Patch update to documentation for release and testing

MSDLLCpapers · Aug 7, 2024 · 2365e10 · 2365e10
2 parents 6a3c80d + 6488efc
commit 2365e10
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diff --git a/demo/Simple single objective.ipynb b/demo/Simple single objective.ipynb
diff --git a/docs/_static/tutorials/Simple single objective.html b/docs/_static/tutorials/Simple single objective.html
diff --git a/docs/_templates/module.rst b/docs/_templates/module.rst
@@ -60,7 +60,7 @@
    :template: module.rst
    :recursive:
 {% for item in modules %}
-{% if not item in ("obsidian.acquisition.aq_config", "obsidian.surrogates.surrogate_config", "obsidian.analysis") %}
+{% if not item in ("aq_config", "surrogate_config", "obj_config") %}
    {{ item }}
 {%- endif %}
 {%- endfor %}

diff --git a/docs/_templates/module_shallow.rst b/docs/_templates/module_shallow.rst
@@ -58,7 +58,7 @@
    :template: module_shallow.rst
    :recursive:
 {% for item in modules %}
-{% if not item in ("obsidian.acquisition.aq_config", "obsidian.surrogates.surrogate_config", "obsidian.analysis") %}
+{% if not item in ("aq_config", "surrogate_config", "obj_config") %}
    {{ item }}
 {%- endif %}
 {%- endfor %}

diff --git a/docs/conf.py b/docs/conf.py
@@ -19,7 +19,6 @@
     'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
     'sphinx.ext.autosummary',
-    'sphinx.ext.autosectionlabel',
     'myst_parser',
 ]
 
@@ -59,14 +58,11 @@
     "member-order": "groupwise",
 }
 
-toc_object_entries_show_parents = 'hide'
-add_module_names = False
-
 autodoc_default_options = {'members': None,  # shows all members
                            'show-inheritance': True}
 
 autodoc_typehints = "signature"
-autoclass_content = "class"
+autoclass_content = "class"  # Use class docstring instead of __init__
 
 # Autosummary Options
 autosummary_imported_members = False

diff --git a/docs/stubs/api_docs.rst b/docs/stubs/api_docs.rst
@@ -4,41 +4,37 @@
 .. automodule:: obsidian
 
 
-
-
-
 .. rubric:: Modules
 
 .. autosummary::
    :toctree: ../build/apidocs
    :recursive:
-   :template: module_shallow.rst
-
-   obsidian.acquisition
+   :template: module.rst
 
-   obsidian.constraints
+   obsidian.parameters
+
+   obsidian.campaign
 
-   obsidian.exceptions
+   obsidian.optimizer
 
-   obsidian.objectives
+   obsidian.surrogates
 
-   obsidian.plotting
+   obsidian.experiment
 
 .. autosummary::
    :toctree: ../build/apidocs
    :recursive:
-   :template: module.rst
-
-   obsidian.campaign
+   :template: module_shallow.rst
 
-   obsidian.experiment
+   obsidian.acquisition
 
-   obsidian.optimizer
+   obsidian.objectives
 
-   obsidian.parameters
+   obsidian.plotting
 
-   obsidian.surrogates
+   obsidian.constraints
 
+   obsidian.exceptions
 
 Indices
 ~~~~~~~~~~~~~~~~~~

diff --git a/docs/wiki/1_APO_Workflow_and_CodeStructure.md b/docs/wiki/1_APO_Workflow_and_CodeStructure.md
diff --git a/obsidian/acquisition/__init__.py b/obsidian/acquisition/__init__.py
@@ -1,15 +1,4 @@
 """Acquisition: Functions to determine the value of sequential experiments"""
 
-from .acquisition_botorch import (
-    qMean,
-    qSpaceFill,
-    qExpectedImprovement,
-    qProbabilityOfImprovement,
-    qUpperConfidenceBound,
-    qNoisyExpectedImprovement,
-    qSimpleRegret,
-    qNoisyExpectedHypervolumeImprovement,
-    qLogNParEGO,
-)
-
-from .aq_config import aq_functions, valid_aqs, aq_hp_defaults
+from .acquisition_botorch import *
+from .aq_config import *
diff --git a/obsidian/acquisition/acquisition_botorch.py b/obsidian/acquisition/acquisition_botorch.py
@@ -11,22 +11,25 @@
 from botorch.acquisition.objective import MCAcquisitionObjective, PosteriorTransform
 
 # Botorch acquisition functions supported in obsidian
-from botorch.acquisition import qExpectedImprovement, qProbabilityOfImprovement, \
-    qUpperConfidenceBound, qNoisyExpectedImprovement, qSimpleRegret
-from botorch.acquisition.multi_objective.monte_carlo import qNoisyExpectedHypervolumeImprovement
+from botorch.acquisition import qProbabilityOfImprovement, qUpperConfidenceBound, qSimpleRegret
+from botorch.acquisition.logei import qLogExpectedImprovement, qLogNoisyExpectedImprovement
+from botorch.acquisition.multi_objective.logei import qLogExpectedHypervolumeImprovement, qLogNoisyExpectedHypervolumeImprovement
 from botorch.acquisition.multi_objective.parego import qLogNParEGO
+from botorch.acquisition.active_learning import qNegIntegratedPosteriorVariance
 
 
 __all__ = [
-    "qExpectedImprovement",
+    "qMean",
+    "qSpaceFill",
     "qProbabilityOfImprovement",
     "qUpperConfidenceBound",
-    "qNoisyExpectedImprovement",
     "qSimpleRegret",
-    "qNoisyExpectedHypervolumeImprovement",
+    "qLogExpectedImprovement",
+    "qLogNoisyExpectedImprovement",
+    "qLogExpectedHypervolumeImprovement",
+    "qLogNoisyExpectedHypervolumeImprovement",
     "qLogNParEGO",
-    "qMean",
-    "qSpaceFill",
+    "qNegIntegratedPosteriorVariance",
 ]
 
 

diff --git a/obsidian/dash/__init__.py b/obsidian/dash/__init__.py
@@ -1,3 +1,5 @@
+"""Dash: Build components for dash web app"""
+
 from .inputs_data import *
 from .inputs_config import *
 from .optimize import *

diff --git a/obsidian/objectives/__init__.py b/obsidian/objectives/__init__.py
@@ -5,3 +5,4 @@
 from .utils import *
 from .sequence import *
 from .base import *
+from .obj_config import *
diff --git a/obsidian/parameters/__init__.py b/obsidian/parameters/__init__.py
@@ -6,3 +6,4 @@
 from .param_space import *
 from .targets import *
 from .transforms import *
+from .utils import *
diff --git a/obsidian/surrogates/__init__.py b/obsidian/surrogates/__init__.py
@@ -4,3 +4,4 @@
 from .GP_custom import *
 from .torch_custom import *
 from .surrogate_config import *
+from .utils import *
diff --git a/obsidian/tests/__init__.py b/obsidian/tests/__init__.py
@@ -1 +0,0 @@
-