fix: move extra sort arguments to sorter init (#241)

* fix: move extra arguments to init

* Apply suggestions from code review

Co-authored-by: Copilot <[email protected]>

* fix: resolving copilot review and adding class attribute with required arguments

* fix: remove SorterUseHint call

* fix: remove arguments from ABC
make all requrements a list
make all arguments required

* style: style fixes by ruff and autoformatting by black

* fix: add check for geology_data

* fix: not initiliase sorter in project.init

* fix: try use SorterUseNetworkX

* fix: adding utils module and fixing tests

* style: style fixes by ruff and autoformatting by black

* fix: sorter arguments optional. Allow project to update attributes from map data

* fix: minage/maxage optional

* fix: add unit relations as optional argument

* fix: default min/max age

* fix: wrong defaults.

---------

Co-authored-by: Copilot <[email protected]>
Co-authored-by: lachlangrose <[email protected]>
Co-authored-by: rabii-chaarani <[email protected]>

Author: 3 people

map2loop/__init__.py

@@ -1,10 +1,6 @@
 import logging
+from map2loop.logging import loggers, ch
 
-loggers = {}
-ch = logging.StreamHandler()
-formatter = logging.Formatter("%(levelname)s: %(asctime)s: %(filename)s:%(lineno)d -- %(message)s")
-ch.setFormatter(formatter)
-ch.setLevel(logging.WARNING)
 from .project import Project
 from .version import __version__
 

map2loop/logging.py

@@ -1,7 +1,11 @@
 import logging
-import map2loop
 
+loggers = {}
 
+ch = ch = logging.StreamHandler()
+formatter = logging.Formatter("%(levelname)s: %(asctime)s: %(filename)s:%(lineno)d -- %(message)s")
+ch.setFormatter(formatter)
+ch.setLevel(logging.WARNING)
 def get_levels():
     """dict for converting to logger levels from string
 
@@ -33,12 +37,12 @@ def getLogger(name: str):
     logging.Logger
         logger object
     """
-    if name in map2loop.loggers:
-        return map2loop.loggers[name]
+    if name in loggers:
+        return loggers[name]
     logger = logging.getLogger(name)
-    logger.addHandler(map2loop.ch)
+    logger.addHandler(ch)
     logger.propagate = False
-    map2loop.loggers[name] = logger
+    loggers[name] = logger
     return logger
 
 
@@ -56,9 +60,9 @@ def set_level(level: str):
     """
     levels = get_levels()
     level = levels.get(level, logging.WARNING)
-    map2loop.ch.setLevel(level)
+    ch.setLevel(level)
 
-    for name in map2loop.loggers:
+    for name in loggers:
         logger = logging.getLogger(name)
         logger.setLevel(level)
     logger.info(f"Logging level set to {level}")

map2loop/project.py

@@ -140,7 +140,7 @@ def __init__(
         self.set_default_samplers()
         self.bounding_box = bounding_box
         self.contact_extractor = None
-        self.sorter = SorterUseHint()
+        self.sorter = SorterUseHint
         self.throw_calculator = ThrowCalculatorAlpha()
         self.fault_orientation = FaultOrientationNearest()
         self.map_data = MapData(verbose_level=verbose_level)
@@ -560,19 +560,22 @@ def calculate_stratigraphic_order(self, take_best=False):
             )
             self.contact_extractor.extract_all_contacts()
         if take_best:
-            sorters = [SorterUseHint(), SorterAgeBased(), SorterAlpha(), SorterUseNetworkX()]
+            sorters = [
+                SorterAgeBased(),
+                SorterAlpha(
+                    contacts=self.contact_extractor.contacts,
+                ),
+                SorterUseNetworkX(
+                    unit_relationships=self.topology.get_unit_unit_relationships(),
+                ),
+            ]
             logger.info(
                 f"Calculating best stratigraphic column from {[sorter.sorter_label for sorter in sorters]}"
             )
 
             columns = [
                 sorter.sort(
                     self.stratigraphic_column.stratigraphicUnits,
-                    self.topology.get_unit_unit_relationships(),
-                    self.contact_extractor.contacts,
-                    self.map_data.get_map_data(Datatype.GEOLOGY),
-                    self.map_data.get_map_data(Datatype.STRUCTURE),
-                    self.map_data.get_map_data(Datatype.DTM),
                 )
                 for sorter in sorters
             ]
@@ -600,13 +603,19 @@ def calculate_stratigraphic_order(self, take_best=False):
             self.stratigraphic_column.column = column
         else:
             logger.info(f'Calculating stratigraphic column using sorter {self.sorter.sorter_label}')
+            # Update sorter with current data based on what it needs
+            if hasattr(self.sorter, 'unit_relationships') and self.sorter.unit_relationships is None:
+                self.sorter.unit_relationships = self.topology.get_unit_unit_relationships()
+            if hasattr(self.sorter, 'contacts') and self.sorter.contacts is None:
+                self.sorter.contacts = self.contact_extractor.contacts
+            if hasattr(self.sorter, 'geology_data') and self.sorter.geology_data is None:
+                self.sorter.geology_data = self.map_data.get_map_data(Datatype.GEOLOGY)
+            if hasattr(self.sorter, 'structure_data') and self.sorter.structure_data is None:
+                self.sorter.structure_data = self.map_data.get_map_data(Datatype.STRUCTURE)
+            if hasattr(self.sorter, 'dtm_data') and self.sorter.dtm_data is None:
+                self.sorter.dtm_data = self.map_data.get_map_data(Datatype.DTM)
             self.stratigraphic_column.column = self.sorter.sort(
                 self.stratigraphic_column.stratigraphicUnits,
-                self.topology.get_unit_unit_relationships(),
-                self.contact_extractor.contacts,
-                self.map_data.get_map_data(Datatype.GEOLOGY),
-                self.map_data.get_map_data(Datatype.STRUCTURE),
-                self.map_data.get_map_data(Datatype.DTM),
             )
 
     @beartype.beartype