documentation fixes

bessagroup · May 29, 2024 · 093ff03 · 093ff03
1 parent 1b25af0
commit 093ff03
Show file tree

Hide file tree

Showing 21 changed files with 20 additions and 2,418 deletions.
diff --git a/docs/source/img/contour_data.png b/docs/source/img/contour_data.png
diff --git a/docs/source/img/contour_samples.png b/docs/source/img/contour_samples.png
diff --git a/docs/source/img/f3dasm-blocks.svg b/docs/source/img/f3dasm-blocks.svg
diff --git a/docs/source/img/f3dasm-cluster.png b/docs/source/img/f3dasm-cluster.png
diff --git a/docs/source/img/f3dasm-datageneration.png b/docs/source/img/f3dasm-datageneration.png
diff --git a/docs/source/img/f3dasm-design.png b/docs/source/img/f3dasm-design.png
diff --git a/docs/source/img/f3dasm-domain.png b/docs/source/img/f3dasm-domain.png
diff --git a/docs/source/img/f3dasm-experimentdata.png b/docs/source/img/f3dasm-experimentdata.png
diff --git a/docs/source/img/f3dasm-logo.png b/docs/source/img/f3dasm-logo.png
diff --git a/docs/source/img/f3dasm-logo.svg b/docs/source/img/f3dasm-logo.svg
diff --git a/docs/source/img/f3dasm-optimizer.png b/docs/source/img/f3dasm-optimizer.png
diff --git a/docs/source/img/f3dasm-parameter.png b/docs/source/img/f3dasm-parameter.png
diff --git a/docs/source/img/performance.png b/docs/source/img/performance.png
diff --git a/docs/source/img/samples.png b/docs/source/img/samples.png
diff --git a/docs/source/rst_doc_files/general/overview.rst b/docs/source/rst_doc_files/general/overview.rst
@@ -51,15 +51,15 @@ Computational framework
 
  - The framework automatically manages I/O processes, saving you time and effort implementing these common procedures.
 
-- :doc:`Easy parallelization <auto_examples/005_workflow/001_cluster_computing>`
+- :doc:`Easy parallelization <../../auto_examples/005_workflow/001_cluster_computing>`
 
  - The framework manages parallelization of experiments, and is compatible with both local and high-performance cluster computing.
 
-- :doc:`Built-in defaults <rst_doc_files/defaults>`
+- :doc:`Built-in defaults <../defaults>`
 
  - The framework includes a collection of :ref:`benchmark functions <implemented-benchmark-functions>`, :ref:`optimization algorithms <implemented optimizers>` and :ref:`sampling strategies <implemented samplers>` to get you started right away!
 
-- :doc:`Hydra integration <auto_examples/006_hydra/001_hydra_usage>`
+- :doc:`Hydra integration <../../auto_examples/006_hydra/001_hydra_usage>`
 
  - The framework is integrated with `hydra <https://hydra.cc/>`_ configuration manager, to easily manage and run experiments.
 

diff --git a/examples/001_domain/001_domain_creation.py b/examples/001_domain/001_domain_creation.py
@@ -2,7 +2,7 @@
 Introduction to domain and parameters
 =====================================
 
-This section will give you information on how to set up your search space with the :ref:`domain <domain>` class and the :ref:`parameters <parameters>`
+This section will give you information on how to set up your search space with the :class:`~f3dasm.design.Domain` class and the paramaters
 The :class:`~f3dasm.design.Domain` is a set of parameter instances that make up the feasible search space.
 """
 ###############################################################################
@@ -21,25 +21,25 @@
 # Now we well add some input parameters:
 # There are four types of parameters that can be created:
 #
-# - :ref:`floating point <continuous-parameter>` parameters
+# - floating point parameters
 
 domain.add_float(name='x1', low=0.0, high=100.0)
 domain.add_float(name='x2', low=0.0, high=4.0)
 
 ###############################################################################
-# - :ref:`discrete integer pramaters <discrete-parameter>`
+# - discrete integer parameters
 
 domain.add_int(name='x3', low=2, high=4)
 domain.add_int(name='x4', low=74, high=99)
 
 ###############################################################################
-# - :ref:`categorical parameters <categorical-parameter>`
+# - categorical parameters
 
 domain.add_category(name='x5', categories=['test1', 'test2', 'test3', 'test4'])
 domain.add_category(name='x6', categories=[0.9, 0.2, 0.1, -2])
 
 ###############################################################################
-# - :ref:`constant parameters<constant-parameter>`
+# - constant parameters
 
 domain.add_constant(name='x7', value=0.9)
 
