changed Design to ExperimentSample

docs/source/index.rst

@@ -24,7 +24,7 @@ f3dasm
    rst_doc_files/classes/design/parameters
    rst_doc_files/classes/design/domain
    rst_doc_files/classes/design/experimentdata
-   rst_doc_files/classes/design/design
+   rst_doc_files/classes/design/experimentsample
    rst_doc_files/classes/sampling/sampling
 
 .. toctree::

docs/source/rst_doc_files/classes/datageneration/datagenerator.rst

@@ -2,7 +2,7 @@ Datagenerator
 =============
 
 The :class:`~f3dasm.datageneration.datagenerator.DataGenerator` class is the main class of the :mod:`~f3dasm.datageneration` module.
-It is used to generate :attr:`~f3dasm.design.experimentdata.ExperimentData.output_data` for the :class:`~f3dasm.design.experimentdata.ExperimentData` by taking a :class:`~f3dasm.design.design.Design` object.
+It is used to generate :attr:`~f3dasm.design.experimentdata.ExperimentData.output_data` for the :class:`~f3dasm.design.experimentdata.ExperimentData` by taking a :class:`~f3dasm.design.experimentsample.ExperimentSample` object.
 
 The :class:`~f3dasm.datageneration.datagenerator.DataGenerator` can serve as the interface between the 
 :class:`~f3dasm.design.experimentdata.ExperimentData` object and any third-party simulation software.
@@ -17,7 +17,7 @@ The :class:`~f3dasm.datageneration.datagenerator.DataGenerator` can serve as the
 Creating a data-generator
 -------------------------
 
-In order to run your simulator on each of the :class:`~f3dasm.design.design.Design` of your :class:`~f3dasm.design.experimentdata.ExperimentData`, you follow these steps:
+In order to run your simulator on each of the :class:`~f3dasm.design.experimentsample.ExperimentSample` of your :class:`~f3dasm.design.experimentdata.ExperimentData`, you follow these steps:
 In this case, we are utilizing a one of the :ref:`benchmark-functions` to mock a simulator.
 
 1. Construct the :class:`~f3dasm.datageneration.datagenerator.DataGenerator` object.
@@ -38,11 +38,11 @@ In this case, we are utilizing a one of the :ref:`benchmark-functions` to mock a
     Any key-word arguments that need to be passed down to the :class:`~f3dasm.datageneration.datagenerator.DataGenerator` :code:`__call__` function can be passed in the :code:`kwargs` argument of the :meth:`~f3dasm.design.experimentdata.ExperimentData.run` function.
 
 
-There are three methods available of handeling the :class:`~f3dasm.design.design.Design` objects:
+There are three methods available of handeling the :class:`~f3dasm.design.experimentsample.ExperimentSample` objects:
 
-* :code:`sequential`: regular for-loop over each of the :class:`~f3dasm.design.design.Design` objects in order
-* :code:`parallel`: utilizing the multiprocessing capabilities, each :class:`~f3dasm.design.design.Design` object is run in a separate core
-* :code:`cluster`: utilizing the multiprocessing capabilities, each :class:`~f3dasm.design.design.Design` object is run in a separate node. After termination of a design, the node will automatically pick the next available design. More information on this mode can be found in the :ref:`cluster-mode` section.
+* :code:`sequential`: regular for-loop over each of the :class:`~f3dasm.design.experimentsample.ExperimentSample` objects in order
+* :code:`parallel`: utilizing the multiprocessing capabilities, each :class:`~f3dasm.design.experimentsample.ExperimentSample` object is run in a separate core
+* :code:`cluster`: utilizing the multiprocessing capabilities, each :class:`~f3dasm.design.experimentsample.ExperimentSample` object is run in a separate node. After completion of an sample, the node will automatically pick the next available sample. More information on this mode can be found in the :ref:`cluster-mode` section.
 
 
 Implemented data-generators
@@ -73,7 +73,7 @@ Create your own data-generator
 In order to use your own simulator or script, you need to comply with either one of the following options:
 
 * Create a class that inherits from the :class:`~f3dasm.datageneration.datagenerator.DataGenerator` class and implement the methods.
-* Create a function that takes a :class:`~f3dasm.design.design.Design` object as an argument (and returns a :class:`~f3dasm.design.design.Design`).
+* Create a function that takes a :class:`~f3dasm.design.experimentsample.ExperimentSample` object as an argument (and returns a :class:`~f3dasm.design.experimentsample.ExperimentSample`).
 
