Pull line lengths back to 120 to match the rest of the CountESS-Proje…

…ct repos

countess/core/config.py

@@ -70,7 +70,9 @@ def read_config(
             if key.startswith("_parent."):
                 node.add_parent(nodes_by_name[val])
 
-        node.config = [(key, ast.literal_eval(val), base_dir) for key, val in config_dict.items() if not key.startswith("_")]
+        node.config = [
+            (key, ast.literal_eval(val), base_dir) for key, val in config_dict.items() if not key.startswith("_")
+        ]
 
         nodes_by_name[section_name] = node
 

countess/core/pipeline.py

@@ -1,9 +1,9 @@
 from dataclasses import dataclass, field
+from itertools import chain
 from multiprocessing import Process, Queue
 from os import cpu_count
 from queue import Empty
 from typing import Any, Iterable, Optional
-from itertools import chain
 
 from countess.core.logger import Logger
 from countess.core.plugins import BasePlugin, FileInputPlugin, ProcessPlugin, get_plugin_classes
@@ -96,10 +96,14 @@ def execute(self, logger: Logger, row_limit: Optional[int] = None):
         elif isinstance(self.plugin, FileInputPlugin):
             num_files = self.plugin.num_files()
             row_limit_each_file = row_limit // num_files if row_limit is not None else None
-            self.result = multi_iterator_map(self.plugin.load_file, range(0, num_files), args=(logger, row_limit_each_file))
+            self.result = multi_iterator_map(
+                self.plugin.load_file, range(0, num_files), args=(logger, row_limit_each_file)
+            )
         elif isinstance(self.plugin, ProcessPlugin):
             self.plugin.prepare([p.name for p in self.parent_nodes], row_limit)
-            self.result = chain(self.plugin.collect(self.process_parent_iterables(logger)), self.plugin.finalize(logger))
+            self.result = chain(
+                self.plugin.collect(self.process_parent_iterables(logger)), self.plugin.finalize(logger)
+            )
 
         if row_limit is not None or len(self.child_nodes) != 1:
             self.result = list(self.result)
@@ -238,7 +242,9 @@ def tidy(self):
                 if len(node.parent_nodes) == 0:
                     stratum[node] = min(stratum[n] for n in node.child_nodes) - 1
                 else:
-                    stratum[node] = (min(stratum[n] for n in node.child_nodes) + max(stratum[n] for n in node.parent_nodes)) // 2
+                    stratum[node] = (
+                        min(stratum[n] for n in node.child_nodes) + max(stratum[n] for n in node.parent_nodes)
+                    ) // 2
 
         max_stratum = max(stratum.values())
 

countess/core/plugins.py

@@ -444,63 +444,81 @@ def series_to_dataframe(self, series: pd.Series) -> pd.DataFrame:
 # Six combinations of the five mixins!
 
 
-class PandasTransformSingleToSinglePlugin(PandasTransformXToSingleMixin, PandasTransformSingleToXMixin, PandasTransformBasePlugin):
+class PandasTransformSingleToSinglePlugin(
+    PandasTransformXToSingleMixin, PandasTransformSingleToXMixin, PandasTransformBasePlugin
+):
     """Transformer which takes a single column and returns a single value"""
 
     def process_value(self, value, logger: Logger):
         raise NotImplementedError(f"{self.__class__}.process_value()")
 
 
-class PandasTransformSingleToTuplePlugin(PandasTransformXToTupleMixin, PandasTransformSingleToXMixin, PandasTransformBasePlugin):
+class PandasTransformSingleToTuplePlugin(
+    PandasTransformXToTupleMixin, PandasTransformSingleToXMixin, PandasTransformBasePlugin
+):
     """Transformer which takes a single column and returns a tuple of values"""
 
     def process_value(self, value, logger: Logger):
         raise NotImplementedError(f"{self.__class__}.process_value()")
 
 
-class PandasTransformSingleToDictPlugin(PandasTransformXToDictMixin, PandasTransformSingleToXMixin, PandasTransformBasePlugin):
+class PandasTransformSingleToDictPlugin(
+    PandasTransformXToDictMixin, PandasTransformSingleToXMixin, PandasTransformBasePlugin
+):
     """Transformer which takes a single column and returns a dictionary of values"""
 
     def process_value(self, value, logger: Logger):
         raise NotImplementedError(f"{self.__class__}.process_value()")
 
 
-class PandasTransformRowToSinglePlugin(PandasTransformXToSingleMixin, PandasTransformRowToXMixin, PandasTransformBasePlugin):
+class PandasTransformRowToSinglePlugin(
+    PandasTransformXToSingleMixin, PandasTransformRowToXMixin, PandasTransformBasePlugin
+):
     """Transformer which takes a whole row and returns a single value"""
 
     def process_row(self, row: pd.Series, logger: Logger):
         raise NotImplementedError(f"{self.__class__}.process_row()")
 
 
-class PandasTransformRowToTuplePlugin(PandasTransformXToTupleMixin, PandasTransformRowToXMixin, PandasTransformBasePlugin):
+class PandasTransformRowToTuplePlugin(
+    PandasTransformXToTupleMixin, PandasTransformRowToXMixin, PandasTransformBasePlugin
+):
     """Transformer which takes a whole row and returns a tuple of values"""
 
     def process_row(self, row: pd.Series, logger: Logger):
         raise NotImplementedError(f"{self.__class__}.process_row()")
 
 
-class PandasTransformRowToDictPlugin(PandasTransformXToDictMixin, PandasTransformRowToXMixin, PandasTransformBasePlugin):
+class PandasTransformRowToDictPlugin(
+    PandasTransformXToDictMixin, PandasTransformRowToXMixin, PandasTransformBasePlugin
+):
     """Transformer which takes a whole row and returns a dictionary of values"""
 
     def process_row(self, row: pd.Series, logger: Logger):
         raise NotImplementedError(f"{self.__class__}.process_row()")
 
 
-class PandasTransformDictToSinglePlugin(PandasTransformXToSingleMixin, PandasTransformDictToXMixin, PandasTransformBasePlugin):
+class PandasTransformDictToSinglePlugin(
+    PandasTransformXToSingleMixin, PandasTransformDictToXMixin, PandasTransformBasePlugin
+):
     """Transformer which takes a whole row and returns a single value"""
 
     def process_dict(self, data, logger: Logger):
         raise NotImplementedError(f"{self.__class__}.process_dict()")
 
 
-class PandasTransformDictToTuplePlugin(PandasTransformXToTupleMixin, PandasTransformDictToXMixin, PandasTransformBasePlugin):
+class PandasTransformDictToTuplePlugin(
+    PandasTransformXToTupleMixin, PandasTransformDictToXMixin, PandasTransformBasePlugin
+):
     """Transformer which takes a whole row and returns a tuple of values"""
 
     def process_dict(self, data, logger: Logger):
         raise NotImplementedError(f"{self.__class__}.process_dict()")
 
 
-class PandasTransformDictToDictPlugin(PandasTransformXToDictMixin, PandasTransformDictToXMixin, PandasTransformBasePlugin):
+class PandasTransformDictToDictPlugin(
+    PandasTransformXToDictMixin, PandasTransformDictToXMixin, PandasTransformBasePlugin
+):
     """Transformer which takes a whole row and returns a dictionary of values"""
 
     def process_dict(self, data, logger: Logger):
@@ -527,8 +545,8 @@ def num_files(self):
     def load_file(self, file_number: int, logger: Logger, row_limit: Optional[int] = None) -> Iterable[pd.DataFrame]:
         raise NotImplementedError(f"{self.__class__}.load_file()")
 
-class PandasInputFilesPlugin(PandasInputPlugin):
 
+class PandasInputFilesPlugin(PandasInputPlugin):
     def num_files(self):
         return len(self.parameters["files"])
 
@@ -541,7 +559,6 @@ def read_file_to_dataframe(self, file_params, logger, row_limit=None) -> pd.Data
         raise NotImplementedError(f"{self.__class__}.read_file_to_dataframe")
 
 
-
 class PandasOutputPlugin(PandasProcessPlugin):
     def process_inputs(self, inputs: Mapping[str, Iterable[pd.DataFrame]], logger: Logger, row_limit: Optional[int]):
         iterators = set(iter(input) for input in inputs.values())

countess/gui/config.py

@@ -93,7 +93,9 @@ def __init__(  # pylint: disable=R0912,R0915
             if parameter.read_only:
                 self.entry["state"] = tk.DISABLED
 
-        elif isinstance(parameter, ArrayParam) and self.level == 0 and not isinstance(parameter.param, TabularMultiParam):
+        elif (
+            isinstance(parameter, ArrayParam) and self.level == 0 and not isinstance(parameter.param, TabularMultiParam)
+        ):
             self.entry = tk.Frame(tk_parent)
             self.entry.columnconfigure(0, weight=1)
             drc = self.delete_row_callback if not parameter.read_only else None
@@ -168,7 +170,11 @@ def update(self):
         else:
             self.entry["fg"] = None
 
-        if isinstance(self.parameter, ArrayParam) and self.level == 0 and not isinstance(self.parameter.param, TabularMultiParam):
+        if (
+            isinstance(self.parameter, ArrayParam)
+            and self.level == 0
+            and not isinstance(self.parameter.param, TabularMultiParam)
+        ):
             self.update_subwrappers_framed(self.parameter.params, self.delete_row_callback)
             if self.button:
                 self.button.grid(row=len(self.parameter.params) + 1, padx=10)
@@ -457,7 +463,9 @@ def update(self) -> None:
             if key in self.wrapper_cache:
                 self.wrapper_cache[key].update()
             else:
-                self.wrapper_cache[key] = ParameterWrapper(self.subframe, parameter, self.change_parameter, level=top_level)
+                self.wrapper_cache[key] = ParameterWrapper(
+                    self.subframe, parameter, self.change_parameter, level=top_level
+                )
             self.wrapper_cache[key].set_row(n + 1)
 
         # Remove any parameter wrappers no longer needed

countess/gui/main.py

@@ -148,7 +148,7 @@ def show_preview_subframe(self):
             self.preview_subframe.destroy()
 
         if all(isinstance(r, (str, bytes)) for r in self.node.result):
-            text_result = ''.join(self.node.result)
+            text_result = "".join(self.node.result)
             self.preview_subframe = tk.Frame(self.frame)
             self.preview_subframe.rowconfigure(1, weight=1)
             n_lines = len(text_result.splitlines())
@@ -230,7 +230,9 @@ class ButtonMenu:  # pylint: disable=R0903
     def __init__(self, tk_parent, buttons):
         self.frame = tk.Frame(tk_parent)
         for button_number, (button_label, button_command) in enumerate(buttons):
-            tk.Button(self.frame, text=button_label, command=button_command).grid(row=0, column=button_number, sticky=tk.EW)
+            tk.Button(self.frame, text=button_label, command=button_command).grid(
+                row=0, column=button_number, sticky=tk.EW
+            )
         self.frame.grid(sticky=tk.NSEW)
 
 

countess/plugins/correlation.py

@@ -1,4 +1,4 @@
-from typing import Optional, Iterable
+from typing import Iterable, Optional
 
 import pandas as pd
 
@@ -22,14 +22,14 @@ class CorrelationPlugin(PandasSimplePlugin):
         "column1": ColumnChoiceParam("Column 1"),
         "column2": ColumnChoiceParam("Column 2"),
     }
-    columns : list[str] = []
-    dataframes : list[pd.DataFrame] = []
+    columns: list[str] = []
+    dataframes: list[pd.DataFrame] = []
 
     def prepare(self, sources: list[str], row_limit: Optional[int]):
         assert isinstance(self.parameters["group"], ColumnOrNoneChoiceParam)
         column1 = self.parameters["column1"].value
         column2 = self.parameters["column2"].value
-        self.columns = [ column1, column2 ]
+        self.columns = [column1, column2]
         if not self.parameters["group"].is_none():
             self.columns.append(self.parameters["group"].value)
         self.dataframes = []

countess/plugins/data_table.py

@@ -83,6 +83,8 @@ def load_file(self, file_number: int, logger: Logger, row_limit: Optional[int] =
         self.fix_columns()
         values = []
         for row in self.parameters["rows"]:
-            values.append(dict((col["name"].value, row[str(num)].value) for num, col in enumerate(self.parameters["columns"])))
+            values.append(
+                dict((col["name"].value, row[str(num)].value) for num, col in enumerate(self.parameters["columns"]))
+            )
 
         yield pd.DataFrame(values)

countess/plugins/group_by.py

@@ -1,4 +1,4 @@
-from typing import Iterable, Optional, List
+from typing import Iterable, List, Optional
 
 import pandas as pd
 
@@ -44,7 +44,7 @@ class GroupByPlugin(PandasSimplePlugin):
         "join": BooleanParam("Join Back?"),
     }
 
-    dataframes : Optional[List[pd.DataFrame]] = None
+    dataframes: Optional[List[pd.DataFrame]] = None
 
     def prepare(self, *_):
         self.dataframes = []

countess/plugins/mutagenize.py

@@ -9,7 +9,9 @@
 from countess.core.plugins import PandasInputPlugin
 
 
-def mutagenize(sequence: str, mutate: bool, delete: bool, insert: bool) -> Iterable[tuple[str, int, Optional[str], Optional[str]]]:
+def mutagenize(
+    sequence: str, mutate: bool, delete: bool, insert: bool
+) -> Iterable[tuple[str, int, Optional[str], Optional[str]]]:
     # XXX it'd be faster, but less neat, to include logic for duplicate
     # removal here instead of producing duplicates and then removing them
     # later.

countess/plugins/pivot.py

@@ -17,7 +17,9 @@ class PivotPlugin(PandasSimplePlugin):
     version = VERSION
     link = "https://countess-project.github.io/CountESS/plugins/#pivot-tool"
 
-    parameters = {"columns": PerColumnArrayParam("Columns", ChoiceParam("Role", choices=["Index", "Pivot", "Expand", "Drop"]))}
+    parameters = {
+        "columns": PerColumnArrayParam("Columns", ChoiceParam("Role", choices=["Index", "Pivot", "Expand", "Drop"]))
+    }
 
     def process_dataframe(self, dataframe: pd.DataFrame, logger: Logger) -> pd.DataFrame:
         assert isinstance(self.parameters["columns"], PerColumnArrayParam)

countess/plugins/regex.py

@@ -125,7 +125,9 @@ def read_file_to_dataframe(self, file_params, logger, row_limit=None):
 
         output_parameters = list(self.parameters["output"])[: compiled_re.groups]
         columns = [p.name.value or f"column_{n+1}" for n, p in enumerate(output_parameters)]
-        index_columns = [p.name.value or f"column_{n+1}" for n, p in enumerate(output_parameters) if p.index.value] or None
+        index_columns = [
+            p.name.value or f"column_{n+1}" for n, p in enumerate(output_parameters) if p.index.value
+        ] or None
 
         records = []
         with open(file_params["filename"].value, "r", encoding="utf-8") as fh:

countess/utils/pandas.py

@@ -8,7 +8,11 @@
 def get_all_indexes(dataframe: pd.DataFrame) -> Dict[str, Any]:
     if dataframe.index.name:
         return {str(dataframe.index.name): dataframe.index.dtype}
-    elif hasattr(dataframe.index, "names") and hasattr(dataframe.index, "dtypes") and dataframe.index.names[0] is not None:
+    elif (
+        hasattr(dataframe.index, "names")
+        and hasattr(dataframe.index, "dtypes")
+        and dataframe.index.names[0] is not None
+    ):
         return dict(zip(dataframe.index.names, dataframe.index.dtypes))
     else:
         return {}

pyproject.toml

@@ -100,7 +100,7 @@ disable = [
     "too-many-public-methods",
     "unidiomatic-typecheck",
 ]
-max-line-length = 132
+max-line-length = 120
 
 [tool.black]
-line-length = 132
+line-length = 120