From 0962846536b9a9c8c35985be27164578245d3c13 Mon Sep 17 00:00:00 2001
From: Jan Janssen <jan-janssen@users.noreply.github.com>
Date: Mon, 27 Jul 2026 06:53:30 +0200
Subject: [PATCH 01/19] Configure Ruff for linting in pyproject.toml

Add Ruff configuration for linting with specified rules.
---
 pyproject.toml | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index c06709a..ba8cf98 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,6 +42,32 @@ plot = [
     "ipython>=7.33.0,<=9.8.0",
 ]
 
+[tool.ruff]
+exclude = [".ci_support", "docs", "notebooks", "tests", "setup.py", "_version.py"]
+
+[tool.ruff.lint]
+select = [
+    # pycodestyle
+    "E",
+    # Pyflakes
+    "F",
+    # pyupgrade
+    "UP",
+    # flake8-bugbear
+    "B",
+    # flake8-simplify
+    "SIM",
+    # isort
+    "I",
+    # flake8-comprehensions
+    "C4",
+    # eradicate
+    "ERA",
+    # pylint
+    "PL",
+]
+ignore = []
+
 [tool.hatch.build]
 include = [
     "src/python_workflow_definition"

From 32bf515c5b75d5a5c4a4786e52dcb56100c18245 Mon Sep 17 00:00:00 2001
From: Jan Janssen <jan-janssen@users.noreply.github.com>
Date: Mon, 27 Jul 2026 06:54:25 +0200
Subject: [PATCH 02/19] Add ruff pre-commit hooks for linting and formatting

---
 .pre-commit-config.yaml | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 .pre-commit-config.yaml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..422cfca
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,10 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.22
+    hooks:
+      - id: ruff
+        name: ruff lint
+        args: ["--fix"]
+        files: ^src/python_workflow_definition/
+      - id: ruff-format
+        name: ruff format

From 6eae8e183df64e4a6c1d6c2f625cd372234059de Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 27 Jul 2026 07:00:37 +0200
Subject: [PATCH 03/19] do not apply on notebooks for now

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ba8cf98..ba59460 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ plot = [
 ]
 
 [tool.ruff]
-exclude = [".ci_support", "docs", "notebooks", "tests", "setup.py", "_version.py"]
+exclude = ["documentation", "example_workflows", "tests", "binder", "_version.py"]
 
 [tool.ruff.lint]
 select = [

From dd8354094fbbda6a5e822c852d0bbd8829f7cf3f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 27 Jul 2026 05:01:04 +0000
Subject: [PATCH 04/19] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/python_workflow_definition/aiida.py       |  1 -
 .../cwl/__init__.py                           | 59 +++++++++----------
 src/python_workflow_definition/executorlib.py |  8 +--
 src/python_workflow_definition/jobflow.py     | 16 +++--
 src/python_workflow_definition/models.py      | 40 ++++++-------
 src/python_workflow_definition/plot.py        |  1 -
 src/python_workflow_definition/purepython.py  | 14 ++---
 src/python_workflow_definition/pyiron_base.py | 20 +++----
 .../pyiron_workflow.py                        | 42 +++++--------
 src/python_workflow_definition/shared.py      |  4 +-
 10 files changed, 88 insertions(+), 117 deletions(-)

diff --git a/src/python_workflow_definition/aiida.py b/src/python_workflow_definition/aiida.py
index 30212b3..9d17dc0 100644
--- a/src/python_workflow_definition/aiida.py
+++ b/src/python_workflow_definition/aiida.py
@@ -99,7 +99,6 @@ def write_workflow_json(wg: WorkGraph, file_name: str) -> None:
     GRAPH_LEVEL_NAMES = ["graph_inputs", "graph_outputs", "graph_ctx"]
 
     for node in wg.tasks:
-
         if node.name in GRAPH_LEVEL_NAMES:
             continue
 
diff --git a/src/python_workflow_definition/cwl/__init__.py b/src/python_workflow_definition/cwl/__init__.py
index 05885fc..96ae76e 100644
--- a/src/python_workflow_definition/cwl/__init__.py
+++ b/src/python_workflow_definition/cwl/__init__.py
@@ -21,8 +21,7 @@
 
 def _get_function_argument(argument: str, position: int = 3) -> dict:
     return {
-        argument
-        + "_file": {
+        argument + "_file": {
             "type": "File",
             "inputBinding": {
                 "prefix": "--arg_" + argument + "=",
@@ -45,8 +44,10 @@ def _get_function_template(function_name: str) -> dict:
 
 def _get_output_name(output_name: str) -> dict:
     return {
-        output_name
-        + "_file": {"type": "File", "outputBinding": {"glob": output_name + ".pickle"}}
+        output_name + "_file": {
+            "type": "File",
+            "outputBinding": {"glob": output_name + ".pickle"},
+        }
     }
 
 
@@ -55,7 +56,7 @@ def _get_function(workflow):
         n["id"]: n["value"] for n in workflow[NODES_LABEL] if n["type"] == "function"
     }
     funct_dict = {}
-    for funct_id in function_nodes_dict.keys():
+    for funct_id in function_nodes_dict:
         target_ports = list(
             set(
                 [
@@ -142,10 +143,7 @@ def _write_workflow_config(workflow, directory_path: str = "."):
     export_path.mkdir(parents=True, exist_ok=True)
     with open(export_path / "workflow.yml", "w") as f:
         dump(
-            {
-                k + "_file": {"class": "File", "path": k + ".pickle"}
-                for k in input_dict.keys()
-            },
+            {k + "_file": {"class": "File", "path": k + ".pickle"} for k in input_dict},
             f,
             Dumper=Dumper,
         )
@@ -170,7 +168,7 @@ def _write_workflow(workflow, directory_path: str = "."):
     last_compute_id = [
         e[SOURCE_LABEL] for e in workflow[EDGES_LABEL] if e[TARGET_LABEL] == result_id
     ][0]
-    workflow_template["inputs"].update({k + "_file": "File" for k in input_dict.keys()})
+    workflow_template["inputs"].update({k + "_file": "File" for k in input_dict})
     if funct_dict[last_compute_id]["sourcePorts"] == [None]:
         workflow_template["outputs"] = {
             "result_file": {
@@ -209,28 +207,29 @@ def _write_workflow(workflow, directory_path: str = "."):
         for k, v in t[1].items():
             if v[SOURCE_LABEL] in input_id_dict:
                 in_dict[k + "_file"] = input_id_dict[v[SOURCE_LABEL]] + "_file"
+            elif v["sourcePort"] is None:
+                in_dict[k + "_file"] = (
+                    step_name_lst[v[SOURCE_LABEL]]
+                    + "_"
+                    + str(v[SOURCE_LABEL])
+                    + "/result_file"
+                )
             else:
-                if v["sourcePort"] is None:
-                    in_dict[k + "_file"] = (
-                        step_name_lst[v[SOURCE_LABEL]]
-                        + "_"
-                        + str(v[SOURCE_LABEL])
-                        + "/result_file"
-                    )
-                else:
-                    in_dict[k + "_file"] = (
-                        step_name_lst[v[SOURCE_LABEL]]
-                        + "_"
-                        + str(v[SOURCE_LABEL])
-                        + "/"
-                        + v[SOURCE_PORT_LABEL]
-                        + "_file"
-                    )
+                in_dict[k + "_file"] = (
+                    step_name_lst[v[SOURCE_LABEL]]
+                    + "_"
+                    + str(v[SOURCE_LABEL])
+                    + "/"
+                    + v[SOURCE_PORT_LABEL]
+                    + "_file"
+                )
         workflow_template["steps"].update(
             {
-                step_name_lst[ind]
-                + "_"
-                + str(ind): {"run": node_script, "in": in_dict, "out": output}
+                step_name_lst[ind] + "_" + str(ind): {
+                    "run": node_script,
+                    "in": in_dict,
+                    "out": output,
+                }
             }
         )
     export_path = Path(directory_path)
@@ -240,7 +239,7 @@ def _write_workflow(workflow, directory_path: str = "."):
 
 
 def write_workflow(file_name: str, directory_path: str = "."):
-    with open(file_name, "r") as f:
+    with open(file_name) as f:
         workflow = json.load(f)
 
     _write_function_cwl(workflow=workflow, directory_path=directory_path)
diff --git a/src/python_workflow_definition/executorlib.py b/src/python_workflow_definition/executorlib.py
index 552d44b..8cb76cb 100644
--- a/src/python_workflow_definition/executorlib.py
+++ b/src/python_workflow_definition/executorlib.py
@@ -11,10 +11,6 @@
     SOURCE_LABEL,
     SOURCE_PORT_LABEL,
     convert_nodes_list_to_dict,
-    get_dict,
-    get_kwargs,
-    get_list,
-    get_source_handles,
     remove_result,
 )
 