 
 Inherit from DataGenerator
@@ -111,13 +111,13 @@ An example is given in the following code block:
 
     def execute(self, any_argument: str, **kwargs) -> None:
         # Retrieve parameters
-        parameter_1 = self.design['parameter1']
+        parameter_1 = self.experiment_sample['parameter1']
 
         # Run a simulation
         ...
 
         # Store the results
-        self.design['result'] = result
+        self.experiment_sample['result'] = result
 
     def post_process(self, any_post_process_arg: str, **kwargs) -> None:
         ...
@@ -133,18 +133,19 @@ Create a data-generator from a functional approach
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The functional approach is a bit more flexible, as it allows you to use any function 
-that takes a :class:`~f3dasm.design.design.Design` object as an argument, and returns a :class:`~f3dasm.design.design.Design` object.
+that takes a :class:`~f3dasm.design.experimentsample.ExperimentSample` object as an argument, and returns a :class:`~f3dasm.design.experimentsample.ExperimentSample` object.
 
 .. note::
 
     The :class:`~f3dasm.datageneration.datagenerator.DataGenerator` class is a wrapper around the functional approach.
 
 
 .. code-block:: python
-    from f3dasm import Design
+    
+    from f3dasm import ExperimentSample
 
-    def my_function(design: f3dasm.Design, some_kwarg: int):
-        # do something with the design
-        return design
+    def my_function(experiment_sample: f3dasm.ExperimentSample, some_kwarg: int):
+        # do something with the sample
+        return experiment_sample
 
     experimentdata.run(my_function, method='sequential', kwargs={'some_kwarg': 1})

docs/source/rst_doc_files/classes/datageneration/functions.rst

@@ -18,12 +18,12 @@ Benchmarkfunction are a submodule of the :code:`f3dasm.datageneration` module un
 Creating the function
 ^^^^^^^^^^^^^^^^^^^^^
 
-First we make a 2-dimensional continous design space with the helper function :func:`~f3dasm.design.design.make_nd_continuous_design`:
+First we make a 2-dimensional continous domain with the helper function :func:`~f3dasm.design.design.make_nd_continuous_design`:
 
 .. code-block:: python
 
   bounds = np.array([[-1.0, 1.0], [-1.0, 1.0]])
-  design = f3dasm.make_nd_continuous_design(bounds=bounds, dimensions=2)
+  domain = f3dasm.make_nd_continuous_design(bounds=bounds, dimensions=2)
 
 Then we create an object of the :class:`~f3dasm.functions.pybenchfunction.Sphere` class, specifying the :attr:`~f3dasm.functions.pybenchfunction.PybenchFunction.dimensionality`:
 

docs/source/rst_doc_files/classes/design/domain.rst

@@ -113,4 +113,4 @@ We can make easily make a :math:`n`-dimensional continous domain with the helper
 .. code-block:: python
 
   bounds = np.array([[-1.0, 1.0], [-1.0, 1.0]])
-  design = f3dasm.make_nd_continuous_domain(bounds=bounds, dimensionality=2)
+  domain = f3dasm.make_nd_continuous_domain(bounds=bounds, dimensionality=2)

docs/source/rst_doc_files/classes/design/design.rst → docs/source/rst_doc_files/classes/design/experimentsample.rst

@@ -1,7 +1,7 @@
 Design
 ======
 
-A :class:`~f3dasm.design.design.Design` object contains a single realization of the design-of-experiment in :class:`~f3dasm.design.experimentdata.ExperimentData`.
+A :class:`~f3dasm.design.experimentsample.ExperimentSample` object contains a single realization of the design-of-experiment in :class:`~f3dasm.design.experimentdata.ExperimentData`.
 
 .. image:: ../../../img/f3dasm-design.png
     :alt: Design
@@ -11,81 +11,81 @@ A :class:`~f3dasm.design.design.Design` object contains a single realization of
 |
 
 .. note:: 
-    A :class:`~f3dasm.design.design.Design` is not constructed manually, but created inside the ExperimentData when it is required by internal processes. 
-    The main use of the :class:`~f3dasm.design.design.Design` is to pass it to your own functions and scripts to extract design variables and store output variables.
+    A :class:`~f3dasm.design.experimentsample.ExperimentSample` is not constructed manually, but created inside the ExperimentData when it is required by internal processes. 
+    The main use of the :class:`~f3dasm.design.experimentsample.ExperimentSample` is to pass it to your own functions and scripts to extract design variables and store output variables.
 
 
 
-For each of the experiments in the :class:`~f3dasm.design.experimentdata.ExperimentData`, a :class:`~f3dasm.design.design.Design` object can be created.
-This object contains the input and output parameters of a single realization of the :class:`~f3dasm.design.experimentdata.ExperimentData`, as well as the index number of the experiment (:attr:`~f3dasm.design.design.Design.job_number`).
+For each of the experiments in the :class:`~f3dasm.design.experimentdata.ExperimentData`, a :class:`~f3dasm.design.experimentsample.ExperimentSample` object can be created.
+This object contains the input and output parameters of a single realization of the :class:`~f3dasm.design.experimentdata.ExperimentData`, as well as the index number of the experiment (:attr:`~f3dasm.design.experimentsample.ExperimentSample.job_number`).
 
