New easycore

.github/workflows/documentation-build.yml

@@ -34,7 +34,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.10.12
+        python-version: 3.11
     - name: Install Pandoc, repo and dependencies
       run: |
         sudo apt install pandoc

.github/workflows/python-ci.yml

@@ -30,7 +30,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.11', '3.12']
         os: [ubuntu-latest, macos-latest, windows-latest]
 
     runs-on: ${{ matrix.os }}

.github/workflows/python-package.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10', '3.11','3.12']
+        python-version: ['3.11','3.12']
     if: "!contains(github.event.head_commit.message, '[ci skip]')"
 
     steps:

CONTRIBUTING.rst

@@ -102,7 +102,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.md.
-3. The pull request should work for Python, 3.10, 3.11 and 3.12, and for PyPy. Check
+3. The pull request should work for Python, 3.11 and 3.12, and for PyPy. Check
    https://travis-ci.com/easyScience/EasyReflectometryLib/pull_requests
    and make sure that the tests pass for all supported Python versions.
 

pyproject.toml

@@ -21,41 +21,40 @@ classifiers = [
     "Topic :: Scientific/Engineering",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Development Status :: 3 - Alpha"
 ]
 
-requires-python = ">=3.10,<3.13"
+requires-python = ">=3.11,<3.13"
 
 dependencies = [
-    "easyscience==1.3.0",
-    "scipp==25.2.0",
-    "refnx==0.1.52",
+    "easyscience",
+    "scipp",
+    "refnx",
     "refl1d[webview]==1.0.0a12",
-    "orsopy==1.2.1",
-    "xhtml2pdf==0.2.17",
-    "bumps==1.0.0b7",
+    "orsopy",
+    "xhtml2pdf",
+    "bumps",
 ]
 
 [project.optional-dependencies]
 dev = [
-    "build==1.2.2.post1",
-    "codecov==2.1.13",
-    "coverage==7.7.0",
-    "coveralls==4.0.1",
-    "flake8==7.1.2",
-    "ipykernel==6.29.5",
-    "jupyter==1.1.1",
-    "jupyterlab==4.3.6",
-    "plopp==25.3.0",
-    "pooch==1.8.2",
-    "pytest==8.3.5",
-    "pytest-cov==6.0.0",
-    "ruff==0.11.0",
-    "toml==0.10.2",
-    "yapf==0.43.0",
+    "build",
+    "codecov",
+    "coverage",
+    "coveralls",
+    "flake8",
+    "ipykernel",
+    "jupyter",
+    "jupyterlab",
+    "plopp",
+    "pooch",
+    "pytest",
+    "pytest-cov",
+    "ruff",
+    "toml",
+    "yapf",
 ]
 
 docs = [
@@ -134,10 +133,9 @@ force-single-line = true
 legacy_tox_ini = """
 [tox]
 isolated_build = True
-envlist = py{3.10,3.11,3.12}
+envlist = py{3.11,3.12}
 [gh-actions]
 python =
-        3.10: py310
         3.11: py311
         3.12: py312
 [gh-actions:env]

src/easyreflectometry/calculators/bornagain/calculator.py

@@ -1,6 +1,6 @@
 __author__ = 'github.com/arm61'
 
-from easyscience.Objects.Inferface import ItemContainer
+from easyscience.fitting.calculators.interface_factory import ItemContainer
 
 from easyreflectometry.model import Model
 from easyreflectometry.sample import Layer

src/easyreflectometry/calculators/calculator_base.py

@@ -4,8 +4,8 @@
 from typing import Callable
 
 import numpy as np
-from easyscience.Objects.core import ComponentSerializer
-from easyscience.Objects.Inferface import ItemContainer
+from easyscience.fitting.calculators.interface_factory import ItemContainer
+from easyscience.io import SerializerComponent
 
 from easyreflectometry.model import Model
 from easyreflectometry.sample import BaseAssembly
@@ -17,7 +17,7 @@
 from .wrapper_base import WrapperBase
 
 
-class CalculatorBase(ComponentSerializer, metaclass=ABCMeta):
+class CalculatorBase(SerializerComponent, metaclass=ABCMeta):
     """
     This class is a template and defines all properties that a calculator should have.
     """

src/easyreflectometry/calculators/factory.py

@@ -1,7 +1,7 @@
 __author__ = 'github.com/wardsimon'
 from typing import Callable
 
-from easyscience.Objects.Inferface import InterfaceFactoryTemplate
+from easyscience.fitting.calculators.interface_factory import InterfaceFactoryTemplate
 
 from easyreflectometry.calculators import CalculatorBase
 

src/easyreflectometry/calculators/refl1d/wrapper.py

@@ -42,9 +42,7 @@ def create_item(self, name: str):
 
         :param name: The name of the item
         """
-        self.storage['item'][name] = Repeat(
-            names.Stack(names.Slab(names.SLD(), thickness=0, interface=0)), name=str(name)
-        )
+        self.storage['item'][name] = Repeat(names.Stack(names.Slab(names.SLD(), thickness=0, interface=0)), name=str(name))
         del self.storage['item'][name].stack[0]
 
     def update_layer(self, name: str, **kwargs):
@@ -66,7 +64,9 @@ def get_layer_value(self, name: str, key: str) -> float:
         :param key: The given value keys
         """
         if key in ['magnetism_rhoM', 'magnetism_thetaM']:
-            return getattr(self.storage['layer'][name].magnetism, key.split('_')[-1]).value #TODO: check if we want to return the raw value or the full Parameter  # noqa: E501
+            return getattr(
+                self.storage['layer'][name].magnetism, key.split('_')[-1]
+            ).value  # TODO: check if we want to return the raw value or the full Parameter  # noqa: E501
         return super().get_layer_value(name, key)
 
     def create_model(self, name: str):

src/easyreflectometry/data/__init__.py

@@ -5,9 +5,9 @@
 from .measurement import merge_datagroups
 
 __all__ = [
-    "load",
-    "load_as_dataset",
-    "merge_datagroups",
-    "ProjectData",
-    "DataSet1D",
+    'load',
+    'load_as_dataset',
+    'merge_datagroups',
+    'ProjectData',
+    'DataSet1D',
 ]

src/easyreflectometry/data/data_store.py

@@ -6,15 +6,16 @@
 from typing import Union
 
 import numpy as np
-from easyscience.Objects.core import ComponentSerializer
-from easyscience.Utils.io.dict import DictSerializer
+from easyscience.io import SerializerComponent
+from easyscience.io import SerializerDict
 
+# from easyscience.utils.io.dict import DictSerializer
 from easyreflectometry.model import Model
 
 T = TypeVar('T')
 
 
-class ProjectData(ComponentSerializer):
+class ProjectData(SerializerComponent):
     def __init__(self, name='DataStore', exp_data=None, sim_data=None):
         self.name = name
         if exp_data is None:
@@ -25,7 +26,7 @@ def __init__(self, name='DataStore', exp_data=None, sim_data=None):
         self.sim_data = sim_data
 
 
-class DataStore(Sequence, ComponentSerializer):
+class DataStore(Sequence, SerializerComponent):
     def __init__(self, *args, name='DataStore'):
         self.name = name
         self.items = list(args)
@@ -55,7 +56,7 @@ def from_dict(cls, d):
         items = d['items']
         del d['items']
         obj = cls.from_dict(d)
-        decoder = DictSerializer()
+        decoder = SerializerDict()
         obj.items = [decoder.decode(item) for item in items]
         return obj
 
@@ -68,7 +69,7 @@ def simulations(self):
         return [self[idx] for idx in range(len(self)) if self[idx].is_simulation]
 
 
-class DataSet1D(ComponentSerializer):
+class DataSet1D(SerializerComponent):
     def __init__(
         self,
         name: str = 'Series',

src/easyreflectometry/data/measurement.py

@@ -105,7 +105,7 @@ def _load_txt(fname: Union[TextIO, str]) -> sc.DataGroup:
 
         # Verify minimum column requirement
         if num_columns < 3:
-            raise ValueError(f"File must contain at least 3 columns (found {num_columns})")
+            raise ValueError(f'File must contain at least 3 columns (found {num_columns})')
 
         # Now unpack the data based on column count
         if num_columns >= 4:
@@ -116,7 +116,7 @@ def _load_txt(fname: Union[TextIO, str]) -> sc.DataGroup:
 
     except (ValueError, IOError) as error:
         # Re-raise with more descriptive message
-        raise ValueError(f"Failed to load data from {fname}: {str(error)}") from error
+        raise ValueError(f'Failed to load data from {fname}: {str(error)}') from error
 
     data_name = 'R_' + basename
     coords_name = 'Qz_' + basename
@@ -131,6 +131,7 @@ def _load_txt(fname: Union[TextIO, str]) -> sc.DataGroup:
     }
     return sc.DataGroup(data=data, coords=coords)
 
+
 def merge_datagroups(*data_groups: sc.DataGroup) -> sc.DataGroup:
     """Merge multiple DataGroups into a single DataGroup."""
     merged_data = {}

src/easyreflectometry/model/__init__.py

@@ -6,10 +6,10 @@
 from .resolution_functions import ResolutionFunction
 
 __all__ = (
-    "LinearSpline",
-    "PercentageFwhm",
-    "Pointwise",
-    "ResolutionFunction",
-    "Model",
-    "ModelCollection",
+    'LinearSpline',
+    'PercentageFwhm',
+    'Pointwise',
+    'ResolutionFunction',
+    'Model',
+    'ModelCollection',
 )

src/easyreflectometry/model/model.py

@@ -8,9 +8,9 @@
 from typing import Union
 
 import numpy as np
+from easyscience import ObjBase as BaseObj
 from easyscience import global_object
-from easyscience.Objects.ObjectClasses import BaseObj
-from easyscience.Objects.variable import Parameter
+from easyscience.variable import Parameter
 
 from easyreflectometry.sample import BaseAssembly
 from easyreflectometry.sample import Sample
@@ -42,7 +42,8 @@
     },
 }
 
-COLORS =["#0173B2", "#DE8F05", "#029E73", "#D55E00", "#CC78BC", "#CA9161", "#FBAFE4", "#949494", "#ECE133", "#56B4E9"]
+COLORS = ['#0173B2', '#DE8F05', '#029E73', '#D55E00', '#CC78BC', '#CA9161', '#FBAFE4', '#949494', '#ECE133', '#56B4E9']
+
 
 class Model(BaseObj):
     """Model is the class that represents the experiment.

src/easyreflectometry/model/model_collection.py

@@ -79,6 +79,6 @@ def from_dict(cls, this_dict: dict) -> ModelCollection:
             collection.add_model(Model.from_dict(model_data))
 
         if len(collection) != len(this_dict['data']):
-            raise ValueError(f"Expected {len(collection)} models, got {len(this_dict['data'])}")
+            raise ValueError(f'Expected {len(collection)} models, got {len(this_dict["data"])}')
 
         return collection

src/easyreflectometry/model/resolution_functions.py

@@ -63,14 +63,14 @@ def as_dict(
     ) -> dict[str, str]:  # skip is kept for consistency of the as_dict signature
         return {'smearing': 'LinearSpline', 'q_data_points': list(self.q_data_points), 'fwhm_values': list(self.fwhm_values)}
 
+
 # add pointwise smearing funtion
 class Pointwise(ResolutionFunction):
     def __init__(self, q_data_points: list[np.ndarray]):
         self.q_data_points = q_data_points
         self.q = None
 
     def smearing(self, q: Union[np.ndarray, float] = None) -> np.ndarray:
-
         Qz = self.q_data_points[0]
         R = self.q_data_points[1]
         sQz = self.q_data_points[2]
@@ -87,19 +87,20 @@ def smearing(self, q: Union[np.ndarray, float] = None) -> np.ndarray:
     def as_dict(
         self, skip: Optional[List[str]] = None
     ) -> dict[str, str]:  # skip is kept for consistency of the as_dict signature
-        return {'smearing': 'Pointwise',
-                'q_data_points': list(self.q_data_points[0]),
-                'R_data_points': list(self.q_data_points[1]),
-                'sQz_data_points': list(self.q_data_points[2])}
+        return {
+            'smearing': 'Pointwise',
+            'q_data_points': list(self.q_data_points[0]),
+            'R_data_points': list(self.q_data_points[1]),
+            'sQz_data_points': list(self.q_data_points[2]),
+        }
 
     def gaussian_smearing(self, qt, Qz, R, sQz):
         weights = np.exp(-0.5 * ((qt - Qz) / sQz) ** 2)
         if np.sum(weights) == 0 or not np.isfinite(np.sum(weights)):
             return np.sum(R)
-        weights /= (sQz * np.sqrt(2 * np.pi))
+        weights /= sQz * np.sqrt(2 * np.pi)
         return np.sum(R * weights) / np.sum(weights)
 
-
     def apply_smooth_smearing(self, Qz, R, sQzs):
         """
         Apply smooth resolution smearing using convolution with Gaussian kernel.

src/easyreflectometry/project.py

@@ -11,7 +11,7 @@
 from easyscience import global_object
 from easyscience.fitting import AvailableMinimizers
 from easyscience.fitting.fitter import DEFAULT_MINIMIZER
-from easyscience.Objects.variable import Parameter
+from easyscience.variable import Parameter
 from scipp import DataGroup
 
 from easyreflectometry.calculators import CalculatorFactory
@@ -173,7 +173,7 @@ def current_experiment_index(self, value: int) -> None:
         if self._current_experiment_index != value:
             self._current_experiment_index = value
             # Resetting the model index to 0 when changing the experiment
-            #self.current_model_index = 0
+            # self.current_model_index = 0
 
     @property
     def created(self) -> bool:
@@ -283,8 +283,7 @@ def load_experiment_for_model_at_index(self, path: Union[Path, str], index: Opti
             q = self._experiments[index].x
             reflectivity = self._experiments[index].y
             q_error = self._experiments[index].xe
-            resolution_function = Pointwise(
-                q_data_points=[q, reflectivity, q_error])
+            resolution_function = Pointwise(q_data_points=[q, reflectivity, q_error])
             # resolution_function = LinearSpline(
             #     q_data_points=self._experiments[index].y,
             #     fwhm_values=np.sqrt(self._experiments[index].ye),