@@ -25,9 +21,9 @@ def get_item(obj, key):
 
 def _get_value(result_dict: dict, nodes_new_dict: dict, link_dict: dict, exe: Executor):
     source, source_handle = link_dict[SOURCE_LABEL], link_dict[SOURCE_PORT_LABEL]
-    if source in result_dict.keys():
+    if source in result_dict:
         result = result_dict[source]
-    elif source in nodes_new_dict.keys():
+    elif source in nodes_new_dict:
         result = nodes_new_dict[source]
     else:
         raise KeyError()
diff --git a/src/python_workflow_definition/jobflow.py b/src/python_workflow_definition/jobflow.py
index b385177..348c446 100644
--- a/src/python_workflow_definition/jobflow.py
+++ b/src/python_workflow_definition/jobflow.py
@@ -196,10 +196,8 @@ def _get_edges_and_extend_nodes(
 
 
 def _resort_total_lst(total_dict: dict, nodes_dict: dict) -> dict:
-    nodes_with_dep_lst = list(sorted(total_dict.keys()))
-    nodes_without_dep_lst = [
-        k for k in nodes_dict.keys() if k not in nodes_with_dep_lst
-    ]
+    nodes_with_dep_lst = sorted(total_dict.keys())
+    nodes_without_dep_lst = [k for k in nodes_dict if k not in nodes_with_dep_lst]
     ordered_lst: list = []
     total_new_dict: dict[Any, dict] = {}
     while len(total_new_dict) < len(total_dict):
@@ -220,7 +218,7 @@ def _group_edges(edges_lst: list) -> dict:
     for ed_major in edges_lst:
         target_id = ed_major[TARGET_LABEL]
         tmp_lst = []
-        if target_id not in total_dict.keys():
+        if target_id not in total_dict:
             for ed in edges_lst:
                 if target_id == ed[TARGET_LABEL]:
                     tmp_lst.append(ed)
@@ -237,15 +235,15 @@ def _get_workflow(
 ) -> list:
     def get_attr_helper(obj, source_handle):
         if source_handle is None:
-            return getattr(obj, "output")
+            return obj.output
         else:
-            return getattr(getattr(obj, "output"), source_handle)
+            return getattr(obj.output, source_handle)
 
     memory_dict: dict[Any, Any] = {}
-    for k in total_dict.keys():
+    for k in total_dict:
         v = nodes_dict[k]
         if isfunction(v):
-            if k in source_handles_dict.keys():
+            if k in source_handles_dict:
                 fn = job(
                     method=v,
                     data=[el for el in source_handles_dict[k] if el is not None],
diff --git a/src/python_workflow_definition/models.py b/src/python_workflow_definition/models.py
index 6ddb583..8265132 100644
--- a/src/python_workflow_definition/models.py
+++ b/src/python_workflow_definition/models.py
@@ -1,7 +1,7 @@
 import json
 import logging
 from pathlib import Path
-from typing import Annotated, Any, List, Literal, Optional, Type, TypeVar, Union
+from typing import Annotated, Any, Literal, TypeVar, Union
 
 from pydantic import (
     BaseModel,
@@ -29,7 +29,7 @@
 JsonPrimitive = Union[str, int, float, bool, None]
 AllowableDefaults = TypeAliasType(
     "AllowableDefaults",
-    "Union[JsonPrimitive, dict[str, AllowableDefaults], list[AllowableDefaults]]",
+    "JsonPrimitive | dict[str, AllowableDefaults] | list[AllowableDefaults]",
 )
 
 
@@ -47,7 +47,7 @@ class PythonWorkflowDefinitionInputNode(PythonWorkflowDefinitionBaseNode):
 
     type: Literal["input"]
     name: str
-    value: Optional[AllowableDefaults] = None
+    value: AllowableDefaults | None = None
 
 
 class PythonWorkflowDefinitionOutputNode(PythonWorkflowDefinitionBaseNode):
@@ -80,11 +80,9 @@ def check_value_format(cls, v: str):
 
 # Discriminated Union for Nodes
 PythonWorkflowDefinitionNode = Annotated[
-    Union[
-        PythonWorkflowDefinitionInputNode,
-        PythonWorkflowDefinitionOutputNode,
-        PythonWorkflowDefinitionFunctionNode,
-    ],
+    PythonWorkflowDefinitionInputNode
+    | PythonWorkflowDefinitionOutputNode
+    | PythonWorkflowDefinitionFunctionNode,
     Field(discriminator="type"),
 ]
 
@@ -93,13 +91,13 @@ class PythonWorkflowDefinitionEdge(BaseModel):
     """Model for edges connecting nodes."""
 
     target: int
-    targetPort: Optional[str] = None
+    targetPort: str | None = None
     source: int
-    sourcePort: Optional[str] = None
+    sourcePort: str | None = None
 
     @field_validator("sourcePort", mode="before")
     @classmethod
-    def handle_default_source(cls, v: Any) -> Optional[str]:
+    def handle_default_source(cls, v: Any) -> str | None:
         """
         Transforms incoming None/null for sourcePort to INTERNAL_DEFAULT_HANDLE.
         Runs before standard validation.
@@ -117,7 +115,7 @@ def handle_default_source(cls, v: Any) -> Optional[str]:
         return v
 
     @field_serializer("sourcePort")
-    def serialize_source_handle(self, v: Optional[str]) -> Optional[str]:
+    def serialize_source_handle(self, v: str | None) -> str | None:
         """
         SERIALIZATION (Output): Converts internal INTERNAL_DEFAULT_HANDLE ("__result__")
         back to None.
@@ -131,13 +129,13 @@ class PythonWorkflowDefinitionWorkflow(BaseModel):
     """The main workflow model."""
 
     version: str
-    nodes: List[PythonWorkflowDefinitionNode]
-    edges: List[PythonWorkflowDefinitionEdge]
+    nodes: list[PythonWorkflowDefinitionNode]
+    edges: list[PythonWorkflowDefinitionEdge]
 
     def dump_json(
         self,
         *,
-        indent: Optional[int] = 2,
+        indent: int | None = 2,
         **kwargs,
     ) -> str:
         """
@@ -171,9 +169,9 @@ def dump_json(
 
     def dump_json_file(
         self,
-        file_name: Union[str, Path],
+        file_name: str | Path,
         *,
-        indent: Optional[int] = 2,
+        indent: int | None = 2,
         **kwargs,
     ) -> None:
         """
@@ -196,14 +194,14 @@ def dump_json_file(
             with open(file_name, "w", encoding="utf-8") as f:
                 f.write(json_string)
             logger.info(f"Successfully wrote workflow model to {file_name}.")
-        except IOError as e:
+        except OSError as e:
             logger.error(
                 f"Error writing workflow model to file {file_name}: {e}", exc_info=True
             )
             raise
 
     @classmethod
-    def load_json_str(cls: Type[T], json_data: Union[str, bytes]) -> dict:
+    def load_json_str(cls: type[T], json_data: str | bytes) -> dict:
         """
         Loads and validates workflow data from a JSON string or bytes.
 
@@ -239,7 +237,7 @@ def load_json_str(cls: Type[T], json_data: Union[str, bytes]) -> dict:
             raise
 
     @classmethod
-    def load_json_file(cls: Type[T], file_name: Union[str, Path]) -> dict:
+    def load_json_file(cls: type[T], file_name: str | Path) -> dict:
         """
         Loads and validates workflow data from a JSON file.
 
@@ -263,6 +261,6 @@ def load_json_file(cls: Type[T], file_name: Union[str, Path]) -> dict:
         except FileNotFoundError:
             logger.error(f"JSON file not found: {file_name}", exc_info=True)
             raise
-        except IOError as e:
+        except OSError as e:
             logger.error(f"Error reading JSON file {file_name}: {e}", exc_info=True)
             raise
diff --git a/src/python_workflow_definition/plot.py b/src/python_workflow_definition/plot.py
index d0ca1b7..04d4413 100644
--- a/src/python_workflow_definition/plot.py
+++ b/src/python_workflow_definition/plot.py
@@ -11,7 +11,6 @@
     SOURCE_LABEL,
     SOURCE_PORT_LABEL,
     convert_nodes_list_to_dict,
-    get_kwargs,
 )
 
 
diff --git a/src/python_workflow_definition/purepython.py b/src/python_workflow_definition/purepython.py
index 0e77bd3..7d0407f 100644
--- a/src/python_workflow_definition/purepython.py
+++ b/src/python_workflow_definition/purepython.py
@@ -9,21 +9,15 @@
     SOURCE_LABEL,
     SOURCE_PORT_LABEL,
     TARGET_LABEL,
-    TARGET_PORT_LABEL,
     convert_nodes_list_to_dict,
-    get_dict,
     get_kwargs,
-    get_list,
-    get_source_handles,
     remove_result,
 )
 
 
 def resort_total_lst(total_lst: list, nodes_dict: dict) -> list:
-    nodes_with_dep_lst = list(sorted([v[0] for v in total_lst]))
-    nodes_without_dep_lst = [
-        k for k in nodes_dict.keys() if k not in nodes_with_dep_lst
-    ]
+    nodes_with_dep_lst = sorted([v[0] for v in total_lst])
+    nodes_without_dep_lst = [k for k in nodes_dict if k not in nodes_with_dep_lst]
     ordered_lst: list = []
     total_new_lst: list[list] = []
     while len(total_new_lst) < len(total_lst):
@@ -55,9 +49,9 @@ def group_edges(edges_lst: list) -> list:
 
 def _get_value(result_dict: dict, nodes_new_dict: dict, link_dict: dict):
     source, source_handle = link_dict[SOURCE_LABEL], link_dict[SOURCE_PORT_LABEL]
-    if source in result_dict.keys():
+    if source in result_dict:
         result = result_dict[source]
-    elif source in nodes_new_dict.keys():
+    elif source in nodes_new_dict:
         result = nodes_new_dict[source]
     else:
         raise KeyError()
diff --git a/src/python_workflow_definition/pyiron_base.py b/src/python_workflow_definition/pyiron_base.py
index 17e4aaa..eb92ec9 100644
--- a/src/python_workflow_definition/pyiron_base.py
+++ b/src/python_workflow_definition/pyiron_base.py
@@ -1,6 +1,6 @@
 from importlib import import_module
 from inspect import isfunction
-from typing import Any, Optional
+from typing import Any
 
 import numpy as np
 from pyiron_base import Project, job
@@ -26,10 +26,8 @@
 
 
 def _resort_total_lst(total_lst: list, nodes_dict: dict) -> list:
-    nodes_with_dep_lst = list(sorted([v[0] for v in total_lst]))
-    nodes_without_dep_lst = [
-        k for k in nodes_dict.keys() if k not in nodes_with_dep_lst
-    ]
+    nodes_with_dep_lst = sorted([v[0] for v in total_lst])
+    nodes_without_dep_lst = [k for k in nodes_dict if k not in nodes_with_dep_lst]
     ordered_lst: list = []
     total_new_lst: list[list] = []
     while len(total_new_lst) < len(total_lst):
@@ -62,11 +60,11 @@ def _group_edges(edges_lst: list) -> list:
 def _get_source(
     nodes_dict: dict, delayed_object_dict: dict, source: str, source_handle: str
 ):
-    if source in delayed_object_dict.keys() and source_handle is not None:
+    if source in delayed_object_dict and source_handle is not None:
         return (
             delayed_object_dict[source].__getattr__("output").__getattr__(source_handle)
         )
-    elif source in delayed_object_dict.keys():
+    elif source in delayed_object_dict:
         return delayed_object_dict[source]
     else:
         return nodes_dict[source]
@@ -103,7 +101,7 @@ def get_list(**kwargs) -> list:
 
 
 def _remove_server_obj(nodes_dict: dict, edges_lst: list):
-    server_lst = [k for k in nodes_dict.keys() if k.startswith("_server_obj_")]
+    server_lst = [k for k in nodes_dict if k.startswith("_server_obj_")]
     for s in server_lst:
         del nodes_dict[s]
         edges_lst = [ep for ep in edges_lst if s not in ep]
@@ -138,7 +136,7 @@ def _get_unique_objects(nodes_dict: dict):
     unique_lst: list = []
     delayed_object_updated_dict: dict[Any, DelayedObject] = {}
     match_dict: dict[Any, Any] = {}
-    for dobj in delayed_object_dict.keys():
+    for dobj in delayed_object_dict:
         match = False
         for obj in unique_lst:
             if (
@@ -180,7 +178,7 @@ def _get_connection_dict(delayed_object_updated_dict: dict, match_dict: dict):
         lookup_dict[i] = k
 
     for k, v in match_dict.items():
-        if v in connection_dict.keys():
+        if v in connection_dict:
             connection_dict[k] = connection_dict[v]
 
     return connection_dict, lookup_dict
@@ -230,7 +228,7 @@ def _get_edges_dict(
     return edges_dict_lst
 
 
-def load_workflow_json(file_name: str, project: Optional[Project] = None):
+def load_workflow_json(file_name: str, project: Project | None = None):
     if project is None:
         project = Project(".")
 
diff --git a/src/python_workflow_definition/pyiron_workflow.py b/src/python_workflow_definition/pyiron_workflow.py
index 73d994b..33f49a3 100644
--- a/src/python_workflow_definition/pyiron_workflow.py
+++ b/src/python_workflow_definition/pyiron_workflow.py
@@ -4,7 +4,7 @@
 from typing import Any
 
 import numpy as np
-from pyiron_workflow import Workflow, as_function_node, function_node
+from pyiron_workflow import Workflow, function_node
 from pyiron_workflow.api import Function
 
 from python_workflow_definition.models import PythonWorkflowDefinitionWorkflow
@@ -111,8 +111,7 @@ def write_workflow_json(graph_as_dict: dict, file_name: str = "workflow.json"):
     item_node_lst = [
         e[SOURCE_LABEL]
         for e in edges_lst
-        if e[TARGET_LABEL] in pyiron_workflow_modules.keys()
-        and e[TARGET_PORT_LABEL] == "item"
+        if e[TARGET_LABEL] in pyiron_workflow_modules and e[TARGET_PORT_LABEL] == "item"
     ]
 
     values_from_dict_lst = [
@@ -129,8 +128,8 @@ def write_workflow_json(graph_as_dict: dict, file_name: str = "workflow.json"):
     nodes_remaining_dict = {
         k: v
         for k, v in nodes_dict.items()
-        if k not in pyiron_workflow_modules.keys()
-        and k not in remap_dict.keys()
+        if k not in pyiron_workflow_modules
+        and k not in remap_dict
         and k not in item_node_lst
         and k not in remap_get_list_dict.values()
     }
@@ -178,7 +177,7 @@ def write_workflow_json(graph_as_dict: dict, file_name: str = "workflow.json"):
                 SOURCE_PORT_LABEL: connected_edge[SOURCE_PORT_LABEL],
             }
             edge_get_list_updated_lst.append(edge_updated)
-        elif edge[SOURCE_LABEL] in remap_dict.keys():
+        elif edge[SOURCE_LABEL] in remap_dict:
             edge_updated = {
                 TARGET_LABEL: edge[TARGET_LABEL],
                 TARGET_PORT_LABEL: edge[TARGET_PORT_LABEL],
@@ -191,7 +190,7 @@ def write_workflow_json(graph_as_dict: dict, file_name: str = "workflow.json"):
 
     target_dict: dict[Any, list] = {}
     for edge in edge_get_list_updated_lst:
-        for k in pyiron_workflow_modules.keys():
+        for k in pyiron_workflow_modules:
             if k == edge[TARGET_LABEL]:
                 if k not in target_dict:
                     target_dict[k] = []
@@ -199,14 +198,14 @@ def write_workflow_json(graph_as_dict: dict, file_name: str = "workflow.json"):
 
     source_dict: dict[Any, list] = {}
     for edge in edge_get_list_updated_lst:
-        for k in pyiron_workflow_modules.keys():
+        for k in pyiron_workflow_modules:
             if k == edge[SOURCE_LABEL]:
                 if k not in source_dict:
                     source_dict[k] = []
                 source_dict[k].append(edge)
 
     edge_new_lst, nodes_to_delete = [], []
-    for k in target_dict.keys():
+    for k in target_dict:
         source, sourcehandle = None, None
         for edge in target_dict[k]:
             if edge[SOURCE_PORT_LABEL] is None:
@@ -214,7 +213,7 @@ def write_workflow_json(graph_as_dict: dict, file_name: str = "workflow.json"):
                 nodes_to_delete.append(edge[SOURCE_LABEL])
             else:
                 source = edge[SOURCE_LABEL]
-        if "s_" == source_dict[k][-1][TARGET_PORT_LABEL][:2]:
+        if source_dict[k][-1][TARGET_PORT_LABEL][:2] == "s_":
             edge_new_lst.append(
                 {
                     SOURCE_LABEL: nodes_final_order_dict[source],
@@ -247,16 +246,7 @@ def write_workflow_json(graph_as_dict: dict, file_name: str = "workflow.json"):
             if (
                 isfunction(source_node)
                 and source_node.__name__ == edge[SOURCE_PORT_LABEL]
-            ):
-                edge_new_lst.append(
-                    {
-                        TARGET_LABEL: nodes_final_order_dict[edge[TARGET_LABEL]],
-                        TARGET_PORT_LABEL: edge[TARGET_PORT_LABEL],
-                        SOURCE_LABEL: nodes_final_order_dict[edge[SOURCE_LABEL]],
-                        SOURCE_PORT_LABEL: None,
-                    }
-                )
-            elif (
+            ) or (
                 isfunction(source_node)
                 and source_node.__name__ == "get_dict"
                 and edge[SOURCE_PORT_LABEL] == "dict"
@@ -328,15 +318,15 @@ def load_workflow_json(file_name: str) -> Workflow:
         PythonWorkflowDefinitionWorkflow.load_json_file(file_name=file_name)
     )
 
