Merge pull request #12 from jluethi/manifest_update

Update manifest and add test that manifest matches function signature

.github/workflows/ci.yml

@@ -48,6 +48,9 @@ jobs:
           python -m pip install -U pip
           python -m pip install .[test]
 
+      - name: Install some testing dependencies (hard-coded)
+        run: python -m pip install pytest devtools jsonschema requests wget
+
       - name: 🧪 Run Tests
         run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
 

src/fractal_faim_hcs/__FRACTAL_MANIFEST__.json

@@ -28,7 +28,7 @@
           },
           "mode": {
             "default": "all",
-            "description": "Mode can be 3 values: \"z-steps\" (only parse the 3D data), \"top-level\" (only parse the 2D data), \"all\" (parse both)",
+            "description": "Mode can be 4 values: \"z-steps\" (only parse the 3D data), \"top-level\" (only parse the 2D data), \"all\" (parse both), \"zmb\" (zmb-parser, detect mode automatically)",
             "title": "Mode",
             "type": "string"
           },
@@ -54,6 +54,12 @@
             "title": "Overwrite",
             "type": "boolean"
           },
+          "query": {
+            "default": "",
+            "description": "Pandas query to filter intput-filenames",
+            "title": "Query",
+            "type": "string"
+          },
           "zarr_name": {
             "default": "Plate",
             "description": "Name of the zarr plate file that will be created",
@@ -90,6 +96,12 @@
             "title": "Component",
             "type": "string"
           },
+          "grid_montage": {
+            "default": true,
+            "description": "Force FOVs into closest grid cells",
+            "title": "Grid Montage",
+            "type": "boolean"
+          },
           "input_paths": {
             "description": "List of paths to the input files (Fractal managed)",
             "items": {

tests/test_valid_args_schemas.py

@@ -0,0 +1,74 @@
+import json
+from pathlib import Path
+
+import fractal_faim_hcs
+import pytest
+from devtools import debug
+from fractal_tasks_core.dev.lib_args_schemas import (
+    create_schema_for_single_task,
+)
+from fractal_tasks_core.dev.lib_signature_constraints import (
+    _extract_function,
+    _validate_function_signature,
+)
+from jsonschema.validators import (
+    Draft7Validator,
+    Draft201909Validator,
+    Draft202012Validator,
+)
+
+FRACTAL_TASKS_CORE_DIR = Path(fractal_faim_hcs.__file__).parent
+with (FRACTAL_TASKS_CORE_DIR / "__FRACTAL_MANIFEST__.json").open("r") as f:
+    MANIFEST = json.load(f)
+TASK_LIST = MANIFEST["task_list"]
+PACKAGE = "fractal_faim_hcs"
+
+
+def test_manifest_has_args_schemas_is_true():
+    debug(MANIFEST)
+    assert MANIFEST["has_args_schemas"]
+
+
+def test_task_functions_have_valid_signatures():
+    """
+    Test that task functions have valid signatures.
+    """
+    for _ind_task, task in enumerate(TASK_LIST):
+        function_name = Path(task["executable"]).with_suffix("").name
+        task_function = _extract_function(
+            task["executable"], function_name, package_name=PACKAGE
+        )
+        _validate_function_signature(task_function)
+
+
+def test_args_schemas_are_up_to_date():
+    """
+    Test that args_schema attributes in the manifest are up-to-date
+    """
+    for ind_task, task in enumerate(TASK_LIST):
+        print(f"Now handling {task['executable']}")
+        old_schema = TASK_LIST[ind_task]["args_schema"]
+        new_schema = create_schema_for_single_task(task["executable"], package=PACKAGE)
+        # The following step is required because some arguments may have a
+        # default which has a non-JSON type (e.g. a tuple), which we need to
+        # convert to JSON type (i.e. an array) before comparison.
+        new_schema = json.loads(json.dumps(new_schema))
+        assert new_schema == old_schema
+
+
+@pytest.mark.parametrize(
+    "jsonschema_validator",
+    [Draft7Validator, Draft201909Validator, Draft202012Validator],
+)
+def test_args_schema_comply_with_jsonschema_specs(jsonschema_validator):
+    """
+    FIXME: it is not clear whether this test is actually useful
+    """
+    for ind_task, task in enumerate(TASK_LIST):
+        schema = TASK_LIST[ind_task]["args_schema"]
+        my_validator = jsonschema_validator(schema=schema)
+        my_validator.check_schema(my_validator.schema)
+        print(
+            f"Schema for task {task['executable']} is valid for "
+            f"{jsonschema_validator}."
+        )

tests/test_valid_manifest.py

@@ -0,0 +1,33 @@
+import json
+import sys
+from pathlib import Path
+
+import fractal_tasks_core
+import requests
+from devtools import debug
+
+
+def test_valid_manifest(tmp_path):
+    """
+    NOTE: to avoid adding a fractal-server dependency, we simply download the
+    relevant file. In the future we may have a fractal-common package, and that
+    one could be easily added as a `dev` dependency.
+    """
+
+    url = (
+        "https://raw.githubusercontent.com/fractal-analytics-platform/"
+        "fractal-common/main/schemas/manifest.py"
+    )
+    r = requests.get(url)
+    debug(tmp_path)
+    with (tmp_path / "fractal_manifest.py").open("wb") as fout:
+        fout.write(r.content)
+
+    sys.path.append(str(tmp_path))
+    from fractal_manifest import ManifestV1
+
+    module_dir = Path(fractal_tasks_core.__file__).parent
+    with (module_dir / "__FRACTAL_MANIFEST__.json").open("r") as fin:
+        manifest_dict = json.load(fin)
+    manifest = ManifestV1(**manifest_dict)
+    debug(manifest)