Merge pull request #210 from EasyScience/develop

Develop

Author: andped10

.github/workflows/documentation-build.yml

@@ -28,7 +28,7 @@ jobs:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install EasyReflectometry and dependencies
       run: |
         sudo apt install pandoc

.github/workflows/macos-windows-build.yml

@@ -32,7 +32,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-            python-version: 3.9
+            python-version: '3.10'
 
       - name: Upgrade Pip
         run: python -m pip install --upgrade pip

CHANGELOG.md

@@ -1,4 +1,8 @@
 # CHANGELOG
+### Changes 0.0.12
+
+- Use the latest version of the lib
+
 ### Changes 0.0.11
 
 - Fix to how surfactant table is displayed in GUI

DEPENDENCIES.md

@@ -5,6 +5,7 @@ The following Open Source projects are used in EasyReflectometry (_if there are
 ## Computational libraries
 
 * [refnx](https://refnx.readthedocs.io/en/latest/): [BSD-3](https://github.com/refnx/refnx/blob/master/LICENSE) 
+* [refl1d](https://refl1d.readthedocs.io/en/latest/): [Public Domain](https://github.com/reflectometry/refl1d/blob/master/LICENSE.txt) 
 * [bornagain](https://www.bornagainproject.org): [GNU General Public License (GPL)](http://www.gnu.org/licenses/gpl-3.0.html)
 
 ## Visualization libraries

EasyReflectometryApp/Gui/Pages/Analysis/SideBarAdvanced.qml

@@ -54,37 +54,14 @@ EaComponents.SideBarColumn {
             EaElements.ComboBox {
                 id: minimizerSelector
 
-                width: (EaStyle.Sizes.sideBarContentWidth - minimizerLabel.width * 2 - EaStyle.Sizes.fontPixelSize * 4) / 2
-
                 model: ExGlobals.Constants.proxy.minimizer.minimizerNames
                 currentIndex: ExGlobals.Constants.proxy.minimizer.currentMinimizerIndex
 
                 onCurrentIndexChanged: {
                     ExGlobals.Constants.proxy.minimizer.currentMinimizerIndex = currentIndex
                 }
             }
-
-            // Spacer
-            Item {}
-
-            // Method
-            EaComponents.TableViewLabel{
-                horizontalAlignment: Text.AlignRight
-                width: minimizerLabel.width
-                text: qsTr("Method:")
-            }
-            EaElements.ComboBox {
-                id: methodSelector
-
-                width: minimizerSelector.width
-                model: ExGlobals.Constants.proxy.minimizer.minimizerMethodNames
-                currentIndex: ExGlobals.Constants.proxy.minimizer.currentMinimizerMethodIndex
-                onCurrentIndexChanged: {
-                    ExGlobals.Constants.proxy.currentMinimizerMethodIndex = currentIndex
-                }
-            }
         }
-
     }
 
     /*

EasyReflectometryApp/Logic/DataStore.py

@@ -4,10 +4,10 @@
 from typing import TypeVar
 
 import numpy as np
-from easyscience.Objects.core import ComponentSerializer
-from easyscience.Utils.io.dict import DictSerializer
 from collections.abc import Sequence
 
+from easyscience.Objects.core import ComponentSerializer
+from easyscience.Utils.io.dict import DictSerializer
 from easyreflectometry.experiment.model import Model
 
 T = TypeVar('T')

EasyReflectometryApp/Logic/Proxies/Calculator.py

@@ -4,7 +4,7 @@
 from PySide2.QtCore import Signal
 from PySide2.QtCore import Property
 
-from easyscience.Utils.UndoRedo import property_stack_deco
+from easyscience.global_object.undo_redo import property_stack_deco
 
 
 class CalculatorProxy(QObject):

EasyReflectometryApp/Logic/Proxies/Data.py

@@ -11,12 +11,12 @@
 import numpy as np
 from easyApp.Logic.Utils.Utils import generalizePath
 
-from EasyReflectometryApp.Logic.DataStore import DataSet1D
-from EasyReflectometryApp.Logic.DataStore import DataStore
-
 from easyreflectometry.data import load
 from easyreflectometry.experiment import PercentageFhwm
 
+from ..DataStore import DataSet1D
+from ..DataStore import DataStore
+
 class DataProxy(QObject):
 
     experimentSkippedChanged = Signal()
@@ -98,7 +98,7 @@ def experimentDataAsObj(self):
             dictionary['model_index'] = self.parent._model_proxy._model.index(experiment.model)
             dictionary['color'] = self.parent._model_proxy._colors[dictionary['model_index']]
             dictionary['model_name'] = self.parent._model_proxy._model[dictionary['model_index']].name
-            dictionary['background'] = self.parent._model_proxy._model[dictionary['model_index']].background.raw_value
+            dictionary['background'] = self.parent._model_proxy._model[dictionary['model_index']].background.value
             experiment_data_as_obj.append(dictionary)
         return experiment_data_as_obj
 
@@ -110,7 +110,7 @@ def setScaling(self, new_scaling: float):
         :param new_scaling: New scaling value
         """
         model_index = self.parent._model_proxy._model.index(self._data[self.currentDataIndex].model)
-        if self.parent._model_proxy._model[model_index].scale.raw_value == new_scaling:
+        if self.parent._model_proxy._model[model_index].scale.value == new_scaling:
             return
         self.parent._model_proxy._model[model_index].scale = new_scaling
         self.parent.layersChanged.emit()
@@ -137,7 +137,7 @@ def setBackground(self, new_background: float):
         :param new_background: New background value
         """
         model_index = self.parent._model_proxy._model.index(self._data[self.currentDataIndex].model)
-        if self.parent._model_proxy._model[model_index].background.raw_value == new_background:
+        if self.parent._model_proxy._model[model_index].background.value == new_background:
             return
         self.parent._model_proxy._model[model_index].background = new_background
         self.parent.layersChanged.emit()
@@ -146,15 +146,15 @@ def setBackground(self, new_background: float):
     def currentScaling(self):
         try:
             model_index = self.parent._model_proxy._model.index(self._data[self.currentDataIndex].model)
-            return self.parent._model_proxy._model[model_index].scale.raw_value
+            return self.parent._model_proxy._model[model_index].scale.value
         except IndexError:
             return 1
 
     @Property(float, notify=experimentChanged)
     def currentBackground(self):
         try:
             model_index = self.parent._model_proxy._model.index(self._data[self.currentDataIndex].model)
-            return self.parent._model_proxy._model[model_index].background.raw_value
+            return self.parent._model_proxy._model[model_index].background.value
         except IndexError:
             return 0
 

EasyReflectometryApp/Logic/Proxies/Fitter.py

@@ -6,7 +6,7 @@
 from PySide2.QtCore import Property
 from PySide2.QtCore import Slot
 
-from easyscience import borg
+from easyscience import global_object
 
 from easyreflectometry.fitting import Fitter as easyFitter
 
@@ -126,7 +126,7 @@ def fit(self):
         # if running, stop the thread
         if not self.isFitFinished:
             self.onStopFit()
-            borg.stack.endMacro()  # need this to close the undo stack properly
+            global_object.stack.endMacro()  # need this to close the undo stack properly
             return
         # macos is possibly problematic with MT, skip on this platform
         # if 'darwin' in sys.platform:
@@ -146,7 +146,7 @@ def nonthreaded_fit(self):
         x = [i.x for i in exp_data]
         y = [i.y for i in exp_data]
         weights = [1 / i.ye for i in exp_data]
-        method = self.parent.minimizer._current_minimizer_method_name
+        method = self.parent.minimizer._current_minimizer.method
 
         res = self.eFitter.easy_f.fit(x, y, weights=weights, method=method)
         self._setFitResults(res)

EasyReflectometryApp/Logic/Proxies/Material.py

@@ -8,7 +8,7 @@
 from PySide2.QtCore import Property
 from PySide2.QtCore import Slot
 
-from easyscience import borg
+from easyscience import global_object
 from easyscience.Utils.io.xml import XMLSerializer
 
 from easyreflectometry.sample import Material
@@ -116,7 +116,7 @@ def addNewMaterials(self):
         """
         Add a new material.
         """
-        borg.stack.enabled = False
+        global_object.stack.enabled = False
         self._materials.append(
             Material(
                 sld=2.074,
@@ -125,7 +125,7 @@ def addNewMaterials(self):
                 interface=self.parent._interface
             )
         )
-        borg.stack.enabled = True
+        global_object.stack.enabled = True
         self.materialsChanged.emit()
         self.parent.layersMaterialsChanged.emit()
 
@@ -134,21 +134,19 @@ def duplicateSelectedMaterials(self):
         """
         Duplicate the currently selected material.
         """
-        # if borg.stack.enabled:
-        #    borg.stack.beginMacro('Loaded default material')
-        borg.stack.enabled = False
+        global_object.stack.enabled = False
         # This is a fix until deepcopy is worked out
         # Manual duplication instead of creating a copy
         to_dup = self._materials[self.currentMaterialsIndex]
         self._materials.append(
             Material(
-                sld=to_dup.sld.raw_value,
-                isld=to_dup.isld.raw_value,
+                sld=to_dup.sld.value,
+                isld=to_dup.isld.value,
                 name=to_dup.name,
                 interface=self.parent._interface
             )
         )
-        borg.stack.enabled = True
+        global_object.stack.enabled = True
         self.materialsChanged.emit()
         self.parent.layersMaterialsChanged.emit()
 
@@ -203,9 +201,9 @@ def setCurrentMaterialsSld(self, sld: float):
 
         :param sld: New SLD value
         """
-        if self._materials[self.currentMaterialsIndex].sld.raw_value == sld:
+        if self._materials[self.currentMaterialsIndex].sld.value == sld:
             return
-        self._materials[self.currentMaterialsIndex].sld = sld
+        self._materials[self.currentMaterialsIndex].sld.value = sld
         self.materialsChanged.emit()
         self.parent.layersChanged.emit()
 
@@ -216,9 +214,9 @@ def setCurrentMaterialsISld(self, isld: float):
 
         :param isld: New iSLD value
         """
-        if self._materials[self.currentMaterialsIndex].isld.raw_value == isld:
+        if self._materials[self.currentMaterialsIndex].isld.value == isld:
             return
-        self._materials[self.currentMaterialsIndex].isld = isld
+        self._materials[self.currentMaterialsIndex].isld.value = isld
         self.materialsChanged.emit()
         self.parent.layersChanged.emit()
 

EasyReflectometryApp/Logic/Proxies/Minimizer.py

@@ -4,8 +4,8 @@
 from PySide2.QtCore import Signal
 from PySide2.QtCore import Property
 
-from easyscience.Utils.UndoRedo import property_stack_deco
-
+from easyscience.global_object.undo_redo import property_stack_deco
+from easyscience.fitting import AvailableMinimizers
 
 class MinimizerProxy(QObject):
 
@@ -17,22 +17,22 @@ def __init__(self, parent=None):
         super().__init__(parent)
         self.parent = parent
 
-        self._current_minimizer_method_index = 0
-        self._current_minimizer_method_name = self.parent._fitter_proxy.eFitter.easy_f.available_methods(
-        )[0]
+        self._current_minimizer = AvailableMinimizers.LMFit_leastsq
         self.currentMinimizerChanged.connect(self._onCurrentMinimizerChanged)
+        self._current_minimizer_method_index = self.currentMinimizerIndex
+        self._current_minimizer_method_name = self._current_minimizer.name
 
     # # #
     # Setters and getters
     # # #
 
     @Property('QVariant', notify=dummySignal)
     def minimizerNames(self):
-        return self.parent._fitter_proxy.eFitter.easy_f.available_engines
+        return [minimizer.name for minimizer in AvailableMinimizers]
 
     @Property(int, notify=currentMinimizerChanged)
     def currentMinimizerIndex(self):
-        current_name = self.parent._fitter_proxy.eFitter.easy_f.current_engine.name
+        current_name = self.parent._fitter_proxy.eFitter.easy_f.minimizer.name
         return self.minimizerNames.index(current_name)
 
     @currentMinimizerIndex.setter
@@ -41,7 +41,7 @@ def currentMinimizerIndex(self, new_index: int):
         if self.currentMinimizerIndex == new_index:
             return
         new_name = self.minimizerNames[new_index]
-        self.parent._fitter_proxy.eFitter.easy_f.switch_engine(new_name)
+        self.parent._fitter_proxy.eFitter.easy_f.switch_minimizer(new_name)
         self.currentMinimizerChanged.emit()
 
     @Property(int, notify=currentMinimizerMethodChanged)
@@ -57,29 +57,14 @@ def currentMinimizerMethodIndex(self, new_index: int):
         self._current_minimizer_method_name = self.minimizerMethodNames[new_index]
         self.currentMinimizerMethodChanged.emit()
 
-    @Property('QVariant', notify=currentMinimizerChanged)
-    def minimizerMethodNames(self):
-        current_minimizer = self.minimizerNames[self.currentMinimizerIndex]
-        tested_methods = {
-            'lmfit': ['leastsq', 'powell', 'cobyla'],
-            'bumps': ['newton', 'lm', 'de'],
-            'DFO_LS': ['leastsq']
-        }
-        return tested_methods[current_minimizer]
-
     # # #
     # Actions
     # # #
 
     def _onCurrentMinimizerChanged(self):
-        idx = 0
-        minimizer_name = self.parent._fitter_proxy.eFitter.easy_f.current_engine.name
-        if minimizer_name == 'lmfit':
-            idx = self.minimizerMethodNames.index('leastsq')
-        elif minimizer_name == 'bumps':
-            idx = self.minimizerMethodNames.index('lm')
-        if -1 < idx != self._current_minimizer_method_index:
+        idx = self.currentMinimizerIndex
+        if idx != self._current_minimizer_method_index:
             # Bypass the property as it would be added to the stack.
             self._current_minimizer_method_index = idx
-            self._current_minimizer_method_name = self.minimizerMethodNames[idx]
-            self.currentMinimizerMethodChanged.emit()
+            self._current_minimizer_method_name = self._current_minimizer.name
+            self.currentMinimizerMethodChanged.emit()