Add black formatting (#72)

Author: jan-janssen

.github/workflows/pipeline.yml

@@ -6,6 +6,19 @@ on:
   pull_request:
 
 jobs:
+  black:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: psf/black@stable
+      with:
+        options: "--check --diff"
+        src: ./python_workflow_definition/src/python_workflow_definition
+    - uses: psf/black@stable
+      with:
+        options: "--check --diff"
+        src: ./qe_xml_parser/src/qe_xml_parser
+
   nfdi4ing:
     runs-on: ubuntu-22.04
     steps:

python_workflow_definition/src/python_workflow_definition/jobflow.py

@@ -33,7 +33,9 @@ def _get_nodes_dict(function_dict: dict):
     return nodes_dict, nodes_mapping_dict
 
 
-def _get_edge_from_dict(target: str, key: str, value_dict: dict, nodes_mapping_dict: dict) -> dict:
+def _get_edge_from_dict(
+    target: str, key: str, value_dict: dict, nodes_mapping_dict: dict
+) -> dict:
     if len(value_dict["attributes"]) == 1:
         return {
             TARGET_LABEL: target,
@@ -50,7 +52,9 @@ def _get_edge_from_dict(target: str, key: str, value_dict: dict, nodes_mapping_d
         }
 
 
-def _get_edges_and_extend_nodes(flow_dict: dict, nodes_mapping_dict: dict, nodes_dict: dict):
+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():
@@ -222,7 +226,9 @@ def _get_input_dict(nodes_dict: dict) -> dict:
     return {k: v for k, v in nodes_dict.items() if not isfunction(v)}
 
 
-def _get_workflow(nodes_dict: dict, input_dict: dict, total_dict: dict, source_handles_dict: dict) -> list:
+def _get_workflow(
+    nodes_dict: dict, input_dict: dict, total_dict: dict, source_handles_dict: dict
+) -> list:
     def get_attr_helper(obj, source_handle):
         if source_handle is None:
             return getattr(obj, "output")

python_workflow_definition/src/python_workflow_definition/pyiron_base.py

@@ -53,7 +53,9 @@ def _group_edges(edges_lst: list) -> list:
     return total_lst
 
 
-def _get_source(nodes_dict: dict, delayed_object_dict: dict, source: str, source_handle: str):
+def _get_source(
+    nodes_dict: dict, delayed_object_dict: dict, source: str, source_handle: str
+):
     if source in delayed_object_dict.keys() and source_handle is not None:
         return (
             delayed_object_dict[source].__getattr__("output").__getattr__(source_handle)
@@ -64,7 +66,9 @@ def _get_source(nodes_dict: dict, delayed_object_dict: dict, source: str, source
         return nodes_dict[source]
 
 
-def _get_delayed_object_dict(total_lst: list, nodes_dict: dict, source_handle_dict: dict, pyiron_project: Project) -> dict:
+def _get_delayed_object_dict(
+    total_lst: list, nodes_dict: dict, source_handle_dict: dict, pyiron_project: Project
+) -> dict:
     delayed_object_dict = {}
     for item in total_lst:
         key, input_dict = item
@@ -175,7 +179,9 @@ def _get_connection_dict(delayed_object_updated_dict: dict, match_dict: dict):
     return connection_dict, lookup_dict
 
 
-def _get_edges_dict(edges_lst: list, nodes_dict: dict, connection_dict: dict, lookup_dict: dict):
+def _get_edges_dict(
+    edges_lst: list, nodes_dict: dict, connection_dict: dict, lookup_dict: dict
+):
     edges_dict_lst = []
     existing_connection_lst = []
     for ep in edges_lst:
@@ -217,7 +223,7 @@ def _get_edges_dict(edges_lst: list, nodes_dict: dict, connection_dict: dict, lo
     return edges_dict_lst
 
 
-def load_workflow_json(file_name: str, project: Optional[Project]=None):
+def load_workflow_json(file_name: str, project: Optional[Project] = None):
     if project is None:
         project = Project(".")
 
@@ -248,7 +254,9 @@ def load_workflow_json(file_name: str, project: Optional[Project]=None):
     return list(delayed_object_dict.values())
 
 
-def write_workflow_json(delayed_object: DelayedObject, file_name: str="workflow.json"):
+def write_workflow_json(
+    delayed_object: DelayedObject, file_name: str = "workflow.json"
+):
     nodes_dict, edges_lst = delayed_object.get_graph()
     nodes_dict, edges_lst = _remove_server_obj(
         nodes_dict=nodes_dict, edges_lst=edges_lst

qe_xml_parser/src/qe_xml_parser/parsers.py

@@ -12,20 +12,34 @@
 def parse_pw(xml_file):
     """Parse a Quantum Espresso XML output file."""
 
-    xml_dict = XMLSchema(str(files(schemas) / 'qes_230310.xsd')).to_dict(xml_file)
+    xml_dict = XMLSchema(str(files(schemas) / "qes_230310.xsd")).to_dict(xml_file)
 
     parsed_results = {}
 
     try:
-        cell = numpy.array(
-            [ v for v in xml_dict['output']['atomic_structure']['cell'].values()]
-        ) * CONSTANTS.bohr_to_ang
-        symbols = [el['@name'] for el in xml_dict['output']['atomic_structure']['atomic_positions']['atom']]
-        positions = numpy.array(
-            [el['$'] for el in xml_dict['output']['atomic_structure']['atomic_positions']['atom']]
-        ) * CONSTANTS.bohr_to_ang
-
-        parsed_results['ase_structure'] = Atoms(
+        cell = (
+            numpy.array(
+                [v for v in xml_dict["output"]["atomic_structure"]["cell"].values()]
+            )
+            * CONSTANTS.bohr_to_ang
+        )
+        symbols = [
+            el["@name"]
+            for el in xml_dict["output"]["atomic_structure"]["atomic_positions"]["atom"]
+        ]
+        positions = (
+            numpy.array(
+                [
+                    el["$"]
+                    for el in xml_dict["output"]["atomic_structure"][
+                        "atomic_positions"
+                    ]["atom"]
+                ]
+            )
+            * CONSTANTS.bohr_to_ang
+        )
+
+        parsed_results["ase_structure"] = Atoms(
             cell=cell,
             positions=positions,
             symbols=symbols,
@@ -35,14 +49,20 @@ def parse_pw(xml_file):
         pass
 
     try:
-        parsed_results['energy'] = xml_dict['output']['total_energy']['etot'] * CONSTANTS.ry_to_ev
+        parsed_results["energy"] = (
+            xml_dict["output"]["total_energy"]["etot"] * CONSTANTS.ry_to_ev
+        )
     except KeyError:
         pass
 
     try:
-        parsed_results['forces'] = (
-            numpy.array(xml_dict['output']['forces']['$']).reshape(xml_dict['output']['forces']['@dims'])
-            * 2 * CONSTANTS.ry_to_ev / CONSTANTS.bohr_to_ang
+        parsed_results["forces"] = (
+            numpy.array(xml_dict["output"]["forces"]["$"]).reshape(
+                xml_dict["output"]["forces"]["@dims"]
+            )
+            * 2
+            * CONSTANTS.ry_to_ev
+            / CONSTANTS.bohr_to_ang
         )
     except KeyError:
         pass