Merge pull request #72 from EasyScience/develop

Release 1.0.0

Author: andped10

.github/workflows/documentation-build.yml

@@ -29,6 +29,9 @@ jobs:
     - name: Upgrade pip
       run: |
         python -m pip install --upgrade pip
+    - name: Force upgrade of sphinx-rtd-theme to build documentation, not compatible with docutils 0.20.1
+      run: |
+        pip install --upgrade --force-reinstall sphinx-rtd-theme
     - name: Set up Python
       uses: actions/setup-python@v5
       with:

Examples/fitting/plot_constraints.py

@@ -4,7 +4,7 @@
 This  example shows the usages of the different constraints.
 """
 
-from easyscience.Fitting import Constraints
+from easyscience.fitting import Constraints
 from easyscience.Objects.ObjectClasses import Parameter
 
 p1 = Parameter('p1', 1)
@@ -15,7 +15,7 @@
     p1.value = value
     print(f'Set Value: {value}, Parameter Value: {p1}')
 
-#%%
+# %%
 # To include embedded rST, use a line of >= 20 ``#``'s or ``#%%`` between your
 # rST and your code. This separates your example
 # into distinct text and code blocks. You can continue writing code below the

docs/src/conf.py

@@ -95,7 +95,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

docs/src/getting-started/installation.rst

@@ -14,7 +14,7 @@ The easiest way of obtaining EasyScience and using it in your project is via pip
     $ pip install EasyScience
 
 Install as an EasyScience developer
---------------------------------
+-----------------------------------
 
 You can obtain the latest development source from our `Github repository
 <https://github.com/easyScience/EasyScience>`_.:

docs/src/reference/base.rst

@@ -5,13 +5,13 @@ Parameters and Objects
 Descriptors
 ===========
 
-.. autoclass:: easyscience.Objects.Base.Descriptor
+.. autoclass:: easyscience.Objects.Variable.Descriptor
   :members:
 
 Parameters
 ==========
 
-.. autoclass:: easyscience.Objects.Base.Parameter
+.. autoclass:: easyscience.Objects.Variable.Parameter
   :members:
   :inherited-members:
 
@@ -22,11 +22,11 @@ Super Classes and Collections
 Super Classes
 =============
 
-.. autoclass:: easyscience.Objects.Base.BasedBase
+.. autoclass:: easyscience.Objects.ObjectClasses.BasedBase
   :members:
   :inherited-members:
 
-.. autoclass:: easyscience.Objects.Base.BaseObj
+.. autoclass:: easyscience.Objects.ObjectClasses.BaseObj
   :members: +_add_component
   :inherited-members:
 

examples_old/example1.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-from easyscience.Fitting import Fitter
+from easyscience.fitting import Fitter
 from easyscience.Objects.ObjectClasses import BaseObj
 from easyscience.Objects.ObjectClasses import Parameter
 

examples_old/example1_dream.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-from easyscience.Fitting import Fitter
+from easyscience.fitting import Fitter
 from easyscience.Objects.ObjectClasses import BaseObj
 from easyscience.Objects.ObjectClasses import Parameter
 

examples_old/example2.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-from easyscience.Fitting import Fitter
+from easyscience.fitting import Fitter
 from easyscience.Objects.ObjectClasses import BaseObj
 from easyscience.Objects.ObjectClasses import Parameter
 

examples_old/example3.py

@@ -5,7 +5,7 @@
 
 import numpy as np
 
-from easyscience.Fitting import Fitter
+from easyscience.fitting import Fitter
 from easyscience.Objects.ObjectClasses import BaseObj
 from easyscience.Objects.ObjectClasses import Parameter
 

examples_old/example4.py

@@ -10,7 +10,7 @@
 import numpy as np
 
 from easyscience import global_object
-from easyscience.Fitting import Fitter
+from easyscience.fitting import Fitter
 from easyscience.Objects.core import ComponentSerializer
 from easyscience.Objects.ObjectClasses import BaseObj
 from easyscience.Objects.ObjectClasses import Parameter

examples_old/example5_broken.py

@@ -9,7 +9,7 @@
 import numpy as np
 
 from easyscience import global_object
-from easyscience.Fitting import Fitter
+from easyscience.fitting import Fitter
 from easyscience.Objects.Base import BaseObj
 from easyscience.Objects.Base import Parameter
 from easyscience.Objects.core import ComponentSerializer

