chore: move testing infra code out of core

.github/workflows/fuzzy_compile_weekly.yml

@@ -97,7 +97,7 @@ jobs:
 
       - name: Generate Sophios Python API Workflows (*.py -> *.wic)
         if: always()
-        run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
+        run: cd sophios/ && pytest -k test_compile_python_workflows 
 
       - name: Generate Sophios Validation Jsonschema
         if: always()
@@ -108,7 +108,7 @@ jobs:
         # WIC Python API workflows as well as the WIC Python API itself.
       - name: Validate Sophios Python API Workflows (*.py -> *.wic)
         if: always()
-        run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
+        run: cd sophios/ && pytest -k test_compile_python_workflows
 
 # Since a randomly chosen subschema is used every time, repeat 10X for more coverage.
 

.github/workflows/lint_and_test.yml

@@ -179,7 +179,7 @@ jobs:
 
       - name: Generate Sophios Python API Workflows (*.py -> *.wic)
         if: always()
-        run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
+        run: cd sophios/ && pytest -k test_compile_python_workflows
 
       - name: Generate Sophios Validation Jsonschema
         if: always()
@@ -190,7 +190,7 @@ jobs:
         # Sophios Python API workflows as well as the Sophios Python API itself.
       - name: Validate sophios Python API Workflows (*.py -> *.wic)
         if: always()
-        run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
+        run: cd sophios/ && pytest -k test_compile_python_workflows
 
       - name: Build Documentation
         if: always()

.github/workflows/lint_and_test_macos.yml

@@ -103,7 +103,7 @@ jobs:
 
       - name: Generate Sophios Python API Workflows (*.py -> *.wic)
         if: always()
-        run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
+        run: cd sophios/ && pytest -k test_compile_python_workflows
 
       - name: Generate Sophios Validation Jsonschema
         if: always()
@@ -114,7 +114,7 @@ jobs:
         # Sophios Python API workflows as well as the Sophios Python API itself.
       - name: Validate Sophios Python API Workflows (*.py -> *.wic)
         if: always()
-        run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
+        run: cd sophios/ && pytest -k test_compile_python_workflows
 
       - name: Build Documentation
         if: always()

.github/workflows/run_workflows.yml

@@ -157,7 +157,7 @@ jobs:
 
     - name: Generate Sophios Python API Workflows (*.py -> *.wic)
       if: always()
-      run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
+      run: cd sophios/ && pytest -k test_compile_python_workflows
 
     - name: Generate Sophios Validation Jsonschema
       if: always()
@@ -168,7 +168,7 @@ jobs:
       # WIC Python API workflows as well as the WIC Python API itself.
     - name: Validate Sophios Python API Workflows (*.py -> *.wic)
       if: always()
-      run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
+      run: cd sophios/ && pytest -k test_compile_python_workflows
 
     - name: cwl-docker-extract (i.e. recursively docker pull)
       if: always()

.github/workflows/run_workflows_weekly.yml

@@ -120,7 +120,7 @@ jobs:
 
     - name: Generate Sophios Python API Workflows (*.py -> *.wic)
       if: always()
-      run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
+      run: cd sophios/ && pytest -k test_compile_python_workflows
 
     - name: Generate Sophios Validation Jsonschema
       if: always()
@@ -131,7 +131,7 @@ jobs:
       # Sophios Python API workflows as well as the WIC Python API itself.
     - name: Validate Sophios Python API Workflows (*.py -> *.wic)
       if: always()
-      run: cd sophios/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()'
+      run: cd sophios/ && pytest -k test_compile_python_workflows
 
     - name: cwl-docker-extract (i.e. recursively docker pull)
       if: always()

src/sophios/plugins.py

@@ -466,69 +466,3 @@ def get_yml_paths(config: Json) -> Dict[str, Dict[str, Path]]:
 
