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Merged
jan-janssen merged 20 commits into from
Jul 27, 2026
Merged

Add Pre-commit-ci #196

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0962846
Configure Ruff for linting in pyproject.toml
jan-janssen Jul 27, 2026
32bf515
Add ruff pre-commit hooks for linting and formatting
jan-janssen Jul 27, 2026
6eae8e1
do not apply on notebooks for now
jan-janssen Jul 27, 2026
dd83540
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 27, 2026
c422a77
fixes
jan-janssen Jul 27, 2026
5898f5d
black fixes
jan-janssen Jul 27, 2026
8ad140d
fixes
jan-janssen Jul 27, 2026
9ae47bd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 27, 2026
6fc3070
remove commended out code
jan-janssen Jul 27, 2026
c6036ef
more fixes
jan-janssen Jul 27, 2026
e36659b
type fix
jan-janssen Jul 27, 2026
aed8d8a
more fixes
jan-janssen Jul 27, 2026
68f3ee9
more fixes
jan-janssen Jul 27, 2026
74def52
black fixes
jan-janssen Jul 27, 2026
d642f29
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 27, 2026
8ac8336
black fixes
jan-janssen Jul 27, 2026
f3b0e93
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 27, 2026
eed7dee
fix
jan-janssen Jul 27, 2026
fe2a204
Merge commit 'f3b0e93c6c1e93a50d794552ddbac8d451894666' into precommit
jan-janssen Jul 27, 2026
6419104
black formatting
jan-janssen Jul 27, 2026
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10 changes: 10 additions & 0 deletions .pre-commit-config.yaml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -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
33 changes: 33 additions & 0 deletions pyproject.toml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -42,6 +42,39 @@ plot = [
"ipython>=7.33.0,<=9.8.0",
]

[tool.ruff]
exclude = ["documentation", "example_workflows", "tests", "binder", "_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 = [
# ignore line-length violations
"E501",
# Too many statements
"PLR0915",
# Too many branches
"PLR0912",
]

[tool.hatch.build]
include = [
"src/python_workflow_definition"
Expand Down
1 change: 0 additions & 1 deletion src/python_workflow_definition/aiida.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -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

Expand Down
102 changes: 47 additions & 55 deletions src/python_workflow_definition/cwl/__init__.py
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -20,17 +20,15 @@


def _get_function_argument(argument: str, position: int = 3) -> dict:
return {
argument
+ "_file": {
"type": "File",
"inputBinding": {
"prefix": "--arg_" + argument + "=",
"separate": False,
"position": position,
},
argument_dict = {
"type": "File",
"inputBinding": {
"prefix": "--arg_" + argument + "=",
"separate": False,
"position": position,
},
}
return {argument + "_file": argument_dict}


def _get_function_template(function_name: str) -> dict:
Expand All@@ -44,35 +42,32 @@ 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_dict = {
"type": "File",
"outputBinding": {"glob": output_name + ".pickle"},
}
return {output_name + "_file": output_dict}


def _get_function(workflow):
function_nodes_dict = {
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(
[
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(
set(
[
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] = {
"targetPorts": target_ports,
Expand All@@ -86,7 +81,7 @@ 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",
Expand DownExpand Up@@ -142,10 +137,7 @@ 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,
)
Expand All@@ -170,7 +162,7 @@ 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": {
Expand DownExpand Up@@ -209,29 +201,29 @@ 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"
)
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)
export_path.mkdir(parents=True, exist_ok=True)
Expand All@@ -240,7 +232,7 @@ 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)
Expand Down
8 changes: 2 additions & 6 deletions src/python_workflow_definition/executorlib.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
)

Expand All@@ -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()
Expand Down
58 changes: 26 additions & 32 deletions src/python_workflow_definition/jobflow.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -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):
Expand DownExpand Up@@ -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
Expand All@@ -72,20 +72,18 @@ 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,
)
)
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()
]
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
Expand DownExpand Up@@ -122,20 +120,18 @@ 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,
}
)
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
]
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
Expand DownExpand Up@@ -172,7 +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,
Expand All@@ -186,7 +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,
Expand All@@ -196,10 +192,8 @@ 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):
Expand All@@ -208,7 +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
Expand All@@ -220,7 +214,7 @@ 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)
Expand All@@ -237,15 +231,15 @@ 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 kin total_dict.keys():
for k, subdict in total_dict.items():
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],
Expand All@@ -261,7 +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())
Expand Down
Loading
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Add Pre-commit-ci#196