examples_old/example_dataset2.py

@@ -5,7 +5,7 @@
 
 import numpy as np
 from easyscience.Datasets.xarray import xr
-from easyscience.Fitting import Fitter
+from easyscience.fitting import Fitter
 from easyscience.Objects.ObjectClasses import BaseObj
 from easyscience.Objects.ObjectClasses import Parameter
 

examples_old/example_dataset2pt2.py

@@ -5,7 +5,7 @@
 
 import numpy as np
 from easyscience.Datasets.xarray import xr
-from easyscience.Fitting import Fitter
+from easyscience.fitting import Fitter
 from easyscience.Objects.ObjectClasses import BaseObj
 from easyscience.Objects.ObjectClasses import Parameter
 

examples_old/example_dataset2pt2_broken.py

@@ -5,7 +5,7 @@
 
 import numpy as np
 from easyscience.Datasets.xarray import xr
-from easyscience.Fitting import Fitter
+from easyscience.fitting import Fitter
 from easyscience.Objects.Base import BaseObj
 from easyscience.Objects.Base import Parameter
 

examples_old/example_dataset3.py

@@ -7,7 +7,7 @@
 
 import numpy as np
 from easyscience.Datasets.xarray import xr
-from easyscience.Fitting import Fitter
+from easyscience.fitting import Fitter
 from easyscience.Objects.ObjectClasses import BaseObj
 from easyscience.Objects.ObjectClasses import Parameter
 

examples_old/example_dataset3pt2.py

@@ -5,7 +5,7 @@
 
 import numpy as np
 from easyscience.Datasets.xarray import xr
-from easyscience.Fitting import Fitter
+from easyscience.fitting import Fitter
 from easyscience.Objects.ObjectClasses import BaseObj
 from easyscience.Objects.ObjectClasses import Parameter
 

examples_old/example_dataset4.py

@@ -5,7 +5,7 @@
 
 import numpy as np
 from easyscience.Datasets.xarray import xr
-from easyscience.Fitting import Fitter
+from easyscience.fitting import Fitter
 from easyscience.Objects.ObjectClasses import BaseObj
 from easyscience.Objects.ObjectClasses import Parameter
 

examples_old/example_dataset4_2.py

@@ -5,7 +5,7 @@
 
 import numpy as np
 from easyscience.Datasets.xarray import xr
-from easyscience.Fitting import Fitter
+from easyscience.fitting import Fitter
 from easyscience.Objects.ObjectClasses import BaseObj
 from easyscience.Objects.ObjectClasses import Parameter
 

src/easyscience/Datasets/xarray.py

@@ -281,14 +281,13 @@ def sigma_generator(
 
         :param variable_label: Name of the DataArray to perform the calculation on
         :type variable_label: str
-        :param sigma_func: Function to generate the sigmas. Must be of the form f(x) and return an array of the same
-        shape as the input. DEFAULT: sqrt(|data|)
+        :param sigma_func: Function to generate the sigmas. Must be of the form f(x) and return an array of the same shape as the input. Default sqrt(\|x\|)
         :type sigma_func: Callable
         :param label_prefix: What prefix should be used to designate a sigma DataArray from a data DataArray
         :type label_prefix: str
         :return: None
         :rtype: None
-        """
+        """  # noqa: E501
         sigma_values = sigma_func(self._obj[variable_label])
         self.sigma_attach(variable_label, sigma_values, label_prefix)
 

src/easyscience/Objects/Groups.py

@@ -22,9 +22,9 @@
 from easyscience.Objects.ObjectClasses import Descriptor
 
 if TYPE_CHECKING:
-    from easyscience.Utils.typing import B
-    from easyscience.Utils.typing import V
-    from easyscience.Utils.typing import iF
+    from easyscience.Objects.Inferface import iF
+    from easyscience.Objects.ObjectClasses import B
+    from easyscience.Objects.Variable import V
 
 
 class BaseCollection(BasedBase, MutableSequence):

src/easyscience/Objects/ObjectClasses.py

@@ -28,9 +28,9 @@
 from .Variable import Parameter
 
 if TYPE_CHECKING:
-    from easyscience.Utils.typing import C
-    from easyscience.Utils.typing import V
-    from easyscience.Utils.typing import iF
+    from easyscience.fitting.Constraints import C
+    from easyscience.Objects.Inferface import iF
+    from easyscience.Objects.Variable import V
 
