Some proposals (#1119)

neurom/core/morphology.py

@@ -408,7 +408,7 @@ def graft_morphology(section):
 class Neurite:
     """Class representing a neurite tree."""
 
-    def __init__(self, root_node, process_subtrees=False):
+    def __init__(self, root_node, *, process_subtrees=False):
         """Constructor.
 
         Args:
@@ -538,7 +538,7 @@ def __repr__(self):
 class Morphology:
     """Class representing a simple morphology."""
 
-    def __init__(self, morphio_morph, name=None, process_subtrees=False):
+    def __init__(self, morphio_morph, name=None, *, process_subtrees=False):
         """Morphology constructor.
 
         Args:

neurom/core/population.py

@@ -53,7 +53,13 @@ class Population:
     """
 
     def __init__(
-        self, files, name='Population', ignored_exceptions=(), cache=False, process_subtrees=False
+        self,
+        files,
+        name='Population',
+        ignored_exceptions=(),
+        *,
+        cache=False,
+        process_subtrees=False,
     ):
         """Construct a morphology population.
 
@@ -67,6 +73,7 @@ def __init__(
                 will be loaded everytime it is accessed within the population. Which is good when
                 population is big. If true then all morphs will be loaded upon the construction
                 and kept in memory.
+            process_subtrees (bool): enable mixed tree processing if set to True
 
         Notes:
             symlinks in paths are not resolved.

neurom/io/utils.py

@@ -120,7 +120,7 @@ def _get_file(stream, extension):
     return temp_file
 
 
-def load_morphology(morph, reader=None, mutable=None, process_subtrees=False):
+def load_morphology(morph, reader=None, *, mutable=None, process_subtrees=False):
     """Build section trees from a morphology or a h5, swc or asc file.
 
     Args:
@@ -132,11 +132,12 @@ def load_morphology(morph, reader=None, mutable=None, process_subtrees=False):
             - a morphio mutable or immutable Morphology object
             - a stream that can be put into a io.StreamIO object. In this case, the READER argument
               must be passed with the corresponding file format (asc, swc and h5)
+        reader (str): Optional, must be provided if morphology is a stream to
+                      specify the file format (asc, swc, h5)
         mutable (bool|None): Whether to enforce mutability. If None and a morphio/neurom object is
                              passed, the initial mutability will be maintained. If None and the
                              morphology is loaded, then it will be immutable by default.
-        reader (str): Optional, must be provided if morphology is a stream to
-                      specify the file format (asc, swc, h5)
+        process_subtrees (bool): enable mixed tree processing if set to True
 
     Returns:
         A Morphology object
@@ -181,7 +182,7 @@ def load_morphology(morph, reader=None, mutable=None, process_subtrees=False):
 
 
 def load_morphologies(
-    morphs, name=None, ignored_exceptions=(), cache=False, process_subtrees=False
+    morphs, name=None, ignored_exceptions=(), *, cache=False, process_subtrees=False
 ):
     """Create a population object.
 
@@ -195,6 +196,7 @@ def load_morphologies(
         ignored_exceptions (tuple): NeuroM and MorphIO exceptions that you want to ignore when
             loading morphologies
         cache (bool): whether to cache the loaded morphologies in memory
+        process_subtrees (bool): enable mixed tree processing if set to True
 
     Returns:
         Population: population object
@@ -205,4 +207,6 @@ def load_morphologies(
     else:
         files = morphs
         name = name or 'Population'
-    return Population(files, name, ignored_exceptions, cache, process_subtrees=process_subtrees)
+    return Population(
+        files, name, ignored_exceptions, cache=cache, process_subtrees=process_subtrees
+    )