Fix tests

packages/python/openproblems/CHANGELOG.md

@@ -6,7 +6,7 @@
   - `resolve_path`: Resolve a path relative to a parent path or project root.
 
 * `project.component_tests`:
-  - `run_check_config` / `check_config`: Validate a component's Viash config (namespace, type, metadata, normalization, variants, Nextflow runner).
+  - `check_config`: Validate a component's Viash config (namespace, type, metadata, normalization, variants, Nextflow runner).
   - `run_and_check_output`: Run a component executable and validate its output files against format specifications.
 
 * `project.docs`:

packages/python/openproblems/README.md

@@ -27,7 +27,7 @@ Utilities for working with Viash projects.
 
 Helpers for writing component tests.
 
-- `run_check_config` / `check_config`: Validate a component's Viash configuration.
+- `check_config`: Validate a component's Viash configuration.
 - `run_and_check_output`: Run a component and validate its output files against format specs.
 
 #### `openproblems.project.docs`

packages/python/openproblems/src/openproblems/project/__init__.py

@@ -1,7 +1,7 @@
 from .find_project_root import find_project_root
 from .read_viash_config import read_viash_config
 from .read_nested_yaml import read_nested_yaml
-from .component_tests.check_config import run_check_config as check_config
+from .component_tests.check_config import check_config
 from .component_tests.run_and_check_output import run_and_check_output
 from .docs.read_task_metadata import read_task_metadata
 from .docs.render_task_readme_qmd import render_task_readme_qmd

packages/python/openproblems/src/openproblems/project/component_tests/__init__.py

@@ -1,41 +1,11 @@
 from .check_config import (
-    check_info,
-    check_links,
-    check_references,
-    check_url,
-    run_check_config,
+    check_config,
 )
 from .run_and_check_output import (
-    check_anndata,
-    check_dataframe,
-    check_dictionary,
-    check_format,
-    check_input_files,
-    check_output_files,
-    check_spatialdata,
-    generate_cmd_args,
-    get_argument_sets,
     run_and_check_output,
-    run_component,
 )
 
 __all__ = [
-    # check_config
-    "check_info",
-    "check_links",
-    "check_references",
-    "check_url",
-    "run_check_config",
-    # run_and_check_output
-    "check_anndata",
-    "check_dataframe",
-    "check_dictionary",
-    "check_format",
-    "check_input_files",
-    "check_output_files",
-    "check_spatialdata",
-    "generate_cmd_args",
-    "get_argument_sets",
+    "check_config",
     "run_and_check_output",
-    "run_component",
 ]

packages/python/openproblems/src/openproblems/project/component_tests/check_config.py

@@ -105,7 +105,7 @@ def check_info(this_info: Dict, this_config: Dict, comp_type: str) -> None:
         check_references(references)
 
 
-def run_check_config(config: dict) -> None:
+def check_config(config: dict) -> None:
     """Validate a viash component config.
 
     Checks namespace, info.type, component metadata, preferred_normalization,

packages/python/openproblems/src/openproblems/project/component_tests/run_and_check_output.py

@@ -215,13 +215,20 @@ def get_argument_sets(config: dict, resources_dir: str) -> dict:
     for arg in config["all_arguments"]:
         new_arg = arg.copy()
         arg_info = new_arg.get("info") or {}
-        example = arg.get("example", [None])[0]
-
-        if example and arg["type"] == "file":
+        default_or_example = None
+        if arg_info.get("default"):
+            default_or_example = arg_info["default"]
+        elif arg_info.get("example"):
+            default_or_example = arg_info["example"]
+        if isinstance(default_or_example, list):
+            default_or_example = default_or_example[0]
+
+        # use example to find test resource file
+        if default_or_example and arg["type"] == "file":
             if arg["direction"] == "input":
-                value = f"{resources_dir}/{example}"
+                value = f"{resources_dir}/{default_or_example}"
             else:
-                ext_res = re.search(r"\.(\w+)$", example)
+                ext_res = re.search(r"\.(\w+)$", default_or_example)
                 if ext_res:
                     value = f"{arg['clean_name']}.{ext_res.group(1)}"
                 else:
@@ -246,7 +253,7 @@ def get_argument_sets(config: dict, resources_dir: str) -> dict:
                     val = test_instance[arg["clean_name"]]
                     if new_arg["type"] == "file" and new_arg["direction"] == "input":
                         val = f"{resources_dir}/{val}"
-                    new_arg["value"] = val
+                    new_arg["value"] = normalize_argument_value(val, new_arg)
                 new_arguments.append(new_arg)
             argument_sets[name] = new_arguments