 
 class BasedBase(ComponentSerializer):
@@ -41,10 +41,10 @@ class BasedBase(ComponentSerializer):
     def __init__(self, name: str, interface: Optional[iF] = None, unique_name: Optional[str] = None):
         self._global_object = global_object
         if unique_name is None:
-            unique_name = self._unique_name_generator()
+            unique_name = self._global_object.generate_unique_name(self.__class__.__name__)
         self._unique_name = unique_name
         self._name = name
-        self._global_object.map.add_vertex(self, obj_type="created")
+        self._global_object.map.add_vertex(self, obj_type='created')
         self.interface = interface
         self.user_data: dict = {}
 
@@ -69,16 +69,16 @@ def __reduce__(self):
 
     @property
     def unique_name(self) -> str:
-        """ Get the unique name of the object."""
+        """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. 
-        
+        """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.")
+            raise TypeError('Unique name has to be a string.')
         self._unique_name = new_unique_name
         self._global_object.map.add_vertex(self)
 
@@ -206,18 +206,6 @@ def get_fit_parameters(self) -> Union[List[Parameter], List[NewParameter]]:
                     fit_list.append(item)
         return fit_list
 
-    def _unique_name_generator(self) -> str:
-        """
-        Generate a generic unique name for the object using the class name and a global iterator.
-        """
-        class_name = self.__class__.__name__
-        iterator_string = str(self._global_object.map._get_name_iterator(class_name))
-        name = class_name + "_" + iterator_string
-        while name in self._global_object.map.vertices():
-            iterator_string = str(self._global_object.map._get_name_iterator(class_name))
-            name = class_name + "_" + iterator_string
-        return name
-
     def __dir__(self) -> Iterable[str]:
         """
         This creates auto-completion and helps out in iPython notebooks.
@@ -226,7 +214,6 @@ def __dir__(self) -> Iterable[str]:
         """
         new_class_objs = list(k for k in dir(self.__class__) if not k.startswith('_'))
         return sorted(new_class_objs)
-    
 
 
 if TYPE_CHECKING:
@@ -267,7 +254,7 @@ def __init__(
         self._kwargs = kwargs
         for key in kwargs.keys():
             if key in known_keys:
-                raise AttributeError("Kwargs cannot overwrite class attributes in BaseObj.")
+                raise AttributeError('Kwargs cannot overwrite class attributes in BaseObj.')
             if issubclass(type(kwargs[key]), (BasedBase, Descriptor, DescriptorBase)) or 'BaseCollection' in [
                 c.__name__ for c in type(kwargs[key]).__bases__
             ]:

src/easyscience/Objects/Variable.py

@@ -37,7 +37,7 @@
 from easyscience.Utils.Exceptions import CoreSetException
 
 if TYPE_CHECKING:
-    from easyscience.Utils.typing import C
+    from easyscience.fitting.Constraints import C
 
 Q_ = ureg.Quantity
 M_ = ureg.Measurement
@@ -109,7 +109,7 @@ def __init__(
         if not hasattr(self, '_args'):
             self._args = {'value': None, 'units': ''}
         if unique_name is None:
-            unique_name = self._unique_name_generator()
+            unique_name = self._global_object.generate_unique_name(self.__class__.__name__)
         self._unique_name = unique_name
         self.name = name
         # Let the collective know we've been assimilated
@@ -190,14 +190,14 @@ def unique_name(self) -> str:
         :return: Unique name of this 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. 
-        
+        """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.")
+            raise TypeError('Unique name has to be a string.')
         self._unique_name = new_unique_name
         self._global_object.map.add_vertex(self)
 
@@ -363,19 +363,6 @@ def convert_unit(self, unit_str: str):
         self._args['value'] = self.raw_value
         self._args['units'] = str(self.unit)
 
-    def _unique_name_generator(self) -> str:
-        """
-        Generate a generic unique name for the object using the class name and a global iterator.
-        """
-        class_name = self.__class__.__name__
-        iterator_string = str(self._global_object.map._get_name_iterator(class_name))
-        name = class_name + "_" + iterator_string
-        while name in self._global_object.map.vertices():
-            iterator_string = str(self._global_object.map._get_name_iterator(class_name))
-            name = class_name + "_" + iterator_string
-        return name
-
-
     # @cached_property
     @property
     def compatible_units(self) -> List[str]: