
 import json
-import os
 
 import pytest
 
+from ._helpers import find_iwc_ga_files, IWC_DIR, iwc_fixture_ids
 from gxformat2.export import from_galaxy_native
 from gxformat2.schema.gxformat2 import (
     GalaxyWorkflow,
@@ -290,35 +289,15 @@ def test_extra_fields_allowed(self):
 
 # --- IWC integration tests ---
 
-IWC_DIR = os.environ.get("GXFORMAT2_TEST_IWC_DIRECTORY")
-
-
-# TODO: remove after https://github.com/galaxyproject/iwc/pull/1167 is merged
-_IWC_PYDANTIC_SKIP = {
-    "hic-fastq-to-cool-hicup-cooler.ga",
-    "chic-fastq-to-cool-hicup-cooler.ga",
-}
-
-
-def _find_ga_files():
-    if not IWC_DIR:
-        return []
-    return sorted(
-        p
-        for p in glob.glob(os.path.join(IWC_DIR, "workflows", "**", "*.ga"), recursive=True)
-        if os.path.basename(p) not in _IWC_PYDANTIC_SKIP
-    )
-
-
-GA_FILES = _find_ga_files()
+GA_FILES = find_iwc_ga_files()
 
 
 @pytest.mark.skipif(IWC_DIR is None, reason="GXFORMAT2_TEST_IWC_DIRECTORY not set")
 class TestIWCPydantic:
 
     @pytest.fixture(
         params=GA_FILES,
-        ids=[os.path.relpath(p, IWC_DIR) if IWC_DIR else p for p in GA_FILES],
+        ids=iwc_fixture_ids(GA_FILES),
     )
     def ga_workflow(self, request):
         with open(request.param) as f: