fix 'None' string parameters, plus code tidy

countess/core/cmd.py

@@ -6,29 +6,27 @@
 import re
 import sys
 
-
 from countess import VERSION
 from countess.core.config import read_config
 
 logger = logging.getLogger(__name__)
 
 
-def run(args : list[str]) -> None:
- options, args = getopt.getopt(args, '', ['version', 'set=', 'log='])
- config : list[tuple[str,str,str]] = []
-
+def run(args: list[str]) -> None:
+ options, args = getopt.getopt(args, "", ["version", "set=", "log="])
+ config: list[tuple[str, str, str]] = []
 
  for opt_key, opt_val in options:
- if opt_key == '--version':
+ if opt_key == "--version":
  print(f"CountESS {VERSION}") # pylint: disable=bad-builtin
- elif opt_key == '--set':
- if m := re.match(r'([^.]+)\.([^=]+)=(.*)', opt_val):
- config.append(m.groups())
+ elif opt_key == "--set":
+ if m := re.match(r"([^.]+)\.([^=]+)=(.*)", opt_val):
+ config.append((m.group(1), m.group(2), m.group(3)))
  else:
  logger.warning("Bad --set option: %s", opt_val)
- elif opt_key == '--log':
+ elif opt_key == "--log":
  try:
- if re.match(r'\d+$', opt_val):
+ if re.match(r"\d+$", opt_val):
  logging.getLogger().setLevel(int(opt_val))
  else:
  logging.getLogger().setLevel(opt_val.upper())
@@ -39,11 +37,15 @@ def run(args : list[str]) -> None:
 
  for filename in args:
  graph = read_config(filename)
- for node_label, config_key, config_val in config:
- try:
- graph.find_node(node_label).set_config(config_key, ast.literal_eval(config_val), '.')
- except (KeyError, ValueError):
- logger.warning("Bad --set option: %s=%s", config_key, config_val)
+ for node_name, config_key, config_val in config:
+ node = graph.find_node(node_name)
+ if node:
+ try:
+ node.set_config(config_key, ast.literal_eval(config_val), ".")
+ except (TypeError, KeyError, ValueError):
+ logger.warning("Bad --set option: %s.%s=%s", node_name, config_key, config_val)
+ else:
+ logger.warning("Bad --set node name: %s", node_name)
 
  graph.run()
 

countess/core/parameters.py

@@ -130,7 +130,7 @@ class StringParam(ScalarWithOperatorsParam):
  _value: Optional[str] = None
 
  def set_value(self, value: Any):
- self._value = str(value)
+ self._value = str(value or "")
 
  # Operator methods which apply only to strings
 
@@ -149,7 +149,7 @@ class TextParam(StringParam):
  long text field and also removes extra blank lines"""
 
  def set_value(self, value):
- self._value = re.sub("\n\n\n+", "\n\n", value)
+ self._value = re.sub("\n\n\n+", "\n\n", value or "")
 
 
 class NumericParam(ScalarWithOperatorsParam):
@@ -270,7 +270,7 @@ def clean_character(self, c: str):
  return ""
 
  def set_value(self, value: Any):
- value_str = str(value)
+ value_str = str(value or "")
  self._value = "".join([self.clean_character(c) for c in value_str])
 
  def copy(self) -> "StringCharacterSetParam":

countess/core/pipeline.py

@@ -79,7 +79,15 @@ class PipelineNode:
  # at config load time, if it is present it is loaded the
  # first time the plugin is prerun.
 
- def __init__(self, name, plugin=None, position=None, notes=None, sort_column=0, sort_descending=0):
+ def __init__(
+ self,
+ name: str,
+ plugin: Optional[BasePlugin] = None,
+ position: Optional[tuple[float, float]] = None,
+ notes: Optional[str] = None,
+ sort_column: int = 0,
+ sort_descending: bool = False,
+ ):
  self.name = name
  self.plugin = plugin
  self.position = position or (0.5, 0.5)
@@ -89,7 +97,7 @@ def __init__(self, name, plugin=None, position=None, notes=None, sort_column=0,
  self.parent_nodes = set()
  self.child_nodes = set()
  self.output_queues = set()
- self.config : list[tuple[str,str,str]] = []
+ self.config: list[tuple[str, str, str]] = []
 
  def set_config(self, key, value, base_dir):
  self.config.append((key, value, base_dir))
@@ -270,9 +278,9 @@ def del_node(self, node: PipelineNode):
  node.detach()
  self.nodes.remove(node)
 
- def find_node(self, label: str) -> Optional[PipelineNode]:
+ def find_node(self, name: str) -> Optional[PipelineNode]:
  for node in self.nodes:
- if node.label == label:
+ if node.name == name:
  return node
  return None
 
@@ -329,7 +337,6 @@ def reset_node_names(self):
  node.name += f" {num + 1}"
  node_names_seen.add(node.name)
 
-
  def tidy(self):
  """Tidies the graph (sets all the node positions)"""
 

countess/gui/config.py

@@ -208,7 +208,10 @@ def update(self):
  elif isinstance(self.parameter, FileParam):
  self.entry["text"] = self.parameter.value
  else:
- self.var.set(self.parameter.value)
+ if self.parameter.value is None:
+ self.var.set("")
+ else:
+ self.var.set(self.parameter.value)
 
  if self.label:
  self.label["text"] = self.parameter.label
@@ -448,7 +451,6 @@ def change_parameter(self, parameter):
  self.change_callback(self)
 
  def update(self) -> None:
-
  # If there's only a single parameter it is presented a little differently.
  top_level = 0 if len(self.plugin.params) == 1 else 1
 

countess/plugins/data_table.py

@@ -36,6 +36,11 @@ class DataTablePlugin(PandasInputPlugin):
  def fix_columns(self):
  old_rows = self.rows.params
 
+ # XXX should deal with duplicate column names more generally
+ for num, col in enumerate(self.columns):
+ if col.name == "":
+ col.name = f"col_{num+1}"
+
  self.params["rows"] = self.rows = ArrayParam(
  "Rows",
  TabularMultiParam("Row", {str(col.name): col.type.get_parameter(str(col.name)) for col in self.columns}),

countess/plugins/python.py

@@ -100,7 +100,7 @@ def process_dataframe(self, dataframe: pd.DataFrame) -> pd.DataFrame:
  b) we don't need to merge afterwards"""
 
  # XXX cache this?
- self.code_object = compile(self.code.value, "<PythonPlugin>", mode="exec")
+ self.code_object = compile(self.code.value or "", "<PythonPlugin>", mode="exec")
 
  dataframe = dataframe.reset_index(drop=dataframe.index.names == [None])
  series = self.dataframe_to_series(dataframe)

tests/test_config.py

@@ -26,7 +26,8 @@ def test_read_config_dict_no_plugin():
 
 
 def test_write_config():
- pn = PipelineNode("node", plugin=NothingPlugin("node"), config=[("foo", "bar", "baz")])
+ pn = PipelineNode("node", plugin=NothingPlugin("node"))
+ pn.set_config("foo", "bar", "baz")
  pg = PipelineGraph([pn])
 
  buf = io.StringIO()

tests/test_pipeline.py

@@ -106,12 +106,10 @@ def test_plugin_config(caplog):
  dnp = DoesNothingPlugin()
  dnn = PipelineNode(
  "node",
- plugin=dnp,
- config=[
- ("param", 1, "."),
- ("noparam", "whatever", "."),
- ],
+ plugin=dnp
  )
+ dnn.set_config("param", "1", ".")
+ dnn.set_config("noparam", "whatever", ".")
  dnn.load_config()
 
  assert "noparam=whatever" in caplog.text