Fix issues from hatch fmt

src/sirocco/core/graph_items.py

@@ -110,7 +110,7 @@ def from_config(cls, config: ConfigBaseData, coordinates: dict) -> Self:
 
     @property
     def path(self) -> Path:
-        # TODO yaml level?
+        # TODO: yaml level?
         return Path(expandvars(self.src))
 
 

src/sirocco/parsing/_yaml_data_models.py

@@ -3,9 +3,9 @@
 import time
 from dataclasses import dataclass
 from datetime import datetime
+from os.path import expandvars
 from pathlib import Path
 from typing import Annotated, Any, ClassVar, Literal
-from os.path import expandvars
 
 from isoduration import parse_duration
 from isoduration.types import Duration  # pydantic needs type # noqa: TCH002
@@ -280,15 +280,14 @@ class ConfigShellTaskSpecs:
 
 
 class ConfigShellTask(ConfigBaseTask, ConfigShellTaskSpecs):
-
     command: str = ""
 
     # PR(COMMENT) tmp hack to make script work, need to find better solution than PWD for tests
     @field_validator("command", "src")
     @classmethod
     def expand_var(cls, value: str) -> str:
         """Expand environemnt variables"""
-        # TODO this might be not intended if we want to use environment variables on remote HPC
+        # TODO: this might be not intended if we want to use environment variables on remote HPC
         return expandvars(value)
 
 
@@ -297,6 +296,7 @@ class ConfigIconTaskSpecs:
     plugin: ClassVar[Literal["icon"]] = "icon"
     namelists: dict[str, str] | None = None
 
+
 class ConfigIconTask(ConfigBaseTask, ConfigIconTaskSpecs):
     pass
 
@@ -331,7 +331,7 @@ def is_file_or_dir(cls, value: str) -> str:
     @classmethod
     def expand_var(cls, value: str | None) -> str | None:
         """Expand environemnt variables"""
-        # TODO this might be not intended if we want to use environment variables on remote HPC
+        # TODO: this might be not intended if we want to use environment variables on remote HPC
         return None if value is None else expandvars(value)
 
 

src/sirocco/workgraph.py

@@ -7,14 +7,15 @@
 import aiida_workgraph.engine.utils  # type: ignore[import-untyped]
 from aiida_workgraph import WorkGraph  # type: ignore[import-untyped]
 
-from sirocco import core
-from sirocco.core import graph_items
 from sirocco.core._tasks.icon_task import IconTask
 from sirocco.core._tasks.shell_task import ShellTask
 
 if TYPE_CHECKING:
     from aiida_workgraph.socket import TaskSocket  # type: ignore[import-untyped]
 
+    from sirocco import core
+    from sirocco.core import graph_items
+
 
 # This is hack to aiida-workgraph, merging this into aiida-workgraph properly would require
 # some major refactor see issue https://github.com/aiidateam/aiida-workgraph/issues/168
@@ -69,7 +70,7 @@ def __init__(self, core_workflow: core.Workflow):
 
         self._validate_workflow()
 
-        self._workgraph = WorkGraph() # core_workflow.name TODO use filename
+        self._workgraph = WorkGraph()  # core_workflow.name TODO: use filename
 
         # stores the input data available on initialization
         self._aiida_data_nodes: dict[str, aiida_workgraph.orm.Data] = {}
@@ -136,7 +137,7 @@ def get_aiida_label_from_unrolled_data(obj: graph_items.GraphItem) -> str:
     @staticmethod
     def get_aiida_label_from_unrolled_task(obj: graph_items.GraphItem) -> str:
         """ """
-        # TODO task is not anymore using cycle name because information is not there
+        # TODO: task is not anymore using cycle name because information is not there
         #      so do we check somewhere that a task is not used in multiple cycles?
         #      Otherwise the label is not unique
         # --> task name + date + parameters
@@ -164,7 +165,7 @@ def _add_aiida_task_nodes(self):
             for task in cycle.tasks:
                 self._add_aiida_task_node(task)
         # after creation we can link the wait_on tasks
-        # TODO check where this is now
+        # TODO: check where this is now
         # for cycle in self._core_workflow.cycles:
         #    for task in cycle.tasks:
         #        self._link_wait_on_to_task(task)
@@ -182,7 +183,7 @@ def _add_aiida_task_node(self, task: graph_items.Task):
             # ? Source file
             env_source_files = task.env_source_files
             env_source_files = [env_source_files] if isinstance(env_source_files, str) else env_source_files
-            prepend_text = '\n'.join([f"source {env_source_file}" for env_source_file in env_source_files])
+            prepend_text = "\n".join([f"source {env_source_file}" for env_source_file in env_source_files])
 
             # Note: We don't pass the `nodes` dictionary here, as then we would need to have the sockets available when
             # we create the task. Instead, they are being updated via the WG internals when linking inputs/outputs to
@@ -193,11 +194,7 @@ def _add_aiida_task_node(self, task: graph_items.Task):
                 name=label,
                 command=command,
                 arguments=argument_list,
-                metadata={
-                        'options': {
-                            'prepend_text': prepend_text
-                        }
-                    }
+                metadata={"options": {"prepend_text": prepend_text}},
             )
 
             self._aiida_task_nodes[label] = workgraph_task
@@ -210,7 +207,7 @@ def _add_aiida_task_node(self, task: graph_items.Task):
             raise NotImplementedError(exc)
 
     def _link_wait_on_to_task(self, task: graph_items.Task):
-        # TODO
+        # TODO: to be done
         msg = ""
         raise NotImplementedError(msg)
         label = AiidaWorkGraph.get_aiida_label_from_unrolled_task(task)
@@ -259,7 +256,7 @@ def _link_input_to_task(self, task: graph_items.Task, input_: graph_items.Data):
         if (workgraph_task_arguments := workgraph_task.inputs.get("arguments")) is None:
             msg = f"Workgraph task {workgraph_task.name!r} did not initialize arguments nodes in the workgraph before linking. This is a bug in the code, please contact devevlopers."
             raise ValueError(msg)
-        # TODO think about that the yaml file should have aiida valid labels
+        # TODO: think about that the yaml file should have aiida valid labels
 