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 Merged

jan-janssen
merged 20 commits into

from

Jul 27, 2026
 Merged


Add Pre-commit-ci
#196
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0962846

Configure Ruff for linting in pyproject.toml


jan-janssen Jul 27, 2026
32bf515

Add ruff pre-commit hooks for linting and formatting


jan-janssen Jul 27, 2026
6eae8e1

do not apply on notebooks for now


jan-janssen Jul 27, 2026
dd83540

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
c422a77

fixes


jan-janssen Jul 27, 2026
5898f5d

black fixes


jan-janssen Jul 27, 2026
8ad140d

fixes


jan-janssen Jul 27, 2026
9ae47bd

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
6fc3070

remove commended out code


jan-janssen Jul 27, 2026
c6036ef

more fixes


jan-janssen Jul 27, 2026
e36659b

type fix


jan-janssen Jul 27, 2026
aed8d8a

more fixes


jan-janssen Jul 27, 2026
68f3ee9

more fixes


jan-janssen Jul 27, 2026
74def52

black fixes


jan-janssen Jul 27, 2026
d642f29

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
8ac8336

black fixes


jan-janssen Jul 27, 2026
f3b0e93

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
eed7dee

fix


jan-janssen Jul 27, 2026
fe2a204

Merge commit 'f3b0e93c6c1e93a50d794552ddbac8d451894666' into precommit


jan-janssen Jul 27, 2026
6419104

black formatting


jan-janssen Jul 27, 2026

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10 changes: 10 additions & 0 deletions
.pre-commit-config.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -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

33 changes: 33 additions & 0 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -42,6 +42,39 @@ plot = [
 "ipython>=7.33.0,<=9.8.0",
]

[tool.ruff]
exclude = ["documentation", "example_workflows", "tests", "binder", "_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 = [
 # ignore line-length violations
 "E501",
 # Too many statements
 "PLR0915",
 # Too many branches
 "PLR0912",
]

[tool.hatch.build]
include = [
 "src/python_workflow_definition"
Expand Down

1 change: 0 additions & 1 deletion
src/python_workflow_definition/aiida.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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

Expand Down

102 changes: 47 additions & 55 deletions
src/python_workflow_definition/cwl/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -20,17 +20,15 @@


def _get_function_argument(argument: str, position: int = 3) -> dict:
 return {
 argument
 + "_file": {
 "type": "File",
 "inputBinding": {
 "prefix": "--arg_" + argument + "=",
 "separate": False,
 "position": position,
 },
 argument_dict = {
 "type": "File",
 "inputBinding": {
 "prefix": "--arg_" + argument + "=",
 "separate": False,
 "position": position,
 },
 }
 return {argument + "_file": argument_dict}


def _get_function_template(function_name: str) -> dict:
Expand All@@ -44,35 +42,32 @@ 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_dict = {
"type": "File",
"outputBinding": {"glob": output_name + ".pickle"},
 }
 return {output_name + "_file": output_dict}


def _get_function(workflow):
 function_nodes_dict = {
 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(
 [
 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(
 set(
 [
 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] = {
 "targetPorts": target_ports,
Expand All@@ -86,7 +81,7 @@ 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",
Expand DownExpand Up@@ -142,10 +137,7 @@ 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,
 )
Expand All@@ -170,7 +162,7 @@ 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": {
Expand DownExpand Up@@ -209,29 +201,29 @@ 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"
 )
 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)
 export_path.mkdir(parents=True, exist_ok=True)
Expand All@@ -240,7 +232,7 @@ 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)
Expand Down

8 changes: 2 additions & 6 deletions
src/python_workflow_definition/executorlib.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
)

Expand All@@ -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()
Expand Down

58 changes: 26 additions & 32 deletions
src/python_workflow_definition/jobflow.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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):
Expand DownExpand Up@@ -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
Expand All@@ -72,20 +72,18 @@ 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,
 )
 )
 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()
 ]
 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
Expand DownExpand Up@@ -122,20 +120,18 @@ 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,
 }
 )
 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
 ]
 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
Expand DownExpand Up@@ -172,7 +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,
Expand All@@ -186,7 +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,
Expand All@@ -196,10 +192,8 @@ 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):
Expand All@@ -208,7 +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
Expand All@@ -220,7 +214,7 @@ 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)
Expand All@@ -237,15 +231,15 @@ 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 kin total_dict.keys():
 for k, subdict in total_dict.items():
 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],
Expand All@@ -261,7 +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())
Expand Down
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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jan-janssen
merged 20 commits into

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Jul 27, 2026
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Add Pre-commit-ci
#196
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0962846

Configure Ruff for linting in pyproject.toml


jan-janssen Jul 27, 2026
32bf515

Add ruff pre-commit hooks for linting and formatting


jan-janssen Jul 27, 2026
6eae8e1

do not apply on notebooks for now


jan-janssen Jul 27, 2026
dd83540

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
c422a77

fixes


jan-janssen Jul 27, 2026
5898f5d

black fixes


jan-janssen Jul 27, 2026
8ad140d

fixes


jan-janssen Jul 27, 2026
9ae47bd

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
6fc3070

remove commended out code


jan-janssen Jul 27, 2026
c6036ef

more fixes


jan-janssen Jul 27, 2026
e36659b

type fix


jan-janssen Jul 27, 2026
aed8d8a

more fixes


jan-janssen Jul 27, 2026
68f3ee9

more fixes


jan-janssen Jul 27, 2026
74def52

black fixes


jan-janssen Jul 27, 2026
d642f29

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
8ac8336

black fixes


jan-janssen Jul 27, 2026
f3b0e93

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
eed7dee

fix


jan-janssen Jul 27, 2026
fe2a204

Merge commit 'f3b0e93c6c1e93a50d794552ddbac8d451894666' into precommit


jan-janssen Jul 27, 2026
6419104

black formatting


jan-janssen Jul 27, 2026

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10 changes: 10 additions & 0 deletions
.pre-commit-config.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -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

33 changes: 33 additions & 0 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -42,6 +42,39 @@ plot = [
 "ipython>=7.33.0,<=9.8.0",
]

[tool.ruff]
exclude = ["documentation", "example_workflows", "tests", "binder", "_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 = [
 # ignore line-length violations
 "E501",
 # Too many statements
 "PLR0915",
 # Too many branches
 "PLR0912",
]

[tool.hatch.build]
include = [
 "src/python_workflow_definition"
Expand Down

1 change: 0 additions & 1 deletion
src/python_workflow_definition/aiida.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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

Expand Down

102 changes: 47 additions & 55 deletions
src/python_workflow_definition/cwl/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -20,17 +20,15 @@


def _get_function_argument(argument: str, position: int = 3) -> dict:
 return {
 argument
 + "_file": {
 "type": "File",
 "inputBinding": {
 "prefix": "--arg_" + argument + "=",
 "separate": False,
 "position": position,
 },
 argument_dict = {
 "type": "File",
 "inputBinding": {
 "prefix": "--arg_" + argument + "=",
 "separate": False,
 "position": position,
 },
 }
 return {argument + "_file": argument_dict}


def _get_function_template(function_name: str) -> dict:
Expand All@@ -44,35 +42,32 @@ 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_dict = {
"type": "File",
"outputBinding": {"glob": output_name + ".pickle"},
 }
 return {output_name + "_file": output_dict}


def _get_function(workflow):
 function_nodes_dict = {
 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(
 [
 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(
 set(
 [
 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] = {
 "targetPorts": target_ports,
Expand All@@ -86,7 +81,7 @@ 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",
Expand DownExpand Up@@ -142,10 +137,7 @@ 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,
 )
Expand All@@ -170,7 +162,7 @@ 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": {
Expand DownExpand Up@@ -209,29 +201,29 @@ 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"
 )
 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)
 export_path.mkdir(parents=True, exist_ok=True)
Expand All@@ -240,7 +232,7 @@ 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)
Expand Down

8 changes: 2 additions & 6 deletions
src/python_workflow_definition/executorlib.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
)

Expand All@@ -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()
Expand Down

58 changes: 26 additions & 32 deletions
src/python_workflow_definition/jobflow.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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):
Expand DownExpand Up@@ -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
Expand All@@ -72,20 +72,18 @@ 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,
 )
 )
 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()
 ]
 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
Expand DownExpand Up@@ -122,20 +120,18 @@ 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,
 }
 )
 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
 ]
 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
Expand DownExpand Up@@ -172,7 +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,
Expand All@@ -186,7 +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,
Expand All@@ -196,10 +192,8 @@ 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):
Expand All@@ -208,7 +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
Expand All@@ -220,7 +214,7 @@ 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)
Expand All@@ -237,15 +231,15 @@ 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 kin total_dict.keys():
 for k, subdict in total_dict.items():
 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],
Expand All@@ -261,7 +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())
Expand Down
Loading
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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jan-janssen
merged 20 commits into

