Morphology parsers & pipeline blocks (#799)

* skip inferring a point at certain morphology transitions

* add shortform to `types`

* add scaffold type hint

* separated parsing code

* deleted old divio folder

* type casting for `property`. closes #681

* lint

* correct docs: params are kwargs

* use `parse_morphology_file`

* remove more dead code replaced by new parse func

* allow pipeline node in morphologies block

* added morphio flags to parser

* reusable morpho pipelines, with customizable parsers

* docstr tweak

* bump dep

* fix docs

---------

Co-authored-by: danilobenozzo <danilo.benozzo@gmail.com>

bsb/config/_attrs.py

@@ -252,15 +252,17 @@ def slot(**kwargs):
     return ConfigurationAttributeSlot(**kwargs)
 
 
-def property(val=None, /, **kwargs):
+def property(val=None, /, type=None, **kwargs):
     """
     Create a configuration property attribute. You may provide a value or a callable. Call
     `setter` on the return value as you would with a regular property.
     """
+    if type is None:
+        type = lambda v: v
 
     def decorator(val):
         prop = val if callable(val) else lambda s: val
-        return ConfigurationProperty(prop, **kwargs)
+        return ConfigurationProperty(prop, type=type, **kwargs)
 
     if val is None:
         return decorator
@@ -440,16 +442,18 @@ def __get__(self, instance, owner):
             return self
         return _getattr(instance, self.attr_name)
 
+    def fset(self, instance, value):
+        return _setattr(instance, self.attr_name, value)
+
     def __set__(self, instance, value):
         if _hasattr(instance, self.attr_name):
             ex_value = _getattr(instance, self.attr_name)
             _unset_nodes(ex_value)
         if value is None:
-            # Don't cast None to a value of the attribute type.
-            return _setattr(instance, self.attr_name, None)
+            # Don't try to cast None to a value of the attribute type.
+            return self.fset(instance, None)
         try:
             value = self.type(value, _parent=instance, _key=self.attr_name)
-            self.flag_dirty(instance)
         except ValueError:
             # This value error should only arise when users are manually setting
             # attributes in an already bootstrapped config tree.
@@ -467,8 +471,9 @@ def __set__(self, instance, value):
                 instance,
                 self.attr_name,
             ) from e
+        self.flag_dirty(instance)
         # The value was cast to its intented type and the new value can be set.
-        _setattr(instance, self.attr_name, value)
+        self.fset(instance, value)
         root = _strict_root(instance)
         if _is_booted(root):
             _boot_nodes(value, root.scaffold)
@@ -1058,7 +1063,7 @@ def __set__(self, instance, value):
             e.node = self
             raise e
         else:
-            return self.fset(instance, value)
+            return super().__set__(instance, value)
 
 
 def _collect_kv(n, d, k, v):

bsb/config/_config.py

@@ -9,7 +9,11 @@
 from ..placement import PlacementStrategy
 from ..postprocessing import PostProcessingHook
 from ..simulation.simulation import Simulation
-from ..storage._files import CodeDependencyNode, MorphologyDependencyNode
+from ..storage._files import (
+    CodeDependencyNode,
+    MorphologyDependencyNode,
+    MorphologyPipelineNode,
+)
 from ..storage.interfaces import StorageNode
 from ..topology import Partition, Region, RegionGroup, create_topology, get_partitions
 from . import types
@@ -60,7 +64,7 @@ class Configuration:
         type=CodeDependencyNode,
     )
     morphologies: cfglist[MorphologyDependencyNode] = config.list(
-        type=MorphologyDependencyNode,
+        type=types.or_(MorphologyDependencyNode, MorphologyPipelineNode),
     )
     storage: StorageNode = config.attr(
         type=StorageNode,

bsb/config/types.py

@@ -705,16 +705,14 @@ def type_handler(value, _parent, _key=None):
     return type_handler
 
 
-def mut_excl(*mutuals, required=True, max=1):
+def mut_excl(*mutuals, required=True, max=1, shortform=False):
     """
     Requirement handler for mutually exclusive attributes.
 
-    :param mutuals: The keys of the mutually exclusive attributes.
-    :type mutuals: str
-    :param required: Whether at least one of the keys is required
-    :type required: bool
-    :param max: The maximum amount of keys that may occur together.
-    :type max: int
+    :param str mutuals: The keys of the mutually exclusive attributes.
+    :param bool required: Whether at least one of the keys is required
+    :param int max: The maximum amount of keys that may occur together.
+    :param bool shortform: Allow the short form alternative.
     :returns: Requirement function
     :rtype: Callable
     """
@@ -723,6 +721,8 @@ def mut_excl(*mutuals, required=True, max=1):
         listed += f" {{}} `{mutuals[-1]}`"
 
     def requirement(section):
+        if shortform and section.is_shortform:
+            return False
         bools = [m in section for m in mutuals]
         given = sum(bools)
         if given > max: