easyscience 2.0.0__tar.gz → 2.1.0__tar.gz

{easyscience-2.0.0 → easyscience-2.1.0}/.gitignore

@@ -23,6 +23,9 @@ dist
 poetry.lock
 *.egg-info
 
+# Pixi
+.pixi/
+
 # PyInstaller
 build
 *.spec

{easyscience-2.0.0 → easyscience-2.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: easyscience
-Version: 2.0.0
+Version: 2.1.0
 Summary: Generic logic for easyScience libraries
 Project-URL: homepage, https://github.com/EasyScience/EasyScience
 Project-URL: documentation, https://easyscience.github.io/EasyScience/
@@ -52,10 +52,15 @@ Requires-Dist: lmfit
 Requires-Dist: numpy
 Requires-Dist: scipp
 Requires-Dist: uncertainties
+Provides-Extra: build
+Requires-Dist: build; extra == 'build'
+Requires-Dist: hatchling<=1.21.0; extra == 'build'
+Requires-Dist: setuptools-git-versioning; extra == 'build'
 Provides-Extra: dev
 Requires-Dist: build; extra == 'dev'
 Requires-Dist: codecov; extra == 'dev'
 Requires-Dist: flake8; extra == 'dev'
+Requires-Dist: jupyterlab; extra == 'dev'
 Requires-Dist: matplotlib; extra == 'dev'
 Requires-Dist: pytest; extra == 'dev'
 Requires-Dist: pytest-cov; extra == 'dev'
@@ -91,6 +96,10 @@ Or direct from the repository:
 
 ```pip install https://github.com/easyScience/EasyScience```
 
+### Development
+
+For development setup and workflow instructions, please see [CONTRIBUTING.md](CONTRIBUTING.md).
+
 ## Test
 
 After installation, launch the test suite:

{easyscience-2.0.0 → easyscience-2.1.0}/README.md

@@ -19,6 +19,10 @@ Or direct from the repository:
 
 ```pip install https://github.com/easyScience/EasyScience```
 
+### Development
+
+For development setup and workflow instructions, please see [CONTRIBUTING.md](CONTRIBUTING.md).
+
 ## Test
 
 After installation, launch the test suite:

{easyscience-2.0.0 → easyscience-2.1.0}/pyproject.toml

@@ -38,6 +38,11 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
+build = [
+    "hatchling <= 1.21.0",
+    "setuptools-git-versioning",
+    "build"
+]
 dev = [
     "build",
     "codecov",
@@ -46,7 +51,8 @@ dev = [
     "pytest",
     "pytest-cov",
     "ruff",
-    "tox-gh-actions"
+    "tox-gh-actions",
+    "jupyterlab"
 ]
 docs = [
     "doc8",
@@ -136,6 +142,7 @@ python =
 PLATFORM =
     ubuntu-latest: linux
     macos-latest: macos
+    macos-15-intel: macos-intel
     windows-latest: windows
 [testenv]
 passenv =

easyscience-2.1.0/src/easyscience/__version__.py

@@ -0,0 +1 @@
+__version__ = '2.1.0'

{easyscience-2.0.0 → easyscience-2.1.0}/src/easyscience/base_classes/__init__.py

@@ -1,9 +1,13 @@
 from .based_base import BasedBase
 from .collection_base import CollectionBase
+from .model_base import ModelBase
+from .new_base import NewBase
 from .obj_base import ObjBase
 
 __all__ = [
     BasedBase,
     CollectionBase,
     ObjBase,
+    ModelBase,
+    NewBase,
 ]

{easyscience-2.0.0 → easyscience-2.1.0}/src/easyscience/base_classes/based_base.py

@@ -3,8 +3,10 @@ from __future__ import annotations
 #  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 inspect import getfullargspec
+from inspect import signature
 from typing import TYPE_CHECKING
+from typing import Any
+from typing import Dict
 from typing import Iterable
 from typing import List
 from typing import Optional
@@ -38,9 +40,9 @@ class BasedBase(SerializerComponent):
     @property
     def _arg_spec(self) -> Set[str]:
         base_cls = getattr(self, '__old_class__', self.__class__)
-        spec = getfullargspec(base_cls.__init__)
-        names = set(spec.args[1:])
-        return names
+        sign = signature(base_cls.__init__)
+        names = [param.name for param in sign.parameters.values() if param.kind == param.POSITIONAL_OR_KEYWORD]
+        return set(names[1:])
 
     def __reduce__(self):
         """
@@ -195,4 +197,17 @@ class BasedBase(SerializerComponent):
         new_obj = self.__class__.from_dict(temp)
         return new_obj
 
+    def as_dict(self, skip: Optional[List[str]] = None) -> Dict[str, Any]:
+        """
+        Convert an object into a full dictionary using `SerializerDict`.
+        This is a shortcut for ```obj.encode(encoder=SerializerDict)```
 
+        :param skip: List of field names as strings to skip when forming the dictionary
+        :return: encoded object containing all information to reform an EasyScience object.
+        """
+        # extend skip to include unique_name by default
+        if skip is None:
+            skip = []
+        if 'unique_name' not in skip:
+            skip.append('unique_name')
+        return super().as_dict(skip=skip)

{easyscience-2.0.0 → easyscience-2.1.0}/src/easyscience/base_classes/collection_base.py

@@ -23,7 +23,6 @@ if TYPE_CHECKING:
     from ..fitting.calculators import InterfaceFactoryTemplate
 
 
-
 class CollectionBase(BasedBase, MutableSequence):
     """
     This is the base class for which all higher level classes are built off of.
@@ -232,7 +231,7 @@ class CollectionBase(BasedBase, MutableSequence):
         return tuple(self._kwargs.values())
 
     def __repr__(self) -> str:
-        return f"{self.__class__.__name__} `{getattr(self, 'name')}` of length {len(self)}"
+        return f'{self.__class__.__name__} `{getattr(self, "name")}` of length {len(self)}'
 
     def sort(self, mapping: Callable[[Union[BasedBase, DescriptorBase]], Any], reverse: bool = False) -> None:
         """

easyscience-2.1.0/src/easyscience/base_classes/model_base.py

@@ -0,0 +1,119 @@
+from __future__ import annotations
+
+#  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 typing import TYPE_CHECKING
+
+from easyscience.variable.descriptor_number import DescriptorNumber
+
+if TYPE_CHECKING:
+    from typing import Any
+    from typing import Dict
+    from typing import List
+    from typing import Optional
+
+from ..io import SerializerBase
+from ..variable import Parameter
+from ..variable.descriptor_base import DescriptorBase
+from .new_base import NewBase
+
+
+class ModelBase(NewBase):
+    """
+    This is the base class for all model classes in EasyScience.
+    It provides methods to get parameters for fitting and analysis as well as proper serialization/deserialization for
+    DescriptorNumber/Parameter attributes.
+
+    It assumes that Parameters/DescriptorNumbers are assigned as properties with the getters returning the parameter
+    but the setter only setting the value of the parameter.
+    e.g.
+    ```python
+    @property
+    def my_param(self) -> Parameter:
+        return self._my_param
+
+    @my_param.setter
+    def my_param(self, new_value: float) -> None:
+        self._my_param.value = new_value
+    ```
+    """
+
+    def __init__(self, unique_name: Optional[str] = None, display_name: Optional[str] = None):
+        super().__init__(unique_name=unique_name, display_name=display_name)
+
+    def get_all_variables(self) -> List[DescriptorBase]:
+        """
+        Get all `Descriptor` and `Parameter` objects as a list.
+
+        :return: List of `Descriptor` and `Parameter` objects.
+        """
+        vars = []
+        for attr_name in dir(self):
+            attr = getattr(self, attr_name)
+            if isinstance(attr, DescriptorBase):
+                vars.append(attr)
+            elif hasattr(attr, 'get_all_variables'):
+                vars += attr.get_all_variables()
+        return vars
+
+    def get_all_parameters(self) -> List[Parameter]:
+        """
+        Get all `Parameter` objects as a list.
+
+        :return: List of `Parameter` objects.
+        """
+        return [param for param in self.get_all_variables() if isinstance(param, Parameter)]
+
+    def get_fittable_parameters(self) -> List[Parameter]:
+        """
+        Get all parameters which can be fitted as a list.
+
+        :return: List of `Parameter` objects.
+        """
+        return [param for param in self.get_all_parameters() if param.independent]
+
+    def get_free_parameters(self) -> List[Parameter]:
+        """
+        Get all parameters which are currently free to be fitted as a list.
+
+        :return: List of `Parameter` objects.
+        """
+        return [param for param in self.get_fittable_parameters() if not param.fixed]
+
+    def get_fit_parameters(self) -> List[Parameter]:
+        """
+        This is an alias for `get_free_parameters`.
+        To be removed when fully moved to new base classes and minimizer can be changed.
+        """
+        return self.get_free_parameters()
+
+    @classmethod
+    def from_dict(cls, obj_dict: Dict[str, Any]) -> ModelBase:
+        """
+        Re-create an EasyScience object with DescriptorNumber attributes from a full encoded dictionary.
+
+        :param obj_dict: dictionary containing the serialized contents (from `SerializerDict`) of an EasyScience object
+        :return: Reformed EasyScience object
+        """
+        if not SerializerBase._is_serialized_easyscience_object(obj_dict):
+            raise ValueError('Input must be a dictionary representing an EasyScience object.')
+        if obj_dict['@class'] == cls.__name__:
+            kwargs = SerializerBase.deserialize_dict(obj_dict)
+            parameter_placeholder = {}
+            for key, value in kwargs.items():
+                if isinstance(value, DescriptorNumber):
+                    parameter_placeholder[key] = value
+                    kwargs[key] = value.value
+            cls_instance = cls(**kwargs)
+            for key, value in parameter_placeholder.items():
+                try:
+                    temp_param = getattr(cls_instance, key)
+                    setattr(cls_instance, '_' + key, value)
+                    cls_instance._global_object.map.prune(temp_param.unique_name)
+                except Exception as e:
+                    raise SyntaxError(f"""Could not set parameter {key} during `from_dict` with full deserialized variable. \n'
+                            This should be fixed in the class definition. Error: {e}""") from e
+            return cls_instance
+        else:
+            raise ValueError(f'Class name in dictionary does not match the expected class: {cls.__name__}.')

easyscience-2.1.0/src/easyscience/base_classes/new_base.py

@@ -0,0 +1,145 @@
+from __future__ import annotations
+
+#  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 inspect import signature
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from typing import Any
+    from typing import Dict
+    from typing import Iterable
+    from typing import List
+    from typing import Optional
+    from typing import Set
+
+from easyscience import global_object
+
+from ..global_object.undo_redo import property_stack
+from ..io.serializer_base import SerializerBase
+
+
+class NewBase:
+    """
+    This is the new base class for easyscience objects.
+    It provides serialization capabilities as well as unique naming and display naming.
+    """
+
+    def __init__(self, unique_name: Optional[str] = None, display_name: Optional[str] = None):
+        self._global_object = global_object
+        if unique_name is None:
+            unique_name = self._global_object.generate_unique_name(self.__class__.__name__)
+            self._default_unique_name = True
+        else:
+            self._default_unique_name = False
+        if not isinstance(unique_name, str):
+            raise TypeError('Unique name has to be a string.')
+        self._unique_name = unique_name
+        self._global_object.map.add_vertex(self, obj_type='created')
+        if display_name is not None and not isinstance(display_name, str):
+            raise TypeError('Display name must be a string or None')
+        self._display_name = display_name
+
+    @property
+    def _arg_spec(self) -> Set[str]:
+        """
+        This method is used by the serializer to determine which arguments are needed
+        by the constructor to deserialize the object.
+        """
+        sign = signature(self.__class__.__init__)
+        names = [param.name for param in sign.parameters.values() if param.kind == param.POSITIONAL_OR_KEYWORD]
+        return set(names[1:])
+
+    @property
+    def unique_name(self) -> str:
+        """Get the unique name of the object."""
+        return self._unique_name
+
+    @unique_name.setter
+    def unique_name(self, new_unique_name: str):
+        """Set a new unique name for the object. The old name is still kept in the map.
+
+        :param new_unique_name: New unique name for the object"""
+        if not isinstance(new_unique_name, str):
+            raise TypeError('Unique name has to be a string.')
+        self._unique_name = new_unique_name
+        self._global_object.map.add_vertex(self)
+        self._default_unique_name = False
+
+    @property
+    def display_name(self) -> str:
+        """
+        Get a pretty display name.
+
+        :return: The pretty display name.
+        """
+        display_name = self._display_name
+        if display_name is None:
+            display_name = self.unique_name
+        return display_name
+
+    @display_name.setter
+    @property_stack
+    def display_name(self, name: str | None) -> None:
+        """
+        Set the pretty display name.
+
+        :param name: Pretty display name of the object.
+        """
+        if name is not None and not isinstance(name, str):
+            raise TypeError('Display name must be a string or None')
+        self._display_name = name
+
+    def to_dict(self, skip: Optional[List[str]] = None) -> Dict[str, Any]:
+        """
+        Convert an EasyScience object into a full dictionary using `SerializerBase`s generic `convert_to_dict` method.
+
+        :param skip: List of field names as strings to skip when forming the dictionary
+        :return: encoded object containing all information to reform an EasyScience object.
+        """
+        serializer = SerializerBase()
+        if skip is None:
+            skip = []
+        if self._default_unique_name and 'unique_name' not in skip:
+            skip.append('unique_name')
+        if self._display_name is None:
+            skip.append('display_name')
+        return serializer._convert_to_dict(self, skip=skip, full_encode=False)
+
+    @classmethod
+    def from_dict(cls, obj_dict: Dict[str, Any]) -> NewBase:
+        """
+        Re-create an EasyScience object from a full encoded dictionary.
+
+        :param obj_dict: dictionary containing the serialized contents (from `SerializerDict`) of an EasyScience object
+        :return: Reformed EasyScience object
+        """
+        if not SerializerBase._is_serialized_easyscience_object(obj_dict):
+            raise ValueError('Input must be a dictionary representing an EasyScience object.')
+        if obj_dict['@class'] == cls.__name__:
+            kwargs = SerializerBase.deserialize_dict(obj_dict)
+            return cls(**kwargs)
+        else:
+            raise ValueError(f'Class name in dictionary does not match the expected class: {cls.__name__}.')
+
+    def __dir__(self) -> Iterable[str]:
+        """
+        This creates auto-completion and helps out in iPython notebooks.
+
+        :return: list of function and parameter names for auto-completion
+        """
+        new_class_objs = list(k for k in dir(self.__class__) if not k.startswith('_'))
+        return sorted(new_class_objs)
+
+    def __copy__(self) -> NewBase:
+        """Return a copy of the object."""
+        temp = self.to_dict(skip=['unique_name'])
+        new_obj = self.__class__.from_dict(temp)
+        return new_obj
+
+    def __deepcopy__(self, memo):
+        return self.__copy__()
+
+    def __repr__(self) -> str:
+        return f'{self.__class__.__name__} `{self.unique_name}`'

{easyscience-2.0.0 → easyscience-2.1.0}/src/easyscience/base_classes/obj_base.py

@@ -15,7 +15,6 @@ if TYPE_CHECKING:
     from ..io import SerializerComponent
 
 
-
 class ObjBase(BasedBase):
     """
     This is the base class for which all higher level classes are built off of.
@@ -69,17 +68,12 @@ class ObjBase(BasedBase):
         Dynamically add a component to the class. This is an internal method, though can be called remotely.
         The recommended alternative is to use typing, i.e.
 
-        class Foo(Bar):
-            def __init__(self, foo: Parameter, bar: Parameter):
-                super(Foo, self).__init__(bar=bar)
-                self._add_component("foo", foo)
+        .. code-block:: python
 
-        Goes to:
-         class Foo(Bar):
-            foo: ClassVar[Parameter]
-            def __init__(self, foo: Parameter, bar: Parameter):
-                super(Foo, self).__init__(bar=bar)
-                self.foo = foo
+            class Foo(Bar):
+                def __init__(self, foo: Parameter, bar: Parameter):
+                    super(Foo, self).__init__(bar=bar)
+                    self._add_component("foo", foo)
 
         :param key: Name of component to be added
         :param component: Component to be added
@@ -127,7 +121,7 @@ class ObjBase(BasedBase):
                 self.generate_bindings()
 
     def __repr__(self) -> str:
-        return f"{self.__class__.__name__} `{getattr(self, 'name')}`"
+        return f'{self.__class__.__name__} `{getattr(self, "name")}`'
 
     @staticmethod
     def __getter(key: str) -> Callable[[SerializerComponent], SerializerComponent]:
@@ -139,9 +133,7 @@ class ObjBase(BasedBase):
     @staticmethod
     def __setter(key: str) -> Callable[[SerializerComponent], None]:
         def setter(obj: SerializerComponent, value: float) -> None:
-            if issubclass(obj._kwargs[key].__class__, (DescriptorBase)) and not issubclass(
-                value.__class__, (DescriptorBase)
-            ):
+            if issubclass(obj._kwargs[key].__class__, (DescriptorBase)) and not issubclass(value.__class__, (DescriptorBase)):
                 obj._kwargs[key].value = value
             else:
                 obj._kwargs[key] = value

{easyscience-2.0.0 → easyscience-2.1.0}/src/easyscience/fitting/fitter.py

@@ -69,6 +69,7 @@ class Fitter:
     def switch_minimizer(self, minimizer_enum: Union[AvailableMinimizers, str]) -> None:
         """
         Switch minimizer and initialize.
+
         :param minimizer_enum: The enum of the minimizer to create and instantiate.
         """
         if isinstance(minimizer_enum, str):

{easyscience-2.0.0 → easyscience-2.1.0}/src/easyscience/fitting/minimizers/__init__.py

@@ -3,7 +3,10 @@
 #  © 2021-2025 Contributors to the EasyScience project <https://github.com/easyScience/easyscience
 
 from .minimizer_base import MinimizerBase
+from .minimizer_bumps import Bumps
+from .minimizer_dfo import DFO
+from .minimizer_lmfit import LMFit
 from .utils import FitError
 from .utils import FitResults
 
-__all__ = [MinimizerBase, FitError, FitResults]
+__all__ = [MinimizerBase, Bumps, DFO, LMFit, FitError, FitResults]

{easyscience-2.0.0 → easyscience-2.1.0}/src/easyscience/fitting/minimizers/minimizer_base.py

@@ -212,7 +212,7 @@ class MinimizerBase(metaclass=ABCMeta):
             for name, value in kwargs.items():
                 par_name = name[1:]
                 if par_name in self._cached_pars.keys():
-                        # This will take into account constraints
+                    # This will take into account constraints
                     if self._cached_pars[par_name].value != value:
                         self._cached_pars[par_name].value = value
 

{easyscience-2.0.0 → easyscience-2.1.0}/src/easyscience/fitting/minimizers/minimizer_bumps.py

@@ -105,13 +105,13 @@ class Bumps(MinimizerBase):
 
         if y.shape != x.shape:
             raise ValueError('x and y must have the same shape.')
-        
+
         if weights.shape != x.shape:
             raise ValueError('Weights must have the same shape as x and y.')
 
         if not np.isfinite(weights).all():
             raise ValueError('Weights cannot be NaN or infinite.')
-        
+
         if (weights <= 0).any():
             raise ValueError('Weights must be strictly positive and non-zero.')
 

{easyscience-2.0.0 → easyscience-2.1.0}/src/easyscience/fitting/minimizers/minimizer_dfo.py

@@ -90,13 +90,13 @@ class DFO(MinimizerBase):
 
         if y.shape != x.shape:
             raise ValueError('x and y must have the same shape.')
-        
+
         if weights.shape != x.shape:
             raise ValueError('Weights must have the same shape as x and y.')
-        
+
         if not np.isfinite(weights).all():
             raise ValueError('Weights cannot be NaN or infinite.')
-        
+
         if (weights <= 0).any():
             raise ValueError('Weights must be strictly positive and non-zero.')
 
@@ -152,7 +152,6 @@ class DFO(MinimizerBase):
 
         def _outer(obj: DFO):
             def _make_func(x, y, weights):
-
                 dfo_pars = {}
                 if not parameters:
                     for name, par in obj._cached_pars.items():

{easyscience-2.0.0 → easyscience-2.1.0}/src/easyscience/fitting/minimizers/minimizer_lmfit.py

@@ -116,13 +116,13 @@ class LMFit(MinimizerBase):  # noqa: S101
 
         if y.shape != x.shape:
             raise ValueError('x and y must have the same shape.')
-        
+
         if weights.shape != x.shape:
             raise ValueError('Weights must have the same shape as x and y.')
-        
+
         if not np.isfinite(weights).all():
             raise ValueError('Weights cannot be NaN or infinite.')
-        
+
         if (weights <= 0).any():
             raise ValueError('Weights must be strictly positive and non-zero.')
 

{easyscience-2.0.0 → easyscience-2.1.0}/src/easyscience/fitting/minimizers/utils.py

@@ -51,6 +51,7 @@ class FitResults:
     def reduced_chi(self):
         return self.chi2 / (len(self.x) - self.n_pars)
 
+
 class FitError(Exception):
     def __init__(self, e: Exception = None):
         self.e = e

{easyscience-2.0.0 → easyscience-2.1.0}/src/easyscience/global_object/__init__.py

@@ -2,3 +2,4 @@ from .global_object import GlobalObject  # noqa: F401
 from .hugger.hugger import ScriptManager  # noqa: F401
 from .logger import Logger  # noqa: F401
 from .map import Map  # noqa: F401
+from .undo_redo import UndoStack  # noqa: F401