 def get_py_paths(config: Json) -> Dict[str, Dict[str, Path]]:
     return get_workflow_paths(config, 'py')
-
-
-def blindly_execute_python_workflows() -> None:
-    """This function imports (read: blindly executes) all python files in 'search_paths_wic'
-       The python files are assumed to have a top-level workflow() function
-       which returns a sophios.api.pythonapi.Workflow object.
-       The python files should NOT call the .run() method!
-       (from any code path that is automatically executed on import)
-    """
-    # I hope u like Remote Code Execution vulnerabilities!
-    # See https://en.wikipedia.org/wiki/Arithmetical_hierarchy
-    from sophios.api import pythonapi  # pylint: disable=C0415:import-outside-toplevel
-    # Since this is completely different test path we have to copy
-    # default .txt files to default global_config.json
-    config_file = Path().home()/'wic'/'global_config.json'
-    global_config = io.read_config_from_disk(config_file)
-    pythonapi.global_config = get_tools_cwl(global_config)  # Use path fallback in the CI
-    paths = get_py_paths(global_config)
-    # Above we are assuming that config is default
-    paths_tuples = [(path_str, path)
-                    for namespace, paths_dict in paths.items()
-                    for path_str, path in paths_dict.items()]
-    any_import_errors = False
-    for path_stem, path in paths_tuples:
-        if 'mm-workflows' in str(path) or 'docs/tutorials/' in str(path):
-            # Exclude paths that only contain 'regular' python files.
-            continue
-        # NOTE: Use anything (unique?) for the python_module_name.
-        try:
-            module = import_python_file(path_stem, path)
-            # Let's require all python API files to define a function, say
-            # def workflow() -> Workflow
-            # so we can programmatically call it here:
-            retval: pythonapi.Workflow = module.workflow()  # no arguments
-            # which allows us to programmatically call Workflow methods:
-            compiler_info = retval.compile()  # hopefully retval is actually a Workflow object!
-            # But since this is python (i.e. not Haskell) that in no way eliminates
-            # the above security considerations.
-
-            # This lets us use path.parent to write a *.wic file in the
-            # auto-discovery path, and thus reuse the existing wic CI
-            retval.write_ast_to_disk(path.parent)
-
-            # Programmatically blacklist subworkflows from running in config_ci.json
-            # (Again, because subworkflows are missing inputs and cannot run.)
-            config_ci = path.parent / 'config_ci.json'
-            json_contents = {}
-            if config_ci.exists():
-                with open(config_ci, mode='r', encoding='utf-8') as r:
-                    json_contents = json.load(r)
-            run_blacklist: list[str] = json_contents.get('run_blacklist', [])
-            # Use [1:] for proper subworkflows only
-            subworkflows: list[pythonapi.Workflow] = retval.flatten_subworkflows()[1:]
-            run_blacklist += [wf.process_name for wf in subworkflows]
-            json_contents['run_blacklist'] = run_blacklist
-            with open(config_ci, mode='w', encoding='utf-8') as f:
-                json.dump(json_contents, f)
-
-        except Exception as e:
-            any_import_errors = True
-            if sys.version_info >= (3, 10):
-                traceback.print_exception(type(e), value=e, tb=None)
-            else:
-                traceback.print_exception(etype=type(e), value=e, tb=None)
-    if any_import_errors:
-        sys.exit(1)  # Make sure the CI fails

tests/test_compile_python_workflows.py

@@ -0,0 +1,73 @@
+import json
+import sys
+import traceback
+from pathlib import Path
+
+import sophios
+import sophios.plugins
+from sophios import input_output as io
+from sophios.python_cwl_adapter import import_python_file
+
+
+def test_compile_python_workflows() -> None:
+    """This function imports (read: blindly executes) all python files in 'search_paths_wic'
+       The python files are assumed to have a top-level workflow() function
+       which returns a sophios.api.pythonapi.Workflow object.
+       The python files should NOT call the .run() method!
+       (from any code path that is automatically executed on import)
+    """
+    from sophios.api import pythonapi  # pylint: disable=C0415:import-outside-toplevel
+    # Since this is completely different test path we have to copy
+    # default .txt files to default global_config.json
+    config_file = Path().home()/'wic'/'global_config.json'
+    global_config = io.read_config_from_disk(config_file)
+    pythonapi.global_config = sophios.plugins.get_tools_cwl(global_config)  # Use path fallback in the CI
+    paths = sophios.plugins.get_py_paths(global_config)
+    # Above we are assuming that config is default
+    paths_tuples = [(path_str, path)
+                    for namespace, paths_dict in paths.items()
+                    for path_str, path in paths_dict.items()]
+    any_import_errors = False
+    for path_stem, path in paths_tuples:
+        if 'mm-workflows' in str(path) or 'docs/tutorials/' in str(path):
+            # Exclude paths that only contain 'regular' python files.
+            continue
+        # NOTE: Use anything (unique?) for the python_module_name.
+        try:
+            module = import_python_file(path_stem, path)
+            # Let's require all python API files to define a function, say
+            # def workflow() -> Workflow
+            # so we can programmatically call it here:
+            retval: pythonapi.Workflow = module.workflow()  # no arguments
+            # which allows us to programmatically call Workflow methods:
+            compiler_info = retval.compile()  # hopefully retval is actually a Workflow object!
+            # But since this is python (i.e. not Haskell) that in no way eliminates
+            # the above security considerations.
+
+            # This lets us use path.parent to write a *.wic file in the
+            # auto-discovery path, and thus reuse the existing wic CI
+            retval.write_ast_to_disk(path.parent)
+
+            # Programmatically blacklist subworkflows from running in config_ci.json
+            # (Again, because subworkflows are missing inputs and cannot run.)
+            config_ci = path.parent / 'config_ci.json'
+            json_contents = {}
+            if config_ci.exists():
+                with open(config_ci, mode='r', encoding='utf-8') as r:
+                    json_contents = json.load(r)
+            run_blacklist: list[str] = json_contents.get('run_blacklist', [])
+            # Use [1:] for proper subworkflows only
+            subworkflows: list[pythonapi.Workflow] = retval.flatten_subworkflows()[1:]
+            run_blacklist += [wf.process_name for wf in subworkflows]
+            json_contents['run_blacklist'] = run_blacklist
+            with open(config_ci, mode='w', encoding='utf-8') as f:
+                json.dump(json_contents, f)
+
+        except Exception as e:
+            any_import_errors = True
+            if sys.version_info >= (3, 10):
+                traceback.print_exception(type(e), value=e, tb=None)
+            else:
+                traceback.print_exception(etype=type(e), value=e, tb=None)
+    if any_import_errors:
+        sys.exit(1)  # Make sure the CI fails