 .. code-block:: python
     
-   from f3dasm import Design
+   from f3dasm import ExperimentSample
 
-    def my_function(design: Design, **kwargs):
-        parameter1 = design['param_1']
-        parameter2 = design['param_2']
-        job_number = design.job_number
+    def my_function(experiment_sample: ExperimentSample, **kwargs):
+        parameter1 = experiment_sample['param_1']
+        parameter2 = experiment_sample['param_2']
+        job_number = experiment_sample.job_number
         ...  # Your own program
 
-        design['output_1'] = output
-        return design
+        experiment_sample['output_1'] = output
+        return experiment_sample
 
-A function with a signature like :code:`my_function` can be used as a callable in the :meth:`~f3dasm.design.experimentdata.ExperimentData.run` method to iterate over every design in the :class:`~f3dasm.design.experimentdata.ExperimentData`.
+A function with a signature like :code:`my_function` can be used as a callable in the :meth:`~f3dasm.design.experimentdata.ExperimentData.run` method to iterate over every sample in the :class:`~f3dasm.design.experimentdata.ExperimentData`.
 
 .. note:: 
-    In order to use :code:`my_function` within :mod:`f3dasm` workflow, the first argument needs to be a :class:`~f3dasm.design.design.Design` object. 
+    In order to use :code:`my_function` within :mod:`f3dasm` workflow, the first argument needs to be a :class:`~f3dasm.design.experimentsample.ExperimentSample` object. 
     The function can have any number of additional arguments, which will be passed to the function when it is called.
-    Lastly, the :class:`~f3dasm.design.design.Design` must be returned.
+    Lastly, the :class:`~f3dasm.design.experimentsample.ExperimentSample` must be returned.
 
-Extract parameters from a design
---------------------------------
+Extract parameters from a experiment sample
+-------------------------------------------
 
-Input parameters of a design can be accessed using the :code:`[]` operator, with the name of the parameter as the key.
-Only input parameters of the design can be accessed this way, and an error will be raised if the key is not found.
+Input parameters of an experiment sample can be accessed using the :code:`[]` operator, with the name of the parameter as the key.
+Only input parameters of the experiment sample can be accessed this way, and an error will be raised if the key is not found.
 
 .. code-block:: python
 
-    >>> design['param_1']
+    >>> experiment_sample['param_1']
     0.0249
 
 
-The job_number of the design can be accessed using the :attr:`~f3dasm.design.design.Design.job_number` attribute and is zero-indexed.
+The job_number of the experiment sample can be accessed using the :attr:`~f3dasm.design.experimentsample.ExperimentSaple.job_number` attribute and is zero-indexed.
 
 .. code-block:: python
 
-    >>> design.job_number
+    >>> experiment_sample.job_number
     0
 
-The input and output parameters of a design can be extracted as a tuple of numpy arrays with the :meth:`~f3dasm.design.Design.to_numpy` method.
+The input and output parameters of an experiment sample can be extracted as a tuple of numpy arrays with the :meth:`~f3dasm.experimentsample.ExperimentSample.to_numpy` method.
 
 .. code-block:: python
 
-    >>> design.to_numpy()
+    >>> experiment_sample.to_numpy()
     (np.array([0.0249, 0.034, 0.100]), np.array([]))
 
-Storing output parameters to the design
----------------------------------------
+Storing output parameters to the experiment sample
+--------------------------------------------------
 
-After running your calculation, you can store the result back into the design in two ways:
+After running your calculation, you can store the result back into the experiment sample in two ways:
 
 * Singular values and small lists can be stored directly to the :attr:`~f3dasm.design.experimentdata.ExperimentData.output_data`
-* Large objects can be stored to disk with the :meth:`f3dasm.design.design.Design.store` method.
+* Large objects can be stored to disk with the :meth:`f3dasm.design.experimentsample.ExperimentSample.store` method.
 
 Single values or small lists
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Single values or small lists can be stored to the design using the :code:`[]` operator, with the name of the parameter as the key. 
+Single values or small lists can be stored to the :class:`~f3dasm.design.experimentdata.ExperimentData` using the :code:`[]` operator, with the name of the parameter as the key. 
 This will create a new output parameter if the parameter name is not found in :attr:`~f3dasm.design.experimentdata.ExperimentData.output_data` of the :class:`~f3dasm.design.experimentdata.ExperimentData`.
 