@@ -61,7 +61,6 @@
 ###############################################################################
 # The :code:`to_disk` argument can be set to :code:`True` to store the output parameter on disk. A reference to the file is stored in the :class:`~f3dasm.ExperimentData` object.
 # This is useful when the output data is very large, or when the output data is an array-like object.
-# More information on storing output can be found in :ref:`this section <storing-output-experiment-sample>`
 
 ###############################################################################
 # Filtering the domain

diff --git a/examples/002_experimentdata/001_experimentdata.py b/examples/002_experimentdata/001_experimentdata.py
@@ -9,17 +9,17 @@
 
 The :class:`~f3dasm.ExperimentData` object consists of the following attributes:
 
-- :ref:`domain <domain-format>`: The feasible :class:`~f3dasm.design.Domain` of the Experiment. Used for sampling and optimization.
-- :ref:`input_data <input-data-format>`: Tabular data containing the input variables of the experiments as column and the experiments as rows.
-- :ref:`output_data <output-data-format>`: Tabular data containing the tracked outputs of the experiments.
-- :ref:`project_dir <filename-format>`: A user-defined project directory where all files related to your data-driven process will be stored. 
+- domain: The feasible :class:`~f3dasm.design.Domain` of the Experiment. Used for sampling and optimization.
+- input_data: Tabular data containing the input variables of the experiments as column and the experiments as rows.
+- output_data: Tabular data containing the tracked outputs of the experiments.
+- project_dir: A user-defined project directory where all files related to your data-driven process will be stored. 
 """
 
 ###############################################################################
 # The :class:`~f3dasm.ExperimentData` object can be constructed in several ways:
 #
-# You can construct a :class:`~f3dasm.ExperimentData` object by providing it :ref:`input_data <input-data-format>`,
-# :ref:`output_data <output-data-format>`, a :ref:`domain <domain-format>` object and a :ref:`project_dir <filename-format>`.
+# You can construct a :class:`~f3dasm.ExperimentData` object by providing it input data,
+# output data, a :class:`~f3dasm.design.Domain` object and a project directory.
 
 import numpy as np
 import pandas as pd

diff --git a/examples/002_experimentdata/002_experimentdata_storing.py b/examples/002_experimentdata/002_experimentdata_storing.py
@@ -10,7 +10,7 @@
 # project directory
 # ^^^^^^^^^^^^^^^^^
 #
-# The ``project_dir`` argument is used to :ref:`store the ExperimentData to disk <experimentdata-store>`
+# The ``project_dir`` argument is used to store the ExperimentData to disk
 # You can provide a string or a path to a directory. This can either be a relative or absolute path.
 # If the directory does not exist, it will be created.
 

diff --git a/examples/005_workflow/001_cluster_computing.py b/examples/005_workflow/001_cluster_computing.py
@@ -23,11 +23,11 @@
 from f3dasm.design import make_nd_continuous_domain
 
 ###############################################################################
-# The following example is the same as in section :ref:`workflow`; only now we are omiting the optimization part and only parallelize the data generation:
+# We will create the following data-driven process:
 #
 # * Create a 20D continuous :class:`~f3dasm.design.Domain`
 # * Sample from the domain using a the Latin-hypercube sampler
-# * With multiple nodes; use a data generation function, which will be the ``"Ackley"`` function a from the :ref:`benchmark-functions`
+# * With multiple nodes; use a data generation function, which will be the ``"Ackley"`` function a from the benchmark functions
 #
 #
 # .. image:: ../../img/f3dasm-workflow-example-cluster.png

diff --git a/examples/006_hydra/002_cluster_hydra.py b/examples/006_hydra/002_cluster_hydra.py
@@ -6,11 +6,11 @@
 """
 ###############################################################################
 #
-# The following example is the same as in section :ref:`workflow`; we will create a workflow for the following data-driven process:
+# The following example is the same as in workflow section; we will create a workflow for the following data-driven process:
 #
 # * Create a 2D continuous :class:`~f3dasm.design.Domain`
 # * Sample from the domain using a the Latin-hypercube sampler
-# * Use a data generation function, which will be the ``"Ackley"`` function a from the :ref:`benchmark-functions`
+# * Use a data generation function, which will be the ``"Ackley"`` function a from the benchmark functions
 #
 # .. image:: ../../img/f3dasm-workflow-example-cluster.png
 # :width: 70%

diff --git a/src/f3dasm/_src/optimization/optimizer.py b/src/f3dasm/_src/optimization/optimizer.py
@@ -56,7 +56,7 @@ class Optimizer:
 
  '''
  def update_step(self, data_generator: DataGenerator)
-  -> Tuple[np.ndarray, np.ndarray]:
+ -> Tuple[np.ndarray, np.ndarray]:
  '''
 
  The method should return a tuple containing the new samples and the