-    input_values: dict[int, object] = (
-        {}
-    )  # Type is actually more restrictive, must be jsonifyable object
+    input_values: dict[
+        int, object
+    ] = {}  # Type is actually more restrictive, must be jsonifyable object
     nodes: dict[int, Function] = {}
     total_counter_dict = Counter(
         [n["value"] for n in content[NODES_LABEL] if n["type"] == "function"]
     )
-    counter_dict = {k: -1 for k in total_counter_dict.keys()}
-    wf = Workflow(file_name.split(".")[0])
+    counter_dict = dict.fromkeys(total_counter_dict.keys(), -1)
+    wf = Workflow(file_name.split(".", maxsplit=1)[0])
     nodes_look_up_dict = {node["id"]: node["value"] for node in content[NODES_LABEL]}
     for node_dict in content[NODES_LABEL]:
         if node_dict["type"] == "function":
@@ -384,7 +374,7 @@ def load_workflow_json(file_name: str) -> Workflow:
         source_port = edge_dict[SOURCE_PORT_LABEL]
 
         if source_port is None:
-            if source_id in input_values.keys():  # Parent input value
+            if source_id in input_values:  # Parent input value
                 upstream = input_values[source_id]
             else:  # Single-output sibling
                 upstream = nodes[source_id]
diff --git a/src/python_workflow_definition/shared.py b/src/python_workflow_definition/shared.py
index 9cc6680..746403c 100644
--- a/src/python_workflow_definition/shared.py
+++ b/src/python_workflow_definition/shared.py
@@ -34,7 +34,7 @@ def get_kwargs(lst: list) -> dict:
 def get_source_handles(edges_lst: list) -> dict:
     source_handle_dict: dict[Any, list] = {}
     for ed in edges_lst:
-        if ed[SOURCE_LABEL] not in source_handle_dict.keys():
+        if ed[SOURCE_LABEL] not in source_handle_dict:
             source_handle_dict[ed[SOURCE_LABEL]] = []
         source_handle_dict[ed[SOURCE_LABEL]].append(ed[SOURCE_PORT_LABEL])
     return {
@@ -67,7 +67,7 @@ def update_node_names(workflow_dict: dict) -> dict:
     }
 
     counter_dict = Counter(node_names_dict.values())
-    node_names_useage_dict = {k: -1 for k in counter_dict.keys()}
+    node_names_useage_dict = dict.fromkeys(counter_dict.keys(), -1)
     for k, v in node_names_dict.items():
         node_names_useage_dict[v] += 1
         if counter_dict[v] > 1:

From c422a77e58388e4781e107d2b7472d9f77fa7695 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 27 Jul 2026 07:03:51 +0200
Subject: [PATCH 05/19] fixes

---
 pyproject.toml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ba59460..0046187 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -66,7 +66,12 @@ select = [
     # pylint
     "PL",
 ]
-ignore = []
+ignore = [
+    # ignore line-length violations
+    "E501",
+    # Too many branches
+    "PLR0912",
+]
 
 [tool.hatch.build]
 include = [

From 5898f5d346a29991c58194d79d47a0149a11e799 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 27 Jul 2026 07:04:20 +0200
Subject: [PATCH 06/19] black fixes

---
 src/python_workflow_definition/cwl/__init__.py    | 10 +++++++---
 src/python_workflow_definition/pyiron_workflow.py |  6 +++---
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/src/python_workflow_definition/cwl/__init__.py b/src/python_workflow_definition/cwl/__init__.py
index 96ae76e..7333a65 100644
--- a/src/python_workflow_definition/cwl/__init__.py
+++ b/src/python_workflow_definition/cwl/__init__.py
@@ -21,7 +21,8 @@
 
 def _get_function_argument(argument: str, position: int = 3) -> dict:
     return {
-        argument + "_file": {
+        argument
+        + "_file": {
             "type": "File",
             "inputBinding": {
                 "prefix": "--arg_" + argument + "=",
@@ -44,7 +45,8 @@ def _get_function_template(function_name: str) -> dict:
 
 def _get_output_name(output_name: str) -> dict:
     return {
-        output_name + "_file": {
+        output_name
+        + "_file": {
             "type": "File",
             "outputBinding": {"glob": output_name + ".pickle"},
         }
@@ -225,7 +227,9 @@ def _write_workflow(workflow, directory_path: str = "."):
                 )
         workflow_template["steps"].update(
             {
-                step_name_lst[ind] + "_" + str(ind): {
+                step_name_lst[ind]
+                + "_"
+                + str(ind): {
                     "run": node_script,
                     "in": in_dict,
                     "out": output,
diff --git a/src/python_workflow_definition/pyiron_workflow.py b/src/python_workflow_definition/pyiron_workflow.py
index 33f49a3..0af64ab 100644
--- a/src/python_workflow_definition/pyiron_workflow.py
+++ b/src/python_workflow_definition/pyiron_workflow.py
@@ -318,9 +318,9 @@ def load_workflow_json(file_name: str) -> Workflow:
         PythonWorkflowDefinitionWorkflow.load_json_file(file_name=file_name)
     )
 
-    input_values: dict[
-        int, object
-    ] = {}  # Type is actually more restrictive, must be jsonifyable object
+    input_values: dict[int, object] = (
+        {}
+    )  # Type is actually more restrictive, must be jsonifyable object
     nodes: dict[int, Function] = {}
     total_counter_dict = Counter(
         [n["value"] for n in content[NODES_LABEL] if n["type"] == "function"]

From 8ad140dcea14ab4b9e63511dda264d372025cc73 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 27 Jul 2026 07:07:04 +0200
Subject: [PATCH 07/19] fixes

---
 src/python_workflow_definition/cwl/__init__.py | 18 +++++++++---------
 src/python_workflow_definition/jobflow.py      | 10 +++-------
 src/python_workflow_definition/purepython.py   |  2 +-
 src/python_workflow_definition/pyiron_base.py  | 14 +++++++-------
 src/python_workflow_definition/shared.py       | 14 +++++++-------
 5 files changed, 27 insertions(+), 31 deletions(-)

diff --git a/src/python_workflow_definition/cwl/__init__.py b/src/python_workflow_definition/cwl/__init__.py
index 7333a65..b0333b2 100644
--- a/src/python_workflow_definition/cwl/__init__.py
+++ b/src/python_workflow_definition/cwl/__init__.py
@@ -60,22 +60,22 @@ def _get_function(workflow):
     funct_dict = {}
     for funct_id in function_nodes_dict:
         target_ports = list(
-            set(
-                [
+            {
+                
                     e[TARGET_PORT_LABEL]
                     for e in workflow[EDGES_LABEL]
                     if e["target"] == funct_id
-                ]
-            )
+                
+            }
         )
         source_ports = list(
-            set(
-                [
+            {
+                
                     e[SOURCE_PORT_LABEL]
                     for e in workflow[EDGES_LABEL]
                     if e["source"] == funct_id
-                ]
-            )
+                
+            }
         )
         funct_dict[funct_id] = {
             "targetPorts": target_ports,
@@ -89,7 +89,7 @@ def _write_function_cwl(workflow, directory_path: str = "."):
     export_path = Path(directory_path)
     export_path.mkdir(parents=True, exist_ok=True)
 
-    for i in function_nodes_dict.keys():
+    for i in function_nodes_dict:
         template: dict[str, Any] = {
             "cwlVersion": "v1.2",
             "class": "CommandLineTool",
diff --git a/src/python_workflow_definition/jobflow.py b/src/python_workflow_definition/jobflow.py
index 348c446..67868fa 100644
--- a/src/python_workflow_definition/jobflow.py
+++ b/src/python_workflow_definition/jobflow.py
@@ -79,13 +79,11 @@ def _get_edges_and_extend_nodes(
                     )
                 )
             elif isinstance(v, dict) and any(
-                [
-                    isinstance(el, dict)
+                isinstance(el, dict)
                     and "@module" in el
                     and "@class" in el
                     and "@version" in el
                     for el in v.values()
-                ]
             ):
                 node_dict_index = len(nodes_dict)
                 nodes_dict[node_dict_index] = get_dict
@@ -129,13 +127,11 @@ def _get_edges_and_extend_nodes(
                     }
                 )
             elif isinstance(v, list) and any(
-                [
-                    isinstance(el, dict)
+                isinstance(el, dict)
                     and "@module" in el
                     and "@class" in el
                     and "@version" in el
                     for el in v
-                ]
             ):
                 node_list_index = len(nodes_dict)
                 nodes_dict[node_list_index] = get_list
@@ -206,7 +202,7 @@ def _resort_total_lst(total_dict: dict, nodes_dict: dict) -> dict:
             if ind not in ordered_lst:
                 source_lst = [sd[SOURCE_LABEL] for sd in connect.values()]
                 if all(
-                    [s in ordered_lst or s in nodes_without_dep_lst for s in source_lst]
+                    s in ordered_lst or s in nodes_without_dep_lst for s in source_lst
                 ):
                     ordered_lst.append(ind)
                     total_new_dict[ind] = connect
diff --git a/src/python_workflow_definition/purepython.py b/src/python_workflow_definition/purepython.py
index 7d0407f..f541edc 100644
--- a/src/python_workflow_definition/purepython.py
+++ b/src/python_workflow_definition/purepython.py
@@ -25,7 +25,7 @@ def resort_total_lst(total_lst: list, nodes_dict: dict) -> list:
             if ind not in ordered_lst:
                 source_lst = [sd[SOURCE_LABEL] for sd in connect.values()]
                 if all(
-                    [s in ordered_lst or s in nodes_without_dep_lst for s in source_lst]
+                    s in ordered_lst or s in nodes_without_dep_lst for s in source_lst
                 ):
                     ordered_lst.append(ind)
                     total_new_lst.append([ind, connect])
diff --git a/src/python_workflow_definition/pyiron_base.py b/src/python_workflow_definition/pyiron_base.py
index eb92ec9..e9d3725 100644
--- a/src/python_workflow_definition/pyiron_base.py
+++ b/src/python_workflow_definition/pyiron_base.py
@@ -35,7 +35,7 @@ def _resort_total_lst(total_lst: list, nodes_dict: dict) -> list:
             if ind not in ordered_lst:
                 source_lst = [sd[SOURCE_LABEL] for sd in connect.values()]
                 if all(
-                    [s in ordered_lst or s in nodes_without_dep_lst for s in source_lst]
+                    s in ordered_lst or s in nodes_without_dep_lst for s in source_lst
                 ):
                     ordered_lst.append(ind)
                     total_new_lst.append([ind, connect])
@@ -93,7 +93,7 @@ def _get_delayed_object_dict(
 
 
 def get_dict(**kwargs) -> dict:
-    return {k: v for k, v in kwargs["kwargs"].items()}
+    return dict(kwargs["kwargs"].items())
 
 
 def get_list(**kwargs) -> list:
@@ -120,12 +120,12 @@ def _get_unique_objects(nodes_dict: dict):
     for k, v in nodes_dict.items():
         if isinstance(v, DelayedObject):
             delayed_object_dict[k] = v
-        elif isinstance(v, list) and any([isinstance(el, DelayedObject) for el in v]):
+        elif isinstance(v, list) and any(isinstance(el, DelayedObject) for el in v):
             delayed_object_dict[k] = DelayedObject(function=get_list)
-            delayed_object_dict[k]._input = {i: el for i, el in enumerate(v)}
+            delayed_object_dict[k]._input = dict(enumerate(v))
             delayed_object_dict[k]._python_function = get_list
         elif isinstance(v, dict) and any(
-            [isinstance(el, DelayedObject) for el in v.values()]
+            isinstance(el, DelayedObject) for el in v.values()
         ):
             delayed_object_dict[k] = DelayedObject(
                 function=get_dict,
@@ -156,11 +156,11 @@ def _get_unique_objects(nodes_dict: dict):
         if not (
             isinstance(v, DelayedObject)
             or (
-                isinstance(v, list) and any([isinstance(el, DelayedObject) for el in v])
+                isinstance(v, list) and any(isinstance(el, DelayedObject) for el in v)
             )
             or (
                 isinstance(v, dict)
-                and any([isinstance(el, DelayedObject) for el in v.values()])
+                and any(isinstance(el, DelayedObject) for el in v.values())
             )
         ):
             update_dict[k] = v
diff --git a/src/python_workflow_definition/shared.py b/src/python_workflow_definition/shared.py
index 746403c..affc9c5 100644
--- a/src/python_workflow_definition/shared.py
+++ b/src/python_workflow_definition/shared.py
@@ -13,7 +13,7 @@
 
 def get_dict(**kwargs) -> dict:
     # NOTE: In WG, this will automatically be wrapped in a dict with the `result` key
-    return {k: v for k, v in kwargs.items()}
+    return dict(kwargs.items())
     # return {'dict': {k: v for k, v in kwargs.items()}}
 
 
@@ -38,7 +38,7 @@ def get_source_handles(edges_lst: list) -> dict:
             source_handle_dict[ed[SOURCE_LABEL]] = []
         source_handle_dict[ed[SOURCE_LABEL]].append(ed[SOURCE_PORT_LABEL])
     return {
-        k: list(range(len(v))) if len(v) > 1 and all([el is None for el in v]) else v
+        k: list(range(len(v))) if len(v) > 1 and all(el is None for el in v) else v
         for k, v in source_handle_dict.items()
     }
 
@@ -55,13 +55,13 @@ def update_node_names(workflow_dict: dict) -> dict:
     input_nodes = [n for n in workflow_dict[NODES_LABEL] if n["type"] == "input"]
     node_names_dict = {
         n["id"]: list(
-            set(
-                [
+            {
+                
                     e[TARGET_PORT_LABEL]
                     for e in workflow_dict[EDGES_LABEL]
                     if e[SOURCE_LABEL] == n["id"]
-                ]
-            )
+                
+            }
         )[0]
         for n in input_nodes
     }
@@ -83,7 +83,7 @@ def update_node_names(workflow_dict: dict) -> dict:
 
 def set_result_node(workflow_dict):
     node_id_lst = [n["id"] for n in workflow_dict[NODES_LABEL]]
-    source_lst = list(set([e[SOURCE_LABEL] for e in workflow_dict[EDGES_LABEL]]))
+    source_lst = list({e[SOURCE_LABEL] for e in workflow_dict[EDGES_LABEL]})
 
     end_node_lst = []
     for ni in node_id_lst:

From 9ae47bdd8cf46f6b53e2b2785f263cdb23d5dd4f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 27 Jul 2026 05:09:40 +0000
Subject: [PATCH 08/19] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../cwl/__init__.py                           | 26 +++++++------------
 src/python_workflow_definition/jobflow.py     | 16 ++++++------
 src/python_workflow_definition/pyiron_base.py |  4 +--
 .../pyiron_workflow.py                        |  6 ++---
 src/python_workflow_definition/shared.py      |  8 +++---
 5 files changed, 24 insertions(+), 36 deletions(-)

diff --git a/src/python_workflow_definition/cwl/__init__.py b/src/python_workflow_definition/cwl/__init__.py
index b0333b2..2bf0afc 100644
--- a/src/python_workflow_definition/cwl/__init__.py
+++ b/src/python_workflow_definition/cwl/__init__.py
@@ -21,8 +21,7 @@
 
 def _get_function_argument(argument: str, position: int = 3) -> dict:
     return {
-        argument
-        + "_file": {
+        argument + "_file": {
             "type": "File",
             "inputBinding": {
                 "prefix": "--arg_" + argument + "=",
@@ -45,8 +44,7 @@ def _get_function_template(function_name: str) -> dict:
 
 def _get_output_name(output_name: str) -> dict:
     return {
-        output_name
-        + "_file": {
+        output_name + "_file": {
             "type": "File",
             "outputBinding": {"glob": output_name + ".pickle"},
         }
@@ -61,20 +59,16 @@ def _get_function(workflow):
     for funct_id in function_nodes_dict:
         target_ports = list(
             {
-                
-                    e[TARGET_PORT_LABEL]
-                    for e in workflow[EDGES_LABEL]
-                    if e["target"] == funct_id
-                
+                e[TARGET_PORT_LABEL]
+                for e in workflow[EDGES_LABEL]
+                if e["target"] == funct_id
             }
         )
         source_ports = list(
             {
-                
-                    e[SOURCE_PORT_LABEL]
-                    for e in workflow[EDGES_LABEL]
-                    if e["source"] == funct_id
-                
+                e[SOURCE_PORT_LABEL]
+                for e in workflow[EDGES_LABEL]
+                if e["source"] == funct_id
             }
         )
         funct_dict[funct_id] = {
@@ -227,9 +221,7 @@ def _write_workflow(workflow, directory_path: str = "."):
                 )
         workflow_template["steps"].update(
             {
-                step_name_lst[ind]
-                + "_"
-                + str(ind): {
+                step_name_lst[ind] + "_" + str(ind): {
                     "run": node_script,
                     "in": in_dict,
                     "out": output,
diff --git a/src/python_workflow_definition/jobflow.py b/src/python_workflow_definition/jobflow.py
index 67868fa..3d9e567 100644
--- a/src/python_workflow_definition/jobflow.py
+++ b/src/python_workflow_definition/jobflow.py
@@ -80,10 +80,10 @@ def _get_edges_and_extend_nodes(
                 )
             elif isinstance(v, dict) and any(
                 isinstance(el, dict)
-                    and "@module" in el
-                    and "@class" in el
-                    and "@version" in el
-                    for el in v.values()
+                and "@module" in el
+                and "@class" in el
+                and "@version" in el
+                for el in v.values()
             ):
                 node_dict_index = len(nodes_dict)
                 nodes_dict[node_dict_index] = get_dict
@@ -128,10 +128,10 @@ def _get_edges_and_extend_nodes(
                 )
             elif isinstance(v, list) and any(
                 isinstance(el, dict)
-                    and "@module" in el
-                    and "@class" in el
-                    and "@version" in el
-                    for el in v
+                and "@module" in el
+                and "@class" in el
+                and "@version" in el
+                for el in v
             ):
                 node_list_index = len(nodes_dict)
                 nodes_dict[node_list_index] = get_list
diff --git a/src/python_workflow_definition/pyiron_base.py b/src/python_workflow_definition/pyiron_base.py
index e9d3725..fdfae42 100644
--- a/src/python_workflow_definition/pyiron_base.py
+++ b/src/python_workflow_definition/pyiron_base.py
@@ -155,9 +155,7 @@ def _get_unique_objects(nodes_dict: dict):
     for k, v in nodes_dict.items():
         if not (
             isinstance(v, DelayedObject)
-            or (
-                isinstance(v, list) and any(isinstance(el, DelayedObject) for el in v)
-            )
+            or (isinstance(v, list) and any(isinstance(el, DelayedObject) for el in v))
             or (
                 isinstance(v, dict)
                 and any(isinstance(el, DelayedObject) for el in v.values())
diff --git a/src/python_workflow_definition/pyiron_workflow.py b/src/python_workflow_definition/pyiron_workflow.py
index 0af64ab..33f49a3 100644
--- a/src/python_workflow_definition/pyiron_workflow.py
+++ b/src/python_workflow_definition/pyiron_workflow.py
@@ -318,9 +318,9 @@ def load_workflow_json(file_name: str) -> Workflow:
         PythonWorkflowDefinitionWorkflow.load_json_file(file_name=file_name)
     )
 
-    input_values: dict[int, object] = (
-        {}
-    )  # Type is actually more restrictive, must be jsonifyable object
+    input_values: dict[
+        int, object
+    ] = {}  # Type is actually more restrictive, must be jsonifyable object
     nodes: dict[int, Function] = {}
     total_counter_dict = Counter(
         [n["value"] for n in content[NODES_LABEL] if n["type"] == "function"]
diff --git a/src/python_workflow_definition/shared.py b/src/python_workflow_definition/shared.py
index affc9c5..d3ed347 100644
--- a/src/python_workflow_definition/shared.py
+++ b/src/python_workflow_definition/shared.py
@@ -56,11 +56,9 @@ def update_node_names(workflow_dict: dict) -> dict:
     node_names_dict = {
         n["id"]: list(
             {
-                
-                    e[TARGET_PORT_LABEL]
-                    for e in workflow_dict[EDGES_LABEL]
-                    if e[SOURCE_LABEL] == n["id"]
-                
+                e[TARGET_PORT_LABEL]
+                for e in workflow_dict[EDGES_LABEL]
+                if e[SOURCE_LABEL] == n["id"]
             }
         )[0]
         for n in input_nodes

From 6fc3070d20e0ad95611344cff9de551dd71c5a81 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 27 Jul 2026 07:16:26 +0200
Subject: [PATCH 09/19] remove commended out code

---
 src/python_workflow_definition/shared.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/python_workflow_definition/shared.py b/src/python_workflow_definition/shared.py
index d3ed347..fe42cfc 100644
--- a/src/python_workflow_definition/shared.py
+++ b/src/python_workflow_definition/shared.py
@@ -12,9 +12,7 @@
 
 
 def get_dict(**kwargs) -> dict:
-    # NOTE: In WG, this will automatically be wrapped in a dict with the `result` key
     return dict(kwargs.items())
-    # return {'dict': {k: v for k, v in kwargs.items()}}
 
 
 def get_list(**kwargs) -> list:

From c6036ef063e6112448bb000803f164c12b59b925 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 27 Jul 2026 07:20:38 +0200
Subject: [PATCH 10/19] more fixes

---
 pyproject.toml                            |  2 ++
 src/python_workflow_definition/jobflow.py | 14 +++++++-------
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0046187..04e61b4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -69,6 +69,8 @@ select = [
 ignore = [
     # ignore line-length violations
     "E501",
+    # Too many statements
+    "PLR0915",
     # Too many branches
     "PLR0912",
 ]
diff --git a/src/python_workflow_definition/jobflow.py b/src/python_workflow_definition/jobflow.py
index 3d9e567..7f4e43c 100644
--- a/src/python_workflow_definition/jobflow.py
+++ b/src/python_workflow_definition/jobflow.py
@@ -27,7 +27,7 @@
 
 
 def _get_function_dict(flow: Flow):
-    return {job.uuid: job.function for job in flow.jobs}
+    return {j.uuid: j.function for j in flow.jobs}
 
 
 def _get_nodes_dict(function_dict: dict):
@@ -62,8 +62,8 @@ def _get_edges_and_extend_nodes(
     flow_dict: dict, nodes_mapping_dict: dict, nodes_dict: dict
 ):
     edges_lst = []
-    for job in flow_dict["jobs"]:
-        for k, v in job["function_kwargs"].items():
+    for j in flow_dict["jobs"]:
+        for k, v in j["function_kwargs"].items():
             if (
                 isinstance(v, dict)
                 and "@module" in v
@@ -72,7 +72,7 @@ def _get_edges_and_extend_nodes(
             ):
                 edges_lst.append(
                     _get_edge_from_dict(
-                        target=nodes_mapping_dict[job["uuid"]],
+                        target=nodes_mapping_dict[j["uuid"]],
                         key=k,
                         value_dict=v,
                         nodes_mapping_dict=nodes_mapping_dict,
@@ -120,7 +120,7 @@ def _get_edges_and_extend_nodes(
                         )
                 edges_lst.append(
                     {
-                        TARGET_LABEL: nodes_mapping_dict[job["uuid"]],
+                        TARGET_LABEL: nodes_mapping_dict[j["uuid"]],
                         TARGET_PORT_LABEL: k,
                         SOURCE_LABEL: node_dict_index,
                         SOURCE_PORT_LABEL: None,
@@ -168,7 +168,7 @@ def _get_edges_and_extend_nodes(
                         )
                 edges_lst.append(
                     {
-                        TARGET_LABEL: nodes_mapping_dict[job["uuid"]],
+                        TARGET_LABEL: nodes_mapping_dict[j["uuid"]],
                         TARGET_PORT_LABEL: k,
                         SOURCE_LABEL: node_list_index,
                         SOURCE_PORT_LABEL: None,
@@ -182,7 +182,7 @@ def _get_edges_and_extend_nodes(
                     node_index = {tv: tk for tk, tv in nodes_dict.items()}[v]
                 edges_lst.append(
                     {
-                        TARGET_LABEL: nodes_mapping_dict[job["uuid"]],
+                        TARGET_LABEL: nodes_mapping_dict[j["uuid"]],
                         TARGET_PORT_LABEL: k,
                         SOURCE_LABEL: node_index,
                         SOURCE_PORT_LABEL: None,

From e36659bd6e2c95b0658d23bcac6f148c6a395ce1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 27 Jul 2026 07:23:01 +0200
Subject: [PATCH 11/19] type fix

---
 src/python_workflow_definition/models.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/python_workflow_definition/models.py b/src/python_workflow_definition/models.py
index 8265132..0f76481 100644
--- a/src/python_workflow_definition/models.py
+++ b/src/python_workflow_definition/models.py
@@ -1,7 +1,7 @@
 import json
 import logging
 from pathlib import Path
-from typing import Annotated, Any, Literal, TypeVar, Union
+from typing import Annotated, Any, Literal, TypeVar, Union, Optional
 
 from pydantic import (
     BaseModel,
@@ -26,7 +26,7 @@
 )
 
 
-JsonPrimitive = Union[str, int, float, bool, None]
+JsonPrimitive = Optional[str | int | float | bool]
 AllowableDefaults = TypeAliasType(
     "AllowableDefaults",
     "JsonPrimitive | dict[str, AllowableDefaults] | list[AllowableDefaults]",

From aed8d8af63152803bc42a3735f77b6d2840a239a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 27 Jul 2026 07:24:17 +0200
Subject: [PATCH 12/19] more fixes

---
 src/python_workflow_definition/models.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/python_workflow_definition/models.py b/src/python_workflow_definition/models.py
index 0f76481..167fa47 100644
--- a/src/python_workflow_definition/models.py
+++ b/src/python_workflow_definition/models.py
@@ -1,7 +1,7 @@
 import json
 import logging
 from pathlib import Path
-from typing import Annotated, Any, Literal, TypeVar, Union, Optional
+from typing import Annotated, Any, Literal, TypeVar
 
 from pydantic import (
     BaseModel,
@@ -26,7 +26,7 @@
 )
 
 
-JsonPrimitive = Optional[str | int | float | bool]
+JsonPrimitive = str | int | float | bool | None
 AllowableDefaults = TypeAliasType(
     "AllowableDefaults",
     "JsonPrimitive | dict[str, AllowableDefaults] | list[AllowableDefaults]",

From 68f3ee9d205f1c29f8c6d6c94691eb5f18e8ce4a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 27 Jul 2026 07:29:55 +0200
Subject: [PATCH 13/19] more fixes

---
 src/python_workflow_definition/jobflow.py         | 4 ++--
 src/python_workflow_definition/pyiron_base.py     | 8 ++++----
 src/python_workflow_definition/pyiron_workflow.py | 4 ++--
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/python_workflow_definition/jobflow.py b/src/python_workflow_definition/jobflow.py
index 7f4e43c..a4dfb05 100644
--- a/src/python_workflow_definition/jobflow.py
+++ b/src/python_workflow_definition/jobflow.py
@@ -236,7 +236,7 @@ def get_attr_helper(obj, source_handle):
             return getattr(obj.output, source_handle)
 
     memory_dict: dict[Any, Any] = {}
-    for k in total_dict:
+    for k, subdict in total_dict.items():
         v = nodes_dict[k]
         if isfunction(v):
             if k in source_handles_dict:
@@ -255,7 +255,7 @@ def get_attr_helper(obj, source_handle):
                         source_handle=vw[SOURCE_PORT_LABEL],
                     )
                 )
-                for kw, vw in total_dict[k].items()
+                for kw, vw in subdict.items()
             }
             memory_dict[k] = fn(**kwargs)
     return list(memory_dict.values())
diff --git a/src/python_workflow_definition/pyiron_base.py b/src/python_workflow_definition/pyiron_base.py
index fdfae42..ae34b1b 100644
--- a/src/python_workflow_definition/pyiron_base.py
+++ b/src/python_workflow_definition/pyiron_base.py
@@ -136,13 +136,13 @@ def _get_unique_objects(nodes_dict: dict):
     unique_lst: list = []
     delayed_object_updated_dict: dict[Any, DelayedObject] = {}
     match_dict: dict[Any, Any] = {}
-    for dobj in delayed_object_dict:
+    for dobj, v in delayed_object_dict.items():
         match = False
         for obj in unique_lst:
             if (
                 delayed_object_updated_dict[obj]._python_function
-                == delayed_object_dict[dobj]._python_function
-                and delayed_object_dict[dobj]._input == delayed_object_dict[obj]._input
+                == v._python_function
+                and v._input == delayed_object_dict[obj]._input
             ):
                 delayed_object_updated_dict[obj] = delayed_object_dict[obj]
                 match_dict[dobj] = obj
@@ -150,7 +150,7 @@ def _get_unique_objects(nodes_dict: dict):
                 break
         if not match:
             unique_lst.append(dobj)
-            delayed_object_updated_dict[dobj] = delayed_object_dict[dobj]
+            delayed_object_updated_dict[dobj] = v
     update_dict = {}
     for k, v in nodes_dict.items():
         if not (
diff --git a/src/python_workflow_definition/pyiron_workflow.py b/src/python_workflow_definition/pyiron_workflow.py
index 33f49a3..5177643 100644
--- a/src/python_workflow_definition/pyiron_workflow.py
+++ b/src/python_workflow_definition/pyiron_workflow.py
@@ -205,9 +205,9 @@ def write_workflow_json(graph_as_dict: dict, file_name: str = "workflow.json"):
                 source_dict[k].append(edge)
 
     edge_new_lst, nodes_to_delete = [], []
-    for k in target_dict:
+    for k, v in target_dict.items():
         source, sourcehandle = None, None
-        for edge in target_dict[k]:
+        for edge in v:
             if edge[SOURCE_PORT_LABEL] is None:
                 sourcehandle = nodes_dict[edge[SOURCE_LABEL]]
                 nodes_to_delete.append(edge[SOURCE_LABEL])

From 74def5261a593422f9fe4522840078f9a78ca669 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 27 Jul 2026 07:34:28 +0200
Subject: [PATCH 14/19] black fixes

---
 src/python_workflow_definition/cwl/__init__.py    | 10 +++++++---
 src/python_workflow_definition/pyiron_base.py     |  3 +--
 src/python_workflow_definition/pyiron_workflow.py |  6 +++---
 3 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/src/python_workflow_definition/cwl/__init__.py b/src/python_workflow_definition/cwl/__init__.py
index 2bf0afc..16a6e9d 100644
--- a/src/python_workflow_definition/cwl/__init__.py
+++ b/src/python_workflow_definition/cwl/__init__.py
@@ -21,7 +21,8 @@
 
 def _get_function_argument(argument: str, position: int = 3) -> dict:
     return {
-        argument + "_file": {
+        argument
+        + "_file": {
             "type": "File",
             "inputBinding": {
                 "prefix": "--arg_" + argument + "=",
@@ -44,7 +45,8 @@ def _get_function_template(function_name: str) -> dict:
 
 def _get_output_name(output_name: str) -> dict:
     return {
-        output_name + "_file": {
+        output_name
+        + "_file": {
             "type": "File",
             "outputBinding": {"glob": output_name + ".pickle"},
         }
@@ -221,7 +223,9 @@ def _write_workflow(workflow, directory_path: str = "."):
                 )
         workflow_template["steps"].update(
             {
-                step_name_lst[ind] + "_" + str(ind): {
+                step_name_lst[ind]
+                + "_"
+                + str(ind): {
                     "run": node_script,
                     "in": in_dict,
                     "out": output,
diff --git a/src/python_workflow_definition/pyiron_base.py b/src/python_workflow_definition/pyiron_base.py
index ae34b1b..53ee1a7 100644
--- a/src/python_workflow_definition/pyiron_base.py
+++ b/src/python_workflow_definition/pyiron_base.py
@@ -140,8 +140,7 @@ def _get_unique_objects(nodes_dict: dict):
         match = False
         for obj in unique_lst:
             if (
-                delayed_object_updated_dict[obj]._python_function
-                == v._python_function
+                delayed_object_updated_dict[obj]._python_function == v._python_function
                 and v._input == delayed_object_dict[obj]._input
             ):
                 delayed_object_updated_dict[obj] = delayed_object_dict[obj]
diff --git a/src/python_workflow_definition/pyiron_workflow.py b/src/python_workflow_definition/pyiron_workflow.py
index 5177643..30c2a77 100644
--- a/src/python_workflow_definition/pyiron_workflow.py
+++ b/src/python_workflow_definition/pyiron_workflow.py
@@ -318,9 +318,9 @@ def load_workflow_json(file_name: str) -> Workflow:
         PythonWorkflowDefinitionWorkflow.load_json_file(file_name=file_name)
     )
 
-    input_values: dict[
-        int, object
-    ] = {}  # Type is actually more restrictive, must be jsonifyable object
+    input_values: dict[int, object] = (
+        {}
+    )  # Type is actually more restrictive, must be jsonifyable object
     nodes: dict[int, Function] = {}
     total_counter_dict = Counter(
         [n["value"] for n in content[NODES_LABEL] if n["type"] == "function"]

