Merge branch 'master' into cornu/clean_mpispike

docs/python/index.rst

@@ -55,6 +55,7 @@ Basic Programming
     programming/dynamiccode.rst
     programming/projectmanagement.rst
     programming/internals.rst
+    programming/neuron_classes.rst
     programming/hoc-from-python.rst
 
 Model Specification

docs/python/programming/neuron_classes.rst

@@ -0,0 +1,87 @@
+NEURON Python Classes and Objects
+=================================
+
+NEURON exposes its internal objects and hoc templates as Python objects via an automatic
+conversion layer, effectively making all entities from the HOC stack available to a Python program.
+
+There are basically two main objects which expose most Neuron entities. The first is `hoc` which
+exposes a number of internal established classes and functions.
+
+.. code-block::
+    python
+
+    >>> from neuron import hoc
+    >>> hoc.
+    hoc.List(
+    hoc.SectionList(
+    hoc.SectionRef(
+    hoc.Vector(
+        ...
+
+However, for *dynamic* entities NEURON provides the `h` gateway object. It gives access to internal
+classes (templates) and objects, even if they were just created. E.g.:
+
+.. code-block::
+    python
+
+    >>> from neuron import h
+    >>> # Create objects in the hoc stack
+    >>> h("objref vec")
+    >>> h("vec = new Vector(5, 1)")
+    >>> # Access to objects
+    >>> h.vec.as_numpy()
+    array([1., 1., 1., 1., 1.])
+    >>>
+    >>> # Access to exposed types
+    >>> vv = h.Vector(5, 2)
+    >>> vv.as_numpy()
+    array([1., 1., 1., 1., 1.])
+
+This is particularly useful as NEURON can dynamically load libraries with more functions and classes.
+
+Class Hierarchy
+---------------
+
+All NEURON's internal interpreter objects are instances of a global top-level type: `HocObject`.
+Until very recently they were considered direct instances, without any intermediate hierarchy.
+
+With #1858 Hoc classes are now associated with actual Python types, created dynamically. Such
+change enables type instances to be properly recognized as such, respecting e.g. `isinstance()`
+predicates and subclassing.
+
+.. code-block::
+    python
+
+    >>> isinstance(hoc.Vector, type)
+    True
+    >>> v = h.Vector()
+    >>> isinstance(v, hoc.HocObject)
+    True
+    >>> isinstance(v, hoc.Vector)
+    True
+    >>> type(v) is hoc.Vector  # direct subclass
+    True
+    >>>isinstance(v, hoc.Deck)  # Not instance of other class
+    False
+
+Subclasses are also recognized properly. For creating them please inherit from `HocBaseObject`
+with `hoc_type` given as argument. E.g.:
+
+.. code-block::
+    python
+
+    >>> class MyStim(neuron.HocBaseObject, hoc_type=h.NetStim):
+        pass
+    >>> issubclass(MyStim, hoc.HocObject)
+    True
+    >>> issubclass(MyStim, neuron.HocBaseObject)
+    True
+    >>> MyStim._hoc_type == h.NetStim
+    True
+    >>> stim = MyStim()
+    >>> isinstance(stim, MyStim)
+    True
+    >>> isinstance(stim, h.NetStim)
+    True
+    >>> isinstance(stim, h.HocObject)
+    True

share/lib/python/neuron/hclass3.py

@@ -12,6 +12,12 @@
 import sys
 
 
+def _is_hoc_pytype(hoc_type):
+    return hoc_type is nrn.Section or (
+        isinstance(hoc_type, type) and issubclass(hoc_type, hoc.HocObject)
+    )
+
+
 def assert_not_hoc_composite(cls):
     """
     Asserts that a class is not directly composed of multiple HOC types.
@@ -58,8 +64,8 @@ class MyVector(myClassTemplate):
         omitted the name of the HOC type is used.
     :deprecated: Inherit from :class:`~neuron.HocBaseObject` instead.
     """
-    if hoc_type == h.Section:
-        return nrn.Section
+    if _is_hoc_pytype(hoc_type):
+        return hoc_type
     if module_name is None:
         module_name = __name__
     if name is None:
@@ -90,23 +96,29 @@ class MyVector(neuron.HocBaseObject, hoc_type=neuron.h.Vector):
     """
 
     def __init_subclass__(cls, hoc_type=None, **kwargs):
-        if hoc_type is not None:
-            if not isinstance(hoc_type, hoc.HocObject):
+        if _is_hoc_pytype(hoc_type):
+            cls_name = cls.__name__
+            raise TypeError(
+                f"Using HocBaseObject with {cls_name} is deprecated."
+                f" Inherit directly from {cls_name} instead."
+            )
+        if hoc_type is None:
+            if not hasattr(cls, "_hoc_type"):
                 raise TypeError(
-                    f"Class's `hoc_type` {hoc_type} is not a valid HOC type."
+                    "Class keyword argument `hoc_type` is required for HocBaseObjects."
                 )
+        elif not isinstance(hoc_type, hoc.HocObject):
+            raise TypeError(f"Class's `hoc_type` {hoc_type} is not a valid HOC type.")
+        else:
             cls._hoc_type = hoc_type
-        elif not hasattr(cls, "_hoc_type"):
-            raise TypeError(
-                "Class keyword argument `hoc_type` is required for HocBaseObjects."
-            )
+        # HOC type classes may not be composed of multiple hoc types
         assert_not_hoc_composite(cls)
-        hobj = hoc.HocObject
-        hbase = HocBaseObject
-        if _overrides(cls, hobj, "__init__") and not _overrides(cls, hbase, "__new__"):
-            # Subclasses that override `__init__` must also implement `__new__` to deal
-            # with the arguments that have to be passed into `HocObject.__new__`.
-            # See https://github.com/neuronsimulator/nrn/issues/1129
+        # Subclasses that override `__init__` must also implement `__new__` to deal
+        # with the arguments that have to be passed into `HocObject.__new__`.
+        # See https://github.com/neuronsimulator/nrn/issues/1129
+        if _overrides(cls, hoc.HocObject, "__init__") and not _overrides(
+            cls, HocBaseObject, "__new__"
+        ):
             raise TypeError(
                 f"`{cls.__qualname__}` implements `__init__` but misses `__new__`. "
                 + "Class must implement `__new__`"
@@ -119,7 +131,7 @@ def __new__(cls, *args, **kwds):
         # To construct HOC objects within NEURON from the Python interface, we use the
         # C-extension module `hoc`. `hoc.HocObject.__new__` both creates an internal
         # representation of the object in NEURON, and hands us back a Python object that
-        # is linked to that internal representation. The `__new__` functions takes the
+        # is linked to that internal representation. The `__new__` function takes the
         # arguments that HOC objects of that type would take, and uses the `hocbase`
         # keyword argument to determine which type of HOC object to create. The `sec`
         # keyword argument can be passed along in case the construction of a HOC object

share/lib/python/neuron/tests/utils/checkresult.py

@@ -1,6 +1,6 @@
 import json
 import math
-from neuron import h
+from neuron import h, hoc
 
 
 class Chk:
@@ -39,7 +39,7 @@ def __call__(self, key, value, tol=0.0):
         """
 
         if key in self.d:
-            if type(value) == type(h.Vector):  # actually hoc.HocObject
+            if isinstance(value, hoc.Vector):
                 # Convert to list to keep the `equal` method below simple
                 value = list(value)
             # Hand-rolled comparison that uses `tol` for arithmetic values
@@ -75,7 +75,7 @@ def equal(a, b):
             assert match
         else:
             print("{} added {}".format(self, key))
-            if type(value) == type(h.Vector):  # actually hoc.HocObject
+            if isinstance(value, hoc.Vector):
                 self.d[key] = value.to_python()
             else:
                 self.d[key] = value

src/nrnoc/init.cpp

@@ -866,13 +866,13 @@ int point_reg_helper(Symbol* s2) {
     return pointtype++;
 }
 
-extern void class2oc(const char*,
-                     void* (*cons)(Object*),
-                     void (*destruct)(void*),
-                     Member_func*,
-                     int (*checkpoint)(void**),
-                     Member_ret_obj_func*,
-                     Member_ret_str_func*);
+extern void class2oc_base(const char*,
+                          void* (*cons)(Object*),
+                          void (*destruct)(void*),
+                          Member_func*,
+                          int (*checkpoint)(void**),
+                          Member_ret_obj_func*,
+                          Member_ret_str_func*);
 
 
 int point_register_mech(const char** m,
@@ -890,7 +890,7 @@ int point_register_mech(const char** m,
     Symlist* sl;
     Symbol *s, *s2;
     nrn_load_name_check(m[1]);
-    class2oc(m[1], constructor, destructor, fmember, nullptr, nullptr, nullptr);
+    class2oc_base(m[1], constructor, destructor, fmember, nullptr, nullptr, nullptr);
     s = hoc_lookup(m[1]);
     sl = hoc_symlist;
     hoc_symlist = s->u.ctemplate->symtable;