Build documentation

.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):

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

src/easyscience/Objects/virtual.py

@@ -18,7 +18,7 @@
 from easyscience.fitting.Constraints import ObjConstraint
 
 if TYPE_CHECKING:
-    from easyscience.Utils.typing import BV
+    from easyscience.Objects.ObjectClasses import BV
 
 
 def raise_(ex):
@@ -48,7 +48,7 @@ def realizer(obj: BV):
         args = []
         if klass in ec_var.__dict__.values():  # is_variable check
             kwargs = obj.encode_data()
-            kwargs["unique_name"] = None
+            kwargs['unique_name'] = None
             return klass(**kwargs)
         else:
             kwargs = {name: realizer(item) for name, item in obj._kwargs.items()}
@@ -97,9 +97,7 @@ def component_realizer(obj: BV, component: str, recursive: bool = True):
                 key = value.unique_name
             if getattr(value, '__old_class__', value.__class__) in ec_var.__dict__.values():
                 continue
-            component._global_object.map.prune_vertex_from_edge(
-                component, component._kwargs[key]
-            )
+            component._global_object.map.prune_vertex_from_edge(component, component._kwargs[key])
             component._global_object.map.add_edge(component, old_component._kwargs[key])
             component._kwargs[key] = old_component._kwargs[key]
             done_mapping = False
@@ -142,12 +140,12 @@ def virtualizer(obj: BV) -> BV:
     # The supplied class
     klass = getattr(obj, '__old_class__', obj.__class__)
     virtual_options = {
-        "_is_virtual": True,
-        "is_virtual": property(fget=lambda self: self._is_virtual),
-        "_derived_from": property(fget=lambda self: obj.unique_name),
-        "__non_virtual_class__": klass,
-        "realize": realizer,
-        "relalize_component": component_realizer,
+        '_is_virtual': True,
+        'is_virtual': property(fget=lambda self: self._is_virtual),
+        '_derived_from': property(fget=lambda self: obj.unique_name),
+        '__non_virtual_class__': klass,
+        'realize': realizer,
+        'relalize_component': component_realizer,
     }
 
     import easyscience.Objects.Variable as ec_var

src/easyscience/Utils/classTools.py

@@ -4,8 +4,8 @@
 
 from __future__ import annotations
 
-__author__ = "github.com/wardsimon"
-__version__ = "0.1.0"
+__author__ = 'github.com/wardsimon'
+__version__ = '0.1.0'
 
 from typing import TYPE_CHECKING
 from typing import List
@@ -15,15 +15,15 @@
 from easyscience.global_object.hugger.property import LoggedProperty
 
 if TYPE_CHECKING:
-    from easyscience.Utils.typing import BV
-    from easyscience.Utils.typing import B
+    from easyscience.Objects.ObjectClasses import BV
+    from easyscience.Objects.ObjectClasses import B
 
 
 def addLoggedProp(inst: BV, name: str, *args, **kwargs) -> None:
     cls = type(inst)
-    annotations = getattr(cls, "__annotations__", False)
-    if not hasattr(cls, "__perinstance"):
-        cls = type(cls.__name__, (cls,), {"__module__": inst.__module__})
+    annotations = getattr(cls, '__annotations__', False)
+    if not hasattr(cls, '__perinstance'):
+        cls = type(cls.__name__, (cls,), {'__module__': inst.__module__})
         cls.__perinstance = True
         if annotations:
             cls.__annotations__ = annotations
@@ -34,9 +34,9 @@ def addLoggedProp(inst: BV, name: str, *args, **kwargs) -> None:
 
 def addProp(inst: BV, name: str, *args, **kwargs) -> None:
     cls = type(inst)
-    annotations = getattr(cls, "__annotations__", False)
-    if not hasattr(cls, "__perinstance"):
-        cls = type(cls.__name__, (cls,), {"__module__": __name__})
+    annotations = getattr(cls, '__annotations__', False)
+    if not hasattr(cls, '__perinstance'):
+        cls = type(cls.__name__, (cls,), {'__module__': __name__})
         cls.__perinstance = True
         if annotations:
             cls.__annotations__ = annotations
@@ -48,8 +48,8 @@ def addProp(inst: BV, name: str, *args, **kwargs) -> None:
 
 def removeProp(inst: BV, name: str) -> None:
     cls = type(inst)
-    if not hasattr(cls, "__perinstance"):
-        cls = type(cls.__name__, (cls,), {"__module__": __name__})
+    if not hasattr(cls, '__perinstance'):
+        cls = type(cls.__name__, (cls,), {'__module__': __name__})
         cls.__perinstance = True
         inst.__old_class__ = inst.__class__
         inst.__class__ = cls
@@ -65,8 +65,8 @@ def generatePath(model_obj: B, skip_first: bool = False) -> Tuple[List[int], Lis
     for par in pars:
         elem = par.unique_name
         route = global_object.map.reverse_route(elem, model_id)
-        objs = [getattr(global_object.map.get_item_by_key(r), "name") for r in route]
+        objs = [getattr(global_object.map.get_item_by_key(r), 'name') for r in route]
         objs.reverse()
-        names.append(".".join(objs[start_idx:]))
+        names.append('.'.join(objs[start_idx:]))
         ids.append(elem.int)
     return ids, names

src/easyscience/Utils/io/template.py

@@ -27,7 +27,7 @@
 import numpy as np
 
 if TYPE_CHECKING:
-    from easyscience.Utils.typing import BV
+    from easyscience.Objects.ObjectClasses import BV
 
 _e = json.JSONEncoder()