From fa616a279c195c94fdb1d8a6e250423ef30fdc60 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Tue, 20 Jun 2023 09:08:58 +0200
Subject: [PATCH 01/36] moved functions and hardcoded inner pydantic models

---
 fractal_tasks_core/dev/lib_args_schemas.py | 51 ++-----------------
 fractal_tasks_core/dev/lib_descriptions.py | 58 ++++++++++++++++++++++
 2 files changed, 62 insertions(+), 47 deletions(-)
 create mode 100644 fractal_tasks_core/dev/lib_descriptions.py

diff --git a/fractal_tasks_core/dev/lib_args_schemas.py b/fractal_tasks_core/dev/lib_args_schemas.py
index 1b0f0b0e8..27a93b123 100644
--- a/fractal_tasks_core/dev/lib_args_schemas.py
+++ b/fractal_tasks_core/dev/lib_args_schemas.py
@@ -13,18 +13,18 @@
 
 Helper functions to handle JSON schemas for task arguments.
 """
-import ast
-from pathlib import Path
 from typing import Any
 
-from docstring_parser import parse
 from pydantic.decorator import ALT_V_ARGS
 from pydantic.decorator import ALT_V_KWARGS
 from pydantic.decorator import V_DUPLICATE_KWARGS
 from pydantic.decorator import V_POSITIONAL_ONLY_NAME
 from pydantic.decorator import ValidatedFunction
 
-import fractal_tasks_core
+from fractal_tasks_core.dev.lib_descriptions import _get_args_descriptions
+from fractal_tasks_core.dev.lib_descriptions import (
+    _include_args_descriptions_in_schema,
+)
 from fractal_tasks_core.dev.lib_signature_constraints import _extract_function
 from fractal_tasks_core.dev.lib_signature_constraints import (
     _validate_function_signature,
@@ -78,49 +78,6 @@ def _remove_pydantic_internals(old_schema: _Schema) -> _Schema:
     return new_schema
 
 
-def _get_args_descriptions(executable) -> dict[str, str]:
-    """
-    Extract argument descriptions for a task function
-    """
-    # Read docstring (via ast)
-    module_path = Path(fractal_tasks_core.__file__).parent / executable
-    module_name = module_path.with_suffix("").name
-    tree = ast.parse(module_path.read_text())
-    function = next(
-        f
-        for f in ast.walk(tree)
-        if (isinstance(f, ast.FunctionDef) and f.name == module_name)
-    )
-    docstring = ast.get_docstring(function)
-    # Parse docstring (via docstring_parser) and prepare output
-    parsed_docstring = parse(docstring)
-    descriptions = {
-        param.arg_name: param.description.replace("\n", " ")
-        for param in parsed_docstring.params
-    }
-    return descriptions
-
-
-def _include_args_descriptions_in_schema(*, schema, descriptions):
-    """
-    Merge the descriptions obtained via `_get_args_descriptions` into an
-    existing JSON Schema for task arguments
-    """
-    new_schema = schema.copy()
-    new_properties = schema["properties"].copy()
-    for key, value in schema["properties"].items():
-        if "description" in value:
-            raise ValueError("Property already has description")
-        else:
-            if key in descriptions:
-                value["description"] = descriptions[key]
-            else:
-                value["description"] = "Missing description"
-            new_properties[key] = value
-    new_schema["properties"] = new_properties
-    return new_schema
-
-
 def create_schema_for_single_task(
     executable: str,
     package: str = "fractal_tasks_core.tasks",
diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
new file mode 100644
index 000000000..97dcd54a0
--- /dev/null
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -0,0 +1,58 @@
+import ast
+from pathlib import Path
+
+from docstring_parser import parse
+
+import fractal_tasks_core
+
+
+inner_pydantic_models = {
+    "OmeroChannel": "fractal_tasks_core.lib_channels.py",
+    "Window": "fractal_tasks_core.lib_channels.py",
+    "Channel": "fractal_tasks_core.tasks._input_models.py",
+    "NapariWorkflowsInput": "fractal_tasks_core.tasks._input_models.py",
+    "NapariWorkflowsOutput": "fractal_tasks_core.tasks._input_models.py",
+}
+
+
+def _get_args_descriptions(executable) -> dict[str, str]:
+    """
+    Extract argument descriptions for a task function
+    """
+    # Read docstring (via ast)
+    module_path = Path(fractal_tasks_core.__file__).parent / executable
+    module_name = module_path.with_suffix("").name
+    tree = ast.parse(module_path.read_text())
+    function = next(
+        f
+        for f in ast.walk(tree)
+        if (isinstance(f, ast.FunctionDef) and f.name == module_name)
+    )
+    docstring = ast.get_docstring(function)
+    # Parse docstring (via docstring_parser) and prepare output
+    parsed_docstring = parse(docstring)
+    descriptions = {
+        param.arg_name: param.description.replace("\n", " ")
+        for param in parsed_docstring.params
+    }
+    return descriptions
+
+
+def _include_args_descriptions_in_schema(*, schema, descriptions):
+    """
+    Merge the descriptions obtained via `_get_args_descriptions` into an
+    existing JSON Schema for task arguments
+    """
+    new_schema = schema.copy()
+    new_properties = schema["properties"].copy()
+    for key, value in schema["properties"].items():
+        if "description" in value:
+            raise ValueError("Property already has description")
+        else:
+            if key in descriptions:
+                value["description"] = descriptions[key]
+            else:
+                value["description"] = "Missing description"
+            new_properties[key] = value
+    new_schema["properties"] = new_properties
+    return new_schema

From 102d63a3eb367232c024a6419442966948a1f343 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Tue, 20 Jun 2023 10:52:34 +0200
Subject: [PATCH 02/36] extract docstrings and var descriptions

---
 fractal_tasks_core/dev/lib_descriptions.py | 51 ++++++++++++++++++----
 tests/test_unit_lib_descriptions.py        |  9 ++++
 2 files changed, 52 insertions(+), 8 deletions(-)
 create mode 100644 tests/test_unit_lib_descriptions.py

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index 97dcd54a0..2a067d512 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -1,20 +1,54 @@
 import ast
 from pathlib import Path
 
-from docstring_parser import parse
+from docstring_parser import parse as docparse
 
 import fractal_tasks_core
 
-
 inner_pydantic_models = {
-    "OmeroChannel": "fractal_tasks_core.lib_channels.py",
-    "Window": "fractal_tasks_core.lib_channels.py",
-    "Channel": "fractal_tasks_core.tasks._input_models.py",
-    "NapariWorkflowsInput": "fractal_tasks_core.tasks._input_models.py",
-    "NapariWorkflowsOutput": "fractal_tasks_core.tasks._input_models.py",
+    "OmeroChannel": "lib_channels.py",
+    "Window": "lib_channels.py",
+    "Channel": "tasks/_input_models.py",
+    "NapariWorkflowsInput": "tasks/_input_models.py",
+    "NapariWorkflowsOutput": "tasks/_input_models.py",
 }
 
 
+def _get_args_model_descriptions():
+
+    descriptions = {}
+
+    for model, module in inner_pydantic_models.items():
+
+        module_path = Path(fractal_tasks_core.__file__).parent / module
+        tree = ast.parse(module_path.read_text())
+        _class = next(
+            c
+            for c in ast.walk(tree)
+            if (isinstance(c, ast.ClassDef) and c.name == model)
+        )
+        if not _class:
+            raise RuntimeError(f"Model {module_path}::{model} not found.")
+        else:
+            descriptions[model] = {}
+
+        docstring = ast.get_docstring(_class)
+        if docstring:
+            descriptions[model]["docstring"] = docstring
+
+        var_name: str = ""
+        for node in _class.body:
+            if isinstance(node, ast.AnnAssign):
+                descriptions[model][node.target.id] = None
+                var_name = node.target.id
+            else:
+                if isinstance(node, ast.Expr) and var_name:
+                    descriptions[model][var_name] = node.value.s
+                    var_name = ""
+
+    return descriptions
+
+
 def _get_args_descriptions(executable) -> dict[str, str]:
     """
     Extract argument descriptions for a task function
@@ -28,9 +62,10 @@ def _get_args_descriptions(executable) -> dict[str, str]:
         for f in ast.walk(tree)
         if (isinstance(f, ast.FunctionDef) and f.name == module_name)
     )
+
     docstring = ast.get_docstring(function)
     # Parse docstring (via docstring_parser) and prepare output
-    parsed_docstring = parse(docstring)
+    parsed_docstring = docparse(docstring)
     descriptions = {
         param.arg_name: param.description.replace("\n", " ")
         for param in parsed_docstring.params
diff --git a/tests/test_unit_lib_descriptions.py b/tests/test_unit_lib_descriptions.py
new file mode 100644
index 000000000..7959528cd
--- /dev/null
+++ b/tests/test_unit_lib_descriptions.py
@@ -0,0 +1,9 @@
+from devtools import debug
+
+from fractal_tasks_core.dev.lib_descriptions import (
+    _get_args_model_descriptions,
+)
+
+
+def test_get_args_model_descriptions():
+    debug(_get_args_model_descriptions())

From 074c36feaeb31122674c866489a69311426a781f Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Tue, 20 Jun 2023 10:56:09 +0200
Subject: [PATCH 03/36] docstring to __docstring__

---
 fractal_tasks_core/dev/lib_descriptions.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index 2a067d512..f7e7ee78c 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -34,7 +34,7 @@ def _get_args_model_descriptions():
 
         docstring = ast.get_docstring(_class)
         if docstring:
-            descriptions[model]["docstring"] = docstring
+            descriptions[model]["__docstring__"] = docstring
 
         var_name: str = ""
         for node in _class.body:

From 1a8512b0b42582185223b91ab8da77e465889b85 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Tue, 20 Jun 2023 11:07:22 +0200
Subject: [PATCH 04/36] moved function and add docs

---
 fractal_tasks_core/dev/lib_descriptions.py | 91 ++++++++++++----------
 1 file changed, 48 insertions(+), 43 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index f7e7ee78c..abcd49cf0 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -5,49 +5,6 @@
 
 import fractal_tasks_core
 
-inner_pydantic_models = {
-    "OmeroChannel": "lib_channels.py",
-    "Window": "lib_channels.py",
-    "Channel": "tasks/_input_models.py",
-    "NapariWorkflowsInput": "tasks/_input_models.py",
-    "NapariWorkflowsOutput": "tasks/_input_models.py",
-}
-
-
-def _get_args_model_descriptions():
-
-    descriptions = {}
-
-    for model, module in inner_pydantic_models.items():
-
-        module_path = Path(fractal_tasks_core.__file__).parent / module
-        tree = ast.parse(module_path.read_text())
-        _class = next(
-            c
-            for c in ast.walk(tree)
-            if (isinstance(c, ast.ClassDef) and c.name == model)
-        )
-        if not _class:
-            raise RuntimeError(f"Model {module_path}::{model} not found.")
-        else:
-            descriptions[model] = {}
-
-        docstring = ast.get_docstring(_class)
-        if docstring:
-            descriptions[model]["__docstring__"] = docstring
-
-        var_name: str = ""
-        for node in _class.body:
-            if isinstance(node, ast.AnnAssign):
-                descriptions[model][node.target.id] = None
-                var_name = node.target.id
-            else:
-                if isinstance(node, ast.Expr) and var_name:
-                    descriptions[model][var_name] = node.value.s
-                    var_name = ""
-
-    return descriptions
-
 
 def _get_args_descriptions(executable) -> dict[str, str]:
     """
@@ -91,3 +48,51 @@ def _include_args_descriptions_in_schema(*, schema, descriptions):
             new_properties[key] = value
     new_schema["properties"] = new_properties
     return new_schema
+
+
+INNER_PYDANTIC_MODELS = {
+    "OmeroChannel": "lib_channels.py",
+    "Window": "lib_channels.py",
+    "Channel": "tasks/_input_models.py",
+    "NapariWorkflowsInput": "tasks/_input_models.py",
+    "NapariWorkflowsOutput": "tasks/_input_models.py",
+}
+
+
+def _get_args_model_descriptions(
+    models: dict[str, str] = INNER_PYDANTIC_MODELS
+):
+    """
+    Extract attribut descriptions for Pydantic models
+    """
+    descriptions = {}
+
+    for model, module in models.items():
+        # get the class
+        module_path = Path(fractal_tasks_core.__file__).parent / module
+        tree = ast.parse(module_path.read_text())
+        _class = next(
+            c
+            for c in ast.walk(tree)
+            if (isinstance(c, ast.ClassDef) and c.name == model)
+        )
+        if not _class:
+            raise RuntimeError(f"Model {module_path}::{model} not found.")
+        else:
+            descriptions[model] = {}
+
+        # extract class docstring and attribute docstrings
+        docstring = ast.get_docstring(_class)
+        if docstring:
+            descriptions[model]["_class_docstring_"] = docstring
+        var_name: str = ""
+        for node in _class.body:
+            if isinstance(node, ast.AnnAssign):
+                descriptions[model][node.target.id] = None
+                var_name = node.target.id
+            else:
+                if isinstance(node, ast.Expr) and var_name:
+                    descriptions[model][var_name] = node.value.s
+                    var_name = ""
+
+    return descriptions

From d52a6af9e048cc864faee0ccf9dc75e5ae3b27fc Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Tue, 20 Jun 2023 11:09:23 +0200
Subject: [PATCH 05/36] change func name

---
 fractal_tasks_core/dev/lib_descriptions.py | 2 +-
 tests/test_unit_lib_descriptions.py        | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index abcd49cf0..6e7666e1b 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -59,7 +59,7 @@ def _include_args_descriptions_in_schema(*, schema, descriptions):
 }
 
 
-def _get_args_model_descriptions(
+def _get_attributes_model_descriptions(
     models: dict[str, str] = INNER_PYDANTIC_MODELS
 ):
     """
diff --git a/tests/test_unit_lib_descriptions.py b/tests/test_unit_lib_descriptions.py
index 7959528cd..fe2534a2d 100644
--- a/tests/test_unit_lib_descriptions.py
+++ b/tests/test_unit_lib_descriptions.py
@@ -1,9 +1,9 @@
 from devtools import debug
 
 from fractal_tasks_core.dev.lib_descriptions import (
-    _get_args_model_descriptions,
+    _get_attributes_model_descriptions,
 )
 
 
 def test_get_args_model_descriptions():
-    debug(_get_args_model_descriptions())
+    debug(_get_attributes_model_descriptions())

From 818f17bcd6a537389dfc316ce2ad09760d859141 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Tue, 20 Jun 2023 11:32:40 +0200
Subject: [PATCH 06/36] implement _include_attributs_descriptions_in_schema

---
 fractal_tasks_core/dev/lib_descriptions.py | 49 ++++++++++++++++++----
 tests/test_unit_lib_descriptions.py        |  4 +-
 2 files changed, 42 insertions(+), 11 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index 6e7666e1b..87cac4f9d 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -8,7 +8,7 @@
 
 def _get_args_descriptions(executable) -> dict[str, str]:
     """
-    Extract argument descriptions for a task function
+    Extract argument descriptions for a task function.
     """
     # Read docstring (via ast)
     module_path = Path(fractal_tasks_core.__file__).parent / executable
@@ -33,7 +33,7 @@ def _get_args_descriptions(executable) -> dict[str, str]:
 def _include_args_descriptions_in_schema(*, schema, descriptions):
     """
     Merge the descriptions obtained via `_get_args_descriptions` into an
-    existing JSON Schema for task arguments
+    existing JSON Schema for task arguments.
     """
     new_schema = schema.copy()
     new_properties = schema["properties"].copy()
@@ -59,11 +59,22 @@ def _include_args_descriptions_in_schema(*, schema, descriptions):
 }
 
 
-def _get_attributes_model_descriptions(
+def _get_attributes_models_descriptions(
     models: dict[str, str] = INNER_PYDANTIC_MODELS
-):
+) -> dict[str, dict[str, str]]:
     """
     Extract attribut descriptions for Pydantic models
+
+    Returns:
+        descriptions == {
+            ... ,
+            'Channel': {
+                '_class_docstring_': '...',
+                'wavelength_id': None,
+                'label': None,
+            },
+            ... ,
+        }
     """
     descriptions = {}
 
@@ -77,14 +88,11 @@ def _get_attributes_model_descriptions(
             if (isinstance(c, ast.ClassDef) and c.name == model)
         )
         if not _class:
-            raise RuntimeError(f"Model {module_path}::{model} not found.")
+            raise ValueError(f"Model {module_path}::{model} not found.")
         else:
             descriptions[model] = {}
 
-        # extract class docstring and attribute docstrings
-        docstring = ast.get_docstring(_class)
-        if docstring:
-            descriptions[model]["_class_docstring_"] = docstring
+        # extract attribute docstrings
         var_name: str = ""
         for node in _class.body:
             if isinstance(node, ast.AnnAssign):
@@ -96,3 +104,26 @@ def _get_attributes_model_descriptions(
                     var_name = ""
 
     return descriptions
+
+
+def _include_attributs_descriptions_in_schema(*, schema, descriptions):
+    """
+    Merge the descriptions obtained via `_get_attributes_models_descriptions`
+    into an existing JSON Schema for task arguments.
+    """
+    new_schema = schema.copy()
+    new_definitions = schema["definitions"].copy()
+
+    for key, value in schema["definitions"].items():
+        if key in descriptions:
+            for attribute in descriptions[key]:
+                if attribute in value["properties"]:
+                    if "description" in value["properties"]:
+                        raise ValueError("Attribute already has description")
+                    else:
+                        new_definitions[key]["properties"][
+                            "description"
+                        ] = descriptions[key][attribute]
+
+    new_schema["definitions"] = new_definitions
+    return new_schema
diff --git a/tests/test_unit_lib_descriptions.py b/tests/test_unit_lib_descriptions.py
index fe2534a2d..0b7275509 100644
--- a/tests/test_unit_lib_descriptions.py
+++ b/tests/test_unit_lib_descriptions.py
@@ -1,9 +1,9 @@
 from devtools import debug
 
 from fractal_tasks_core.dev.lib_descriptions import (
-    _get_attributes_model_descriptions,
+    _get_attributes_models_descriptions,
 )
 
 
 def test_get_args_model_descriptions():
-    debug(_get_attributes_model_descriptions())
+    debug(_get_attributes_models_descriptions())

From 5b28e543e6f4099acea3728082c1bd5e9cec6209 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Wed, 21 Jun 2023 09:18:35 +0200
Subject: [PATCH 07/36] BROKEN stash

---
 fractal_tasks_core/dev/lib_descriptions.py |  3 ++-
 tests/test_unit_lib_descriptions.py        | 21 +++++++++++++++++++--
 2 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index 87cac4f9d..fff3bac98 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -1,4 +1,5 @@
 import ast
+import logging
 from pathlib import Path
 
 from docstring_parser import parse as docparse
@@ -119,7 +120,7 @@ def _include_attributs_descriptions_in_schema(*, schema, descriptions):
             for attribute in descriptions[key]:
                 if attribute in value["properties"]:
                     if "description" in value["properties"]:
-                        raise ValueError("Attribute already has description")
+                        logging.warning("Attribute already has description")
                     else:
                         new_definitions[key]["properties"][
                             "description"
diff --git a/tests/test_unit_lib_descriptions.py b/tests/test_unit_lib_descriptions.py
index 0b7275509..e30ee27fd 100644
--- a/tests/test_unit_lib_descriptions.py
+++ b/tests/test_unit_lib_descriptions.py
@@ -1,9 +1,26 @@
-from devtools import debug
+import json
 
 from fractal_tasks_core.dev.lib_descriptions import (
     _get_attributes_models_descriptions,
 )
+from fractal_tasks_core.dev.lib_descriptions import (
+    _include_attributs_descriptions_in_schema,
+)
 
 
 def test_get_args_model_descriptions():
-    debug(_get_attributes_models_descriptions())
+
+    descriptions = _get_attributes_models_descriptions()
+
+    with open("fractal_tasks_core/__FRACTAL_MANIFEST__.json", "r") as f:
+        manifest = json.load(f)
+
+    schemas = [task["args_schema"] for task in manifest["task_list"]]
+
+    for schema in schemas:
+        new_schema = _include_attributs_descriptions_in_schema(
+            schema=schema, descriptions=descriptions
+        )
+        for _, definition in new_schema["definitions"].items():
+            for prop in definition["properties"]:
+                assert "description" in prop

From 75b18f466e8efa8c1b6fccf36a100601a368d297 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Wed, 21 Jun 2023 14:01:26 +0200
Subject: [PATCH 08/36] fix _include_attributs_descriptions_in_schema and test

---
 fractal_tasks_core/dev/lib_descriptions.py | 41 ++++++++++++----------
 fractal_tasks_core/lib_input_models.py     |  8 +++++
 tests/test_unit_lib_descriptions.py        | 13 ++++---
 3 files changed, 38 insertions(+), 24 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index fff3bac98..3fc20042e 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -54,9 +54,9 @@ def _include_args_descriptions_in_schema(*, schema, descriptions):
 INNER_PYDANTIC_MODELS = {
     "OmeroChannel": "lib_channels.py",
     "Window": "lib_channels.py",
-    "Channel": "tasks/_input_models.py",
-    "NapariWorkflowsInput": "tasks/_input_models.py",
-    "NapariWorkflowsOutput": "tasks/_input_models.py",
+    "Channel": "lib_input_models.py",
+    "NapariWorkflowsInput": "lib_input_models.py",
+    "NapariWorkflowsOutput": "lib_input_models.py",
 }
 
 
@@ -70,9 +70,8 @@ def _get_attributes_models_descriptions(
         descriptions == {
             ... ,
             'Channel': {
-                '_class_docstring_': '...',
-                'wavelength_id': None,
-                'label': None,
+                'wavelength_id': TBD,
+                'label': TBD,
             },
             ... ,
         }
@@ -97,7 +96,7 @@ def _get_attributes_models_descriptions(
         var_name: str = ""
         for node in _class.body:
             if isinstance(node, ast.AnnAssign):
-                descriptions[model][node.target.id] = None
+                descriptions[model][node.target.id] = "Missing description"
                 var_name = node.target.id
             else:
                 if isinstance(node, ast.Expr) and var_name:
@@ -113,18 +112,22 @@ def _include_attributs_descriptions_in_schema(*, schema, descriptions):
     into an existing JSON Schema for task arguments.
     """
     new_schema = schema.copy()
-    new_definitions = schema["definitions"].copy()
-
-    for key, value in schema["definitions"].items():
-        if key in descriptions:
-            for attribute in descriptions[key]:
-                if attribute in value["properties"]:
-                    if "description" in value["properties"]:
-                        logging.warning("Attribute already has description")
-                    else:
-                        new_definitions[key]["properties"][
-                            "description"
-                        ] = descriptions[key][attribute]
 
+    if "definitions" not in schema:
+        return new_schema
+    else:
+        new_definitions = schema["definitions"].copy()
+
+    for name, definition in schema["definitions"].items():
+        if name in descriptions.keys():
+            for prop in definition["properties"]:
+                if "description" in new_definitions[name]["properties"][prop]:
+                    logging.warning(
+                        f"Property {name}.{prop} already has description"
+                    )
+                else:
+                    new_definitions[name]["properties"][prop][
+                        "description"
+                    ] = descriptions[name][prop]
     new_schema["definitions"] = new_definitions
     return new_schema
diff --git a/fractal_tasks_core/lib_input_models.py b/fractal_tasks_core/lib_input_models.py
index f6f70de57..3ff278e28 100644
--- a/fractal_tasks_core/lib_input_models.py
+++ b/fractal_tasks_core/lib_input_models.py
@@ -26,7 +26,9 @@ class Channel(BaseModel):
     """
 
     wavelength_id: Optional[str] = None
+    """TBD"""
     label: Optional[str] = None
+    """TBD"""
 
     @validator("label", always=True)
     def mutually_exclusive_channel_attributes(cls, v, values):
@@ -53,8 +55,11 @@ class NapariWorkflowsInput(BaseModel):
     """
 
     type: Literal["image", "label"]
+    """TBD"""
     label_name: Optional[str]
+    """TBD"""
     channel: Optional[Channel]
+    """TBD"""
 
     @validator("label_name", always=True)
     def label_name_is_present(cls, v, values):
@@ -79,8 +84,11 @@ class NapariWorkflowsOutput(BaseModel):
     """
 
     type: Literal["label", "dataframe"]
+    """TBD"""
     label_name: Optional[str] = None
+    """TBD"""
     table_name: Optional[str] = None
+    """TBD"""
 
     @validator("label_name", always=True)
     def label_name_only_for_label_type(cls, v, values):
diff --git a/tests/test_unit_lib_descriptions.py b/tests/test_unit_lib_descriptions.py
index e30ee27fd..8bfba4b56 100644
--- a/tests/test_unit_lib_descriptions.py
+++ b/tests/test_unit_lib_descriptions.py
@@ -1,5 +1,7 @@
 import json
 
+from devtools import debug
+
 from fractal_tasks_core.dev.lib_descriptions import (
     _get_attributes_models_descriptions,
 )
@@ -9,18 +11,19 @@
 
 
 def test_get_args_model_descriptions():
-
     descriptions = _get_attributes_models_descriptions()
+    debug(descriptions)
 
     with open("fractal_tasks_core/__FRACTAL_MANIFEST__.json", "r") as f:
         manifest = json.load(f)
 
     schemas = [task["args_schema"] for task in manifest["task_list"]]
 
-    for schema in schemas:
+    for i, schema in enumerate(schemas):
         new_schema = _include_attributs_descriptions_in_schema(
             schema=schema, descriptions=descriptions
         )
-        for _, definition in new_schema["definitions"].items():
-            for prop in definition["properties"]:
-                assert "description" in prop
+        if "definitions" in schema:
+            for _, definition in new_schema["definitions"].items():
+                for prop in definition["properties"]:
+                    assert "description" in definition["properties"][prop]

From b9e098fe1d556c0e78cf3e4de5759e706b9b4b8f Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Wed, 21 Jun 2023 14:13:58 +0200
Subject: [PATCH 09/36] change log warning to raise error

---
 fractal_tasks_core/dev/lib_descriptions.py | 19 +++++++++----------
 tests/test_unit_lib_descriptions.py        | 10 ++++++++++
 2 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index 3fc20042e..f65cea615 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -1,5 +1,4 @@
 import ast
-import logging
 from pathlib import Path
 
 from docstring_parser import parse as docparse
@@ -82,15 +81,15 @@ def _get_attributes_models_descriptions(
         # get the class
         module_path = Path(fractal_tasks_core.__file__).parent / module
         tree = ast.parse(module_path.read_text())
-        _class = next(
-            c
-            for c in ast.walk(tree)
-            if (isinstance(c, ast.ClassDef) and c.name == model)
-        )
-        if not _class:
-            raise ValueError(f"Model {module_path}::{model} not found.")
-        else:
+        try:
+            _class = next(
+                c
+                for c in ast.walk(tree)
+                if (isinstance(c, ast.ClassDef) and c.name == model)
+            )
             descriptions[model] = {}
+        except StopIteration:
+            raise ValueError(f"Model {module_path}::{model} not found.")
 