From d642f29b1301296e6c2d83954f05590797532595 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 27 Jul 2026 05:34:50 +0000
Subject: [PATCH 15/19] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/python_workflow_definition/cwl/__init__.py    | 10 +++-------
 src/python_workflow_definition/pyiron_workflow.py |  6 +++---
 2 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/src/python_workflow_definition/cwl/__init__.py b/src/python_workflow_definition/cwl/__init__.py
index 16a6e9d..2bf0afc 100644
--- a/src/python_workflow_definition/cwl/__init__.py
+++ b/src/python_workflow_definition/cwl/__init__.py
@@ -21,8 +21,7 @@
 
 def _get_function_argument(argument: str, position: int = 3) -> dict:
     return {
-        argument
-        + "_file": {
+        argument + "_file": {
             "type": "File",
             "inputBinding": {
                 "prefix": "--arg_" + argument + "=",
@@ -45,8 +44,7 @@ def _get_function_template(function_name: str) -> dict:
 
 def _get_output_name(output_name: str) -> dict:
     return {
-        output_name
-        + "_file": {
+        output_name + "_file": {
             "type": "File",
             "outputBinding": {"glob": output_name + ".pickle"},
         }
@@ -223,9 +221,7 @@ def _write_workflow(workflow, directory_path: str = "."):
                 )
         workflow_template["steps"].update(
             {
-                step_name_lst[ind]
-                + "_"
-                + str(ind): {
+                step_name_lst[ind] + "_" + str(ind): {
                     "run": node_script,
                     "in": in_dict,
                     "out": output,
diff --git a/src/python_workflow_definition/pyiron_workflow.py b/src/python_workflow_definition/pyiron_workflow.py
index 30c2a77..5177643 100644
--- a/src/python_workflow_definition/pyiron_workflow.py
+++ b/src/python_workflow_definition/pyiron_workflow.py
@@ -318,9 +318,9 @@ def load_workflow_json(file_name: str) -> Workflow:
         PythonWorkflowDefinitionWorkflow.load_json_file(file_name=file_name)
     )
 
-    input_values: dict[int, object] = (
-        {}
-    )  # Type is actually more restrictive, must be jsonifyable object
+    input_values: dict[
+        int, object
+    ] = {}  # Type is actually more restrictive, must be jsonifyable object
     nodes: dict[int, Function] = {}
     total_counter_dict = Counter(
         [n["value"] for n in content[NODES_LABEL] if n["type"] == "function"]

From 8ac833667efa063a7357688b27fe8af8d2437406 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 27 Jul 2026 07:41:22 +0200
Subject: [PATCH 16/19] black fixes

---
 .../cwl/__init__.py                           | 31 ++++++++++---------
 .../pyiron_workflow.py                        |  4 +--
 2 files changed, 18 insertions(+), 17 deletions(-)

diff --git a/src/python_workflow_definition/cwl/__init__.py b/src/python_workflow_definition/cwl/__init__.py
index 2bf0afc..af465c5 100644
--- a/src/python_workflow_definition/cwl/__init__.py
+++ b/src/python_workflow_definition/cwl/__init__.py
@@ -20,14 +20,15 @@
 
 
 def _get_function_argument(argument: str, position: int = 3) -> dict:
+    input_dict = {
+        "prefix": "--arg_" + argument + "=",
+        "separate": False,
+        "position": position,
+    }
     return {
         argument + "_file": {
             "type": "File",
-            "inputBinding": {
-                "prefix": "--arg_" + argument + "=",
-                "separate": False,
-                "position": position,
-            },
+            "inputBinding": input_dict,
         },
     }
 
@@ -43,11 +44,12 @@ def _get_function_template(function_name: str) -> dict:
 
 
 def _get_output_name(output_name: str) -> dict:
+    output_dict = {
+        "type": "File",
+        "outputBinding": {"glob": output_name + ".pickle"},
+    }
     return {
-        output_name + "_file": {
-            "type": "File",
-            "outputBinding": {"glob": output_name + ".pickle"},
-        }
+        output_name + "_file": output_dict
     }
 
 
@@ -219,13 +221,14 @@ def _write_workflow(workflow, directory_path: str = "."):
                     + v[SOURCE_PORT_LABEL]
                     + "_file"
                 )
+        step_dict = {
+            "run": node_script,
+            "in": in_dict,
+            "out": output,
+        }
         workflow_template["steps"].update(
             {
-                step_name_lst[ind] + "_" + str(ind): {
-                    "run": node_script,
-                    "in": in_dict,
-                    "out": output,
-                }
+                step_name_lst[ind] + "_" + str(ind): step_dict
             }
         )
     export_path = Path(directory_path)
diff --git a/src/python_workflow_definition/pyiron_workflow.py b/src/python_workflow_definition/pyiron_workflow.py
index 5177643..ffdcd5b 100644
--- a/src/python_workflow_definition/pyiron_workflow.py
+++ b/src/python_workflow_definition/pyiron_workflow.py
@@ -318,9 +318,7 @@ def load_workflow_json(file_name: str) -> Workflow:
         PythonWorkflowDefinitionWorkflow.load_json_file(file_name=file_name)
     )
 
-    input_values: dict[
-        int, object
-    ] = {}  # Type is actually more restrictive, must be jsonifyable object
+    input_values: dict[int, object] = {}
     nodes: dict[int, Function] = {}
     total_counter_dict = Counter(
         [n["value"] for n in content[NODES_LABEL] if n["type"] == "function"]

From f3b0e93c6c1e93a50d794552ddbac8d451894666 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 27 Jul 2026 05:42:10 +0000
Subject: [PATCH 17/19] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/python_workflow_definition/cwl/__init__.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/src/python_workflow_definition/cwl/__init__.py b/src/python_workflow_definition/cwl/__init__.py
index af465c5..ee5961e 100644
--- a/src/python_workflow_definition/cwl/__init__.py
+++ b/src/python_workflow_definition/cwl/__init__.py
@@ -48,9 +48,7 @@ def _get_output_name(output_name: str) -> dict:
         "type": "File",
         "outputBinding": {"glob": output_name + ".pickle"},
     }
-    return {
-        output_name + "_file": output_dict
-    }
+    return {output_name + "_file": output_dict}
 
 
 def _get_function(workflow):
@@ -227,9 +225,7 @@ def _write_workflow(workflow, directory_path: str = "."):
             "out": output,
         }
         workflow_template["steps"].update(
-            {
-                step_name_lst[ind] + "_" + str(ind): step_dict
-            }
+            {step_name_lst[ind] + "_" + str(ind): step_dict}
         )
     export_path = Path(directory_path)
     export_path.mkdir(parents=True, exist_ok=True)

From eed7dee45880b49b24ed95b36f46eb73039ca0ac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 27 Jul 2026 07:44:24 +0200
Subject: [PATCH 18/19] fix

---
 src/python_workflow_definition/cwl/__init__.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/python_workflow_definition/cwl/__init__.py b/src/python_workflow_definition/cwl/__init__.py
index af465c5..5d090b2 100644
--- a/src/python_workflow_definition/cwl/__init__.py
+++ b/src/python_workflow_definition/cwl/__init__.py
@@ -20,16 +20,16 @@
 
 
 def _get_function_argument(argument: str, position: int = 3) -> dict:
-    input_dict = {
-        "prefix": "--arg_" + argument + "=",
-        "separate": False,
-        "position": position,
+    argument_dict = {
+        "type": "File",
+        "inputBinding": {
+            "prefix": "--arg_" + argument + "=",
+            "separate": False,
+            "position": position,
+        },
     }
     return {
-        argument + "_file": {
-            "type": "File",
-            "inputBinding": input_dict,
-        },
+        argument + "_file": argument_dict
     }
 
 

From 6419104ab155708e10071df9cd1612a1e05a7b05 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 27 Jul 2026 07:45:01 +0200
Subject: [PATCH 19/19] black formatting

---
 src/python_workflow_definition/cwl/__init__.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/python_workflow_definition/cwl/__init__.py b/src/python_workflow_definition/cwl/__init__.py
index afb8454..e8bf3ea 100644
--- a/src/python_workflow_definition/cwl/__init__.py
+++ b/src/python_workflow_definition/cwl/__init__.py
@@ -28,9 +28,7 @@ def _get_function_argument(argument: str, position: int = 3) -> dict:
             "position": position,
         },
     }
-    return {
-        argument + "_file": argument_dict
-    }
+    return {argument + "_file": argument_dict}
 
 
 def _get_function_template(function_name: str) -> dict: