code tidy

Author: nickzoic

countess/gui/main.py

@@ -33,17 +33,20 @@
 
 preview_row_limit: Optional[int] = 10000000
 
-usage = """usage: countess_gui [--log LEVEL] [INIFILE]
+usage = (
+    """usage: countess_gui [--log LEVEL] [INIFILE]
 
 Start the CountESS GUI.
 
 options:
     --help                         show this message & exit.
     --version                      show version
-    --preview LIMIT                set preview mode row limit (default: %d)
+    --preview LIMIT                set preview mode row limit (default: %s)
     --log LEVEL                    set log level to LEVEL
     INIFILE                        load configuration file
-""" % preview_row_limit
+"""
+    % preview_row_limit or "NONE"
+)
 
 
 # import faulthandler
@@ -237,13 +240,13 @@ def notes_modified_callback(self, *_):
 
     def config_change_callback(self, *_):
         """Called immediately if a change to config has occurred."""
-        logger.debug("config_change_callback")
+        # logger.debug("config_change_callback")
         self.node.mark_dirty()
 
         # Leave it a bit (2500ms) to see if the user is still typing, if so cancel
         # the previous task and make a new task for another 2.5 seconds away ...
         if self.config_change_task:
-            logger.debug("config_change_callback: cancelling task")
+            # logger.debug("config_change_callback: cancelling task")
             self.frame.after_cancel(self.config_change_task)
         self.config_change_task = self.frame.after(2500, self.config_change_task_callback)
 
@@ -674,7 +677,6 @@ def main() -> None:
     logging.getLogger().addHandler(logging.handlers.QueueHandler(logging_queue))
     # logging.getLogger().addHandler(logging.StreamHandler())
 
-
     root = make_root()
     SplashScreen(root)
     MainWindow(root, args[0] if args else None)

countess/plugins/expression.py

@@ -46,10 +46,10 @@
     "upper",
 }
 CASTOPS = {
-        "int": "integer",
-        "float": "float",
-        "str": "string",
-        "bool": "boolean",
+    "int": "integer",
+    "float": "float",
+    "str": "string",
+    "bool": "boolean",
 }
 LISTOPS = {
     "sum": "list_sum",

countess/plugins/pivot.py

@@ -33,6 +33,7 @@ def execute(
         pivot_cols = [p.label for p in self.columns if p.value == "Pivot" and p.label in source.columns]
         expand_cols = [p.label for p in self.columns if p.value == "Expand" and p.label in source.columns]
 
+        logger.debug("PivotPlugin.execute columns %s", source.columns)
         logger.debug("PivotPlugin.execute index_cols %s", index_cols)
         logger.debug("PivotPlugin.execute pivot_cols %s", pivot_cols)
         logger.debug("PivotPlugin.execute expand_cols %s", expand_cols)
@@ -66,6 +67,7 @@ def execute(
             query_str = f"{query_str} GROUP BY {group_str}"
 
         logger.debug("PivotPlugin.execute query_str %s", query_str)
+        rel = ddbc.sql(query_str)
 
         project_str = f"COLUMNS('(.*)_{pivot_char}(.*)')"
         if self.default_0:
@@ -80,5 +82,6 @@ def execute(
             project_str = (", ".join([duckdb_escape_identifier(ic) for ic in index_cols])) + ", " + project_str
 
         logger.debug("PivotPlugin.execute project_str %s", project_str)
+        logger.debug("PivotPlugin.execute project columns %s", rel.columns)
 
-        return ddbc.sql(query_str).project(project_str)
+        return rel.project(project_str)

countess/plugins/score_scale.py

@@ -55,8 +55,8 @@ def __init__(self, *a, **k):
         super().__init__(*a, **k)
 
         # override classifiers labels
-        self.classifiers[0].label = 'Scale to 0.0'
-        self.classifiers[1].label = 'Scale to 1.0'
+        self.classifiers[0].label = "Scale to 0.0"
+        self.classifiers[1].label = "Scale to 1.0"
 
     def execute(
         self, ddbc: DuckDBPyConnection, source: DuckDBPyRelation, row_limit: Optional[int] = None

countess/plugins/vampseq.py

@@ -4,7 +4,7 @@
 from duckdb import DuckDBPyConnection, DuckDBPyRelation
 
 from countess import VERSION
-from countess.core.parameters import FloatParam, PerNumericColumnArrayParam, TabularMultiParam, ColumnOrNoneChoiceParam
+from countess.core.parameters import ColumnOrNoneChoiceParam, FloatParam, PerNumericColumnArrayParam, TabularMultiParam
 from countess.core.plugins import DuckdbSimplePlugin
 from countess.utils.duckdb import duckdb_escape_identifier, duckdb_escape_literal
 
@@ -23,14 +23,14 @@ class VampSeqScorePlugin(DuckdbSimplePlugin):
     columns = PerNumericColumnArrayParam("Columns", CountColumnParam("Column"))
     group_col = ColumnOrNoneChoiceParam("Group By")
 
-    def prepare(self, ddbc: DuckDBPyConnection, source: DuckDBPyRelation) -> None:
+    def prepare(self, ddbc: DuckDBPyConnection, source: Optional[DuckDBPyRelation]) -> None:
         super().prepare(ddbc, source)
 
         # set default values for weights on "count" columns
         if all(c.weight.value is None for c in self.columns):
-            count_cols = [ c for c in self.columns if c.label.startswith('count') ]
+            count_cols = [c for c in self.columns if c.label.startswith("count")]
             for n, c in enumerate(count_cols):
-                c.weight.value = (n+1)/len(count_cols)
+                c.weight.value = (n + 1) / len(count_cols)
 
     def execute(
         self, ddbc: DuckDBPyConnection, source: DuckDBPyRelation, row_limit: Optional[int] = None

countess/plugins/variant.py

@@ -18,8 +18,8 @@
     StringParam,
 )
 from countess.core.plugins import DuckdbParallelTransformPlugin, DuckdbSimplePlugin
-from countess.utils.variant import TooManyVariationsException, find_variant_string
 from countess.utils.duckdb import duckdb_escape_identifier
+from countess.utils.variant import TooManyVariationsException, find_variant_string
 
 logger = logging.getLogger(__name__)