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Jul 27, 2026
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#196
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0962846

Configure Ruff for linting in pyproject.toml


jan-janssen Jul 27, 2026
32bf515

Add ruff pre-commit hooks for linting and formatting


jan-janssen Jul 27, 2026
6eae8e1

do not apply on notebooks for now


jan-janssen Jul 27, 2026
dd83540

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
c422a77

fixes


jan-janssen Jul 27, 2026
5898f5d

black fixes


jan-janssen Jul 27, 2026
8ad140d

fixes


jan-janssen Jul 27, 2026
9ae47bd

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
6fc3070

remove commended out code


jan-janssen Jul 27, 2026
c6036ef

more fixes


jan-janssen Jul 27, 2026
e36659b

type fix


jan-janssen Jul 27, 2026
aed8d8a

more fixes


jan-janssen Jul 27, 2026
68f3ee9

more fixes


jan-janssen Jul 27, 2026
74def52

black fixes


jan-janssen Jul 27, 2026
d642f29

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
8ac8336

black fixes


jan-janssen Jul 27, 2026
f3b0e93

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
eed7dee

fix


jan-janssen Jul 27, 2026
fe2a204

Merge commit 'f3b0e93c6c1e93a50d794552ddbac8d451894666' into precommit


jan-janssen Jul 27, 2026
6419104

black formatting


jan-janssen Jul 27, 2026

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10 changes: 10 additions & 0 deletions
.pre-commit-config.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -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

33 changes: 33 additions & 0 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -42,6 +42,39 @@ plot = [
 "ipython>=7.33.0,<=9.8.0",
]

[tool.ruff]
exclude = ["documentation", "example_workflows", "tests", "binder", "_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 = [
 # ignore line-length violations
 "E501",
 # Too many statements
 "PLR0915",
 # Too many branches
 "PLR0912",
]

[tool.hatch.build]
include = [
 "src/python_workflow_definition"
Expand Down

1 change: 0 additions & 1 deletion
src/python_workflow_definition/aiida.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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

Expand Down

102 changes: 47 additions & 55 deletions
src/python_workflow_definition/cwl/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -20,17 +20,15 @@


def _get_function_argument(argument: str, position: int = 3) -> dict:
 return {
 argument
 + "_file": {
 "type": "File",
 "inputBinding": {
 "prefix": "--arg_" + argument + "=",
 "separate": False,
 "position": position,
 },
 argument_dict = {
 "type": "File",
 "inputBinding": {
 "prefix": "--arg_" + argument + "=",
 "separate": False,
 "position": position,
 },
 }
 return {argument + "_file": argument_dict}


def _get_function_template(function_name: str) -> dict:
Expand All@@ -44,35 +42,32 @@ 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_dict = {
"type": "File",
"outputBinding": {"glob": output_name + ".pickle"},
 }
 return {output_name + "_file": output_dict}


def _get_function(workflow):
 function_nodes_dict = {
 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(
 [
 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(
 set(
 [
 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] = {
 "targetPorts": target_ports,
Expand All@@ -86,7 +81,7 @@ 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",
Expand DownExpand Up@@ -142,10 +137,7 @@ 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,
 )
Expand All@@ -170,7 +162,7 @@ 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": {
Expand DownExpand Up@@ -209,29 +201,29 @@ 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"
 )
 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)
 export_path.mkdir(parents=True, exist_ok=True)
Expand All@@ -240,7 +232,7 @@ 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)
Expand Down

8 changes: 2 additions & 6 deletions
src/python_workflow_definition/executorlib.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
)

Expand All@@ -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()
Expand Down

58 changes: 26 additions & 32 deletions
src/python_workflow_definition/jobflow.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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):
Expand DownExpand Up@@ -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
Expand All@@ -72,20 +72,18 @@ 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,
 )
 )
 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()
 ]
 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
Expand DownExpand Up@@ -122,20 +120,18 @@ 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,
 }
 )
 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
 ]
 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
Expand DownExpand Up@@ -172,7 +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,
Expand All@@ -186,7 +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,
Expand All@@ -196,10 +192,8 @@ 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):
Expand All@@ -208,7 +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
Expand All@@ -220,7 +214,7 @@ 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)
Expand All@@ -237,15 +231,15 @@ 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 kin total_dict.keys():
 for k, subdict in total_dict.items():
 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],
Expand All@@ -261,7 +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())
Expand Down
Loading
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
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to your account

 Merged

jan-janssen
merged 20 commits into

from

Jul 27, 2026
 Merged


Add Pre-commit-ci
#196
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0962846

Configure Ruff for linting in pyproject.toml


jan-janssen Jul 27, 2026
32bf515

Add ruff pre-commit hooks for linting and formatting


jan-janssen Jul 27, 2026
6eae8e1

do not apply on notebooks for now


jan-janssen Jul 27, 2026
dd83540

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
c422a77

fixes


jan-janssen Jul 27, 2026
5898f5d

black fixes


jan-janssen Jul 27, 2026
8ad140d

fixes


jan-janssen Jul 27, 2026
9ae47bd

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
6fc3070

remove commended out code


jan-janssen Jul 27, 2026
c6036ef

more fixes


jan-janssen Jul 27, 2026
e36659b

type fix


jan-janssen Jul 27, 2026
aed8d8a

more fixes


jan-janssen Jul 27, 2026
68f3ee9

more fixes


jan-janssen Jul 27, 2026
74def52

black fixes


jan-janssen Jul 27, 2026
d642f29

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
8ac8336

black fixes


jan-janssen Jul 27, 2026
f3b0e93

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
eed7dee

fix


jan-janssen Jul 27, 2026
fe2a204

Merge commit 'f3b0e93c6c1e93a50d794552ddbac8d451894666' into precommit


jan-janssen Jul 27, 2026
6419104

black formatting


jan-janssen Jul 27, 2026

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Conversations

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10 changes: 10 additions & 0 deletions
.pre-commit-config.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -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

33 changes: 33 additions & 0 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -42,6 +42,39 @@ plot = [
 "ipython>=7.33.0,<=9.8.0",
]

[tool.ruff]
exclude = ["documentation", "example_workflows", "tests", "binder", "_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 = [
 # ignore line-length violations
 "E501",
 # Too many statements
 "PLR0915",
 # Too many branches
 "PLR0912",
]

[tool.hatch.build]
include = [
 "src/python_workflow_definition"
Expand Down

1 change: 0 additions & 1 deletion
src/python_workflow_definition/aiida.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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

Expand Down

102 changes: 47 additions & 55 deletions
src/python_workflow_definition/cwl/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -20,17 +20,15 @@


def _get_function_argument(argument: str, position: int = 3) -> dict:
 return {
 argument
 + "_file": {
 "type": "File",
 "inputBinding": {
 "prefix": "--arg_" + argument + "=",
 "separate": False,
 "position": position,
 },
 argument_dict = {
 "type": "File",
 "inputBinding": {
 "prefix": "--arg_" + argument + "=",
 "separate": False,
 "position": position,
 },
 }
 return {argument + "_file": argument_dict}


def _get_function_template(function_name: str) -> dict:
Expand All@@ -44,35 +42,32 @@ 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_dict = {
"type": "File",
"outputBinding": {"glob": output_name + ".pickle"},
 }
 return {output_name + "_file": output_dict}


def _get_function(workflow):
 function_nodes_dict = {
 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(
 [
 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(
 set(
 [
 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] = {
 "targetPorts": target_ports,
Expand All@@ -86,7 +81,7 @@ 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",
Expand DownExpand Up@@ -142,10 +137,7 @@ 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,
 )
Expand All@@ -170,7 +162,7 @@ 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": {
Expand DownExpand Up@@ -209,29 +201,29 @@ 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"
 )
 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)
 export_path.mkdir(parents=True, exist_ok=True)
Expand All@@ -240,7 +232,7 @@ 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)
Expand Down

8 changes: 2 additions & 6 deletions
src/python_workflow_definition/executorlib.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
)

Expand All@@ -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()
Expand Down

58 changes: 26 additions & 32 deletions
src/python_workflow_definition/jobflow.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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):
Expand DownExpand Up@@ -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
Expand All@@ -72,20 +72,18 @@ 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,
 )
 )
 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()
 ]
 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
Expand DownExpand Up@@ -122,20 +120,18 @@ 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,
 }
 )
 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
 ]
 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
Expand DownExpand Up@@ -172,7 +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,
Expand All@@ -186,7 +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,
Expand All@@ -196,10 +192,8 @@ 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):
Expand All@@ -208,7 +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
Expand All@@ -220,7 +214,7 @@ 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)
Expand All@@ -237,15 +231,15 @@ 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 kin total_dict.keys():
 for k, subdict in total_dict.items():
 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],
Expand All@@ -261,7 +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())
Expand Down
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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jan-janssen
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Jul 27, 2026
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Add Pre-commit-ci
#196
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0962846

Configure Ruff for linting in pyproject.toml


jan-janssen Jul 27, 2026
32bf515

Add ruff pre-commit hooks for linting and formatting


jan-janssen Jul 27, 2026
6eae8e1

do not apply on notebooks for now


jan-janssen Jul 27, 2026
dd83540

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
c422a77

fixes


jan-janssen Jul 27, 2026
5898f5d

black fixes


jan-janssen Jul 27, 2026
8ad140d

fixes


jan-janssen Jul 27, 2026
9ae47bd

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
6fc3070

remove commended out code


jan-janssen Jul 27, 2026
c6036ef

more fixes


jan-janssen Jul 27, 2026
e36659b

type fix


jan-janssen Jul 27, 2026
aed8d8a

more fixes


jan-janssen Jul 27, 2026
68f3ee9

more fixes


jan-janssen Jul 27, 2026
74def52

black fixes


jan-janssen Jul 27, 2026
d642f29

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
8ac8336

black fixes


jan-janssen Jul 27, 2026
f3b0e93

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
eed7dee

fix


jan-janssen Jul 27, 2026
fe2a204

Merge commit 'f3b0e93c6c1e93a50d794552ddbac8d451894666' into precommit


jan-janssen Jul 27, 2026
6419104

black formatting


jan-janssen Jul 27, 2026

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10 changes: 10 additions & 0 deletions
.pre-commit-config.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -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

33 changes: 33 additions & 0 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -42,6 +42,39 @@ plot = [
 "ipython>=7.33.0,<=9.8.0",
]

[tool.ruff]
exclude = ["documentation", "example_workflows", "tests", "binder", "_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 = [
 # ignore line-length violations
 "E501",
 # Too many statements
 "PLR0915",
 # Too many branches
 "PLR0912",
]

[tool.hatch.build]
include = [
 "src/python_workflow_definition"
Expand Down

1 change: 0 additions & 1 deletion
src/python_workflow_definition/aiida.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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

Expand Down

102 changes: 47 additions & 55 deletions
src/python_workflow_definition/cwl/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -20,17 +20,15 @@


def _get_function_argument(argument: str, position: int = 3) -> dict:
 return {
 argument
 + "_file": {
 "type": "File",
 "inputBinding": {
 "prefix": "--arg_" + argument + "=",
 "separate": False,
 "position": position,
 },
 argument_dict = {
 "type": "File",
 "inputBinding": {
 "prefix": "--arg_" + argument + "=",
 "separate": False,
 "position": position,
 },
 }
 return {argument + "_file": argument_dict}


def _get_function_template(function_name: str) -> dict:
Expand All@@ -44,35 +42,32 @@ 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_dict = {
"type": "File",
"outputBinding": {"glob": output_name + ".pickle"},
 }
 return {output_name + "_file": output_dict}


def _get_function(workflow):
 function_nodes_dict = {
 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(
 [
 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(
 set(
 [
 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] = {
 "targetPorts": target_ports,
Expand All@@ -86,7 +81,7 @@ 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",
Expand DownExpand Up@@ -142,10 +137,7 @@ 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,
 )
Expand All@@ -170,7 +162,7 @@ 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": {
Expand DownExpand Up@@ -209,29 +201,29 @@ 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"
 )
 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)
 export_path.mkdir(parents=True, exist_ok=True)
Expand All@@ -240,7 +232,7 @@ 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)
Expand Down

8 changes: 2 additions & 6 deletions
src/python_workflow_definition/executorlib.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
)

Expand All@@ -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()
Expand Down

58 changes: 26 additions & 32 deletions
src/python_workflow_definition/jobflow.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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):
Expand DownExpand Up@@ -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
Expand All@@ -72,20 +72,18 @@ 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,
 )
 )
 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()
 ]
 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
Expand DownExpand Up@@ -122,20 +120,18 @@ 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,
 }
 )
 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
 ]
 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
Expand DownExpand Up@@ -172,7 +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,
Expand All@@ -186,7 +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,
Expand All@@ -196,10 +192,8 @@ 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):
Expand All@@ -208,7 +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
Expand All@@ -220,7 +214,7 @@ 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)
Expand All@@ -237,15 +231,15 @@ 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 kin total_dict.keys():
 for k, subdict in total_dict.items():
 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],
Expand All@@ -261,7 +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())
Expand Down
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Jul 27, 2026
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0962846

Configure Ruff for linting in pyproject.toml


jan-janssen Jul 27, 2026
32bf515

Add ruff pre-commit hooks for linting and formatting


jan-janssen Jul 27, 2026
6eae8e1

do not apply on notebooks for now


jan-janssen Jul 27, 2026
dd83540

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
c422a77

fixes


jan-janssen Jul 27, 2026
5898f5d

black fixes


jan-janssen Jul 27, 2026
8ad140d

fixes


jan-janssen Jul 27, 2026
9ae47bd

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
6fc3070

remove commended out code


jan-janssen Jul 27, 2026
c6036ef

more fixes


jan-janssen Jul 27, 2026
e36659b

type fix


jan-janssen Jul 27, 2026
aed8d8a

more fixes


jan-janssen Jul 27, 2026
68f3ee9

more fixes


jan-janssen Jul 27, 2026
74def52

black fixes


jan-janssen Jul 27, 2026
d642f29

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
8ac8336

black fixes


jan-janssen Jul 27, 2026
f3b0e93

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
eed7dee

fix


jan-janssen Jul 27, 2026
fe2a204

Merge commit 'f3b0e93c6c1e93a50d794552ddbac8d451894666' into precommit


jan-janssen Jul 27, 2026
6419104

black formatting


jan-janssen Jul 27, 2026

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10 changes: 10 additions & 0 deletions
.pre-commit-config.yaml

View file


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Original file line numberDiff line numberDiff line change
@@ -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

33 changes: 33 additions & 0 deletions
pyproject.toml

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -42,6 +42,39 @@ plot = [
 "ipython>=7.33.0,<=9.8.0",
]

[tool.ruff]
exclude = ["documentation", "example_workflows", "tests", "binder", "_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 = [
 # ignore line-length violations
 "E501",
 # Too many statements
 "PLR0915",
 # Too many branches
 "PLR0912",
]

[tool.hatch.build]
include = [
 "src/python_workflow_definition"
Expand Down

1 change: 0 additions & 1 deletion
src/python_workflow_definition/aiida.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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

Expand Down

102 changes: 47 additions & 55 deletions
src/python_workflow_definition/cwl/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -20,17 +20,15 @@


def _get_function_argument(argument: str, position: int = 3) -> dict:
 return {
 argument
 + "_file": {
 "type": "File",
 "inputBinding": {
 "prefix": "--arg_" + argument + "=",
 "separate": False,
 "position": position,
 },
 argument_dict = {
 "type": "File",
 "inputBinding": {
 "prefix": "--arg_" + argument + "=",
 "separate": False,
 "position": position,
 },
 }
 return {argument + "_file": argument_dict}


def _get_function_template(function_name: str) -> dict:
Expand All@@ -44,35 +42,32 @@ 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_dict = {
"type": "File",
"outputBinding": {"glob": output_name + ".pickle"},
 }
 return {output_name + "_file": output_dict}


def _get_function(workflow):
 function_nodes_dict = {
 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(
 [
 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(
 set(
 [
 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] = {
 "targetPorts": target_ports,
Expand All@@ -86,7 +81,7 @@ 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",
Expand DownExpand Up@@ -142,10 +137,7 @@ 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,
 )
Expand All@@ -170,7 +162,7 @@ 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": {
Expand DownExpand Up@@ -209,29 +201,29 @@ 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"
 )
 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)
 export_path.mkdir(parents=True, exist_ok=True)
Expand All@@ -240,7 +232,7 @@ 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)
Expand Down

8 changes: 2 additions & 6 deletions
src/python_workflow_definition/executorlib.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
)

Expand All@@ -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()
Expand Down

58 changes: 26 additions & 32 deletions
src/python_workflow_definition/jobflow.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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):
Expand DownExpand Up@@ -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
Expand All@@ -72,20 +72,18 @@ 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,
 )
 )
 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()
 ]
 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
Expand DownExpand Up@@ -122,20 +120,18 @@ 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,
 }
 )
 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
 ]
 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
Expand DownExpand Up@@ -172,7 +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,
Expand All@@ -186,7 +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,
Expand All@@ -196,10 +192,8 @@ 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):
Expand All@@ -208,7 +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
Expand All@@ -220,7 +214,7 @@ 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)
Expand All@@ -237,15 +231,15 @@ 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 kin total_dict.keys():
 for k, subdict in total_dict.items():
 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],
Expand All@@ -261,7 +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())
Expand Down
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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jan-janssen
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Jul 27, 2026
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Add Pre-commit-ci
#196
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0962846

Configure Ruff for linting in pyproject.toml


jan-janssen Jul 27, 2026
32bf515

Add ruff pre-commit hooks for linting and formatting


jan-janssen Jul 27, 2026
6eae8e1

do not apply on notebooks for now


jan-janssen Jul 27, 2026
dd83540

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
c422a77

fixes


jan-janssen Jul 27, 2026
5898f5d

black fixes


jan-janssen Jul 27, 2026
8ad140d

fixes


jan-janssen Jul 27, 2026
9ae47bd

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
6fc3070

remove commended out code


jan-janssen Jul 27, 2026
c6036ef

more fixes


jan-janssen Jul 27, 2026
e36659b

type fix


jan-janssen Jul 27, 2026
aed8d8a

more fixes


jan-janssen Jul 27, 2026
68f3ee9

more fixes


jan-janssen Jul 27, 2026
74def52

black fixes


jan-janssen Jul 27, 2026
d642f29

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
8ac8336

black fixes


jan-janssen Jul 27, 2026
f3b0e93

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Jul 27, 2026
eed7dee

fix


jan-janssen Jul 27, 2026
fe2a204

Merge commit 'f3b0e93c6c1e93a50d794552ddbac8d451894666' into precommit


jan-janssen Jul 27, 2026
6419104

black formatting


jan-janssen Jul 27, 2026

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10 changes: 10 additions & 0 deletions
.pre-commit-config.yaml

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Original file line numberDiff line numberDiff line change
@@ -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

33 changes: 33 additions & 0 deletions
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -42,6 +42,39 @@ plot = [
 "ipython>=7.33.0,<=9.8.0",
]

[tool.ruff]
exclude = ["documentation", "example_workflows", "tests", "binder", "_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 = [
 # ignore line-length violations
 "E501",
 # Too many statements
 "PLR0915",
 # Too many branches
 "PLR0912",
]

[tool.hatch.build]
include = [
 "src/python_workflow_definition"
Expand Down

1 change: 0 additions & 1 deletion
src/python_workflow_definition/aiida.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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

Expand Down

102 changes: 47 additions & 55 deletions
src/python_workflow_definition/cwl/__init__.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -20,17 +20,15 @@


def _get_function_argument(argument: str, position: int = 3) -> dict:
 return {
 argument
 + "_file": {
 "type": "File",
 "inputBinding": {
 "prefix": "--arg_" + argument + "=",
 "separate": False,
 "position": position,
 },
 argument_dict = {
 "type": "File",
 "inputBinding": {
 "prefix": "--arg_" + argument + "=",
 "separate": False,
 "position": position,
 },
 }
 return {argument + "_file": argument_dict}


def _get_function_template(function_name: str) -> dict:
Expand All@@ -44,35 +42,32 @@ 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_dict = {
"type": "File",
"outputBinding": {"glob": output_name + ".pickle"},
 }
 return {output_name + "_file": output_dict}


def _get_function(workflow):
 function_nodes_dict = {
 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(
 [
 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(
 set(
 [
 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] = {
 "targetPorts": target_ports,
Expand All@@ -86,7 +81,7 @@ 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",
Expand DownExpand Up@@ -142,10 +137,7 @@ 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,
 )
Expand All@@ -170,7 +162,7 @@ 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": {
Expand DownExpand Up@@ -209,29 +201,29 @@ 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"
 )
 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)
 export_path.mkdir(parents=True, exist_ok=True)
Expand All@@ -240,7 +232,7 @@ 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)
Expand Down

8 changes: 2 additions & 6 deletions
src/python_workflow_definition/executorlib.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
)

Expand All@@ -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()
Expand Down

58 changes: 26 additions & 32 deletions
src/python_workflow_definition/jobflow.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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):
Expand DownExpand Up@@ -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
Expand All@@ -72,20 +72,18 @@ 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,
 )
 )
 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()
 ]
 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
Expand DownExpand Up@@ -122,20 +120,18 @@ 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,
 }
 )
 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
 ]
 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
Expand DownExpand Up@@ -172,7 +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,
Expand All@@ -186,7 +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,
Expand All@@ -196,10 +192,8 @@ 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):
Expand All@@ -208,7 +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
Expand All@@ -220,7 +214,7 @@ 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)
Expand All@@ -237,15 +231,15 @@ 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 kin total_dict.keys():
 for k, subdict in total_dict.items():
 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],
Expand All@@ -261,7 +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())
Expand Down
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