         # extract attribute docstrings
         var_name: str = ""
@@ -122,7 +121,7 @@ def _include_attributs_descriptions_in_schema(*, schema, descriptions):
         if name in descriptions.keys():
             for prop in definition["properties"]:
                 if "description" in new_definitions[name]["properties"][prop]:
-                    logging.warning(
+                    raise ValueError(
                         f"Property {name}.{prop} already has description"
                     )
                 else:
diff --git a/tests/test_unit_lib_descriptions.py b/tests/test_unit_lib_descriptions.py
index 8bfba4b56..067824459 100644
--- a/tests/test_unit_lib_descriptions.py
+++ b/tests/test_unit_lib_descriptions.py
@@ -1,5 +1,6 @@
 import json
 
+import pytest
 from devtools import debug
 
 from fractal_tasks_core.dev.lib_descriptions import (
@@ -11,6 +12,10 @@
 
 
 def test_get_args_model_descriptions():
+
+    with pytest.raises(ValueError):
+        _get_attributes_models_descriptions(models={"Foo": "__init__.py"})
+
     descriptions = _get_attributes_models_descriptions()
     debug(descriptions)
 
@@ -27,3 +32,8 @@ def test_get_args_model_descriptions():
             for _, definition in new_schema["definitions"].items():
                 for prop in definition["properties"]:
                     assert "description" in definition["properties"][prop]
+
+    with pytest.raises(ValueError):
+        _include_attributs_descriptions_in_schema(
+            schema=new_schema, descriptions=descriptions
+        )

From f3a601e0f7551077f640901062f5f151fb3879eb Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Wed, 21 Jun 2023 14:45:42 +0200
Subject: [PATCH 10/36] Update autodoc_member_orderautodoc_member_order option
 in docs

---
 docs/source/conf.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 9b3fc042f..7f1d043ab 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -29,6 +29,7 @@
     "private-members": True,
     "show-inheritance": True,
     "autosummary-no-nesting": True,
+    "autodoc_member_order": "bysource"  # valid options: bysource, groupwise, alphabetical
 }
 autodata_content = "both"
 source_suffix = ".rst"

From cc0400f27e627b0e535f107f007c380a16cc8551 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Wed, 21 Jun 2023 14:52:53 +0200
Subject: [PATCH 11/36] Fix precommit

---
 docs/source/conf.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 7f1d043ab..63f7e1a2a 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -29,7 +29,8 @@
     "private-members": True,
     "show-inheritance": True,
     "autosummary-no-nesting": True,
-    "autodoc_member_order": "bysource"  # valid options: bysource, groupwise, alphabetical
+    # valid options: bysource, groupwise, alphabetical
+    "autodoc_member_order": "bysource",
 }
 autodata_content = "both"
 source_suffix = ".rst"

From b11fc4ed356220e5abaeeca9a9dc2574f124cd5d Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Wed, 21 Jun 2023 16:14:10 +0200
Subject: [PATCH 12/36] class attribute docstrings back to """..."""

---
 fractal_tasks_core/lib_channels.py     | 11 +++++++++++
 fractal_tasks_core/lib_input_models.py |  5 +++++
 2 files changed, 16 insertions(+)

diff --git a/fractal_tasks_core/lib_channels.py b/fractal_tasks_core/lib_channels.py
index a7053ed4d..1899bc9ca 100644
--- a/fractal_tasks_core/lib_channels.py
+++ b/fractal_tasks_core/lib_channels.py
@@ -45,10 +45,13 @@ class Window(BaseModel):
 
     min: Optional[int]
     """TBD"""
+
     max: Optional[int]
     """TBD"""
+
     start: int
     """TBD"""
+
     end: int
     """TBD"""
 
@@ -68,22 +71,30 @@ class OmeroChannel(BaseModel):
     """
 
     # Custom
+
     wavelength_id: str
     """TBD"""
+
     index: Optional[int]
     """TBD"""
 
     # From OME-NGFF v0.4 transitional metadata
+
     window: Optional[Window]
     """TBD"""
+
     color: Optional[str]
     """TBD"""
+
     label: Optional[str]
     """TBD"""
+
     active: bool = True
     """TBD"""
+
     coefficient: int = 1
     """TBD"""
+
     inverted: bool = False
     """TBD"""
 
diff --git a/fractal_tasks_core/lib_input_models.py b/fractal_tasks_core/lib_input_models.py
index 3ff278e28..4c41e9b82 100644
--- a/fractal_tasks_core/lib_input_models.py
+++ b/fractal_tasks_core/lib_input_models.py
@@ -27,6 +27,7 @@ class Channel(BaseModel):
 
     wavelength_id: Optional[str] = None
     """TBD"""
+
     label: Optional[str] = None
     """TBD"""
 
@@ -56,8 +57,10 @@ class NapariWorkflowsInput(BaseModel):
 
     type: Literal["image", "label"]
     """TBD"""
+
     label_name: Optional[str]
     """TBD"""
+
     channel: Optional[Channel]
     """TBD"""
 
@@ -85,8 +88,10 @@ class NapariWorkflowsOutput(BaseModel):
 
     type: Literal["label", "dataframe"]
     """TBD"""
+
     label_name: Optional[str] = None
     """TBD"""
+
     table_name: Optional[str] = None
     """TBD"""
 

From e35555fc1d50a3dbe208a93b6bd164dfe6a593ba Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Wed, 21 Jun 2023 16:17:53 +0200
Subject: [PATCH 13/36] Simplify docstring to fix docs build

---
 fractal_tasks_core/dev/lib_descriptions.py | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index f65cea615..3f0ed5c76 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -64,16 +64,6 @@ def _get_attributes_models_descriptions(
 ) -> dict[str, dict[str, str]]:
     """
     Extract attribut descriptions for Pydantic models
-
-    Returns:
-        descriptions == {
-            ... ,
-            'Channel': {
-                'wavelength_id': TBD,
-                'label': TBD,
-            },
-            ... ,
-        }
     """
     descriptions = {}
 

From 36b072abefcf0521161af6f1b41d3d6468f1009e Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Wed, 21 Jun 2023 16:33:58 +0200
Subject: [PATCH 14/36] STASH

---
 fractal_tasks_core/dev/lib_descriptions.py | 45 +++++++++++++++++-----
 tests/test_unit_lib_descriptions.py        |  9 +++++
 2 files changed, 44 insertions(+), 10 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index f65cea615..d72862620 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -1,10 +1,45 @@
 import ast
+from importlib import import_module
 from pathlib import Path
 
 from docstring_parser import parse as docparse
 
 import fractal_tasks_core
 
+# import inspect
+# from inspect import signature
+# from typing import Callable
+
+
+"""
+pkg_name = fractal_task_core
+relative_module_path = lib_channels.py
+object_name = {class_name} / {function_name}
+
+
+_get_function_args_descriptions: dict[str, str]
+_get_class_attrs_descriptions: dict[str, str]
+
+l'import deve essere fatto tipo:
+    module = import_module(f"{package}.{module_name}")
+    task_function = getattr(module, module_name)
+
+Per una funzione deve ritornare quello che già abbiamo
+Per una classe dobbiamo fare quello che facciamo ma per una sola classe
+"""
+
+
+def _get_function_args_descriptions(
+    package_name: str, module_relative_path: str, function_name: str
+) -> dict[str, str]:
+
+    if not module_relative_path.endswith(".py"):
+        raise ValueError(f"Module {module_relative_path} must end with '.py'")
+
+    module = import_module(f"{package_name}.{module_relative_path}")
+    x = getattr(module, function_name)
+    return x
+
 
 def _get_args_descriptions(executable) -> dict[str, str]:
     """
@@ -64,16 +99,6 @@ def _get_attributes_models_descriptions(
 ) -> dict[str, dict[str, str]]:
     """
     Extract attribut descriptions for Pydantic models
-
-    Returns:
-        descriptions == {
-            ... ,
-            'Channel': {
-                'wavelength_id': TBD,
-                'label': TBD,
-            },
-            ... ,
-        }
     """
     descriptions = {}
 
diff --git a/tests/test_unit_lib_descriptions.py b/tests/test_unit_lib_descriptions.py
index 067824459..4dd989bdf 100644
--- a/tests/test_unit_lib_descriptions.py
+++ b/tests/test_unit_lib_descriptions.py
@@ -6,6 +6,9 @@
 from fractal_tasks_core.dev.lib_descriptions import (
     _get_attributes_models_descriptions,
 )
+from fractal_tasks_core.dev.lib_descriptions import (
+    _get_function_args_descriptions,
+)
 from fractal_tasks_core.dev.lib_descriptions import (
     _include_attributs_descriptions_in_schema,
 )
@@ -13,6 +16,12 @@
 
 def test_get_args_model_descriptions():
 
+    x = _get_function_args_descriptions(
+        "fractal_tasks_core", "lib_input_models.py", "Channel"
+    )
+    debug(x, dir(x))
+    # assert False
+
     with pytest.raises(ValueError):
         _get_attributes_models_descriptions(models={"Foo": "__init__.py"})
 

From 10f21571714f6bb2a9eb2cd161fb131bb5fe5956 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Wed, 21 Jun 2023 16:42:30 +0200
Subject: [PATCH 15/36] Improve docstrings (ref #421)

---
 fractal_tasks_core/lib_channels.py     | 32 +++++++++++++-------------
 fractal_tasks_core/lib_input_models.py | 30 ++++++++++++++++--------
 2 files changed, 37 insertions(+), 25 deletions(-)

diff --git a/fractal_tasks_core/lib_channels.py b/fractal_tasks_core/lib_channels.py
index 1899bc9ca..2db8388fb 100644
--- a/fractal_tasks_core/lib_channels.py
+++ b/fractal_tasks_core/lib_channels.py
@@ -40,20 +40,20 @@ class Window(BaseModel):
     Main difference from the specs:
 
         1. ``min`` and ``max`` are optional, since we have custom logic to set
-            their values.
+           their values.
     """
 
     min: Optional[int]
-    """TBD"""
+    """If not provided, it will be set to ``0``."""
 
     max: Optional[int]
-    """TBD"""
+    """If not provided, it will be set according to bit-depth."""
 
     start: int
-    """TBD"""
+    """Start value of the visualization window."""
 
     end: int
-    """TBD"""
+    """End value of the visualization window."""
 
 
 class OmeroChannel(BaseModel):
@@ -61,7 +61,7 @@ class OmeroChannel(BaseModel):
     Custom class for Omero channels, related to OME-NGFF v0.4.
 
     Differences from OME-NGFF v0.4 specs
-    (https://ngff.openmicroscopy.org/0.4/#omero-md)
+    (https://ngff.openmicroscopy.org/0.4/#omero-md):
 
         1. Additional attributes ``wavelength_id`` and ``index``.
         2. We make ``color`` an optional attribute, since we have custom
@@ -73,30 +73,30 @@ class OmeroChannel(BaseModel):
     # Custom
 
     wavelength_id: str
-    """TBD"""
+    """Custom attribute (e.g. ``A01_C01``)."""
 
     index: Optional[int]
-    """TBD"""
+    """For internal use only."""
 
     # From OME-NGFF v0.4 transitional metadata
 
+    label: Optional[str]
+    """Channel label."""
+
     window: Optional[Window]
-    """TBD"""
+    """A ``Window`` object to display this channel in napari."""
 
     color: Optional[str]
-    """TBD"""
-
-    label: Optional[str]
-    """TBD"""
+    """A colormap to display the channel in napari (e.g. ``00FFFF``)."""
 
     active: bool = True
-    """TBD"""
+    """Omero-channel attribute."""
 
     coefficient: int = 1
-    """TBD"""
+    """Omero-channel attribute."""
 
     inverted: bool = False
-    """TBD"""
+    """Omero-channel attribute."""
 
 
 class ChannelNotFoundError(ValueError):
diff --git a/fractal_tasks_core/lib_input_models.py b/fractal_tasks_core/lib_input_models.py
index 4c41e9b82..0fcefa928 100644
--- a/fractal_tasks_core/lib_input_models.py
+++ b/fractal_tasks_core/lib_input_models.py
@@ -26,15 +26,15 @@ class Channel(BaseModel):
     """
 
     wavelength_id: Optional[str] = None
-    """TBD"""
+    """Unique ID for the channel wavelength, e.g. ``A01_C01``."""
 
     label: Optional[str] = None
-    """TBD"""
+    """Channel label."""
 
     @validator("label", always=True)
     def mutually_exclusive_channel_attributes(cls, v, values):
         """
-        Attributes ``label`` and ``wavelength_id`` are mutually exclusive.
+        Check that either ``label`` or ``wavelength_id`` is set.
         """
         wavelength_id = values.get("wavelength_id")
         label = v
@@ -56,16 +56,19 @@ class NapariWorkflowsInput(BaseModel):
     """
 
     type: Literal["image", "label"]
-    """TBD"""
+    """Input type (supported: ``image`` or ``label``)."""
 
     label_name: Optional[str]
-    """TBD"""
+    """Label name (for label inputs only)."""
 
     channel: Optional[Channel]
-    """TBD"""
+    """Channel object (for image inputs only)."""
 
     @validator("label_name", always=True)
     def label_name_is_present(cls, v, values):
+        """
+        Check that label inputs have ``label_name`` set.
+        """
         _type = values.get("type")
         if _type == "label" and not v:
             raise ValueError(
@@ -75,6 +78,9 @@ def label_name_is_present(cls, v, values):
 
     @validator("channel", always=True)
     def channel_is_present(cls, v, values):
+        """
+        Check that image inputs have ``channel`` set.
+        """
         _type = values.get("type")
         if _type == "image" and not v:
             raise ValueError(f"Input item has type={_type} but channel={v}.")
@@ -87,16 +93,19 @@ class NapariWorkflowsOutput(BaseModel):
     """
 
     type: Literal["label", "dataframe"]
-    """TBD"""
+    """Output type (supported: ``label`` or ``dataframe``)."""
 
     label_name: Optional[str] = None
-    """TBD"""
+    """Label name (for label outputs only)."""
 
     table_name: Optional[str] = None
-    """TBD"""
+    """Table name (for dataframe outputs only)."""
 
     @validator("label_name", always=True)
     def label_name_only_for_label_type(cls, v, values):
+        """
+        Check that label_name is set only for label outputs.
+        """
         _type = values.get("type")
         if (_type == "label" and (not v)) or (_type != "label" and v):
             raise ValueError(
@@ -106,6 +115,9 @@ def label_name_only_for_label_type(cls, v, values):
 
     @validator("table_name", always=True)
     def table_name_only_for_dataframe_type(cls, v, values):
+        """
+        Check that table_name is set only for dataframe outputs.
+        """
         _type = values.get("type")
         if (_type == "dataframe" and (not v)) or (_type != "dataframe" and v):
             raise ValueError(

From 78579e38286cabdb9d843fb8e8a0b0670a28d6eb Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Wed, 21 Jun 2023 16:43:24 +0200
Subject: [PATCH 16/36] Update manifest

---
 fractal_tasks_core/__FRACTAL_MANIFEST__.json | 24 ++++++++++----------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/fractal_tasks_core/__FRACTAL_MANIFEST__.json b/fractal_tasks_core/__FRACTAL_MANIFEST__.json
index 3a0f097bc..cb35e034d 100644
--- a/fractal_tasks_core/__FRACTAL_MANIFEST__.json
+++ b/fractal_tasks_core/__FRACTAL_MANIFEST__.json
@@ -77,7 +77,7 @@
         "definitions": {
           "Window": {
             "title": "Window",
-            "description": "Custom class for Omero-channel window, related to OME-NGFF v0.4\n\nSee https://ngff.openmicroscopy.org/0.4/#omero-md.\nMain difference from the specs:\n\n    1. ``min`` and ``max`` are optional, since we have custom logic to set\n        their values.",
+            "description": "Custom class for Omero-channel window, related to OME-NGFF v0.4\n\nSee https://ngff.openmicroscopy.org/0.4/#omero-md.\nMain difference from the specs:\n\n    1. ``min`` and ``max`` are optional, since we have custom logic to set\n       their values.",
             "type": "object",
             "properties": {
               "min": {
@@ -104,7 +104,7 @@
           },
           "OmeroChannel": {
             "title": "OmeroChannel",
-            "description": "Custom class for Omero channels, related to OME-NGFF v0.4.\n\nDifferences from OME-NGFF v0.4 specs\n(https://ngff.openmicroscopy.org/0.4/#omero-md)\n\n    1. Additional attributes ``wavelength_id`` and ``index``.\n    2. We make ``color`` an optional attribute, since we have custom\n       logic to set its value.\n    3. We make ``window`` an optional attribute, so that we can also\n       process zarr arrays which do not have this attribute.",
+            "description": "Custom class for Omero channels, related to OME-NGFF v0.4.\n\nDifferences from OME-NGFF v0.4 specs\n(https://ngff.openmicroscopy.org/0.4/#omero-md):\n\n    1. Additional attributes ``wavelength_id`` and ``index``.\n    2. We make ``color`` an optional attribute, since we have custom\n       logic to set its value.\n    3. We make ``window`` an optional attribute, so that we can also\n       process zarr arrays which do not have this attribute.",
             "type": "object",
             "properties": {
               "wavelength_id": {
@@ -115,6 +115,10 @@
                 "title": "Index",
                 "type": "integer"
               },
+              "label": {
+                "title": "Label",
+                "type": "string"
+              },
               "window": {
                 "$ref": "#/definitions/Window"
               },
@@ -122,10 +126,6 @@
                 "title": "Color",
                 "type": "string"
               },
-              "label": {
-                "title": "Label",
-                "type": "string"
-              },
               "active": {
                 "title": "Active",
                 "default": true,
@@ -804,7 +804,7 @@
         "definitions": {
           "Window": {
             "title": "Window",
-            "description": "Custom class for Omero-channel window, related to OME-NGFF v0.4\n\nSee https://ngff.openmicroscopy.org/0.4/#omero-md.\nMain difference from the specs:\n\n    1. ``min`` and ``max`` are optional, since we have custom logic to set\n        their values.",
+            "description": "Custom class for Omero-channel window, related to OME-NGFF v0.4\n\nSee https://ngff.openmicroscopy.org/0.4/#omero-md.\nMain difference from the specs:\n\n    1. ``min`` and ``max`` are optional, since we have custom logic to set\n       their values.",
             "type": "object",
             "properties": {
               "min": {
@@ -831,7 +831,7 @@
           },
           "OmeroChannel": {
             "title": "OmeroChannel",
-            "description": "Custom class for Omero channels, related to OME-NGFF v0.4.\n\nDifferences from OME-NGFF v0.4 specs\n(https://ngff.openmicroscopy.org/0.4/#omero-md)\n\n    1. Additional attributes ``wavelength_id`` and ``index``.\n    2. We make ``color`` an optional attribute, since we have custom\n       logic to set its value.\n    3. We make ``window`` an optional attribute, so that we can also\n       process zarr arrays which do not have this attribute.",
+            "description": "Custom class for Omero channels, related to OME-NGFF v0.4.\n\nDifferences from OME-NGFF v0.4 specs\n(https://ngff.openmicroscopy.org/0.4/#omero-md):\n\n    1. Additional attributes ``wavelength_id`` and ``index``.\n    2. We make ``color`` an optional attribute, since we have custom\n       logic to set its value.\n    3. We make ``window`` an optional attribute, so that we can also\n       process zarr arrays which do not have this attribute.",
             "type": "object",
             "properties": {
               "wavelength_id": {
@@ -842,6 +842,10 @@
                 "title": "Index",
                 "type": "integer"
               },
+              "label": {
+                "title": "Label",
+                "type": "string"
+              },
               "window": {
                 "$ref": "#/definitions/Window"
               },
@@ -849,10 +853,6 @@
                 "title": "Color",
                 "type": "string"
               },
-              "label": {
-                "title": "Label",
-                "type": "string"
-              },
               "active": {
                 "title": "Active",
                 "default": true,

From 932aa6ba8975bcdd2711a677649d58a6b0aaea6d Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Wed, 21 Jun 2023 16:53:16 +0200
Subject: [PATCH 17/36] Minor fix to docs config

---
 docs/source/conf.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 63f7e1a2a..bd9e635dd 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -29,8 +29,9 @@
     "private-members": True,
     "show-inheritance": True,
     "autosummary-no-nesting": True,
+    "autosummary_no_nesting": True,
     # valid options: bysource, groupwise, alphabetical
-    "autodoc_member_order": "bysource",
+    "autodoc_member_order": "groupwise",
 }
 autodata_content = "both"
 source_suffix = ".rst"

From daed7e1cafd9065b6fda068becb89e29b2b3969b Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Wed, 21 Jun 2023 17:44:48 +0200
Subject: [PATCH 18/36] implement _get_function_args_descriptions

---
 fractal_tasks_core/dev/lib_descriptions.py | 20 +++++++++++++++++---
 tests/test_unit_lib_descriptions.py        | 11 ++++++-----
 2 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index d72862620..91401cc77 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -32,13 +32,27 @@
 def _get_function_args_descriptions(
     package_name: str, module_relative_path: str, function_name: str
 ) -> dict[str, str]:
+    """
+    Extract argument descriptions from a function
+    """
 
     if not module_relative_path.endswith(".py"):
         raise ValueError(f"Module {module_relative_path} must end with '.py'")
+    else:
+        module_relative_path = module_relative_path.rstrip(".py")
+    module_name = Path(package_name).with_suffix("").name
+    module = import_module(f"{module_name}.{module_relative_path}")
+    function = getattr(module, function_name)
 
-    module = import_module(f"{package_name}.{module_relative_path}")
-    x = getattr(module, function_name)
-    return x
+    docstring = function.__doc__
+
+    # Parse docstring (via docstring_parser) and prepare output
+    parsed_docstring = docparse(docstring)
+    descriptions = {
+        param.arg_name: param.description.replace("\n", " ")
+        for param in parsed_docstring.params
+    }
+    return descriptions
 
 
 def _get_args_descriptions(executable) -> dict[str, str]:
diff --git a/tests/test_unit_lib_descriptions.py b/tests/test_unit_lib_descriptions.py
index 4dd989bdf..1fa695553 100644
--- a/tests/test_unit_lib_descriptions.py
+++ b/tests/test_unit_lib_descriptions.py
@@ -14,13 +14,14 @@
 )
 
 
-def test_get_args_model_descriptions():
+def test_descriptions():
 
-    x = _get_function_args_descriptions(
-        "fractal_tasks_core", "lib_input_models.py", "Channel"
+    function_doc = _get_function_args_descriptions(
+        "fractal_tasks_core",
+        "dev.lib_signature_constraints.py",
+        "_extract_function",
     )
-    debug(x, dir(x))
-    # assert False
+    assert function_doc.keys() == set(("executable", "package"))
 
     with pytest.raises(ValueError):
         _get_attributes_models_descriptions(models={"Foo": "__init__.py"})

From 4a4b993f5c9d5cc182785a72b93110f674dfafb4 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Wed, 21 Jun 2023 17:45:48 +0200
Subject: [PATCH 19/36] separate tests

---
 tests/test_unit_lib_descriptions.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/test_unit_lib_descriptions.py b/tests/test_unit_lib_descriptions.py
index 1fa695553..bb04c6808 100644
--- a/tests/test_unit_lib_descriptions.py
+++ b/tests/test_unit_lib_descriptions.py
@@ -14,8 +14,7 @@
 )
 
 
-def test_descriptions():
-
+def test_get_function_args_descriptions():
     function_doc = _get_function_args_descriptions(
         "fractal_tasks_core",
         "dev.lib_signature_constraints.py",
@@ -23,6 +22,9 @@ def test_descriptions():
     )
     assert function_doc.keys() == set(("executable", "package"))
 
+
+def test_descriptions():
+
     with pytest.raises(ValueError):
         _get_attributes_models_descriptions(models={"Foo": "__init__.py"})
 

From b3dd0b2cc1134b96107823781ef72c8cb964f5cf Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Wed, 21 Jun 2023 18:10:17 +0200
Subject: [PATCH 20/36] implement _get_class_attrs_descriptions and test

---
 fractal_tasks_core/dev/lib_descriptions.py | 52 +++++++++++++---------
 tests/test_unit_lib_descriptions.py        | 14 +++++-
 2 files changed, 42 insertions(+), 24 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index 91401cc77..6aaaa782e 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -6,28 +6,6 @@
 
 import fractal_tasks_core
 
-# import inspect
-# from inspect import signature
-# from typing import Callable
-
-
-"""
-pkg_name = fractal_task_core
-relative_module_path = lib_channels.py
-object_name = {class_name} / {function_name}
-
-
-_get_function_args_descriptions: dict[str, str]
-_get_class_attrs_descriptions: dict[str, str]
-
-l'import deve essere fatto tipo:
-    module = import_module(f"{package}.{module_name}")
-    task_function = getattr(module, module_name)
-
-Per una funzione deve ritornare quello che già abbiamo
-Per una classe dobbiamo fare quello che facciamo ma per una sola classe
-"""
-
 
 def _get_function_args_descriptions(
     package_name: str, module_relative_path: str, function_name: str
@@ -55,6 +33,36 @@ def _get_function_args_descriptions(
     return descriptions
 
 
+def _get_class_attrs_descriptions(
+    package_name: str, module_relative_path: str, class_name: str
+) -> dict[str, str]:
+    if not module_relative_path.endswith(".py"):
+        raise ValueError(f"Module {module_relative_path} must end with '.py'")
+
+    # get the class
+    module_path = Path(package_name) / module_relative_path
+    tree = ast.parse(module_path.read_text())
+
+    _class = next(
+        c
+        for c in ast.walk(tree)
+        if (isinstance(c, ast.ClassDef) and c.name == class_name)
+    )
+    attrs_descriptions = {}
+
+    # extract attribute docstrings
+    var_name: str = ""
+    for node in _class.body:
+        if isinstance(node, ast.AnnAssign):
+            attrs_descriptions[node.target.id] = "Missing description"
+            var_name = node.target.id
+        else:
+            if isinstance(node, ast.Expr) and var_name:
+                attrs_descriptions[var_name] = node.value.s
+                var_name = ""
+    return attrs_descriptions
+
+
 def _get_args_descriptions(executable) -> dict[str, str]:
     """
     Extract argument descriptions for a task function.
diff --git a/tests/test_unit_lib_descriptions.py b/tests/test_unit_lib_descriptions.py
index bb04c6808..d0fc49bca 100644
--- a/tests/test_unit_lib_descriptions.py
+++ b/tests/test_unit_lib_descriptions.py
@@ -6,6 +6,9 @@
 from fractal_tasks_core.dev.lib_descriptions import (
     _get_attributes_models_descriptions,
 )
+from fractal_tasks_core.dev.lib_descriptions import (
+    _get_class_attrs_descriptions,
+)
 from fractal_tasks_core.dev.lib_descriptions import (
     _get_function_args_descriptions,
 )
@@ -15,12 +18,19 @@
 
 
 def test_get_function_args_descriptions():
-    function_doc = _get_function_args_descriptions(
+    args_descriptions = _get_function_args_descriptions(
         "fractal_tasks_core",
         "dev.lib_signature_constraints.py",
         "_extract_function",
     )
-    assert function_doc.keys() == set(("executable", "package"))
+    assert args_descriptions.keys() == set(("executable", "package"))
+
+
+def test_get_class_attrs_descriptions():
+    attrs_descriptions = _get_class_attrs_descriptions(
+        "fractal_tasks_core", "lib_input_models.py", "Channel"
+    )
+    assert attrs_descriptions.keys() == set(("wavelength_id", "label"))
 
 
 def test_descriptions():

From 77cb15a8607c968d02683e005a1564df84767a1e Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Thu, 22 Jun 2023 10:16:25 +0200
Subject: [PATCH 21/36] clean lib_descriptions

---
 fractal_tasks_core/dev/lib_args_schemas.py    |   9 ++
 fractal_tasks_core/dev/lib_descriptions.py    | 103 +++---------------
 tests/{ => dev}/test_unit_lib_descriptions.py |  42 ++++---
 3 files changed, 47 insertions(+), 107 deletions(-)
 rename tests/{ => dev}/test_unit_lib_descriptions.py (52%)

diff --git a/fractal_tasks_core/dev/lib_args_schemas.py b/fractal_tasks_core/dev/lib_args_schemas.py
index 27a93b123..e9fe3b11a 100644
--- a/fractal_tasks_core/dev/lib_args_schemas.py
+++ b/fractal_tasks_core/dev/lib_args_schemas.py
@@ -34,6 +34,15 @@
 _Schema = dict[str, Any]
 
 
+INNER_PYDANTIC_MODELS = {
+    "OmeroChannel": "lib_channels.py",
+    "Window": "lib_channels.py",
+    "Channel": "lib_input_models.py",
+    "NapariWorkflowsInput": "lib_input_models.py",
+    "NapariWorkflowsOutput": "lib_input_models.py",
+}
+
+
 def _remove_args_kwargs_properties(old_schema: _Schema) -> _Schema:
     """
     Remove ``args`` and ``kwargs`` schema properties
diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index 6aaaa782e..7ea4d7d64 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -1,11 +1,8 @@
 import ast
-from importlib import import_module
 from pathlib import Path
 
 from docstring_parser import parse as docparse
 
-import fractal_tasks_core
-
 
 def _get_function_args_descriptions(
     package_name: str, module_relative_path: str, function_name: str
@@ -16,13 +13,17 @@ def _get_function_args_descriptions(
 
     if not module_relative_path.endswith(".py"):
         raise ValueError(f"Module {module_relative_path} must end with '.py'")
-    else:
-        module_relative_path = module_relative_path.rstrip(".py")
-    module_name = Path(package_name).with_suffix("").name
-    module = import_module(f"{module_name}.{module_relative_path}")
-    function = getattr(module, function_name)
 
-    docstring = function.__doc__
+    # get the function
+    module_path = Path(package_name) / module_relative_path
+    tree = ast.parse(module_path.read_text())
+
+    _function = next(
+        f
+        for f in ast.walk(tree)
+        if (isinstance(f, ast.FunctionDef) and f.name == function_name)
+    )
+    docstring = ast.get_docstring(_function)
 
     # Parse docstring (via docstring_parser) and prepare output
     parsed_docstring = docparse(docstring)
@@ -36,6 +37,7 @@ def _get_function_args_descriptions(
 def _get_class_attrs_descriptions(
     package_name: str, module_relative_path: str, class_name: str
 ) -> dict[str, str]:
+
     if not module_relative_path.endswith(".py"):
         raise ValueError(f"Module {module_relative_path} must end with '.py'")
 
@@ -48,46 +50,22 @@ def _get_class_attrs_descriptions(
         for c in ast.walk(tree)
         if (isinstance(c, ast.ClassDef) and c.name == class_name)
     )
-    attrs_descriptions = {}
 
+    descriptions = {}
     # extract attribute docstrings
     var_name: str = ""
     for node in _class.body:
         if isinstance(node, ast.AnnAssign):
-            attrs_descriptions[node.target.id] = "Missing description"
+            descriptions[node.target.id] = "Missing description"
             var_name = node.target.id
         else:
             if isinstance(node, ast.Expr) and var_name:
-                attrs_descriptions[var_name] = node.value.s
+                descriptions[var_name] = node.value.s
                 var_name = ""
-    return attrs_descriptions
-
-
-def _get_args_descriptions(executable) -> dict[str, str]:
-    """
-    Extract argument descriptions for a task function.
-    """
-    # Read docstring (via ast)
-    module_path = Path(fractal_tasks_core.__file__).parent / executable
-    module_name = module_path.with_suffix("").name
-    tree = ast.parse(module_path.read_text())
-    function = next(
-        f
-        for f in ast.walk(tree)
-        if (isinstance(f, ast.FunctionDef) and f.name == module_name)
-    )
-
-    docstring = ast.get_docstring(function)
-    # Parse docstring (via docstring_parser) and prepare output
-    parsed_docstring = docparse(docstring)
-    descriptions = {
-        param.arg_name: param.description.replace("\n", " ")
-        for param in parsed_docstring.params
-    }
     return descriptions
 
 
-def _include_args_descriptions_in_schema(*, schema, descriptions):
+def _insert_function_args_descriptions(*, schema, descriptions):
     """
     Merge the descriptions obtained via `_get_args_descriptions` into an
     existing JSON Schema for task arguments.
@@ -107,52 +85,7 @@ def _include_args_descriptions_in_schema(*, schema, descriptions):
     return new_schema
 
 
-INNER_PYDANTIC_MODELS = {
-    "OmeroChannel": "lib_channels.py",
-    "Window": "lib_channels.py",
-    "Channel": "lib_input_models.py",
-    "NapariWorkflowsInput": "lib_input_models.py",
-    "NapariWorkflowsOutput": "lib_input_models.py",
-}
-
-
-def _get_attributes_models_descriptions(
-    models: dict[str, str] = INNER_PYDANTIC_MODELS
-) -> dict[str, dict[str, str]]:
-    """
-    Extract attribut descriptions for Pydantic models
-    """
-    descriptions = {}
-
-    for model, module in models.items():
-        # get the class
-        module_path = Path(fractal_tasks_core.__file__).parent / module
-        tree = ast.parse(module_path.read_text())
-        try:
-            _class = next(
-                c
-                for c in ast.walk(tree)
-                if (isinstance(c, ast.ClassDef) and c.name == model)
-            )
-            descriptions[model] = {}
-        except StopIteration:
-            raise ValueError(f"Model {module_path}::{model} not found.")
-
-        # extract attribute docstrings
-        var_name: str = ""
-        for node in _class.body:
-            if isinstance(node, ast.AnnAssign):
-                descriptions[model][node.target.id] = "Missing description"
-                var_name = node.target.id
-            else:
-                if isinstance(node, ast.Expr) and var_name:
-                    descriptions[model][var_name] = node.value.s
-                    var_name = ""
-
-    return descriptions
-
-
-def _include_attributs_descriptions_in_schema(*, schema, descriptions):
+def _insert_class_attrs_descriptions(*, schema, class_name, descriptions):
     """
     Merge the descriptions obtained via `_get_attributes_models_descriptions`
     into an existing JSON Schema for task arguments.
@@ -165,7 +98,7 @@ def _include_attributs_descriptions_in_schema(*, schema, descriptions):
         new_definitions = schema["definitions"].copy()
 
     for name, definition in schema["definitions"].items():
-        if name in descriptions.keys():
+        if name == class_name:
             for prop in definition["properties"]:
                 if "description" in new_definitions[name]["properties"][prop]:
                     raise ValueError(
@@ -174,6 +107,6 @@ def _include_attributs_descriptions_in_schema(*, schema, descriptions):
                 else:
                     new_definitions[name]["properties"][prop][
                         "description"
-                    ] = descriptions[name][prop]
+                    ] = descriptions[prop]
     new_schema["definitions"] = new_definitions
     return new_schema
diff --git a/tests/test_unit_lib_descriptions.py b/tests/dev/test_unit_lib_descriptions.py
similarity index 52%
rename from tests/test_unit_lib_descriptions.py
rename to tests/dev/test_unit_lib_descriptions.py
index d0fc49bca..5a9dae9d8 100644
--- a/tests/test_unit_lib_descriptions.py
+++ b/tests/dev/test_unit_lib_descriptions.py
@@ -1,11 +1,7 @@
 import json
 
-import pytest
 from devtools import debug
 
-from fractal_tasks_core.dev.lib_descriptions import (
-    _get_attributes_models_descriptions,
-)
 from fractal_tasks_core.dev.lib_descriptions import (
     _get_class_attrs_descriptions,
 )
@@ -13,16 +9,21 @@
     _get_function_args_descriptions,
 )
 from fractal_tasks_core.dev.lib_descriptions import (
-    _include_attributs_descriptions_in_schema,
+    _insert_class_attrs_descriptions,
 )
 
+# from fractal_tasks_core.dev.lib_descriptions import (
+#     _insert_function_args_descriptions,
+# )
+
 
 def test_get_function_args_descriptions():
     args_descriptions = _get_function_args_descriptions(
         "fractal_tasks_core",
-        "dev.lib_signature_constraints.py",
+        "dev/lib_signature_constraints.py",
         "_extract_function",
     )
+    debug(args_descriptions)
     assert args_descriptions.keys() == set(("executable", "package"))
 
 
@@ -30,32 +31,29 @@ def test_get_class_attrs_descriptions():
     attrs_descriptions = _get_class_attrs_descriptions(
         "fractal_tasks_core", "lib_input_models.py", "Channel"
     )
+    debug(attrs_descriptions)
     assert attrs_descriptions.keys() == set(("wavelength_id", "label"))
 
 
 def test_descriptions():
+    FILE = "lib_channels.py"
+    CLASS = "OmeroChannel"
 
-    with pytest.raises(ValueError):
-        _get_attributes_models_descriptions(models={"Foo": "__init__.py"})
-
-    descriptions = _get_attributes_models_descriptions()
-    debug(descriptions)
+    descriptions = _get_class_attrs_descriptions(
+        "fractal_tasks_core", FILE, CLASS
+    )
 
     with open("fractal_tasks_core/__FRACTAL_MANIFEST__.json", "r") as f:
         manifest = json.load(f)
 
     schemas = [task["args_schema"] for task in manifest["task_list"]]
 
-    for i, schema in enumerate(schemas):
-        new_schema = _include_attributs_descriptions_in_schema(
-            schema=schema, descriptions=descriptions
+    for _, schema in enumerate(schemas):
+        new_schema = _insert_class_attrs_descriptions(
+            schema=schema, class_name=CLASS, descriptions=descriptions
         )
         if "definitions" in schema:
-            for _, definition in new_schema["definitions"].items():
-                for prop in definition["properties"]:
-                    assert "description" in definition["properties"][prop]
-
-    with pytest.raises(ValueError):
-        _include_attributs_descriptions_in_schema(
-            schema=new_schema, descriptions=descriptions
-        )
+            for class_name, definition in new_schema["definitions"].items():
+                if class_name == "OmeroChannel":
+                    for prop in definition["properties"]:
+                        assert "description" in definition["properties"][prop]

From 612ea70b04e4b60db7bc06b474a532baec1c0cb8 Mon Sep 17 00:00:00 2001
From: Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
Date: Thu, 22 Jun 2023 11:00:40 +0200
Subject: [PATCH 22/36] changed lib_args_schemas

---
 fractal_tasks_core/dev/lib_args_schemas.py | 50 ++++++++++++++++------
 1 file changed, 36 insertions(+), 14 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_args_schemas.py b/fractal_tasks_core/dev/lib_args_schemas.py
index e9fe3b11a..d974f2f0c 100644
--- a/fractal_tasks_core/dev/lib_args_schemas.py
+++ b/fractal_tasks_core/dev/lib_args_schemas.py
@@ -15,15 +15,24 @@
 """
 from typing import Any
 
+import Path
 from pydantic.decorator import ALT_V_ARGS
 from pydantic.decorator import ALT_V_KWARGS
 from pydantic.decorator import V_DUPLICATE_KWARGS
 from pydantic.decorator import V_POSITIONAL_ONLY_NAME
 from pydantic.decorator import ValidatedFunction
 
-from fractal_tasks_core.dev.lib_descriptions import _get_args_descriptions
 from fractal_tasks_core.dev.lib_descriptions import (
-    _include_args_descriptions_in_schema,
+    _get_class_attrs_descriptions,
+)
+from fractal_tasks_core.dev.lib_descriptions import (
+    _get_function_args_descriptions,
+)
+from fractal_tasks_core.dev.lib_descriptions import (
+    _insert_class_attrs_descriptions,
+)
+from fractal_tasks_core.dev.lib_descriptions import (
+    _insert_function_args_descriptions,
 )
 from fractal_tasks_core.dev.lib_signature_constraints import _extract_function
 from fractal_tasks_core.dev.lib_signature_constraints import (
@@ -34,15 +43,6 @@
 _Schema = dict[str, Any]
 
 
-INNER_PYDANTIC_MODELS = {
-    "OmeroChannel": "lib_channels.py",
-    "Window": "lib_channels.py",
-    "Channel": "lib_input_models.py",
-    "NapariWorkflowsInput": "lib_input_models.py",
-    "NapariWorkflowsOutput": "lib_input_models.py",
-}
-
-
 def _remove_args_kwargs_properties(old_schema: _Schema) -> _Schema:
     """
     Remove ``args`` and ``kwargs`` schema properties
@@ -107,9 +107,31 @@ def create_schema_for_single_task(
     schema = _remove_pydantic_internals(schema)
 
     # Include arg descriptions
-    descriptions = _get_args_descriptions(executable)
-    schema = _include_args_descriptions_in_schema(
-        schema=schema, descriptions=descriptions
+    function_name = Path(executable).with_suffix("").name
+    function_args_descriptions = _get_function_args_descriptions(
+        package_name=package,
+        module_relative_path=executable,
+        function_name=function_name,
+    )
+    schema = _insert_function_args_descriptions(
+        schema=schema, descriptions=function_args_descriptions
     )
+    # Include inner Pydantic models attrs descriprions
+    INNER_PYDANTIC_MODELS = {
+        "OmeroChannel": "lib_channels.py",
+        "Window": "lib_channels.py",
+        "Channel": "lib_input_models.py",
+        "NapariWorkflowsInput": "lib_input_models.py",
+        "NapariWorkflowsOutput": "lib_input_models.py",
+    }
+    for _class, module in INNER_PYDANTIC_MODELS.items():
+        descriptions = _get_class_attrs_descriptions(
+            package_name=package,
+            module_relative_path=module,
+            class_name=_class,
+        )
+        schema = _insert_class_attrs_descriptions(
+            schema=schema, class_name=_class, descriptions=descriptions
+        )
 
     return schema

From 02f5437eb21941b16f65787479a6641c7d5584a2 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Thu, 22 Jun 2023 11:10:08 +0200
Subject: [PATCH 23/36] Clean up lib_descriptions.py

---
 fractal_tasks_core/dev/lib_descriptions.py | 23 +++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index 7ea4d7d64..9f96c9340 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -9,6 +9,12 @@ def _get_function_args_descriptions(
 ) -> dict[str, str]:
     """
     Extract argument descriptions from a function
+
+    TODO: use ast instead of import, as in _get_class_attrs_descriptions
+
+    :param package_name: Example ``fractal_tasks_core``
+    :param module_relative_path: Example ``tasks/create_ome_zarr.py``
+    :param function_name: Example ``create_ome_zarr``
     """
 
     if not module_relative_path.endswith(".py"):
@@ -37,6 +43,13 @@ def _get_function_args_descriptions(
 def _get_class_attrs_descriptions(
     package_name: str, module_relative_path: str, class_name: str
 ) -> dict[str, str]:
+    """
+    Extract attribute descriptions from a class
+
+    :param package_name: Example ``fractal_tasks_core``
+    :param module_relative_path: Example ``lib_channels.py``
+    :param class_name: Example ``OmeroChannel``
+    """
 
     if not module_relative_path.endswith(".py"):
         raise ValueError(f"Module {module_relative_path} must end with '.py'")
@@ -67,8 +80,9 @@ def _get_class_attrs_descriptions(
 
 def _insert_function_args_descriptions(*, schema, descriptions):
     """
-    Merge the descriptions obtained via `_get_args_descriptions` into an
-    existing JSON Schema for task arguments.
+    Merge the descriptions obtained via `_get_args_descriptions` into the
+    properties of an existing JSON Schema.
+
     """
     new_schema = schema.copy()
     new_properties = schema["properties"].copy()
@@ -88,15 +102,14 @@ def _insert_function_args_descriptions(*, schema, descriptions):
 def _insert_class_attrs_descriptions(*, schema, class_name, descriptions):
     """
     Merge the descriptions obtained via `_get_attributes_models_descriptions`
-    into an existing JSON Schema for task arguments.
+    into the ``class_name`` definition, within an existing JSON Schema
     """
     new_schema = schema.copy()
-
     if "definitions" not in schema:
         return new_schema
     else:
         new_definitions = schema["definitions"].copy()
-
+    # Loop over existing definitions
     for name, definition in schema["definitions"].items():
         if name == class_name:
             for prop in definition["properties"]:

From f50d793edcb0c9765daf35af1ee2d2ca5a84590c Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Thu, 22 Jun 2023 14:13:47 +0200
Subject: [PATCH 24/36] Update extract_function, and make its interface
 compatible with functions in lib_descriptions.py

---
 .../dev/lib_signature_constraints.py          | 29 ++++++++++---------
 1 file changed, 15 insertions(+), 14 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_signature_constraints.py b/fractal_tasks_core/dev/lib_signature_constraints.py
index fc28f05cd..dd68f9967 100644
--- a/fractal_tasks_core/dev/lib_signature_constraints.py
+++ b/fractal_tasks_core/dev/lib_signature_constraints.py
@@ -3,6 +3,7 @@
 from inspect import signature
 from pathlib import Path
 from typing import Callable
+from typing import Optional
 
 from pydantic.decorator import ALT_V_ARGS
 from pydantic.decorator import ALT_V_KWARGS
@@ -20,25 +21,25 @@
 
 
 def _extract_function(
-    executable: str,
-    package: str = "fractal_tasks_core.tasks",
+    module_relative_path: str,
+    package_name: str = "fractal_tasks_core",
+    function_name: Optional[str] = None,
 ) -> Callable:
     """
     Extract function from a module with the same name
 
-    This for instance extracts the function `my_function` from the module
-    `my_function.py`.
-
-    :param executable: Path to Python task script. Valid examples:
-                       `tasks/my_function.py` or `my_function.py`.
-    :param package: Name of the tasks subpackage (e.g.
-                    `fractal_tasks_core.tasks`).
+    :param package_name: Example ``fractal_tasks_core``
+    :param module_relative_path: Example ``tasks/create_ome_zarr.py``
+    :param function_name: Example ``create_ome_zarr``
     """
-    if not executable.endswith(".py"):
-        raise ValueError(f"{executable=} must end with '.py'")
-    module_name = Path(executable).with_suffix("").name
-    module = import_module(f"{package}.{module_name}")
-    task_function = getattr(module, module_name)
+    if not module_relative_path.endswith(".py"):
+        raise ValueError(f"{module_relative_path=} must end with '.py'")
+    module_relative_path_no_py = str(
+        Path(module_relative_path).with_suffix("")
+    )
+    module_relative_path_dots = module_relative_path_no_py.replace("/", ".")
+    module = import_module(f"{package_name}.{module_relative_path_dots}")
+    task_function = getattr(module, function_name)
     return task_function
 
 

From 7c428fe29d9c3df1101731c7b0ae11a90690ec90 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Thu, 22 Jun 2023 14:14:05 +0200
Subject: [PATCH 25/36] Fix setting of `module_path` in lib_descriptions.py

---
 fractal_tasks_core/dev/lib_descriptions.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index 9f96c9340..25e03a208 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -1,4 +1,5 @@
 import ast
+from importlib import import_module
 from pathlib import Path
 
 from docstring_parser import parse as docparse
@@ -20,15 +21,17 @@ def _get_function_args_descriptions(
     if not module_relative_path.endswith(".py"):
         raise ValueError(f"Module {module_relative_path} must end with '.py'")
 
-    # get the function
-    module_path = Path(package_name) / module_relative_path
+    # Get the function ast.FunctionDef object
+    package_path = Path(import_module(package_name).__file__).parent
+    module_path = package_path / module_relative_path
     tree = ast.parse(module_path.read_text())
-
     _function = next(
         f
         for f in ast.walk(tree)
         if (isinstance(f, ast.FunctionDef) and f.name == function_name)
     )
+
+    # Extract docstring from ast.FunctionDef
     docstring = ast.get_docstring(_function)
 
     # Parse docstring (via docstring_parser) and prepare output
@@ -54,10 +57,10 @@ def _get_class_attrs_descriptions(
     if not module_relative_path.endswith(".py"):
         raise ValueError(f"Module {module_relative_path} must end with '.py'")
 
-    # get the class
-    module_path = Path(package_name) / module_relative_path
+    # Get the class ast.ClassDef object
+    package_path = Path(import_module(package_name).__file__).parent
+    module_path = package_path / module_relative_path
     tree = ast.parse(module_path.read_text())
-
     _class = next(
         c
         for c in ast.walk(tree)

From 1a1a7e905fe28a0221f725df13e11e6780c3124e Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Thu, 22 Jun 2023 14:18:22 +0200
Subject: [PATCH 26/36] Fix missing import and update
 create_schema_for_single_task interface

---
 fractal_tasks_core/dev/lib_args_schemas.py | 34 +++++++++++++++-------
 1 file changed, 23 insertions(+), 11 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_args_schemas.py b/fractal_tasks_core/dev/lib_args_schemas.py
index d974f2f0c..14c329e43 100644
--- a/fractal_tasks_core/dev/lib_args_schemas.py
+++ b/fractal_tasks_core/dev/lib_args_schemas.py
@@ -5,6 +5,7 @@
 
     Original authors:
     Tommaso Comparin <tommaso.comparin@exact-lab.it>
+    Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
 
     This file is part of Fractal and was originally developed by eXact lab
     S.r.l.  <exact-lab.it> under contract with Liberali Lab from the Friedrich
@@ -13,9 +14,9 @@
 
 Helper functions to handle JSON schemas for task arguments.
 """
+from pathlib import Path
 from typing import Any
 
-import Path
 from pydantic.decorator import ALT_V_ARGS
 from pydantic.decorator import ALT_V_KWARGS
 from pydantic.decorator import V_DUPLICATE_KWARGS
@@ -42,6 +43,14 @@
 
 _Schema = dict[str, Any]
 
+INNER_PYDANTIC_MODELS = {
+    "OmeroChannel": "lib_channels.py",
+    "Window": "lib_channels.py",
+    "Channel": "lib_input_models.py",
+    "NapariWorkflowsInput": "lib_input_models.py",
+    "NapariWorkflowsOutput": "lib_input_models.py",
+}
+
 
 def _remove_args_kwargs_properties(old_schema: _Schema) -> _Schema:
     """
@@ -89,13 +98,23 @@ def _remove_pydantic_internals(old_schema: _Schema) -> _Schema:
 
 def create_schema_for_single_task(
     executable: str,
-    package: str = "fractal_tasks_core.tasks",
+    package: str = "fractal_tasks_core",
+    inner_pydantic_models: dict[str, str] = INNER_PYDANTIC_MODELS,
 ) -> _Schema:
     """
     Main function to create a JSON Schema of task arguments
     """
+
+    # Extract the function name. Note: this could be made more general, but for
+    # the moment we assume the function has the same name as the module)
+    function_name = Path(executable).with_suffix("").name
+
     # Extract function from module
-    task_function = _extract_function(executable=executable, package=package)
+    task_function = _extract_function(
+        package_name=package,
+        module_relative_path=executable,
+        function_name=function_name,
+    )
 
     # Validate function signature against some custom constraints
     _validate_function_signature(task_function)
@@ -107,7 +126,6 @@ def create_schema_for_single_task(
     schema = _remove_pydantic_internals(schema)
 
     # Include arg descriptions
-    function_name = Path(executable).with_suffix("").name
     function_args_descriptions = _get_function_args_descriptions(
         package_name=package,
         module_relative_path=executable,
@@ -117,13 +135,7 @@ def create_schema_for_single_task(
         schema=schema, descriptions=function_args_descriptions
     )
     # Include inner Pydantic models attrs descriprions
-    INNER_PYDANTIC_MODELS = {
-        "OmeroChannel": "lib_channels.py",
-        "Window": "lib_channels.py",
-        "Channel": "lib_input_models.py",
-        "NapariWorkflowsInput": "lib_input_models.py",
-        "NapariWorkflowsOutput": "lib_input_models.py",
-    }
+
     for _class, module in INNER_PYDANTIC_MODELS.items():
         descriptions = _get_class_attrs_descriptions(
             package_name=package,

From 4eb8334522d08abd296c785b7e9807e5dc9a3da5 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Thu, 22 Jun 2023 14:18:38 +0200
Subject: [PATCH 27/36] Improve error-handling in new_args_schema.py

---
 fractal_tasks_core/dev/new_args_schema.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/fractal_tasks_core/dev/new_args_schema.py b/fractal_tasks_core/dev/new_args_schema.py
index daee63869..33bea8a57 100644
--- a/fractal_tasks_core/dev/new_args_schema.py
+++ b/fractal_tasks_core/dev/new_args_schema.py
@@ -44,10 +44,8 @@
         print(f"[{executable}] Start")
         try:
             schema = create_schema_for_single_task(executable)
-        except AttributeError:
-            print(f"[{executable}] Skip, due to AttributeError")
-            print()
-            continue
+        except Exception as e:
+            print(f"[{executable}] Skip. Original error:\n{str(e)}")
 
         manifest["task_list"][ind]["args_schema"] = schema
         print("Schema added to manifest")

From b428e94e1fbdf3c4f1a0e29659d906845239013b Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Thu, 22 Jun 2023 14:18:52 +0200
Subject: [PATCH 28/36] Include class-attributes descriptions in manifest

---
 fractal_tasks_core/__FRACTAL_MANIFEST__.json | 102 ++++++++++++-------
 1 file changed, 68 insertions(+), 34 deletions(-)

diff --git a/fractal_tasks_core/__FRACTAL_MANIFEST__.json b/fractal_tasks_core/__FRACTAL_MANIFEST__.json
index cb35e034d..99dae8b44 100644
--- a/fractal_tasks_core/__FRACTAL_MANIFEST__.json
+++ b/fractal_tasks_core/__FRACTAL_MANIFEST__.json
@@ -82,19 +82,23 @@
             "properties": {
               "min": {
                 "title": "Min",
-                "type": "integer"
+                "type": "integer",
+                "description": "If not provided, it will be set to ``0``."
               },
               "max": {
                 "title": "Max",
-                "type": "integer"
+                "type": "integer",
+                "description": "If not provided, it will be set according to bit-depth."
               },
               "start": {
                 "title": "Start",
-                "type": "integer"
+                "type": "integer",
+                "description": "Start value of the visualization window."
               },
               "end": {
                 "title": "End",
-                "type": "integer"
+                "type": "integer",
+                "description": "End value of the visualization window."
               }
             },
             "required": [
@@ -109,37 +113,45 @@
             "properties": {
               "wavelength_id": {
                 "title": "Wavelength Id",
-                "type": "string"
+                "type": "string",
+                "description": "Custom attribute (e.g. ``A01_C01``)."
               },
               "index": {
                 "title": "Index",
-                "type": "integer"
+                "type": "integer",
+                "description": "For internal use only."
               },
               "label": {
                 "title": "Label",
-                "type": "string"
+                "type": "string",
+                "description": "Channel label."
               },
               "window": {
-                "$ref": "#/definitions/Window"
+                "$ref": "#/definitions/Window",
+                "description": "A ``Window`` object to display this channel in napari."
               },
               "color": {
                 "title": "Color",
-                "type": "string"
+                "type": "string",
+                "description": "A colormap to display the channel in napari (e.g. ``00FFFF``)."
               },
               "active": {
                 "title": "Active",
                 "default": true,
-                "type": "boolean"
+                "type": "boolean",
+                "description": "Omero-channel attribute."
               },
               "coefficient": {
                 "title": "Coefficient",
                 "default": 1,
-                "type": "integer"
+                "type": "integer",
+                "description": "Omero-channel attribute."
               },
               "inverted": {
                 "title": "Inverted",
                 "default": false,
-                "type": "boolean"
+                "type": "boolean",
+                "description": "Omero-channel attribute."
               }
             },
             "required": [
@@ -462,11 +474,13 @@
             "properties": {
               "wavelength_id": {
                 "title": "Wavelength Id",
-                "type": "string"
+                "type": "string",
+                "description": "Unique ID for the channel wavelength, e.g. ``A01_C01``."
               },
               "label": {
                 "title": "Label",
-                "type": "string"
+                "type": "string",
+                "description": "Channel label."
               }
             }
           }
@@ -654,11 +668,13 @@
             "properties": {
               "wavelength_id": {
                 "title": "Wavelength Id",
-                "type": "string"
+                "type": "string",
+                "description": "Unique ID for the channel wavelength, e.g. ``A01_C01``."
               },
               "label": {
                 "title": "Label",
-                "type": "string"
+                "type": "string",
+                "description": "Channel label."
               }
             }
           },
@@ -673,14 +689,17 @@
                   "image",
                   "label"
                 ],
-                "type": "string"
+                "type": "string",
+                "description": "Input type (supported: ``image`` or ``label``)."
               },
               "label_name": {
                 "title": "Label Name",
-                "type": "string"
+                "type": "string",
+                "description": "Label name (for label inputs only)."
               },
               "channel": {
-                "$ref": "#/definitions/Channel"
+                "$ref": "#/definitions/Channel",
+                "description": "Channel object (for image inputs only)."
               }
             },
             "required": [
@@ -698,15 +717,18 @@
                   "label",
                   "dataframe"
                 ],
-                "type": "string"
+                "type": "string",
+                "description": "Output type (supported: ``label`` or ``dataframe``)."
               },
               "label_name": {
                 "title": "Label Name",
-                "type": "string"
+                "type": "string",
+                "description": "Label name (for label outputs only)."
               },
               "table_name": {
                 "title": "Table Name",
-                "type": "string"
+                "type": "string",
+                "description": "Table name (for dataframe outputs only)."
               }
             },
             "required": [
@@ -809,19 +831,23 @@
             "properties": {
               "min": {
                 "title": "Min",
-                "type": "integer"
+                "type": "integer",
+                "description": "If not provided, it will be set to ``0``."
               },
               "max": {
                 "title": "Max",
-                "type": "integer"
+                "type": "integer",
+                "description": "If not provided, it will be set according to bit-depth."
               },
               "start": {
                 "title": "Start",
-                "type": "integer"
+                "type": "integer",
+                "description": "Start value of the visualization window."
               },
               "end": {
                 "title": "End",
-                "type": "integer"
+                "type": "integer",
+                "description": "End value of the visualization window."
               }
             },
             "required": [
@@ -836,37 +862,45 @@
             "properties": {
               "wavelength_id": {
                 "title": "Wavelength Id",
-                "type": "string"
+                "type": "string",
+                "description": "Custom attribute (e.g. ``A01_C01``)."
               },
               "index": {
                 "title": "Index",
-                "type": "integer"
+                "type": "integer",
+                "description": "For internal use only."
               },
               "label": {
                 "title": "Label",
-                "type": "string"
+                "type": "string",
+                "description": "Channel label."
               },
               "window": {
-                "$ref": "#/definitions/Window"
+                "$ref": "#/definitions/Window",
+                "description": "A ``Window`` object to display this channel in napari."
               },
               "color": {
                 "title": "Color",
-                "type": "string"
+                "type": "string",
+                "description": "A colormap to display the channel in napari (e.g. ``00FFFF``)."
               },
               "active": {
                 "title": "Active",
                 "default": true,
-                "type": "boolean"
+                "type": "boolean",
+                "description": "Omero-channel attribute."
               },
               "coefficient": {
                 "title": "Coefficient",
                 "default": 1,
-                "type": "integer"
+                "type": "integer",
+                "description": "Omero-channel attribute."
               },
               "inverted": {
                 "title": "Inverted",
                 "default": false,
-                "type": "boolean"
+                "type": "boolean",
+                "description": "Omero-channel attribute."
               }
             },
             "required": [

From 2782f4cd0a084241515c8805224c2f1b6e3db7e7 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Thu, 22 Jun 2023 14:20:33 +0200
Subject: [PATCH 29/36] Remove obsolete comment and `from __future__ import
 annotations`

---
 fractal_tasks_core/tasks/_utils.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/fractal_tasks_core/tasks/_utils.py b/fractal_tasks_core/tasks/_utils.py
index 5e408e6e2..a0657acd0 100644
--- a/fractal_tasks_core/tasks/_utils.py
+++ b/fractal_tasks_core/tasks/_utils.py
@@ -13,11 +13,6 @@
 
 Standard input/output interface for tasks
 """
-# Starting from Python 3.9 (see PEP 585) we can use type hints like
-# `type[BaseModel]`. For versions 3.7 and 3.8, this is available through an
-# additional import
-from __future__ import annotations
-
 import json
 import logging
 from argparse import ArgumentParser

From 11ccfc60ade5d27131d799b13482e7145db7ec62 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Thu, 22 Jun 2023 14:21:25 +0200
Subject: [PATCH 30/36] Remove TODO comment

---
 fractal_tasks_core/dev/lib_descriptions.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_descriptions.py b/fractal_tasks_core/dev/lib_descriptions.py
index 25e03a208..8bbc82b32 100644
--- a/fractal_tasks_core/dev/lib_descriptions.py
+++ b/fractal_tasks_core/dev/lib_descriptions.py
@@ -11,8 +11,6 @@ def _get_function_args_descriptions(
     """
     Extract argument descriptions from a function
 
-    TODO: use ast instead of import, as in _get_class_attrs_descriptions
-
     :param package_name: Example ``fractal_tasks_core``
     :param module_relative_path: Example ``tasks/create_ome_zarr.py``
     :param function_name: Example ``create_ome_zarr``

From 6f8d5ba2a872cb7a17476b8e1f3f381a3bc50805 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Thu, 22 Jun 2023 14:23:20 +0200
Subject: [PATCH 31/36] move blank line

---
 fractal_tasks_core/dev/lib_args_schemas.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fractal_tasks_core/dev/lib_args_schemas.py b/fractal_tasks_core/dev/lib_args_schemas.py
index 14c329e43..e4d7ce731 100644
--- a/fractal_tasks_core/dev/lib_args_schemas.py
+++ b/fractal_tasks_core/dev/lib_args_schemas.py
@@ -134,8 +134,8 @@ def create_schema_for_single_task(
     schema = _insert_function_args_descriptions(
         schema=schema, descriptions=function_args_descriptions
     )
-    # Include inner Pydantic models attrs descriprions
 
+    # Include inner Pydantic models attrs descriprions
     for _class, module in INNER_PYDANTIC_MODELS.items():
         descriptions = _get_class_attrs_descriptions(
             package_name=package,

From 26a30b670f418b8b84ee6605ceee495aefd45d48 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Thu, 22 Jun 2023 14:28:34 +0200
Subject: [PATCH 32/36] Update test_unit_lib_descriptions.py

1. Remove `test_descriptions`, since it would always fail because descriptions are already in the manifest;
2. Update other tests.
---
 tests/dev/test_unit_lib_descriptions.py | 37 ++-----------------------
 1 file changed, 3 insertions(+), 34 deletions(-)

diff --git a/tests/dev/test_unit_lib_descriptions.py b/tests/dev/test_unit_lib_descriptions.py
index 5a9dae9d8..969bff985 100644
--- a/tests/dev/test_unit_lib_descriptions.py
+++ b/tests/dev/test_unit_lib_descriptions.py
@@ -1,5 +1,3 @@
-import json
-
 from devtools import debug
 
 from fractal_tasks_core.dev.lib_descriptions import (
@@ -8,13 +6,6 @@
 from fractal_tasks_core.dev.lib_descriptions import (
     _get_function_args_descriptions,
 )
-from fractal_tasks_core.dev.lib_descriptions import (
-    _insert_class_attrs_descriptions,
-)
-
-# from fractal_tasks_core.dev.lib_descriptions import (
-#     _insert_function_args_descriptions,
-# )
 
 
 def test_get_function_args_descriptions():
@@ -24,7 +15,9 @@ def test_get_function_args_descriptions():
         "_extract_function",
     )
     debug(args_descriptions)
-    assert args_descriptions.keys() == set(("executable", "package"))
+    assert args_descriptions.keys() == set(
+        ("package_name", "module_relative_path", "function_name")
+    )
 
 
 def test_get_class_attrs_descriptions():
@@ -33,27 +26,3 @@ def test_get_class_attrs_descriptions():
     )
     debug(attrs_descriptions)
     assert attrs_descriptions.keys() == set(("wavelength_id", "label"))
-
-
-def test_descriptions():
-    FILE = "lib_channels.py"
-    CLASS = "OmeroChannel"
-
-    descriptions = _get_class_attrs_descriptions(
-        "fractal_tasks_core", FILE, CLASS
-    )
-
-    with open("fractal_tasks_core/__FRACTAL_MANIFEST__.json", "r") as f:
-        manifest = json.load(f)
-
-    schemas = [task["args_schema"] for task in manifest["task_list"]]
-
-    for _, schema in enumerate(schemas):
-        new_schema = _insert_class_attrs_descriptions(
-            schema=schema, class_name=CLASS, descriptions=descriptions
-        )
-        if "definitions" in schema:
-            for class_name, definition in new_schema["definitions"].items():
-                if class_name == "OmeroChannel":
-                    for prop in definition["properties"]:
-                        assert "description" in definition["properties"][prop]

From 7f31edd18354addf44fe88b4bd37f930b9a687d7 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Thu, 22 Jun 2023 14:31:28 +0200
Subject: [PATCH 33/36] Update test_valid_args_schemas.py

---
 tests/tasks/test_valid_args_schemas.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/tasks/test_valid_args_schemas.py b/tests/tasks/test_valid_args_schemas.py
index 5cdd2cd4f..6c37ab6ce 100644
--- a/tests/tasks/test_valid_args_schemas.py
+++ b/tests/tasks/test_valid_args_schemas.py
@@ -99,7 +99,8 @@ def test_task_functions_have_valid_signatures():
     Test that task functions have valid signatures.
     """
     for ind_task, task in enumerate(TASK_LIST):
-        task_function = _extract_function(task["executable"])
+        function_name = Path(task["executable"]).with_suffix("").name
+        task_function = _extract_function(task["executable"], function_name)
         _validate_function_signature(task_function)
 
 

From 2fbe417f85ab1b281cac2614a702e2989d9a3b61 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Thu, 22 Jun 2023 14:31:45 +0200
Subject: [PATCH 34/36] Make _extract_function more strict

---
 fractal_tasks_core/dev/lib_signature_constraints.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/fractal_tasks_core/dev/lib_signature_constraints.py b/fractal_tasks_core/dev/lib_signature_constraints.py
index dd68f9967..22ac64edc 100644
--- a/fractal_tasks_core/dev/lib_signature_constraints.py
+++ b/fractal_tasks_core/dev/lib_signature_constraints.py
@@ -3,7 +3,6 @@
 from inspect import signature
 from pathlib import Path
 from typing import Callable
-from typing import Optional
 
 from pydantic.decorator import ALT_V_ARGS
 from pydantic.decorator import ALT_V_KWARGS
@@ -22,8 +21,8 @@
 
 def _extract_function(
     module_relative_path: str,
+    function_name: str,
     package_name: str = "fractal_tasks_core",
-    function_name: Optional[str] = None,
 ) -> Callable:
     """
     Extract function from a module with the same name

From e3f518ee4bffa172563d0c6c75597ee2f9f900bc Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Thu, 22 Jun 2023 14:37:22 +0200
Subject: [PATCH 35/36] Update CHANGELOG

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 812ed5cb2..35e9829b6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,7 +14,8 @@
     * Modify arguments of `illumination_correction` task (\#431);
     * Modify arguments of `create_ome_zarr` and `create_ome_zarr_multiplex` (\#433).
 * JSON Schemas for task arguments:
-    * Add JSON schemas for task arguments in the package manifest (\#369, \#384).
+    * Add JSON Schemas for task arguments in the package manifest (\#369, \#384).
+    * Add JSON Schemas for attributes of custom task-argument Pydantic models (\#436).
     * Remove `TaskArguments` models and switch to Pydantic V1 `validate_arguments` (\#369).
     * Make coercing&validating task arguments required, rather than optional (\#408).
     * Remove `default_args` from manifest (\#379, \#393).

From 2148cabe13b1414b37177fa8d836769ffde80359 Mon Sep 17 00:00:00 2001
From: Tommaso Comparin <3862206+tcompa@users.noreply.github.com>
Date: Thu, 22 Jun 2023 14:44:37 +0200
Subject: [PATCH 36/36] Simplify docstrings (ref #421)

---
 fractal_tasks_core/__FRACTAL_MANIFEST__.json | 16 +++++++-------
 fractal_tasks_core/lib_channels.py           | 23 ++++----------------
 2 files changed, 12 insertions(+), 27 deletions(-)

diff --git a/fractal_tasks_core/__FRACTAL_MANIFEST__.json b/fractal_tasks_core/__FRACTAL_MANIFEST__.json
index 99dae8b44..baa1ed298 100644
--- a/fractal_tasks_core/__FRACTAL_MANIFEST__.json
+++ b/fractal_tasks_core/__FRACTAL_MANIFEST__.json
@@ -77,7 +77,7 @@
         "definitions": {
           "Window": {
             "title": "Window",
-            "description": "Custom class for Omero-channel window, related to OME-NGFF v0.4\n\nSee https://ngff.openmicroscopy.org/0.4/#omero-md.\nMain difference from the specs:\n\n    1. ``min`` and ``max`` are optional, since we have custom logic to set\n       their values.",
+            "description": "Custom class for Omero-channel window, based on OME-NGFF v0.4.",
             "type": "object",
             "properties": {
               "min": {
@@ -108,7 +108,7 @@
           },
           "OmeroChannel": {
             "title": "OmeroChannel",
-            "description": "Custom class for Omero channels, related to OME-NGFF v0.4.\n\nDifferences from OME-NGFF v0.4 specs\n(https://ngff.openmicroscopy.org/0.4/#omero-md):\n\n    1. Additional attributes ``wavelength_id`` and ``index``.\n    2. We make ``color`` an optional attribute, since we have custom\n       logic to set its value.\n    3. We make ``window`` an optional attribute, so that we can also\n       process zarr arrays which do not have this attribute.",
+            "description": "Custom class for Omero channels, based on OME-NGFF v0.4.",
             "type": "object",
             "properties": {
               "wavelength_id": {
@@ -128,12 +128,12 @@
               },
               "window": {
                 "$ref": "#/definitions/Window",
-                "description": "A ``Window`` object to display this channel in napari."
+                "description": "Optional ``Window`` object to display this channel in napari."
               },
               "color": {
                 "title": "Color",
                 "type": "string",
-                "description": "A colormap to display the channel in napari (e.g. ``00FFFF``)."
+                "description": "Optional colormap to display the channel in napari (e.g. ``00FFFF``)."
               },
               "active": {
                 "title": "Active",
@@ -826,7 +826,7 @@
         "definitions": {
           "Window": {
             "title": "Window",
-            "description": "Custom class for Omero-channel window, related to OME-NGFF v0.4\n\nSee https://ngff.openmicroscopy.org/0.4/#omero-md.\nMain difference from the specs:\n\n    1. ``min`` and ``max`` are optional, since we have custom logic to set\n       their values.",
+            "description": "Custom class for Omero-channel window, based on OME-NGFF v0.4.",
             "type": "object",
             "properties": {
               "min": {
@@ -857,7 +857,7 @@
           },
           "OmeroChannel": {
             "title": "OmeroChannel",
-            "description": "Custom class for Omero channels, related to OME-NGFF v0.4.\n\nDifferences from OME-NGFF v0.4 specs\n(https://ngff.openmicroscopy.org/0.4/#omero-md):\n\n    1. Additional attributes ``wavelength_id`` and ``index``.\n    2. We make ``color`` an optional attribute, since we have custom\n       logic to set its value.\n    3. We make ``window`` an optional attribute, so that we can also\n       process zarr arrays which do not have this attribute.",
+            "description": "Custom class for Omero channels, based on OME-NGFF v0.4.",
             "type": "object",
             "properties": {
               "wavelength_id": {
@@ -877,12 +877,12 @@
               },
               "window": {
                 "$ref": "#/definitions/Window",
-                "description": "A ``Window`` object to display this channel in napari."
+                "description": "Optional ``Window`` object to display this channel in napari."
               },
               "color": {
                 "title": "Color",
                 "type": "string",
-                "description": "A colormap to display the channel in napari (e.g. ``00FFFF``)."
+                "description": "Optional colormap to display the channel in napari (e.g. ``00FFFF``)."
               },
               "active": {
                 "title": "Active",
diff --git a/fractal_tasks_core/lib_channels.py b/fractal_tasks_core/lib_channels.py
index 2db8388fb..2f65666b7 100644
--- a/fractal_tasks_core/lib_channels.py
+++ b/fractal_tasks_core/lib_channels.py
@@ -34,13 +34,7 @@
 
 class Window(BaseModel):
     """
-    Custom class for Omero-channel window, related to OME-NGFF v0.4
-
-    See https://ngff.openmicroscopy.org/0.4/#omero-md.
-    Main difference from the specs:
-
-        1. ``min`` and ``max`` are optional, since we have custom logic to set
-           their values.
+    Custom class for Omero-channel window, based on OME-NGFF v0.4.
     """
 
     min: Optional[int]
@@ -58,16 +52,7 @@ class Window(BaseModel):
 
 class OmeroChannel(BaseModel):
     """
-    Custom class for Omero channels, related to OME-NGFF v0.4.
-
-    Differences from OME-NGFF v0.4 specs
-    (https://ngff.openmicroscopy.org/0.4/#omero-md):
-
-        1. Additional attributes ``wavelength_id`` and ``index``.
-        2. We make ``color`` an optional attribute, since we have custom
-           logic to set its value.
-        3. We make ``window`` an optional attribute, so that we can also
-           process zarr arrays which do not have this attribute.
+    Custom class for Omero channels, based on OME-NGFF v0.4.
     """
 
     # Custom
@@ -84,10 +69,10 @@ class OmeroChannel(BaseModel):
     """Channel label."""
 
     window: Optional[Window]
-    """A ``Window`` object to display this channel in napari."""
+    """Optional ``Window`` object to display this channel in napari."""
 
     color: Optional[str]
-    """A colormap to display the channel in napari (e.g. ``00FFFF``)."""
+    """Optional colormap to display the channel in napari (e.g. ``00FFFF``)."""
 
     active: bool = True
     """Omero-channel attribute."""