 .. code-block:: python
 
-    >>> design['output_1'] = 0.123
-    >>> design['output_2'] = [0.123, 0.456, 0.789]
-    >>> design['output_3'] = 'Hello world'
+    >>> experiment_sample['output_1'] = 0.123
+    >>> experiment_sample['output_2'] = [0.123, 0.456, 0.789]
+    >>> experiment_sample['output_3'] = 'Hello world'
 
-All built-in types are supported for storing to the design this way. Array-like data such as numpy arrays and pandas dataframes are **not** supported and will raise an error.
+All built-in types are supported for storing to the :class:`~f3dasm.design.experimentdata.ExperimentData` this way. Array-like data such as numpy arrays and pandas dataframes are **not** supported and will raise an error.
 
 .. note:: 
     Outputs stored directly to the :attr:`~f3dasm.design.experimentdata.ExperimentData.output_data` will be stored within the :class:`~f3dasm.design.experimentdata.ExperimentData` object.
@@ -94,13 +94,13 @@ All built-in types are supported for storing to the design this way. Array-like
 Large objects and array-like data
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-In order to store large objects or array-like data, the :meth:`~f3dasm.design.design.Design.store` method can be used. A reference (:code:`Path`) will be saved to the :attr:`~f3dasm.design.experimentdata.ExperimentData.output_data`.
+In order to store large objects or array-like data, the :meth:`~f3dasm.design.experimentsample.ExperimentSample.store` method can be used. A reference (:code:`Path`) will be saved to the :attr:`~f3dasm.design.experimentdata.ExperimentData.output_data`.
 
 .. code-block:: python
 
-    >>> design.store('output_1', my_large_object)
+    >>> experiment_sample.store('output_1', my_large_object)
 
-:mod:`f3dasm` will automatically create a new directory for each output parameter and store the object with a generated filename referencing the :attr:`~f3dasm.design.design.Design.job_number` of the design.
+:mod:`f3dasm` will automatically create a new directory for each output parameter and store the object with a generated filename referencing the :attr:`~f3dasm.design.experimentsample.ExperimentSample.job_number` of the design.
 
 .. code-block:: none
    :caption: Directory Structure
@@ -120,13 +120,13 @@ In the :attr:`~f3dasm.design.experimentdata.ExperimentData.output_data`, a refer
 
 .. code-block:: python
 
-    >>> design['output_1_path']
+    >>> experiment_sample['output_1_path']
     'my_project/output_1/0.npy'
 
 
 
 :mod:`f3dasm` has built-in storing functions for numpy arrays, pandas DataFrames and xarray DataArrays and Datasets. 
-For any other type of object, you can provide a storing function to the :meth:`~f3dasm.design.design.Design.store` method call:
+For any other type of object, you can provide a storing function to the :meth:`~f3dasm.design.experimentsample.ExperimentSample.store` method call:
 
 * The arguments must be the object itself and the path that it should store to
 * The function should store the object to disk.
@@ -141,8 +141,8 @@ You can take the following function as an example:
         return '.npy'
 
 
-After defining the storing function, it can be used as a callable in the :meth:`~f3dasm.design.design.Design.store` method:
+After defining the storing function, it can be used as a callable in the :meth:`~f3dasm.design.experimentsample.ExperimentSample.store` method:
 
 .. code-block:: python
 
-    >>> design.store('output_1', my_large_object, numpy_storing_function)
+    >>> experiment_sample.store('output_1', my_large_object, numpy_storing_function)

docs/source/rst_doc_files/classes/optimization/optimizers.rst

@@ -4,7 +4,7 @@ Optimizer
 The :class:`~f3dasm.optimization.optimizer.Optimizer` class is used to find the minimum of a particular quantity of interest through an iterative fashion.
 
 * The :meth:`~f3dasm.optimization.optimizer.Optimizer.update_step` method takes a :class:`~f3dasm.datageneration.functions.function.Function` object and outputs a tuple containing the position and evaluated value of the next iteration.
-* The :meth:`~f3dasm.optimization.optimizer.Optimizer.iterate` method is used to start the optimization process. It takes the number of iterations and a :class:`~f3dasm.base.function.Function` object as arguments. For every iteration, the :meth:`~f3dasm.optimization.optimizer.Optimizer.update_step` method is called and the results are stored as new :class:`~f3dasm.design.design.Design` in the :class:`~f3dasm.design.experimentdata.ExperimentData` object.
+* The :meth:`~f3dasm.optimization.optimizer.Optimizer.iterate` method is used to start the optimization process. It takes the number of iterations and a :class:`~f3dasm.base.function.Function` object as arguments. For every iteration, the :meth:`~f3dasm.optimization.optimizer.Optimizer.update_step` method is called and the results are stored as new :class:`~f3dasm.design.experimentsample.ExperimentSample` in the :class:`~f3dasm.design.experimentdata.ExperimentData` object.
 
 
 .. image:: ../../../img/f3dasm-optimizer.png