         # Avoid appending the same argument twice
         argument_placeholder = f"{{{input_label}}}"

tests/conftest.py

@@ -1 +1 @@
-pytest_plugins = ['aiida.tools.pytest_fixtures']
+pytest_plugins = ["aiida.tools.pytest_fixtures"]

tests/files/scripts/cleanup.py

@@ -1,9 +1,10 @@
 #!/usr/bin/env python
 
+
 def main():
     # Main script execution continues here
     print("Cleaning")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

tests/files/scripts/icon.py

@@ -15,29 +15,29 @@
 
 LOG_FILE = Path("icon.log")
 
+
 def log(text: str):
     print(text)
     with LOG_FILE.open("a") as f:
         f.write(text)
 
-def main():
-    parser = argparse.ArgumentParser(description='A script mocking parts of icon in a form of a shell script.')
-    parser.add_argument('--init', nargs='?', type=str, help='The icon init file.')
-    parser.add_argument('namelist', nargs='?', default=None)
-    parser.add_argument('--restart', nargs='?', type=str, help='The icon restart file.')
-    parser.add_argument('--forcing', nargs='?', type=str, help='The icon forcing file.')
 
+def main():
+    parser = argparse.ArgumentParser(description="A script mocking parts of icon in a form of a shell script.")
+    parser.add_argument("--init", nargs="?", type=str, help="The icon init file.")
+    parser.add_argument("namelist", nargs="?", default=None)
+    parser.add_argument("--restart", nargs="?", type=str, help="The icon restart file.")
+    parser.add_argument("--forcing", nargs="?", type=str, help="The icon forcing file.")
 
     args = parser.parse_args()
 
-
-    output = Path('icon_output')
+    output = Path("icon_output")
     output.write_text("")
 
-    if args.restart and args.init:
-        msg = "Cannot use '--init' and '--restart' option at the same time."
-        raise ValueError(msg)
-    elif args.restart:
+    if args.restart:
+        if args.init:
+            msg = "Cannot use '--init' and '--restart' option at the same time."
+            raise ValueError(msg)
         if not Path(args.restart).exists():
             msg = f"The icon restart file {args.restart!r} was not found."
             raise FileNotFoundError(msg)
@@ -62,10 +62,9 @@ def main():
     # Main script execution continues here
     log("Script finished running calculations")
 
-    restart = Path('restart')
+    restart = Path("restart")
     restart.write_text("")
 
-if __name__ == '__main__':
-    main()
-
 
+if __name__ == "__main__":
+    main()

tests/test_wc_workflow.py

@@ -8,15 +8,19 @@
 from sirocco.workgraph import AiidaWorkGraph
 
 
-@pytest.mark.parametrize("config_path", [
-    "tests/files/configs/test_config_small.yml",
-    "tests/files/configs/test_config_parameters.yml",
-])
+@pytest.mark.parametrize(
+    "config_path",
+    [
+        "tests/files/configs/test_config_small.yml",
+        "tests/files/configs/test_config_parameters.yml",
+    ],
+)
 def test_run_workgraph(config_path):
     core_workflow = Workflow.from_yaml(config_path)
     aiida_workflow = AiidaWorkGraph(core_workflow)
     out = aiida_workflow.run()
-    assert out.get('execution_count', None).value == 0 # TODO should be 1 but we need to update workgraph for this
+    assert out.get("execution_count", None).value == 0  # TODO: should be 1 but we need to update workgraph for this
+
 
 # configs that are tested only tested parsing
 config_test_files = [
@@ -25,6 +29,7 @@ def test_run_workgraph(config_path):
     "tests/files/configs/test_config_parameters.yml",
 ]
 
+
 @pytest.fixture(params=config_test_files)
 def config_paths(request):
     config_path = Path(request.param)
@@ -34,17 +39,21 @@ def config_paths(request):
         "svg": (config_path.parent.parent / "svgs" / config_path.name).with_suffix(".svg"),
     }
 
+
 @pytest.fixture
 def pprinter():
     return PrettyPrinter()
 
+
 def test_parse_config_file(config_paths, pprinter):
     reference_str = config_paths["txt"].read_text()
     test_str = pprinter.format(Workflow.from_yaml(config_paths["yml"]))
     if test_str != reference_str:
         new_path = Path(config_paths["txt"]).with_suffix(".new.txt")
         new_path.write_text(test_str)
-        assert reference_str == test_str, f"Workflow graph doesn't match serialized data. New graph string dumped to {new_path}."
+        assert (
+            reference_str == test_str
+        ), f"Workflow graph doesn't match serialized data. New graph string dumped to {new_path}."
 
 
 @pytest.mark.skip(reason="don't run it each time, uncomment to regenerate serilaized data")