fix: pre-commit errors

examples/data/JSON/Readme.md

@@ -4,13 +4,13 @@
 ### peacetreaties
 This file was created by [Lena Jaskov](https://github.com/yaslena). It is is based on data that is available online in a database focused on European peace treaties from 1450 to 1789 (https://www.ieg-friedensvertraege.de/vertraege).
 
-The database was created as part of a project that was funded by the DFG (German Research Foundation) 
+The database was created as part of a project that was funded by the DFG (German Research Foundation)
 and contains a selection of some 1800 treaties. One extra treaty between Tsarist Russia and the Qing Empire (1689) was manually added by Lena Jaskov.
 
-The data sample here only shows a selection of that data, i.e. filterd on treaties that involve Russia. 
+The data sample here only shows a selection of that data, i.e. filterd on treaties that involve Russia.
 There are only edges between treaties and countries. If a country was involved in a treaty, there will be an edge between that country and the respective treaty.
 
-The data was first scraped into a table in a first step. The original scraped table (CSV) can be found in this [repository](https://github.com/DHARPA-Project/kiara_plugin.network_analysis/blob/develop/examples/data/treaties). The scraping code can be found [here](https://github.com/yaslena/WebScraping). 
+The data was first scraped into a table in a first step. The original scraped table (CSV) can be found in this [repository](https://github.com/DHARPA-Project/kiara_plugin.network_analysis/blob/develop/examples/data/treaties). The scraping code can be found [here](https://github.com/yaslena/WebScraping).
 In a second step the data from the scraping process was restructured to fit the requirements of creating a dynamic bipartite graph with networkX.
 Code for restructuring the table data and for generating a bipartite graph with python networkX can be found [here](https://github.com/yaslena/NetworkAnalysis).
 The restructured data was converted into JSON with networkX for visualization in JavaScript on [Observable](https://observablehq.com/@yaslena/dynamic-network-graph).

examples/data/gexf/Readme.md

@@ -5,26 +5,26 @@ Most datasets come from here https://github.com/gephi/gephi/wiki/Datasets if not
 ### lesmis
 
 #### gexf file version: 1.3
-The lesmis gephi file represents the same data as the one in gml format found in 
+The lesmis gephi file represents the same data as the one in gml format found in
 Marc Newmans GML dataset collection: http://www-personal.umich.edu/~mejn/netdata/
 It also has some additional graph data, like node positions, node colors (by modularity group), node size etc because the gexf format can also store that kind of data.
 
 This gefx file is included as sample data with the installation of the Gephi software.
 It seems to be a converted version of Marc Newmans GML file. The reference is the same as for the GML file:
 
-"Les Miserables: coappearance weighted network of characters in the novel Les Miserables. 
+"Les Miserables: coappearance weighted network of characters in the novel Les Miserables.
 D. E. Knuth, The Stanford GraphBase: A Platform for Combinatorial Computing, Addison-Wesley, Reading, MA (1993)."
 
-As the title reveals this data represents a coappearance network. This makes it an **undirected** network. 
-It is furthermore a **weighted** network, edge weights are named "value" in the gml file. 
+As the title reveals this data represents a coappearance network. This makes it an **undirected** network.
+It is furthermore a **weighted** network, edge weights are named "value" in the gml file.
 This is a **one-mode** network because there is only one type of nodes (book characters).
 - 77 nodes
 - 254 edges (undirected)
 
 ### ChineseBuddhism_SNA
 
 #### gexf file version:1.2draft
-This gexf file is located in another [repository](https://github.com/DHARPA-Project/kiara.examples/blob/main/examples/data/network_analysis/gexf), 
+This gexf file is located in another [repository](https://github.com/DHARPA-Project/kiara.examples/blob/main/examples/data/network_analysis/gexf),
 because it is too large (20,4 MB).
 
 It comes from this website:

examples/data/gexf/lesmis.gexf

@@ -884,4 +884,4 @@
       <edge id="249" source="76" target="66"/>
     </edges>
   </graph>
-</gexf>
+</gexf>

examples/data/gml/Readme.md

@@ -24,7 +24,7 @@ Anthropological Research 33, 452-473 (1977)."
 
 See also: https://en.wikipedia.org/wiki/Zachary%27s_karate_club#cite_note-Data-3
 
-This is a **one-mode** network where nodes represent friends. It is **undirected** and **unweighted**. 
+This is a **one-mode** network where nodes represent friends. It is **undirected** and **unweighted**.
 - 34 nodes
 - 78 edges (undirected)
 
@@ -62,7 +62,7 @@ adjacencies for the novel "David Copperfield" by Charles Dickens, as
 described by M. Newman.  Nodes represent the most commonly occurring
 adjectives and nouns in the book.  Node values are 0 for adjectives and 1
 for nouns.  Edges connect any pair of words that occur in adjacent position
-in the text of the book.  
+in the text of the book.
 
 Please cite M. E. J. Newman, Finding community
 structure in networks using the eigenvectors of matrices, Preprint
@@ -91,14 +91,14 @@ Additional information on the network can be found in
 
   D. Lusseau, Evidence for social role in a dolphin social network,
   Preprint q-bio/0607048 (http://arxiv.org/abs/q-bio.PE/0607048)"
-  
+
 This data represents a **one-mode**, **undirected**, **unweighted** network.
-  
+
 - nodes 62
 - edges 159 (undirected)
-  
+
 ### football
- 
+
  "The file football.gml contains the network of American football games
 between Division IA colleges during regular season Fall 2000, as compiled
 by M. Girvan and M. Newman.  The nodes have values that indicate to which
@@ -168,8 +168,8 @@ These data can be cited (as an updated version of)
 
   M. E. J. Newman, The structure of scientific collaboration networks,
   Proc. Natl. Acad. Sci. USA 98, 404-409 (2001)."
-  
+
 This dataset represents a **one-mode** (scientists), **undirected**, **weighted** network.
- 
+
  - nodes 40421
  - edges 175692 (undirected)

examples/data/quakers/Readme.md

@@ -1,2 +1,2 @@
-This data comes from a programming historian tutorial on network analysis with python. 
+This data comes from a programming historian tutorial on network analysis with python.
 For more context see the Readme file under quakers [here](https://github.com/DHARPA-Project/kiara_plugin.network_analysis/tree/develop/examples/data/gexf).

examples/data/treaties/Readme.md

@@ -1,2 +1,2 @@
-This data was created by [Lena Jaskov](https://github.com/yaslena). 
+This data was created by [Lena Jaskov](https://github.com/yaslena).
 For more context see under *peacetreaties* [here](https://github.com/DHARPA-Project/kiara_plugin.network_analysis/blob/develop/examples/data/JSON/Readme.md).

examples/data/treaties/peace_treaties_rus.csv

@@ -5,7 +5,7 @@ Präliminarvertrag von Krakau,"                   Polen, Russland",1523 II 22
 Waffenstillstand von Nowgorod,"                   Russland, Schweden",1524 IV 3
 Waffenstillstand von Nowgorod,"                   Russland, Schweden",1537 III 25_IV 4
 "Waffenstillstands-, Grenz- und Handelsvertrag von Nowgorod","                   Russland, Schweden",1561 VIII
-Waffenstillstand von Dorpat,"                   Russland, Schweden",1564 IX 
+Waffenstillstand von Dorpat,"                   Russland, Schweden",1564 IX
 Waffenstillstand von Narva,"                   Russland, Schweden",1583 VIII 10
 Ewiger Friede von Tjawzin,"                   Russland, Schweden",1595 V 18
 Friedensvertrag von Teusina,"                   Polen, Russland, Schweden",1595 V 18
@@ -15,7 +15,7 @@ Waffenstillstand von Dederino,"                   Russland, Schweden",1616 II 22
 Friedensvertrag von Stolbovo (Beta-Version),"                   Russland, Schweden",1617 II 27_III 9
 Freundschaftsvertrag von Livny,"                   Russland, Siebenbürgen",1623 VI 28_VII 8
 Friedensvertrag von Moskau,"                   Russland, Siebenbürgen",1627 XII 18_28
-Freundschaftsvertrag von Walujki,"                   Russland, Siebenbürgen",1629 IX 
+Freundschaftsvertrag von Walujki,"                   Russland, Siebenbürgen",1629 IX
 Friedensvertrag von Poljanovka,"                   Polen, Russland",1634 V 17_27
 Friedensvertrag (Ewiger Friede) von Poljanovka (Polanów),"                   Polen, Russland",1634 VI 14
 Friedensvertrag von Ilančik,"                   Russland, Siebenbürgen",1638 IX
@@ -25,10 +25,10 @@ Präliminarvertrag von Moskau,"                   Russland, Schweden",1658 V 25
 Stillstandsvertrag von Valiesar,"                   Russland, Schweden",1658 XII 20
 Friedensvertrag von Kardis,"                   Russland, Schweden",1661 VI 21
 Friedensvertrag von Andrusovo,"                   Polen, Russland",1667 I 20_30
-"Bestätigung des Vertrags von Andrusovo (1667 I 20), Radzin","                   Polen, Russland",1670 III 7_17 
+"Bestätigung des Vertrags von Andrusovo (1667 I 20), Radzin","                   Polen, Russland",1670 III 7_17
 Vertrag über eine Verlängerung von Andrusovo (1667 I 20),"                   Polen, Russland",1672 IV 9
 Waffenstillstand von Moskau,"                   Polen, Russland",1678 VIII 13
-Ewiger Friede von Moskau,"                   Polen, Russland",1686 IV 26 / V 6  
+Ewiger Friede von Moskau,"                   Polen, Russland",1686 IV 26 / V 6
 Angriffsbündnis von Wien,"                   Kaiser, Russland, Venedig",1697 I 29
 Waffenstillstand von Karlowitz (Beta-Version),"                   Osmanisches Reich, Russland",1698 XII 25
 Allianzvertrag von Moskau,"                   Russland, Sachsen / Polen",1699 XI 11_21

pixi.toml

@@ -7,7 +7,7 @@ channels = ["conda-forge", "dharpa"]
 platforms = ["linux-64", "win-64", "osx-64", "osx-arm64"]
 
 [tasks]
-install-dev-env = "pip install -e '.[dev_utils]'
+install-dev-env = "pip install -e '.[dev_utils]'"
 pre-commit-check = ".pixi/env/bin/pre-commit run --all-files"
 kiara = ".pixi/env/bin/kiara"
 show-versions = ".pixi/env/bin/kiara --version"

src/kiara_plugin/network_analysis/data_types.py

@@ -2,7 +2,7 @@
 
 """This module contains the value type classes that are used in the ``kiara_plugin.network_analysis`` package.
 """
-from typing import Any, List, Mapping, Type, Union, ClassVar
+from typing import Any, ClassVar, List, Mapping, Type, Union
 
 from rich.console import Group
 
@@ -34,7 +34,7 @@ class NetworkDataType(TablesType):
 
     @classmethod
     def python_class(cls) -> Type:
-        return NetworkData
+        return NetworkData  # type: ignore
 
     def parse_python_obj(self, data: Any) -> NetworkData:
 

src/kiara_plugin/network_analysis/models/__init__.py

@@ -10,14 +10,15 @@
 """
 from typing import (
     TYPE_CHECKING,
+    ClassVar,
     Dict,
     Iterable,
     List,
     Literal,
     Protocol,
     Type,
     TypeVar,
-    Union, ClassVar,
+    Union,
 )
 
 from pydantic import BaseModel, Field
@@ -132,7 +133,7 @@ def create_network_data(
                 nodes_table, edges_table
             )
 
-        network_data = cls.create_tables(
+        network_data: NetworkData = cls.create_tables(
             {NODES_TABLE_NAME: nodes_table, EDGES_TABLE_NAME: edges_table}
         )
 
@@ -356,7 +357,7 @@ def query_edges(
         import duckdb
 
         con = duckdb.connect()
-        edges = self.edges.arrow_table  # noqak
+        edges = self.edges.arrow_table  # noqa: F841
         if relation_name != EDGES_TABLE_NAME:
             sql_query = sql_query.replace(relation_name, EDGES_TABLE_NAME)
 
@@ -514,7 +515,7 @@ def as_networkx_graph(
 
         """
 
-        graph = graph_type()
+        graph: NETWORKX_GRAPH_TYPE = graph_type()
 
         def add_node(_node_id: int, **attrs):
             graph.add_node(_node_id, **attrs)

src/kiara_plugin/network_analysis/models/inputs.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
-from typing import Any, Dict, Union, ClassVar
+from typing import Any, ClassVar, Dict, Union
 
-from pydantic import model_validator, Field
+from pydantic import Field, model_validator
 
 from kiara.models import KiaraModel
 from kiara_plugin.core_types.defaults import DEFAULT_MODEL_KEY

src/kiara_plugin/network_analysis/models/metadata.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 from typing import ClassVar
 
-from pydantic import field_validator, Field
+from pydantic import Field, field_validator
 
 from kiara.models import KiaraModel
 from kiara.models.documentation import DocumentationMetadataModel

src/kiara_plugin/network_analysis/modules/components.py

@@ -175,7 +175,7 @@ def create_outputs_schema(self):
             }
         }
 
-    def process(self, inputs, outputs):
+    def process(self, inputs, outputs) -> None:
 
         import pyarrow as pa
         import rustworkx as rx
@@ -199,7 +199,8 @@ def process(self, inputs, outputs):
         if not cut_points:
             raise NotImplementedError()
         cut_points_column = [
-            x in translated_cut_points for x in range(0, network_data.num_nodes)
+            x in translated_cut_points
+            for x in range(0, network_data.num_nodes)  # noqa: PIE808
         ]
 
         nodes = network_data.nodes.arrow_table

src/kiara_plugin/network_analysis/modules/create.py

@@ -398,7 +398,7 @@ def process(self, inputs: ValueMap, outputs: ValueMap, job_log: JobLog) -> None:
         )
 
         if nodes_arrow_dataframe is None:
-            new_node_ids = range(0, len(unique_node_ids_old))
+            new_node_ids = range(0, len(unique_node_ids_old))  # noqa: PIE808
             node_id_map = dict(zip(unique_node_ids_old, new_node_ids))
             # node_id_map = {
             #     node_id: new_node_id
@@ -421,7 +421,7 @@ def process(self, inputs: ValueMap, outputs: ValueMap, job_log: JobLog) -> None:
                 ~(unique_node_ids_old.is_in(unique_node_ids_nodes_table))
                 raise NotImplementedError("MISSING NODE IDS NOT IMPLEMENTED YET")
             else:
-                new_node_ids = range(0, len(id_column_old))
+                new_node_ids = range(0, len(id_column_old))  # noqa: PIE808
                 node_id_map = dict(zip(id_column_old, new_node_ids))
                 # node_id_map = {
                 #     node_id: new_node_id