From 1992f22089fafa721ee78939ba0c00121fd3c274 Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Wed, 18 Mar 2026 14:03:41 +0100
Subject: [PATCH 1/5] rebased against the current develop

---
 src/easyscience/base_classes/__init__.py      |   3 +-
 .../base_classes/collection_base_easylist.py  | 483 ++++++++++++++++++
 .../test_collection_base_easylist.py          |  81 +++
 3 files changed, 566 insertions(+), 1 deletion(-)
 create mode 100644 src/easyscience/base_classes/collection_base_easylist.py
 create mode 100644 tests/unit/base_classes/test_collection_base_easylist.py

diff --git a/src/easyscience/base_classes/__init__.py b/src/easyscience/base_classes/__init__.py
index b5dc0418..b60c5e54 100644
--- a/src/easyscience/base_classes/__init__.py
+++ b/src/easyscience/base_classes/__init__.py
@@ -3,9 +3,10 @@
 
 from .based_base import BasedBase
 from .collection_base import CollectionBase
+from .collection_base_easylist import CollectionBase as CollectionBaseEasyList
 from .easy_list import EasyList
 from .model_base import ModelBase
 from .new_base import NewBase
 from .obj_base import ObjBase
 
-__all__ = [BasedBase, CollectionBase, ObjBase, ModelBase, NewBase, EasyList]
+__all__ = [BasedBase, CollectionBase, CollectionBaseEasyList, ObjBase, ModelBase, NewBase, EasyList]
diff --git a/src/easyscience/base_classes/collection_base_easylist.py b/src/easyscience/base_classes/collection_base_easylist.py
new file mode 100644
index 00000000..2256135b
--- /dev/null
+++ b/src/easyscience/base_classes/collection_base_easylist.py
@@ -0,0 +1,483 @@
+#  SPDX-FileCopyrightText: 2025 EasyScience contributors  <core@easyscience.software>
+#  SPDX-License-Identifier: BSD-3-Clause
+#  © 2021-2025 Contributors to the EasyScience project <https://github.com/easyScience/EasyScience
+
+from __future__ import annotations
+
+import copy
+import warnings
+from collections.abc import Iterable
+from importlib import import_module
+from numbers import Number
+from typing import Any
+from typing import Optional
+
+from easyscience.io.serializer_base import SerializerBase
+from easyscience.io.serializer_dict import SerializerDict
+
+from ..variable.descriptor_base import DescriptorBase
+from ..variable.parameter import Parameter
+from .based_base import BasedBase
+from .easy_list import EasyList
+from .new_base import NewBase
+
+
+class CollectionBase(EasyList):
+    """
+    EasyList-backed collection with a small compatibility layer for migration.
+
+    The collection delegates storage and MutableSequence behavior to EasyList,
+    adding only scientific-parameter aggregation methods and a thin compatibility
+    layer for existing callers.
+    """
+
+    # Base types that items in this collection must be instances of when no
+    # custom ``protected_types`` are supplied by the caller.  The validation
+    # check in ``_validate_item`` uses this list to reject plain Python objects
+    # that are not part of the EasyScience type hierarchy.
+    # ``BasedBase`` is only kept for backwards compatibility.
+    _DEFAULT_PROTECTED_TYPES = (DescriptorBase, BasedBase, NewBase)
+
+    # Mapping checked by ``SerializerBase._convert_to_dict`` to
+    # decide how to serialise each constructor argument.  ``None``
+    # tells the serialiser to skip that attribute entirely,
+    # a callable value would be invoked to produce the serialised form.
+    # ``interface`` should never be persistent and it will soon be removed.
+    _REDIRECT = {'interface': None}
+
+    def __init__(
+        self,
+        *items: Any,
+        name: Optional[str] = None,
+        protected_types: type | Iterable[type] | None = None,
+        unique_name: Optional[str] = None,
+        display_name: Optional[str] = None,
+        interface: Any = None,  # legacy, should be None and will soon be removed
+        data: Optional[Iterable[Any]] = None,
+    ):
+        """Create a new collection of EasyScience objects.
+
+        Items can be supplied as positional arguments or via the *data*
+        iterable.  Both sources are merged in order.
+
+        If the first positional argument is a string and *name* is not given,
+        it is consumed as the collection name.
+
+        :param items: EasyScience objects to include in the collection.
+        :param name: Human-readable name for the collection.
+        :param protected_types: Allowed item types.  Defaults to
+            ``_DEFAULT_PROTECTED_TYPES``.
+        :param unique_name: Machine-friendly unique identifier.
+        :param display_name: Display label; defaults to *name*.
+        :param interface: Reserved internal attribute — must be ``None``.
+        :param data: Additional iterable of items to append.
+        :raises AttributeError: If *interface* is not ``None`` or an item
+            fails type validation.
+        """
+        if items and isinstance(items[0], str) and name is None:
+            name = items[0]
+            items = items[1:]
+
+        if display_name is None and name is not None:
+            display_name = name
+
+        super().__init__(unique_name=unique_name, display_name=display_name)
+
+        if interface is not None:
+            raise AttributeError('Given kwarg: `interface`, is an internal attribute. Please rename.')
+
+        self._protected_types = self._normalize_protected_types(protected_types)
+        self._name = name if name is not None else self.display_name
+        self.user_data: dict[str, Any] = {}
+        self.interface = None
+
+        all_items = self._collect_items(items, data=data)
+        for item in all_items:
+            try:
+                self._validate_item(item)
+            except TypeError as exc:
+                raise AttributeError('A collection can only be formed from easyscience objects.') from exc
+            if item in self:
+                warnings.warn(f'Item with unique name "{self._get_key(item)}" already in CollectionBase, it will be ignored')
+                continue
+            self._data.append(item)
+
+    @property
+    def name(self) -> str:
+        """Human-readable name of the collection."""
+        return self._name
+
+    @name.setter
+    def name(self, new_name: str) -> None:
+        """Set the collection name and sync *display_name*."""
+        if not isinstance(new_name, str):
+            raise TypeError('Name must be a string')
+        self._name = new_name
+        self.display_name = new_name
+
+    # --- Minimal overrides (compatibility shims) ---
+
+    def __getitem__(self, idx: int | slice | str) -> Any:
+        """Retrieve items by integer index, slice, unique-name key, or display name.
+
+        String lookup first tries the EasyList key (unique_name), then falls
+        back to matching on the item's *name* attribute.  If multiple items
+        share the same name a new ``CollectionBase`` containing all matches is
+        returned.
+        """
+        if isinstance(idx, bool):
+            raise TypeError('Boolean indexing is not supported at the moment')
+        if isinstance(idx, slice):
+            return self._clone_with_items(self._data[idx])
+        if isinstance(idx, str):
+            try:
+                return super().__getitem__(idx)
+            except KeyError:
+                pass
+            name_matches = [item for item in self._data if getattr(item, 'name', None) == idx]
+            if len(name_matches) == 1:
+                return name_matches[0]
+            if len(name_matches) > 1:
+                return self._clone_with_items(name_matches)
+            raise KeyError(f'No item with key or name "{idx}" found')
+        return super().__getitem__(idx)
+
+    def __setitem__(self, idx: int | slice, value: Any) -> None:
+        """Set an item by index.
+
+        When *value* is a plain number and the existing item has a ``value``
+        attribute, the number is assigned to ``item.value`` (in-place update).
+        Otherwise the item is replaced via the EasyList, which
+        enforces type validation.
+        """
+        if isinstance(idx, int) and isinstance(value, Number):
+            item = self[idx]
+            if not hasattr(item, 'value'):
+                raise NotImplementedError('At the moment only numerical values or EasyScience objects can be set.')
+            item.value = value
+            return
+        try:
+            super().__setitem__(idx, value)
+        except TypeError as exc:
+            raise NotImplementedError('At the moment only numerical values or EasyScience objects can be set.') from exc
+
+    def insert(self, index: int, value: Any) -> None:
+        """Insert *value* before *index*, validating it against protected types."""
+        try:
+            super().insert(index, value)
+        except TypeError as exc:
+            raise AttributeError('Only EasyScience objects can be put into an EasyScience group') from exc
+
+    def __repr__(self) -> str:
+        return f'{self.__class__.__name__} `{self.name}` of length {len(self)}'
+
+    def sort(self, key=None, reverse: bool = False, mapping=None) -> None:
+        """Sort items in place.
+
+        :param key: Single-argument function used to extract a comparison key.
+        :param reverse: If ``True``, sort in descending order.
+        :param mapping: Deprecated alias for *key*.
+        """
+        if mapping is not None:
+            if key is not None:
+                raise TypeError('Use either key or mapping, not both')
+            warnings.warn('sort(mapping=...) is deprecated; use sort(key=...) instead', DeprecationWarning)
+            key = mapping
+        super().sort(key=key, reverse=reverse)
+
+    # --- Parameter/variable aggregation ---
+
+    def get_all_variables(self) -> list[DescriptorBase]:
+        """Return all descriptors in this collection, recursing into nested items."""
+        variables: list[DescriptorBase] = []
+        for item in self._data:
+            if isinstance(item, DescriptorBase):
+                variables.append(item)
+            elif hasattr(item, 'get_all_variables'):
+                variables.extend(item.get_all_variables())
+        return variables
+
+    def get_all_parameters(self) -> list[Parameter]:
+        """Return all parameters in this collection, recursing into nested items.
+
+        Each parameter appears at most once (deduplicated by identity).
+        """
+        parameters: list[Parameter] = []
+        seen = set()
+        for item in self._data:
+            if isinstance(item, Parameter):
+                parameters.append(item)
+                seen.add(id(item))
+                continue
+            if hasattr(item, 'get_all_parameters'):
+                for parameter in item.get_all_parameters():
+                    if id(parameter) not in seen:
+                        parameters.append(parameter)
+                        seen.add(id(parameter))
+                continue
+            if hasattr(item, 'get_parameters'):
+                for parameter in item.get_parameters():
+                    if id(parameter) not in seen:
+                        parameters.append(parameter)
+                        seen.add(id(parameter))
+                continue
+            if hasattr(item, 'get_all_variables'):
+                for variable in item.get_all_variables():
+                    if isinstance(variable, Parameter) and id(variable) not in seen:
+                        parameters.append(variable)
+                        seen.add(id(variable))
+        return parameters
+
+    def get_parameters(self) -> list[Parameter]:
+        """Alias for :meth:`get_all_parameters`."""
+        return self.get_all_parameters()
+
+    def get_fittable_parameters(self) -> list[Parameter]:
+        """Return all independent (fittable) parameters."""
+        return [parameter for parameter in self.get_all_parameters() if parameter.independent]
+
+    def get_free_parameters(self) -> list[Parameter]:
+        """Return all fittable parameters that are not fixed."""
+        return [parameter for parameter in self.get_fittable_parameters() if not parameter.fixed]
+
+    def get_fit_parameters(self) -> list[Parameter]:
+        """Legacy alias for :meth:`get_free_parameters`."""
+        return self.get_free_parameters()
+
+    @property
+    def data(self) -> tuple[Any, ...]:
+        """Read-only snapshot of the collection items as a tuple."""
+        return tuple(self._data)
+
+    # --- Serialization ---
+
+    def as_dict(self, skip: Optional[list[str]] = None) -> dict[str, Any]:
+        """Legacy. Serialize to a dict, always excluding ``unique_name``."""
+        if skip is None:
+            skip = []
+        if 'unique_name' not in skip:
+            skip = [*skip, 'unique_name']
+        return self.to_dict(skip=skip)
+
+    def encode(self, skip: Optional[list[str]] = None, encoder=None, **kwargs: Any) -> Any:
+        """Legacy. Encode the collection using the given encoder (default: ``SerializerDict``)."""
+        if encoder is None:
+            encoder = SerializerDict
+        return encoder().encode(self, skip=skip, **kwargs)
+
+    @classmethod
+    def decode(cls, obj: Any, decoder=None) -> Any:
+        """Reconstruct a ``CollectionBase`` from a previously encoded object."""
+        if decoder is None or decoder is SerializerDict:
+            return cls.from_dict(obj)
+        return decoder.decode(obj)
+
+    def to_dict(self, skip: Optional[list[str]] = None) -> dict[str, Any]:
+        """Full serialization including ``@module``, ``@class``, and ``@version`` metadata.
+
+        :param skip: List of attribute names to exclude from the output.
+        """
+        if skip is None:
+            skip = []
+
+        try:
+            parent_module = self.__module__.split('.')[0]
+            module_version = import_module(parent_module).__version__
+        except (AttributeError, ImportError):
+            module_version = None
+
+        dict_repr: dict[str, Any] = {
+            '@module': self.__module__,
+            '@class': self.__class__.__name__,
+            '@version': module_version,
+        }
+
+        if 'name' not in skip:
+            dict_repr['name'] = self.name
+        if 'display_name' not in skip and self._display_name is not None and self._display_name != self.name:
+            dict_repr['display_name'] = self._display_name
+        if 'unique_name' not in skip:
+            dict_repr['unique_name'] = self.unique_name
+        if self._protected_types != list(self._DEFAULT_PROTECTED_TYPES) and 'protected_types' not in skip:
+            dict_repr['protected_types'] = [
+                {'@module': cls_.__module__, '@class': cls_.__name__} for cls_ in self._protected_types
+            ]
+        dict_repr['data'] = [self._serialize_item(item, skip=skip) for item in self._data]
+        return dict_repr
+
+    @classmethod
+    def from_dict(cls, obj_dict: dict[str, Any]) -> CollectionBase:
+        """Reconstruct a ``CollectionBase`` from a dict produced by :meth:`to_dict`.
+
+        :param obj_dict: Dictionary containing ``@module``, ``@class``, and ``data`` keys.
+        :raises ValueError: If the dictionary structure or class name is invalid.
+        """
+        if not isinstance(obj_dict, dict) or '@class' not in obj_dict or '@module' not in obj_dict:
+            raise ValueError('Input must be a dictionary representing an EasyScience CollectionBase object.')
+        accepted_names = {base.__name__ for base in cls.__mro__ if issubclass(base, CollectionBase)}
+        if obj_dict['@class'] not in accepted_names:
+            raise ValueError(f'Class name in dictionary does not match the expected class: {cls.__name__}.')
+
+        temp_dict = copy.deepcopy(obj_dict)
+        protected_types = temp_dict.pop('protected_types', None)
+        if protected_types is not None:
+            protected_types = cls._deserialize_protected_types(protected_types)
+
+        raw_data = temp_dict.pop('data', [])
+        kwargs = SerializerBase.deserialize_dict(temp_dict)
+        data = [cls._deserialize_item(item) for item in raw_data]
+        name = kwargs.pop('name', None)
+        kwargs.pop('unique_name', None)
+        return cls(*data, name=name, protected_types=protected_types, **kwargs)
+
+    def _convert_to_dict(
+        self,
+        in_dict: dict[str, Any],
+        encoder: Any,
+        skip: Optional[list[str]] = None,
+        **kwargs: Any,
+    ) -> dict[str, Any]:
+        """Legacy. Hook used by ``SerializerBase`` to populate *in_dict* with collection data."""
+        if skip is None:
+            skip = []
+        if 'name' not in skip:
+            in_dict['name'] = self.name
+        if self._display_name is not None and self._display_name != self.name and 'display_name' not in skip:
+            in_dict['display_name'] = self._display_name
+        in_dict['data'] = [encoder._convert_to_dict(item, skip=skip, **kwargs) for item in self._data]
+        return in_dict
+
+    @staticmethod
+    def _deserialize_protected_types(protected_types: list[dict[str, str]]) -> list[type]:
+        """Resolve serialized ``{@module, @class}`` dicts back to live type objects."""
+        deserialized_types: list[type] = []
+        for type_dict in protected_types:
+            if '@module' not in type_dict or '@class' not in type_dict:
+                raise ValueError('Each protected type must contain @module and @class keys')
+            module = __import__(type_dict['@module'], globals(), locals(), [type_dict['@class']], 0)
+            deserialized_types.append(getattr(module, type_dict['@class']))
+        return deserialized_types
+
+    def _clone_with_items(self, items: Iterable[Any]) -> CollectionBase:
+        """Create a shallow copy of this collection containing the given *items*."""
+        return self.__class__(
+            *list(items),
+            name=self.name,
+            protected_types=list(self._protected_types),
+            display_name=self._display_name,
+        )
+
+    # --- Compatibility surface ---
+
+    def __dir__(self) -> Iterable[str]:
+        # Names that exist on the class but should not be shown to users.
+        # These are internal/new-API names
+        hidden = {
+            'display_name',
+            'get_all_parameters',
+            'get_all_variables',
+            'get_fittable_parameters',
+            'get_free_parameters',
+            'to_dict',
+        }
+        # Names that the old BasedBase/BaseObj API exposed and that
+        # downstream code may rely on for introspection
+        legacy = {
+            'append',
+            'as_dict',
+            'clear',
+            'constraints',
+            'count',
+            'data',
+            'decode',
+            'encode',
+            'extend',
+            'from_dict',
+            'generate_bindings',
+            'get_fit_parameters',
+            'get_parameters',
+            'index',
+            'insert',
+            'interface',
+            'name',
+            'pop',
+            'remove',
+            'reverse',
+            'sort',
+            'switch_interface',
+            'unique_name',
+            'user_data',
+        }
+        public_names = {name for name in dir(self.__class__) if not name.startswith('_')}
+        return sorted((public_names | legacy) - hidden)
+
+    @property
+    def constraints(self) -> list[Any]:
+        """Compatibility stub — always returns an empty list."""
+        return []
+
+    def generate_bindings(self) -> None:
+        """Compatibility stub — requires ``interface`` to be set."""
+        if self.interface is None:
+            raise AttributeError('Interface error for generating bindings. `interface` has to be set.')
+
+    def switch_interface(self, new_interface_name: str) -> None:
+        """Compatibility stub — requires ``interface`` to be set."""
+        if self.interface is None:
+            raise AttributeError('Interface error for generating bindings. `interface` has to be set.')
+
+    # --- Internal helpers ---
+
+    def _collect_items(
+        self,
+        items: tuple[Any, ...],
+        data: Optional[Iterable[Any]] = None,
+    ) -> list[Any]:
+        """Merge positional *items* and *data* into a flat list.
+
+        Lists inside *items* are flattened one level.
+        """
+        collected: list[Any] = []
+        for item in items:
+            if isinstance(item, list):
+                collected.extend(item)
+            else:
+                collected.append(item)
+        if data is not None:
+            collected.extend(data)
+        return collected
+
+    def _normalize_protected_types(self, protected_types: type | Iterable[type] | None) -> list[type]:
+        """Coerce *protected_types* into a list, falling back to the class default."""
+        if protected_types is None:
+            return list(self._DEFAULT_PROTECTED_TYPES)
+        if isinstance(protected_types, type):
+            return [protected_types]
+        if isinstance(protected_types, Iterable):
+            normalized = list(protected_types)
+            if all(isinstance(item, type) for item in normalized):
+                return normalized
+        raise TypeError('protected_types must be a type or an iterable of types')
+
+    def _serialize_item(self, item: Any, skip: Optional[list[str]] = None) -> dict[str, Any]:
+        """Serialize a single item via its ``to_dict`` or ``as_dict`` method."""
+        if hasattr(item, 'to_dict'):
+            return item.to_dict()
+        if hasattr(item, 'as_dict'):
+            return item.as_dict(skip=skip)
+        raise TypeError(f'Unable to serialize item of type {type(item)}')
+
+    @staticmethod
+    def _deserialize_item(item: Any) -> Any:
+        """Deserialize a single item dict back into an EasyScience object."""
+        if not SerializerBase._is_serialized_easyscience_object(item):
+            return SerializerBase._deserialize_value(item)
+
+        normalized_item = copy.deepcopy(item)
+        normalized_item.pop('unique_name', None)
+        return SerializerBase._deserialize_value(normalized_item)
+
+    def _validate_item(self, item: Any) -> None:
+        """Raise ``TypeError`` if *item* is not an instance of a protected type."""
+        if not isinstance(item, tuple(self._protected_types)):
+            raise TypeError(f'Items must be one of {self._protected_types}, got {type(item)}')
diff --git a/tests/unit/base_classes/test_collection_base_easylist.py b/tests/unit/base_classes/test_collection_base_easylist.py
new file mode 100644
index 00000000..a54c52c5
--- /dev/null
+++ b/tests/unit/base_classes/test_collection_base_easylist.py
@@ -0,0 +1,81 @@
+#  SPDX-FileCopyrightText: 2025 EasyScience contributors  <core@easyscience.software>
+#  SPDX-License-Identifier: BSD-3-Clause
+#  © 2021-2025 Contributors to the EasyScience project <https://github.com/easyScience/EasyScience
+
+import pytest
+
+from easyscience import DescriptorNumber
+from easyscience import ObjBase
+from easyscience import Parameter
+from easyscience import global_object
+from easyscience.base_classes import CollectionBaseEasyList as CollectionBase
+
+
+@pytest.fixture(autouse=True)
+def clear():
+    global_object.map._clear()
+
+
+def test_collection_base_getitem_supports_unique_name_and_name_fallback():
+    p1 = Parameter('dup', 1.0, unique_name='p1')
+    p2 = Parameter('dup', 2.0, unique_name='p2')
+
+    collection = CollectionBase('test', p1, p2)
+
+    assert collection['p1'] is p1
+    same_name = collection['dup']
+    assert isinstance(same_name, CollectionBase)
+    assert len(same_name) == 2
+    assert list(same_name) == [p1, p2]
+
+
+def test_collection_base_get_all_variables_includes_direct_leaf_items():
+    descriptor = DescriptorNumber('d1', 1.0)
+    parameter = Parameter('p1', 2.0)
+
+    collection = CollectionBase('test', descriptor, parameter)
+
+    variables = collection.get_all_variables()
+
+    assert variables == [descriptor, parameter]
+
+
+def test_collection_base_get_parameters_recurses_into_nested_objects():
+    nested = ObjBase('nested', p1=Parameter('p1', 1.0), p2=Parameter('p2', 2.0, fixed=True))
+    collection = CollectionBase('test', nested, Parameter('p3', 3.0))
+
+    parameters = collection.get_parameters()
+    free_parameters = collection.get_fit_parameters()
+
+    assert [parameter.name for parameter in parameters] == ['p1', 'p2', 'p3']
+    assert [parameter.name for parameter in free_parameters] == ['p1', 'p3']
+
+
+def test_collection_base_supports_numeric_item_assignment():
+    parameter = Parameter('p1', 1.0)
+    collection = CollectionBase('test', parameter)
+
+    collection[0] = 4.0
+
+    assert collection[0].value == 4.0
+
+
+def test_collection_base_to_dict_round_trip_preserves_name_and_data():
+    p1 = Parameter('p1', 1.0)
+    p2 = Parameter('p2', 2.0)
+    collection = CollectionBase('test', p1, p2)
+
+    encoded = collection.to_dict()
+    decoded = CollectionBase.from_dict(encoded)
+
+    assert decoded.name == 'test'
+    assert [item.name for item in decoded] == ['p1', 'p2']
+    assert [item.value for item in decoded] == [1.0, 2.0]
+
+
+def test_collection_base_sort_accepts_mapping_alias():
+    collection = CollectionBase('test', Parameter('p1', 3.0), Parameter('p2', 1.0), Parameter('p3', 2.0))
+
+    collection.sort(mapping=lambda item: item.value)
+
+    assert [item.value for item in collection] == [1.0, 2.0, 3.0]
\ No newline at end of file

From 408f4b64394c90785454f92ecc81bfb3405f7184 Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Wed, 18 Mar 2026 15:29:38 +0100
Subject: [PATCH 2/5] fixed formatting

---
 src/easyscience/base_classes/__init__.py      | 10 ++-
 .../base_classes/collection_base_easylist.py  | 80 ++++++++++++++-----
 2 files changed, 70 insertions(+), 20 deletions(-)

diff --git a/src/easyscience/base_classes/__init__.py b/src/easyscience/base_classes/__init__.py
index b60c5e54..d315cf0d 100644
--- a/src/easyscience/base_classes/__init__.py
+++ b/src/easyscience/base_classes/__init__.py
@@ -9,4 +9,12 @@
 from .new_base import NewBase
 from .obj_base import ObjBase
 
-__all__ = [BasedBase, CollectionBase, CollectionBaseEasyList, ObjBase, ModelBase, NewBase, EasyList]
+__all__ = [
+    BasedBase,
+    CollectionBase,
+    CollectionBaseEasyList,
+    ObjBase,
+    ModelBase,
+    NewBase,
+    EasyList,
+]
diff --git a/src/easyscience/base_classes/collection_base_easylist.py b/src/easyscience/base_classes/collection_base_easylist.py
index 2256135b..9b55108f 100644
--- a/src/easyscience/base_classes/collection_base_easylist.py
+++ b/src/easyscience/base_classes/collection_base_easylist.py
@@ -84,7 +84,9 @@ def __init__(
         super().__init__(unique_name=unique_name, display_name=display_name)
 
         if interface is not None:
-            raise AttributeError('Given kwarg: `interface`, is an internal attribute. Please rename.')
+            raise AttributeError(
+                'Given kwarg: `interface`, is an internal attribute. Please rename.'
+            )
 
         self._protected_types = self._normalize_protected_types(protected_types)
         self._name = name if name is not None else self.display_name
@@ -96,9 +98,13 @@ def __init__(
             try:
                 self._validate_item(item)
             except TypeError as exc:
-                raise AttributeError('A collection can only be formed from easyscience objects.') from exc
+                raise AttributeError(
+                    'A collection can only be formed from easyscience objects.'
+                ) from exc
             if item in self:
-                warnings.warn(f'Item with unique name "{self._get_key(item)}" already in CollectionBase, it will be ignored')
+                warnings.warn(
+                    f'Item with unique name "{self._get_key(item)}" already in CollectionBase, it will be ignored'
+                )
                 continue
             self._data.append(item)
 
@@ -153,20 +159,26 @@ def __setitem__(self, idx: int | slice, value: Any) -> None:
         if isinstance(idx, int) and isinstance(value, Number):
             item = self[idx]
             if not hasattr(item, 'value'):
-                raise NotImplementedError('At the moment only numerical values or EasyScience objects can be set.')
+                raise NotImplementedError(
+                    'At the moment only numerical values or EasyScience objects can be set.'
+                )
             item.value = value
             return
         try:
             super().__setitem__(idx, value)
         except TypeError as exc:
-            raise NotImplementedError('At the moment only numerical values or EasyScience objects can be set.') from exc
+            raise NotImplementedError(
+                'At the moment only numerical values or EasyScience objects can be set.'
+            ) from exc
 
     def insert(self, index: int, value: Any) -> None:
         """Insert *value* before *index*, validating it against protected types."""
         try:
             super().insert(index, value)
         except TypeError as exc:
-            raise AttributeError('Only EasyScience objects can be put into an EasyScience group') from exc
+            raise AttributeError(
+                'Only EasyScience objects can be put into an EasyScience group'
+            ) from exc
 
     def __repr__(self) -> str:
         return f'{self.__class__.__name__} `{self.name}` of length {len(self)}'
@@ -181,7 +193,9 @@ def sort(self, key=None, reverse: bool = False, mapping=None) -> None:
         if mapping is not None:
             if key is not None:
                 raise TypeError('Use either key or mapping, not both')
-            warnings.warn('sort(mapping=...) is deprecated; use sort(key=...) instead', DeprecationWarning)
+            warnings.warn(
+                'sort(mapping=...) is deprecated; use sort(key=...) instead', DeprecationWarning
+            )
             key = mapping
         super().sort(key=key, reverse=reverse)
 
@@ -294,13 +308,21 @@ def to_dict(self, skip: Optional[list[str]] = None) -> dict[str, Any]:
 
         if 'name' not in skip:
             dict_repr['name'] = self.name
-        if 'display_name' not in skip and self._display_name is not None and self._display_name != self.name:
+        if (
+            'display_name' not in skip
+            and self._display_name is not None
+            and self._display_name != self.name
+        ):
             dict_repr['display_name'] = self._display_name
         if 'unique_name' not in skip:
             dict_repr['unique_name'] = self.unique_name
-        if self._protected_types != list(self._DEFAULT_PROTECTED_TYPES) and 'protected_types' not in skip:
+        if (
+            self._protected_types != list(self._DEFAULT_PROTECTED_TYPES)
+            and 'protected_types' not in skip
+        ):
             dict_repr['protected_types'] = [
-                {'@module': cls_.__module__, '@class': cls_.__name__} for cls_ in self._protected_types
+                {'@module': cls_.__module__, '@class': cls_.__name__}
+                for cls_ in self._protected_types
             ]
         dict_repr['data'] = [self._serialize_item(item, skip=skip) for item in self._data]
         return dict_repr
@@ -313,10 +335,16 @@ def from_dict(cls, obj_dict: dict[str, Any]) -> CollectionBase:
         :raises ValueError: If the dictionary structure or class name is invalid.
         """
         if not isinstance(obj_dict, dict) or '@class' not in obj_dict or '@module' not in obj_dict:
-            raise ValueError('Input must be a dictionary representing an EasyScience CollectionBase object.')
-        accepted_names = {base.__name__ for base in cls.__mro__ if issubclass(base, CollectionBase)}
+            raise ValueError(
+                'Input must be a dictionary representing an EasyScience CollectionBase object.'
+            )
+        accepted_names = {
+            base.__name__ for base in cls.__mro__ if issubclass(base, CollectionBase)
+        }
         if obj_dict['@class'] not in accepted_names:
-            raise ValueError(f'Class name in dictionary does not match the expected class: {cls.__name__}.')
+            raise ValueError(
+                f'Class name in dictionary does not match the expected class: {cls.__name__}.'
+            )
 
         temp_dict = copy.deepcopy(obj_dict)
         protected_types = temp_dict.pop('protected_types', None)
@@ -342,9 +370,15 @@ def _convert_to_dict(
             skip = []
         if 'name' not in skip:
             in_dict['name'] = self.name
-        if self._display_name is not None and self._display_name != self.name and 'display_name' not in skip:
+        if (
+            self._display_name is not None
+            and self._display_name != self.name
+            and 'display_name' not in skip
+        ):
             in_dict['display_name'] = self._display_name
-        in_dict['data'] = [encoder._convert_to_dict(item, skip=skip, **kwargs) for item in self._data]
+        in_dict['data'] = [
+            encoder._convert_to_dict(item, skip=skip, **kwargs) for item in self._data
+        ]
         return in_dict
 
     @staticmethod
@@ -354,7 +388,9 @@ def _deserialize_protected_types(protected_types: list[dict[str, str]]) -> list[
         for type_dict in protected_types:
             if '@module' not in type_dict or '@class' not in type_dict:
                 raise ValueError('Each protected type must contain @module and @class keys')
-            module = __import__(type_dict['@module'], globals(), locals(), [type_dict['@class']], 0)
+            module = __import__(
+                type_dict['@module'], globals(), locals(), [type_dict['@class']], 0
+            )
             deserialized_types.append(getattr(module, type_dict['@class']))
         return deserialized_types
 
@@ -419,12 +455,16 @@ def constraints(self) -> list[Any]:
     def generate_bindings(self) -> None:
         """Compatibility stub — requires ``interface`` to be set."""
         if self.interface is None:
-            raise AttributeError('Interface error for generating bindings. `interface` has to be set.')
+            raise AttributeError(
+                'Interface error for generating bindings. `interface` has to be set.'
+            )
 
     def switch_interface(self, new_interface_name: str) -> None:
         """Compatibility stub — requires ``interface`` to be set."""
         if self.interface is None:
-            raise AttributeError('Interface error for generating bindings. `interface` has to be set.')
+            raise AttributeError(
+                'Interface error for generating bindings. `interface` has to be set.'
+            )
 
     # --- Internal helpers ---
 
@@ -447,7 +487,9 @@ def _collect_items(
             collected.extend(data)
         return collected
 
-    def _normalize_protected_types(self, protected_types: type | Iterable[type] | None) -> list[type]:
+    def _normalize_protected_types(
+        self, protected_types: type | Iterable[type] | None
+    ) -> list[type]:
         """Coerce *protected_types* into a list, falling back to the class default."""
         if protected_types is None:
             return list(self._DEFAULT_PROTECTED_TYPES)

From 3cb07c89a34cdc1a2021d413ea7a38c6e3967616 Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Wed, 18 Mar 2026 16:41:04 +0100
Subject: [PATCH 3/5] more formatting

---
 tests/unit/base_classes/test_collection_base_easylist.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/unit/base_classes/test_collection_base_easylist.py b/tests/unit/base_classes/test_collection_base_easylist.py
index a54c52c5..0c4637cb 100644
--- a/tests/unit/base_classes/test_collection_base_easylist.py
+++ b/tests/unit/base_classes/test_collection_base_easylist.py
@@ -74,8 +74,10 @@ def test_collection_base_to_dict_round_trip_preserves_name_and_data():
 
 
 def test_collection_base_sort_accepts_mapping_alias():
-    collection = CollectionBase('test', Parameter('p1', 3.0), Parameter('p2', 1.0), Parameter('p3', 2.0))
+    collection = CollectionBase(
+        'test', Parameter('p1', 3.0), Parameter('p2', 1.0), Parameter('p3', 2.0)
+    )
 
     collection.sort(mapping=lambda item: item.value)
 
-    assert [item.value for item in collection] == [1.0, 2.0, 3.0]
\ No newline at end of file
+    assert [item.value for item in collection] == [1.0, 2.0, 3.0]

From 80e76e78298b9e653c32ac8b353a1824978e17de Mon Sep 17 00:00:00 2001
From: Piotr Rozyczko <piotr.rozyczko@gmail.com>
Date: Wed, 18 Mar 2026 16:48:01 +0100
Subject: [PATCH 4/5] doc-format-fix

---
 .../base_classes/collection_base_easylist.py  | 73 +++++++++++++------
 1 file changed, 52 insertions(+), 21 deletions(-)

diff --git a/src/easyscience/base_classes/collection_base_easylist.py b/src/easyscience/base_classes/collection_base_easylist.py
index 9b55108f..3e967c82 100644
--- a/src/easyscience/base_classes/collection_base_easylist.py
+++ b/src/easyscience/base_classes/collection_base_easylist.py
@@ -23,12 +23,12 @@
 
 
 class CollectionBase(EasyList):
-    """
-    EasyList-backed collection with a small compatibility layer for migration.
+    """EasyList-backed collection with a small compatibility layer for
+    migration.
 
-    The collection delegates storage and MutableSequence behavior to EasyList,
-    adding only scientific-parameter aggregation methods and a thin compatibility
-    layer for existing callers.
+    The collection delegates storage and MutableSequence behavior to
+    EasyList, adding only scientific-parameter aggregation methods and a
+    thin compatibility layer for existing callers.
     """
 
     # Base types that items in this collection must be instances of when no
@@ -124,7 +124,8 @@ def name(self, new_name: str) -> None:
     # --- Minimal overrides (compatibility shims) ---
 
     def __getitem__(self, idx: int | slice | str) -> Any:
-        """Retrieve items by integer index, slice, unique-name key, or display name.
+        """Retrieve items by integer index, slice, unique-name key, or
+        display name.
 
         String lookup first tries the EasyList key (unique_name), then falls
         back to matching on the item's *name* attribute.  If multiple items
@@ -172,7 +173,9 @@ def __setitem__(self, idx: int | slice, value: Any) -> None:
             ) from exc
 
     def insert(self, index: int, value: Any) -> None:
-        """Insert *value* before *index*, validating it against protected types."""
+        """Insert *value* before *index*, validating it against
+        protected types.
+        """
         try:
             super().insert(index, value)
         except TypeError as exc:
@@ -202,7 +205,9 @@ def sort(self, key=None, reverse: bool = False, mapping=None) -> None:
     # --- Parameter/variable aggregation ---
 
     def get_all_variables(self) -> list[DescriptorBase]:
-        """Return all descriptors in this collection, recursing into nested items."""
+        """Return all descriptors in this collection, recursing into
+        nested items.
+        """
         variables: list[DescriptorBase] = []
         for item in self._data:
             if isinstance(item, DescriptorBase):
@@ -212,7 +217,8 @@ def get_all_variables(self) -> list[DescriptorBase]:
         return variables
 
     def get_all_parameters(self) -> list[Parameter]:
-        """Return all parameters in this collection, recursing into nested items.
+        """Return all parameters in this collection, recursing into
+        nested items.
 
         Each parameter appears at most once (deduplicated by identity).
         """
@@ -266,7 +272,10 @@ def data(self) -> tuple[Any, ...]:
     # --- Serialization ---
 
     def as_dict(self, skip: Optional[list[str]] = None) -> dict[str, Any]:
-        """Legacy. Serialize to a dict, always excluding ``unique_name``."""
+        """Legacy.
+
+        Serialize to a dict, always excluding ``unique_name``.
+        """
         if skip is None:
             skip = []
         if 'unique_name' not in skip:
@@ -274,20 +283,26 @@ def as_dict(self, skip: Optional[list[str]] = None) -> dict[str, Any]:
         return self.to_dict(skip=skip)
 
     def encode(self, skip: Optional[list[str]] = None, encoder=None, **kwargs: Any) -> Any:
-        """Legacy. Encode the collection using the given encoder (default: ``SerializerDict``)."""
+        """Legacy.
+
+        Encode the collection using the given encoder (default: ``SerializerDict``).
+        """
         if encoder is None:
             encoder = SerializerDict
         return encoder().encode(self, skip=skip, **kwargs)
 
     @classmethod
     def decode(cls, obj: Any, decoder=None) -> Any:
-        """Reconstruct a ``CollectionBase`` from a previously encoded object."""
+        """Reconstruct a ``CollectionBase`` from a previously encoded
+        object.
+        """
         if decoder is None or decoder is SerializerDict:
             return cls.from_dict(obj)
         return decoder.decode(obj)
 
     def to_dict(self, skip: Optional[list[str]] = None) -> dict[str, Any]:
-        """Full serialization including ``@module``, ``@class``, and ``@version`` metadata.
+        """Full serialization including ``@module``, ``@class``, and
+        ``@version`` metadata.
 
         :param skip: List of attribute names to exclude from the output.
         """
@@ -329,7 +344,8 @@ def to_dict(self, skip: Optional[list[str]] = None) -> dict[str, Any]:
 
     @classmethod
     def from_dict(cls, obj_dict: dict[str, Any]) -> CollectionBase:
-        """Reconstruct a ``CollectionBase`` from a dict produced by :meth:`to_dict`.
+        """Reconstruct a ``CollectionBase`` from a dict produced by
+        :meth:`to_dict`.
 
         :param obj_dict: Dictionary containing ``@module``, ``@class``, and ``data`` keys.
         :raises ValueError: If the dictionary structure or class name is invalid.
@@ -365,7 +381,10 @@ def _convert_to_dict(
         skip: Optional[list[str]] = None,
         **kwargs: Any,
     ) -> dict[str, Any]:
-        """Legacy. Hook used by ``SerializerBase`` to populate *in_dict* with collection data."""
+        """Legacy.
+
+        Hook used by ``SerializerBase`` to populate *in_dict* with collection data.
+        """
         if skip is None:
             skip = []
         if 'name' not in skip:
@@ -383,7 +402,9 @@ def _convert_to_dict(
 
     @staticmethod
     def _deserialize_protected_types(protected_types: list[dict[str, str]]) -> list[type]:
-        """Resolve serialized ``{@module, @class}`` dicts back to live type objects."""
+        """Resolve serialized ``{@module, @class}`` dicts back to live
+        type objects.
+        """
         deserialized_types: list[type] = []
         for type_dict in protected_types:
             if '@module' not in type_dict or '@class' not in type_dict:
@@ -395,7 +416,9 @@ def _deserialize_protected_types(protected_types: list[dict[str, str]]) -> list[
         return deserialized_types
 
     def _clone_with_items(self, items: Iterable[Any]) -> CollectionBase:
-        """Create a shallow copy of this collection containing the given *items*."""
+        """Create a shallow copy of this collection containing the given
+        *items*.
+        """
         return self.__class__(
             *list(items),
             name=self.name,
@@ -490,7 +513,9 @@ def _collect_items(
     def _normalize_protected_types(
         self, protected_types: type | Iterable[type] | None
     ) -> list[type]:
-        """Coerce *protected_types* into a list, falling back to the class default."""
+        """Coerce *protected_types* into a list, falling back to the
+        class default.
+        """
         if protected_types is None:
             return list(self._DEFAULT_PROTECTED_TYPES)
         if isinstance(protected_types, type):
@@ -502,7 +527,9 @@ def _normalize_protected_types(
         raise TypeError('protected_types must be a type or an iterable of types')
 
     def _serialize_item(self, item: Any, skip: Optional[list[str]] = None) -> dict[str, Any]:
-        """Serialize a single item via its ``to_dict`` or ``as_dict`` method."""
+        """Serialize a single item via its ``to_dict`` or ``as_dict``
+        method.
+        """
         if hasattr(item, 'to_dict'):
             return item.to_dict()
         if hasattr(item, 'as_dict'):
@@ -511,7 +538,9 @@ def _serialize_item(self, item: Any, skip: Optional[list[str]] = None) -> dict[s
 
     @staticmethod
     def _deserialize_item(item: Any) -> Any:
-        """Deserialize a single item dict back into an EasyScience object."""
+        """Deserialize a single item dict back into an EasyScience
+        object.
+        """
         if not SerializerBase._is_serialized_easyscience_object(item):
             return SerializerBase._deserialize_value(item)
 
@@ -520,6 +549,8 @@ def _deserialize_item(item: Any) -> Any:
         return SerializerBase._deserialize_value(normalized_item)
 
     def _validate_item(self, item: Any) -> None:
-        """Raise ``TypeError`` if *item* is not an instance of a protected type."""
+        """Raise ``TypeError`` if *item* is not an instance of a
+        protected type.
+        """
         if not isinstance(item, tuple(self._protected_types)):
             raise TypeError(f'Items must be one of {self._protected_types}, got {type(item)}')

From bd25383ced649a7313ce57512211bdd027ee7f12 Mon Sep 17 00:00:00 2001
From: rozyczko <piotr.rozyczko@gmail.com>
Date: Thu, 19 Mar 2026 18:40:02 +0100
Subject: [PATCH 5/5] removed vestiges of BasedBase backward compatibility
 layer

---
 pixi.lock                                     | 1312 ++++++++---------
 pyproject.toml                                |    1 -
 .../base_classes/collection_base_easylist.py  |  372 ++---
 .../test_collection_base_easylist.py          |  130 +-
 4 files changed, 834 insertions(+), 981 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index 5d5f40a6..d88eaabe 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -52,8 +52,8 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/ed/c9/d7977eaacb9df673210491da99e6a247e93df98c715fc43fd136ce1d3d33/arrow-1.4.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/99/31/6cf181011dc738c33bf6ba7aea2e8e1d3c1f71b7dab1942f3054f66f6202/asteval-1.0.8-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/d2/39/e7eaf1799466a4aef85b6a4fe7bd175ad2b1c6345066aa33f1f58d4b18d0/asttokens-3.0.1-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/13/5c/af990f019b8dd11c5492a6371fe74a5b0276357370030b67254a87329944/async_lru-2.2.0-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/3a/2a/7cc015f5b9f5db42b7d48157e23356022889fc354a2813c15934b7cb5c0e/attrs-25.4.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/e5/e2/c2e3abf398f80732e58b03be77bde9022550d221dd8781bf586bd4d97cc1/async_lru-2.3.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/64/b4/17d4b0b2a2dc85a6df63d1157e028ed19f90d4cd97c36717afef2bc2f395/attrs-26.1.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/9e/43/53afb8ba17218f19b77c7834128566c5bbb100a0ad9ba2e8e89d089d7079/autopep8-2.3.2-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/77/f5/21d2de20e8b8b0408f0681956ca2c69f1320a3848ac50e6e7f39c6159675/babel-2.18.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/c5/71/c754b1737ad99102e03fa3235acb6cb6d3ac9d6f596cbc3e5f236705abd8/backrefs-6.2-py313-none-any.whl
@@ -66,20 +66,20 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/9a/3c/c17fb3ca2d9c3acff52e30b309f538586f9f5b9c9cf454f3845fc9af4881/certifi-2026.2.25-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/98/df/0a1755e750013a2081e863e7cd37e0cdd02664372c754e5560099eb7aa44/cffi-2.0.0-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/db/3c/33bac158f8ab7f89b2e59426d5fe2e4f63f7ed25df84c036890172b412b5/cfgv-3.5.0-py2.py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/b9/45/860a82d618e5c3930faef0a0fe205b752323e5d10ce0c18fe5016fd4f8d2/chardet-7.0.1-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
-      - pypi: https://files.pythonhosted.org/packages/f5/83/6ab5883f57c9c801ce5e5677242328aa45592be8a00644310a008d04f922/charset_normalizer-3.4.4-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
+      - pypi: https://files.pythonhosted.org/packages/e6/19/f474429b3c6f829b0eeaaeb964c06737c7dc148c97822937b1a2def55b40/chardet-7.2.0-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
+      - pypi: https://files.pythonhosted.org/packages/2b/58/a199d245894b12db0b957d627516c78e055adc3a0d978bc7f65ddaf7c399/charset_normalizer-3.4.6-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/98/78/01c019cdb5d6498122777c1a43056ebb3ebfeef2076d9d026bfe15583b2b/click-8.3.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/88/39/799be3f2f0f38cc727ee3b4f1445fe6d5e4133064ec2e4115069418a5bb6/cloudpickle-3.1.2-py3-none-any.whl
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-  sha256: 70b18734b607bd1da571d097d236cfcfacaf01de45717d59e6e04b96877532e0
+  version: 82.0.1
+  sha256: a59e362652f08dcd477c78bb6e7bd9d80a7995bc73ce773050228a348ce2e5bb
   requires_dist:
   - pytest>=6,!=8.1.* ; extra == 'test'
   - virtualenv>=13.0.0 ; extra == 'test'
@@ -9672,7 +9635,6 @@ packages:
   - importlib-metadata>=6 ; python_full_version < '3.10' and extra == 'core'
   - tomli>=2.0.1 ; python_full_version < '3.11' and extra == 'core'
   - wheel>=0.43.0 ; extra == 'core'
-  - platformdirs>=4.2.2 ; extra == 'core'
   - jaraco-functools>=4 ; extra == 'core'
   - more-itertools ; extra == 'core'
   - pytest-checkdocs>=2.4 ; extra == 'check'
@@ -9702,10 +9664,10 @@ packages:
   version: 1.17.0
   sha256: 4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274
   requires_python: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*'
-- pypi: https://files.pythonhosted.org/packages/04/be/d09147ad1ec7934636ad912901c5fd7667e1c858e19d355237db0d0cd5e4/smmap-5.0.2-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/c1/d4/59e74daffcb57a07668852eeeb6035af9f32cbfd7a1d2511f17d2fe6a738/smmap-5.0.3-py3-none-any.whl
   name: smmap
-  version: 5.0.2
-  sha256: b30115f0def7d7531d22a0fb6502488d879e75b260a9db4d0819cfb25403af5e
+  version: 5.0.3
+  sha256: c106e05d5a61449cf6ba9a1e650227ecfb141590d2a98412103ff35d89fc7b2f
   requires_python: '>=3.7'
 - pypi: https://files.pythonhosted.org/packages/46/2c/1462b1d0a634697ae9e55b3cecdcb64788e8b7d63f54d923fcd0bb140aed/soupsieve-2.8.3-py3-none-any.whl
   name: soupsieve
@@ -9747,13 +9709,13 @@ packages:
   - pygments ; extra == 'tests'
   - littleutils ; extra == 'tests'
   - cython ; extra == 'tests'
-- pypi: https://files.pythonhosted.org/packages/40/44/4a5f08c96eb108af5cb50b41f76142f0afa346dfa99d5296fe7202a11854/tabulate-0.9.0-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/99/55/db07de81b5c630da5cbf5c7df646580ca26dfaefa593667fc6f2fe016d2e/tabulate-0.10.0-py3-none-any.whl
   name: tabulate
-  version: 0.9.0
-  sha256: 024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f
+  version: 0.10.0
+  sha256: f0b0622e567335c8fabaaa659f1b33bcb6ddfe2e496071b743aa113f8774f2d3
   requires_dist:
   - wcwidth ; extra == 'widechars'
-  requires_python: '>=3.7'
+  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/6a/9e/2064975477fdc887e47ad42157e214526dcad8f317a948dee17e1659a62f/terminado-0.18.1-py3-none-any.whl
   name: terminado
   version: 0.18.1
@@ -9875,25 +9837,25 @@ packages:
   version: 2.4.0
   sha256: 5e3f639a7a8f10069d0e15408c0b96a2a828cfdec6fca05296ebcdcc28ca7c76
   requires_python: '>=3.8'
-- pypi: https://files.pythonhosted.org/packages/50/d4/e51d52047e7eb9a582da59f32125d17c0482d065afd5d3bc435ff2120dc5/tornado-6.5.4-cp39-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+- pypi: https://files.pythonhosted.org/packages/2c/23/f6c6112a04d28eed765e374435fb1a9198f73e1ec4b4024184f21faeb1ad/tornado-6.5.5-cp39-abi3-win_amd64.whl
   name: tornado
-  version: 6.5.4
-  sha256: e5fb5e04efa54cf0baabdd10061eb4148e0be137166146fff835745f59ab9f7f
+  version: 6.5.5
+  sha256: 6443a794ba961a9f619b1ae926a2e900ac20c34483eea67be4ed8f1e58d3ef7b
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/ab/a9/e94a9d5224107d7ce3cc1fab8d5dc97f5ea351ccc6322ee4fb661da94e35/tornado-6.5.4-cp39-abi3-macosx_10_9_universal2.whl
+- pypi: https://files.pythonhosted.org/packages/59/8c/77f5097695f4dd8255ecbd08b2a1ed8ba8b953d337804dd7080f199e12bf/tornado-6.5.5-cp39-abi3-macosx_10_9_universal2.whl
   name: tornado
-  version: 6.5.4
-  sha256: d6241c1a16b1c9e4cc28148b1cda97dd1c6cb4fb7068ac1bedc610768dff0ba9
+  version: 6.5.5
+  sha256: 487dc9cc380e29f58c7ab88f9e27cdeef04b2140862e5076a66fb6bb68bb1bfa
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/d6/6d/c69be695a0a64fd37a97db12355a035a6d90f79067a3cf936ec2b1dc38cd/tornado-6.5.4-cp39-abi3-win_amd64.whl
+- pypi: https://files.pythonhosted.org/packages/ab/5e/7625b76cd10f98f1516c36ce0346de62061156352353ef2da44e5c21523c/tornado-6.5.5-cp39-abi3-macosx_10_9_x86_64.whl
   name: tornado
-  version: 6.5.4
-  sha256: fa07d31e0cd85c60713f2b995da613588aa03e1303d75705dca6af8babc18ddc
+  version: 6.5.5
+  sha256: 65a7f1d46d4bb41df1ac99f5fcb685fb25c7e61613742d5108b010975a9a6521
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/db/7e/f7b8d8c4453f305a51f80dbb49014257bb7d28ccb4bbb8dd328ea995ecad/tornado-6.5.4-cp39-abi3-macosx_10_9_x86_64.whl
+- pypi: https://files.pythonhosted.org/packages/b2/04/7b5705d5b3c0fab088f434f9c83edac1573830ca49ccf29fb83bf7178eec/tornado-6.5.5-cp39-abi3-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
   name: tornado
-  version: 6.5.4
-  sha256: 2d50f63dda1d2cac3ae1fa23d254e16b5e38153758470e9956cbc3d813d40843
+  version: 6.5.5
+  sha256: e74c92e8e65086b338fd56333fb9a68b9f6f2fe7ad532645a290a464bcf46be5
   requires_python: '>=3.9'
 - pypi: https://files.pythonhosted.org/packages/00/c0/8f5d070730d7836adc9c9b6408dec68c6ced86b304a9b26a14df072a6e8c/traitlets-5.14.3-py3-none-any.whl
   name: traitlets
@@ -10071,10 +10033,10 @@ packages:
   - mypy ; extra == 'test'
   - pretend ; extra == 'test'
   - pytest ; extra == 'test'
-- pypi: https://files.pythonhosted.org/packages/78/55/896b06bf93a49bec0f4ae2a6f1ed12bd05c8860744ac3a70eda041064e4d/virtualenv-21.1.0-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/c6/59/7d02447a55b2e55755011a647479041bc92a82e143f96a8195cb33bd0a1c/virtualenv-21.2.0-py3-none-any.whl
   name: virtualenv
-  version: 21.1.0
-  sha256: 164f5e14c5587d170cf98e60378eb91ea35bf037be313811905d3a24ea33cc07
+  version: 21.2.0
+  sha256: 1bd755b504931164a5a496d217c014d098426cddc79363ad66ac78125f9d908f
   requires_dist:
   - distlib>=0.3.7,<1
   - filelock>=3.24.2,<4 ; python_full_version >= '3.10'
@@ -10237,30 +10199,6 @@ packages:
   - multidict>=4.0
   - propcache>=0.2.1
   requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/2e/54/647ade08bf0db230bfea292f893923872fd20be6ac6f53b2b936ba839d75/zipp-3.23.0-py3-none-any.whl
-  name: zipp
-  version: 3.23.0
-  sha256: 071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e
-  requires_dist:
-  - pytest>=6,!=8.1.* ; extra == 'test'
-  - jaraco-itertools ; extra == 'test'
-  - jaraco-functools ; extra == 'test'
-  - more-itertools ; extra == 'test'
-  - big-o ; extra == 'test'
-  - pytest-ignore-flaky ; extra == 'test'
-  - jaraco-test ; extra == 'test'
-  - sphinx>=3.5 ; extra == 'doc'
-  - jaraco-packaging>=9.3 ; extra == 'doc'
-  - rst-linker>=1.9 ; extra == 'doc'
-  - furo ; extra == 'doc'
-  - sphinx-lint ; extra == 'doc'
-  - jaraco-tidelift>=1.4 ; extra == 'doc'
-  - pytest-checkdocs>=2.4 ; extra == 'check'
-  - pytest-ruff>=0.2.1 ; sys_platform != 'cygwin' and extra == 'check'
-  - pytest-cov ; extra == 'cover'
-  - pytest-enabler>=2.2 ; extra == 'enabler'
-  - pytest-mypy ; extra == 'type'
-  requires_python: '>=3.9'
 - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
   sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
   md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
diff --git a/pyproject.toml b/pyproject.toml
index c4cba0c2..272acc94 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -181,7 +181,6 @@ preview = true                # Enable new rules that are not yet stable, like D
 docstring-code-format = true    # Whether to format code snippets in docstrings
 docstring-code-line-length = 72 # Line length for code snippets in docstrings
 indent-style = 'space'          # PEP 8 recommends using spaces over tabs
-line-ending = 'lf'              # Line endings will be converted to \n
 quote-style = 'single'          # But double quotes in docstrings (PEP 8, PEP 257)
 
 # https://docs.astral.sh/ruff/rules/
diff --git a/src/easyscience/base_classes/collection_base_easylist.py b/src/easyscience/base_classes/collection_base_easylist.py
index 3e967c82..9497458a 100644
--- a/src/easyscience/base_classes/collection_base_easylist.py
+++ b/src/easyscience/base_classes/collection_base_easylist.py
@@ -5,45 +5,30 @@
 from __future__ import annotations
 
 import copy
-import warnings
 from collections.abc import Iterable
+from collections.abc import MutableSequence
 from importlib import import_module
 from numbers import Number
 from typing import Any
 from typing import Optional
 
 from easyscience.io.serializer_base import SerializerBase
-from easyscience.io.serializer_dict import SerializerDict
 
 from ..variable.descriptor_base import DescriptorBase
-from ..variable.parameter import Parameter
-from .based_base import BasedBase
-from .easy_list import EasyList
-from .new_base import NewBase
+from .model_base import ModelBase
 
 
-class CollectionBase(EasyList):
-    """EasyList-backed collection with a small compatibility layer for
-    migration.
+class CollectionBase(ModelBase, MutableSequence):
+    """A ModelBase-backed collection that can contain only models and
+    other collections.
 
-    The collection delegates storage and MutableSequence behavior to
-    EasyList, adding only scientific-parameter aggregation methods and a
-    thin compatibility layer for existing callers.
+    Inherits from ``ModelBase`` (identity, serialisation, parameter aggregation)
+    and ``MutableSequence`` (list-like interface).  Parameter aggregation
+    methods are overridden to recurse into the contained items rather than
+    using ``dir()`` introspection.
     """
 
-    # Base types that items in this collection must be instances of when no
-    # custom ``protected_types`` are supplied by the caller.  The validation
-    # check in ``_validate_item`` uses this list to reject plain Python objects
-    # that are not part of the EasyScience type hierarchy.
-    # ``BasedBase`` is only kept for backwards compatibility.
-    _DEFAULT_PROTECTED_TYPES = (DescriptorBase, BasedBase, NewBase)
-
-    # Mapping checked by ``SerializerBase._convert_to_dict`` to
-    # decide how to serialise each constructor argument.  ``None``
-    # tells the serialiser to skip that attribute entirely,
-    # a callable value would be invoked to produce the serialised form.
-    # ``interface`` should never be persistent and it will soon be removed.
-    _REDIRECT = {'interface': None}
+    _DEFAULT_PROTECTED_TYPES = (ModelBase,)
 
     def __init__(
         self,
@@ -52,10 +37,9 @@ def __init__(
         protected_types: type | Iterable[type] | None = None,
         unique_name: Optional[str] = None,
         display_name: Optional[str] = None,
-        interface: Any = None,  # legacy, should be None and will soon be removed
         data: Optional[Iterable[Any]] = None,
     ):
-        """Create a new collection of EasyScience objects.
+        """Create a new collection of model objects.
 
         Items can be supplied as positional arguments or via the *data*
         iterable.  Both sources are merged in order.
@@ -63,16 +47,14 @@ def __init__(
         If the first positional argument is a string and *name* is not given,
         it is consumed as the collection name.
 
-        :param items: EasyScience objects to include in the collection.
+        :param items: Model objects to include in the collection.
         :param name: Human-readable name for the collection.
         :param protected_types: Allowed item types.  Defaults to
             ``_DEFAULT_PROTECTED_TYPES``.
         :param unique_name: Machine-friendly unique identifier.
         :param display_name: Display label; defaults to *name*.
-        :param interface: Reserved internal attribute — must be ``None``.
         :param data: Additional iterable of items to append.
-        :raises AttributeError: If *interface* is not ``None`` or an item
-            fails type validation.
+        :raises AttributeError: If an item fails type validation.
         """
         if items and isinstance(items[0], str) and name is None:
             name = items[0]
@@ -83,15 +65,9 @@ def __init__(
 
         super().__init__(unique_name=unique_name, display_name=display_name)
 
-        if interface is not None:
-            raise AttributeError(
-                'Given kwarg: `interface`, is an internal attribute. Please rename.'
-            )
-
         self._protected_types = self._normalize_protected_types(protected_types)
         self._name = name if name is not None else self.display_name
-        self.user_data: dict[str, Any] = {}
-        self.interface = None
+        self._data: list[Any] = []
 
         all_items = self._collect_items(items, data=data)
         for item in all_items:
@@ -99,12 +75,9 @@ def __init__(
                 self._validate_item(item)
             except TypeError as exc:
                 raise AttributeError(
-                    'A collection can only be formed from easyscience objects.'
+                    'A collection can only be formed from model objects.'
                 ) from exc
             if item in self:
-                warnings.warn(
-                    f'Item with unique name "{self._get_key(item)}" already in CollectionBase, it will be ignored'
-                )
                 continue
             self._data.append(item)
 
@@ -121,185 +94,161 @@ def name(self, new_name: str) -> None:
         self._name = new_name
         self.display_name = new_name
 
-    # --- Minimal overrides (compatibility shims) ---
+    # --- MutableSequence abstract methods ---
 
     def __getitem__(self, idx: int | slice | str) -> Any:
         """Retrieve items by integer index, slice, unique-name key, or
         display name.
 
-        String lookup first tries the EasyList key (unique_name), then falls
-        back to matching on the item's *name* attribute.  If multiple items
-        share the same name a new ``CollectionBase`` containing all matches is
-        returned.
+        String lookup first tries the unique_name, then falls back to matching
+        on the item's *name* attribute.  If multiple items share the same name
+        a new ``CollectionBase`` containing all matches is returned.
         """
         if isinstance(idx, bool):
             raise TypeError('Boolean indexing is not supported at the moment')
         if isinstance(idx, slice):
             return self._clone_with_items(self._data[idx])
         if isinstance(idx, str):
-            try:
-                return super().__getitem__(idx)
-            except KeyError:
-                pass
+            element = next((r for r in self._data if self._get_key(r) == idx), None)
+            if element is not None:
+                return element
             name_matches = [item for item in self._data if getattr(item, 'name', None) == idx]
             if len(name_matches) == 1:
                 return name_matches[0]
             if len(name_matches) > 1:
                 return self._clone_with_items(name_matches)
             raise KeyError(f'No item with key or name "{idx}" found')
-        return super().__getitem__(idx)
+        return self._data[idx]
 
     def __setitem__(self, idx: int | slice, value: Any) -> None:
         """Set an item by index.
 
         When *value* is a plain number and the existing item has a ``value``
         attribute, the number is assigned to ``item.value`` (in-place update).
-        Otherwise the item is replaced via the EasyList, which
-        enforces type validation.
+        Otherwise the item is replaced after type validation.
         """
         if isinstance(idx, int) and isinstance(value, Number):
             item = self[idx]
             if not hasattr(item, 'value'):
                 raise NotImplementedError(
-                    'At the moment only numerical values or EasyScience objects can be set.'
+                    'At the moment only numerical values or model objects can be set.'
                 )
             item.value = value
             return
-        try:
-            super().__setitem__(idx, value)
-        except TypeError as exc:
-            raise NotImplementedError(
-                'At the moment only numerical values or EasyScience objects can be set.'
-            ) from exc
+        if isinstance(idx, int):
+            self._validate_item(value)
+            if value is not self._data[idx] and value in self:
+                return
+            self._data[idx] = value
+            return
+        if isinstance(idx, slice):
+            if not isinstance(value, Iterable):
+                raise TypeError('Value must be an iterable for slice assignment')
+            new_values = list(value)
+            for v in new_values:
+                self._validate_item(v)
+            self._data[idx] = new_values
+            return
+        raise TypeError('Index must be an int or slice')
+
+    def __delitem__(self, idx: int | slice | str) -> None:
+        """Delete an item by index, slice, or unique_name."""
+        if isinstance(idx, (int, slice)):
+            del self._data[idx]
+        elif isinstance(idx, str):
+            for i, item in enumerate(self._data):
+                if self._get_key(item) == idx:
+                    del self._data[i]
+                    return
+            raise KeyError(f'No item with unique name "{idx}" found')
+        else:
+            raise TypeError('Index must be an int, slice, or str')
+
+    def __len__(self) -> int:
+        """Return the number of items in the collection."""
+        return len(self._data)
 
     def insert(self, index: int, value: Any) -> None:
         """Insert *value* before *index*, validating it against
         protected types.
         """
         try:
-            super().insert(index, value)
+            self._validate_item(value)
         except TypeError as exc:
-            raise AttributeError(
-                'Only EasyScience objects can be put into an EasyScience group'
-            ) from exc
+            raise AttributeError('Only model objects can be put into a CollectionBase') from exc
+        if value in self:
+            return
+        self._data.insert(index, value)
+
+    # --- Additional list-like methods ---
+
+    def __contains__(self, item: Any) -> bool:
+        if isinstance(item, str):
+            return any(self._get_key(r) == item for r in self._data)
+        return item in self._data
 
     def __repr__(self) -> str:
         return f'{self.__class__.__name__} `{self.name}` of length {len(self)}'
 
-    def sort(self, key=None, reverse: bool = False, mapping=None) -> None:
+    def sort(self, key=None, reverse: bool = False) -> None:
         """Sort items in place.
 
         :param key: Single-argument function used to extract a comparison key.
         :param reverse: If ``True``, sort in descending order.
-        :param mapping: Deprecated alias for *key*.
         """
-        if mapping is not None:
-            if key is not None:
-                raise TypeError('Use either key or mapping, not both')
-            warnings.warn(
-                'sort(mapping=...) is deprecated; use sort(key=...) instead', DeprecationWarning
-            )
-            key = mapping
-        super().sort(key=key, reverse=reverse)
+        self._data.sort(key=key, reverse=reverse)
+
+    def index(self, value: Any, start: int = 0, stop: int | None = None) -> int:
+        if stop is None:
+            stop = len(self._data)
+        if isinstance(value, str):
+            for i in range(start, min(stop, len(self._data))):
+                if self._get_key(self._data[i]) == value:
+                    return i
+            raise ValueError(f'{value} is not in CollectionBase')
+        return self._data.index(value, start, stop)
+
+    def pop(self, index: int | str = -1) -> Any:
+        """Remove and return an item at the given index or
+        unique_name.
+        """
+        if isinstance(index, int):
+            return self._data.pop(index)
+        if isinstance(index, str):
+            for i, item in enumerate(self._data):
+                if self._get_key(item) == index:
+                    return self._data.pop(i)
+            raise KeyError(f'No item with unique name "{index}" found')
+        raise TypeError('Index must be an int or str')
+
+    @staticmethod
+    def _get_key(obj: Any) -> str:
+        """Return the unique name used as the item key."""
+        return obj.unique_name
 
-    # --- Parameter/variable aggregation ---
+    # --- Parameter/variable aggregation (override ModelBase) ---
 
     def get_all_variables(self) -> list[DescriptorBase]:
         """Return all descriptors in this collection, recursing into
         nested items.
-        """
-        variables: list[DescriptorBase] = []
-        for item in self._data:
-            if isinstance(item, DescriptorBase):
-                variables.append(item)
-            elif hasattr(item, 'get_all_variables'):
-                variables.extend(item.get_all_variables())
-        return variables
 
-    def get_all_parameters(self) -> list[Parameter]:
-        """Return all parameters in this collection, recursing into
-        nested items.
-
-        Each parameter appears at most once (deduplicated by identity).
+        Each variable appears at most once (deduplicated by identity).
         """
-        parameters: list[Parameter] = []
-        seen = set()
+        variables: list[DescriptorBase] = []
+        seen: set[int] = set()
         for item in self._data:
-            if isinstance(item, Parameter):
-                parameters.append(item)
-                seen.add(id(item))
-                continue
-            if hasattr(item, 'get_all_parameters'):
-                for parameter in item.get_all_parameters():
-                    if id(parameter) not in seen:
-                        parameters.append(parameter)
-                        seen.add(id(parameter))
-                continue
-            if hasattr(item, 'get_parameters'):
-                for parameter in item.get_parameters():
-                    if id(parameter) not in seen:
-                        parameters.append(parameter)
-                        seen.add(id(parameter))
-                continue
             if hasattr(item, 'get_all_variables'):
                 for variable in item.get_all_variables():
-                    if isinstance(variable, Parameter) and id(variable) not in seen:
-                        parameters.append(variable)
+                    if id(variable) not in seen:
+                        variables.append(variable)
                         seen.add(id(variable))
-        return parameters
-
-    def get_parameters(self) -> list[Parameter]:
-        """Alias for :meth:`get_all_parameters`."""
-        return self.get_all_parameters()
-
-    def get_fittable_parameters(self) -> list[Parameter]:
-        """Return all independent (fittable) parameters."""
-        return [parameter for parameter in self.get_all_parameters() if parameter.independent]
-
-    def get_free_parameters(self) -> list[Parameter]:
-        """Return all fittable parameters that are not fixed."""
-        return [parameter for parameter in self.get_fittable_parameters() if not parameter.fixed]
-
-    def get_fit_parameters(self) -> list[Parameter]:
-        """Legacy alias for :meth:`get_free_parameters`."""
-        return self.get_free_parameters()
+        return variables
 
     @property
     def data(self) -> tuple[Any, ...]:
         """Read-only snapshot of the collection items as a tuple."""
         return tuple(self._data)
 
-    # --- Serialization ---
-
-    def as_dict(self, skip: Optional[list[str]] = None) -> dict[str, Any]:
-        """Legacy.
-
-        Serialize to a dict, always excluding ``unique_name``.
-        """
-        if skip is None:
-            skip = []
-        if 'unique_name' not in skip:
-            skip = [*skip, 'unique_name']
-        return self.to_dict(skip=skip)
-
-    def encode(self, skip: Optional[list[str]] = None, encoder=None, **kwargs: Any) -> Any:
-        """Legacy.
-
-        Encode the collection using the given encoder (default: ``SerializerDict``).
-        """
-        if encoder is None:
-            encoder = SerializerDict
-        return encoder().encode(self, skip=skip, **kwargs)
-
-    @classmethod
-    def decode(cls, obj: Any, decoder=None) -> Any:
-        """Reconstruct a ``CollectionBase`` from a previously encoded
-        object.
-        """
-        if decoder is None or decoder is SerializerDict:
-            return cls.from_dict(obj)
-        return decoder.decode(obj)
-
     def to_dict(self, skip: Optional[list[str]] = None) -> dict[str, Any]:
         """Full serialization including ``@module``, ``@class``, and
         ``@version`` metadata.
@@ -339,7 +288,7 @@ def to_dict(self, skip: Optional[list[str]] = None) -> dict[str, Any]:
                 {'@module': cls_.__module__, '@class': cls_.__name__}
                 for cls_ in self._protected_types
             ]
-        dict_repr['data'] = [self._serialize_item(item, skip=skip) for item in self._data]
+        dict_repr['data'] = [item.to_dict(skip=skip) for item in self._data]
         return dict_repr
 
     @classmethod
@@ -374,32 +323,6 @@ def from_dict(cls, obj_dict: dict[str, Any]) -> CollectionBase:
         kwargs.pop('unique_name', None)
         return cls(*data, name=name, protected_types=protected_types, **kwargs)
 
-    def _convert_to_dict(
-        self,
-        in_dict: dict[str, Any],
-        encoder: Any,
-        skip: Optional[list[str]] = None,
-        **kwargs: Any,
-    ) -> dict[str, Any]:
-        """Legacy.
-
-        Hook used by ``SerializerBase`` to populate *in_dict* with collection data.
-        """
-        if skip is None:
-            skip = []
-        if 'name' not in skip:
-            in_dict['name'] = self.name
-        if (
-            self._display_name is not None
-            and self._display_name != self.name
-            and 'display_name' not in skip
-        ):
-            in_dict['display_name'] = self._display_name
-        in_dict['data'] = [
-            encoder._convert_to_dict(item, skip=skip, **kwargs) for item in self._data
-        ]
-        return in_dict
-
     @staticmethod
     def _deserialize_protected_types(protected_types: list[dict[str, str]]) -> list[type]:
         """Resolve serialized ``{@module, @class}`` dicts back to live
@@ -426,69 +349,6 @@ def _clone_with_items(self, items: Iterable[Any]) -> CollectionBase:
             display_name=self._display_name,
         )
 
-    # --- Compatibility surface ---
-
-    def __dir__(self) -> Iterable[str]:
-        # Names that exist on the class but should not be shown to users.
-        # These are internal/new-API names
-        hidden = {
-            'display_name',
-            'get_all_parameters',
-            'get_all_variables',
-            'get_fittable_parameters',
-            'get_free_parameters',
-            'to_dict',
-        }
-        # Names that the old BasedBase/BaseObj API exposed and that
-        # downstream code may rely on for introspection
-        legacy = {
-            'append',
-            'as_dict',
-            'clear',
-            'constraints',
-            'count',
-            'data',
-            'decode',
-            'encode',
-            'extend',
-            'from_dict',
-            'generate_bindings',
-            'get_fit_parameters',
-            'get_parameters',
-            'index',
-            'insert',
-            'interface',
-            'name',
-            'pop',
-            'remove',
-            'reverse',
-            'sort',
-            'switch_interface',
-            'unique_name',
-            'user_data',
-        }
-        public_names = {name for name in dir(self.__class__) if not name.startswith('_')}
-        return sorted((public_names | legacy) - hidden)
-
-    @property
-    def constraints(self) -> list[Any]:
-        """Compatibility stub — always returns an empty list."""
-        return []
-
-    def generate_bindings(self) -> None:
-        """Compatibility stub — requires ``interface`` to be set."""
-        if self.interface is None:
-            raise AttributeError(
-                'Interface error for generating bindings. `interface` has to be set.'
-            )
-
-    def switch_interface(self, new_interface_name: str) -> None:
-        """Compatibility stub — requires ``interface`` to be set."""
-        if self.interface is None:
-            raise AttributeError(
-                'Interface error for generating bindings. `interface` has to be set.'
-            )
-
     # --- Internal helpers ---
 
     def _collect_items(
@@ -518,23 +378,15 @@ class default.
         """
         if protected_types is None:
             return list(self._DEFAULT_PROTECTED_TYPES)
-        if isinstance(protected_types, type):
+        if isinstance(protected_types, type) and issubclass(protected_types, ModelBase):
             return [protected_types]
         if isinstance(protected_types, Iterable):
             normalized = list(protected_types)
-            if all(isinstance(item, type) for item in normalized):
+            if all(isinstance(item, type) and issubclass(item, ModelBase) for item in normalized):
                 return normalized
-        raise TypeError('protected_types must be a type or an iterable of types')
-
-    def _serialize_item(self, item: Any, skip: Optional[list[str]] = None) -> dict[str, Any]:
-        """Serialize a single item via its ``to_dict`` or ``as_dict``
-        method.
-        """
-        if hasattr(item, 'to_dict'):
-            return item.to_dict()
-        if hasattr(item, 'as_dict'):
-            return item.as_dict(skip=skip)
-        raise TypeError(f'Unable to serialize item of type {type(item)}')
+        raise TypeError(
+            'protected_types must be a ModelBase type or an iterable of ModelBase types'
+        )
 
     @staticmethod
     def _deserialize_item(item: Any) -> Any:
diff --git a/tests/unit/base_classes/test_collection_base_easylist.py b/tests/unit/base_classes/test_collection_base_easylist.py
index 0c4637cb..09eaa3f8 100644
--- a/tests/unit/base_classes/test_collection_base_easylist.py
+++ b/tests/unit/base_classes/test_collection_base_easylist.py
@@ -2,13 +2,53 @@
 #  SPDX-License-Identifier: BSD-3-Clause
 #  © 2021-2025 Contributors to the EasyScience project <https://github.com/easyScience/EasyScience
 
+from typing import Any
+from typing import cast
+
 import pytest
 
-from easyscience import DescriptorNumber
-from easyscience import ObjBase
-from easyscience import Parameter
 from easyscience import global_object
 from easyscience.base_classes import CollectionBaseEasyList as CollectionBase
+from easyscience.base_classes import ModelBase
+from easyscience.variable import Parameter
+
+
+def make_parameter(name: str, value: Any, **kwargs: Any) -> Parameter:
+    return Parameter(name, cast(Any, value), **kwargs)
+
+
+class DummyModel(ModelBase):
+    def __init__(
+        self,
+        name: str,
+        value: Any,
+        unique_name: str | None = None,
+        display_name: str | None = None,
+    ):
+        if display_name is None:
+            display_name = name
+        super().__init__(unique_name=unique_name, display_name=display_name)
+        self._name = name
+        self._value = (
+            value if isinstance(value, Parameter) else make_parameter(f'{name}_value', value)
+        )
+
+    @property
+    def name(self) -> str:
+        return self._name
+
+    @name.setter
+    def name(self, new_name: str) -> None:
+        self._name = new_name
+        self.display_name = new_name
+
+    @property
+    def value(self) -> Parameter:
+        return self._value
+
+    @value.setter
+    def value(self, new_value: float) -> None:
+        self._value.value = new_value
 
 
 @pytest.fixture(autouse=True)
@@ -17,67 +57,91 @@ def clear():
 
 
 def test_collection_base_getitem_supports_unique_name_and_name_fallback():
-    p1 = Parameter('dup', 1.0, unique_name='p1')
-    p2 = Parameter('dup', 2.0, unique_name='p2')
+    m1 = DummyModel('dup', make_parameter('p1', 1.0), unique_name='m1')
+    m2 = DummyModel('dup', make_parameter('p2', 2.0), unique_name='m2')
 
-    collection = CollectionBase('test', p1, p2)
+    collection = CollectionBase('test', m1, m2)
 
-    assert collection['p1'] is p1
+    assert collection['m1'] is m1
     same_name = collection['dup']
     assert isinstance(same_name, CollectionBase)
     assert len(same_name) == 2
-    assert list(same_name) == [p1, p2]
+    assert list(same_name) == [m1, m2]
 
 
-def test_collection_base_get_all_variables_includes_direct_leaf_items():
-    descriptor = DescriptorNumber('d1', 1.0)
-    parameter = Parameter('p1', 2.0)
+def test_collection_base_get_all_variables_recurses_into_models():
+    p1 = make_parameter('p1', 1.0)
+    p2 = make_parameter('p2', 2.0)
+    model1 = DummyModel('m1', p1)
+    model2 = DummyModel('m2', p2)
 
-    collection = CollectionBase('test', descriptor, parameter)
+    collection = CollectionBase('test', model1, model2)
 
     variables = collection.get_all_variables()
 
-    assert variables == [descriptor, parameter]
+    assert p1 in variables
+    assert p2 in variables
 
 
 def test_collection_base_get_parameters_recurses_into_nested_objects():
-    nested = ObjBase('nested', p1=Parameter('p1', 1.0), p2=Parameter('p2', 2.0, fixed=True))
-    collection = CollectionBase('test', nested, Parameter('p3', 3.0))
+    nested = CollectionBase(
+        'nested',
+        DummyModel('m1', make_parameter('p1', 1.0)),
+        DummyModel('m2', make_parameter('p2', 2.0, fixed=True)),
+    )
+    model = DummyModel('model', make_parameter('p3', 3.0))
+    collection = CollectionBase('test', nested, model)
 
-    parameters = collection.get_parameters()
-    free_parameters = collection.get_fit_parameters()
+    parameters = collection.get_all_parameters()
+    free_parameters = collection.get_free_parameters()
 
     assert [parameter.name for parameter in parameters] == ['p1', 'p2', 'p3']
     assert [parameter.name for parameter in free_parameters] == ['p1', 'p3']
 
 
-def test_collection_base_supports_numeric_item_assignment():
-    parameter = Parameter('p1', 1.0)
-    collection = CollectionBase('test', parameter)
+def test_collection_base_rejects_non_model_items():
+    with pytest.raises(AttributeError, match='model objects'):
+        CollectionBase('test', make_parameter('p1', 1.0))
+
+
+def test_collection_base_rejects_basedbase_objects():
+    with pytest.raises(AttributeError, match='model objects'):
+        from easyscience import ObjBase
+
+        CollectionBase('test', ObjBase('legacy', p=make_parameter('p1', 1.0)))
 
-    collection[0] = 4.0
 
-    assert collection[0].value == 4.0
+def test_collection_base_accepts_nested_collections():
+    inner = CollectionBase('inner', DummyModel('m', make_parameter('p', 1.0)))
+    outer = CollectionBase('outer', inner)
+
+    assert len(outer) == 1
+    assert outer[0] is inner
 
 
 def test_collection_base_to_dict_round_trip_preserves_name_and_data():
-    p1 = Parameter('p1', 1.0)
-    p2 = Parameter('p2', 2.0)
-    collection = CollectionBase('test', p1, p2)
+    m1 = DummyModel('m1', make_parameter('p1', 1.0))
+    m2 = DummyModel('m2', make_parameter('p2', 2.0))
+    collection = CollectionBase('test', m1, m2)
 
     encoded = collection.to_dict()
     decoded = CollectionBase.from_dict(encoded)
 
     assert decoded.name == 'test'
-    assert [item.name for item in decoded] == ['p1', 'p2']
-    assert [item.value for item in decoded] == [1.0, 2.0]
+    assert [item.name for item in decoded] == ['m1', 'm2']
 
 
-def test_collection_base_sort_accepts_mapping_alias():
-    collection = CollectionBase(
-        'test', Parameter('p1', 3.0), Parameter('p2', 1.0), Parameter('p3', 2.0)
-    )
+def test_collection_base_sort_accepts_key():
+    m1 = DummyModel('m1', make_parameter('p1', 3.0))
+    m2 = DummyModel('m2', make_parameter('p2', 1.0))
+    m3 = DummyModel('m3', make_parameter('p3', 2.0))
+    collection = CollectionBase('test', m1, m2, m3)
+
+    collection.sort(key=lambda item: item.value.value)
+
+    assert [item.name for item in collection] == ['m2', 'm3', 'm1']
 
-    collection.sort(mapping=lambda item: item.value)
 
-    assert [item.value for item in collection] == [1.0, 2.0, 3.0]
+def test_collection_base_isinstance_model_base():
+    collection = CollectionBase('test')
+    assert isinstance(collection, ModelBase)