Merge branch 'main' of github.com:PinguDevTeam/ICF-MI-framework into …

…main
PinguDevTeam · Nov 30, 2022 · f35355a · f35355a
2 parents fbb7d23 + 339ce03
commit f35355a
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -14,7 +14,7 @@ repos:
     - id: check-merge-conflict
 
 -   repo: https://github.com/ambv/black
-    rev: 22.3.0
+    rev: 22.10.0
     hooks:
     - id: black
       language: python
@@ -25,7 +25,7 @@ repos:
     rev: 5.0.4
     hooks:
     - id: flake8
-      args: ["--max-line-length=88"]
+      args: ["--max-line-length=88", "--extend-ignore=E203", "--doctests"]
 
 -   repo: https://github.com/pre-commit/mirrors-clang-format
     rev: v14.0.6

diff --git a/GIM/README.md b/GIM/README.md
diff --git a/LSTM/README.md b/LSTM/README.md
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_build/readme.md b/docs/_build/readme.md
@@ -0,0 +1 @@
+This is the build folder
diff --git a/docs/conf.py b/docs/conf.py
@@ -0,0 +1,37 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../"))
+sys.path.insert(0, os.path.abspath("../GIM/"))
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html\
+# project-information
+
+project = "ICF-MI"
+copyright = "2022, Sahil Bhola"
+author = "Sahil Bhola, Doruk Aksoy, Carleen McKenna, Codie Kawaguchi"
+release = "0.0.1"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-
+# configuration
+
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.napoleon", "sphinx.ext.viewcode"]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-
+# html-output
+
+# html_theme = 'alabaster'
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
diff --git a/docs/index.rst b/docs/index.rst
@@ -0,0 +1,28 @@
+.. ICF-MI documentation master file, created by
+   sphinx-quickstart on Tue Nov 22 16:11:51 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to ICF-MI's documentation!
+==================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Introduction:
+
+   introduction
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/introduction.rst b/docs/introduction.rst
@@ -0,0 +1,32 @@
+Introduction
+^^^^^^^^^^^^^
+**ICF-MI** combines two statistical algorithms, **TT-ICE** which is an incremental tensor-train decomposition alogorithm suitable for data streams and **GIM** which is a model identification alogorithm.
+The Algorithm has the following salient features:
+
+* **TT-ICE** is a novel incremental tensor-train (TT) decomposition algorithm which is developed to decompose high dimensional data streams into tensor-train format.
+**TT-ICE** uses orthogonal projections and sequential application of SVD to compute the missing orthogonal directions in the TT-cores.
+For a stream of d-dimensional tensors, **TT-ICE** accumulates the stream along an additional (d+1)-th dimension and trains d 3 dimensional TT-cores that span the first d dimensions of the stream.
+The (d+1)-th TT-core resulting from the decomposition process contains coefficient vectors unique to each datum.
+Within the scope of our pipeline, we will treat **TT-ICE** as a multilinear dimensionality reduction tool and use the coefficient vectors contained in the last TT-core to train the surrogate model.
+
+* **GIM** is an information-theoretic model identification algorithm which can be used to identify the model which best fits the data.
+
+* **ICF-MI** is a combination of **TT-ICE** and **GIM** and can therefore be used to identify the model parameter in a cost efficient manner.
+
+.. HEADING:
+.. ===============
+.. * If necessart mention some points here.
+
+REFERENCES:
+===============
+* `Google <https://www.google.com>`_ , search engine has been used throughout the project.
+*  Aksoy et al., An Incremental Tensor-Train Decomposition Algorithm, 'arXiv preprint <https://arxiv.org/abs/2211.12487>'_
+*  Other kind of text ``Bold reference``.
+*  Bold **letters**.
+
+Developers:
+========
+| Sahil Bhola (University of Michgan, Ann Arbor)
+| Doruk Aksoy (University of Michgan, Ann Arbor)
+| Carleen McKenna (University of Michgan, Ann Arbor)
+| Codie Kawaguchi (University of Michgan, Ann Arbor)
diff --git a/docs/make.bat b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/scripts/create_documentation.sh b/scripts/create_documentation.sh
@@ -6,7 +6,7 @@ cd docs
 echo $PWD
 
 rm `find . -name "*rst" ! -name "index.rst" ! -name "introduction.rst"`
-sphinx-apidoc -o . ../
+sphinx-apidoc -o . ../src
 make html
 make latexpdf
 firefox ./_build/html/index.html
diff --git a/GIM/__init__.py → src/GIM/__init__.py b/GIM/__init__.py → src/GIM/__init__.py
diff --git a/GIM/template_GIM_documentation.py → src/GIM/template_GIM_documentation.py b/GIM/template_GIM_documentation.py → src/GIM/template_GIM_documentation.py
diff --git a/LSTM/__init__.py → src/LSTM/__init__.py b/LSTM/__init__.py → src/LSTM/__init__.py
diff --git a/LSTM/template_LSTM_documentation.py → src/LSTM/template_LSTM_documentation.py b/LSTM/template_LSTM_documentation.py → src/LSTM/template_LSTM_documentation.py
diff --git a/TTICE/__init__.py → src/TTICE/__init__.py b/TTICE/__init__.py → src/TTICE/__init__.py
diff --git a/TTICE/template_TT_ICE_documentation.py → src/TTICE/template_TT_ICE_documentation.py b/TTICE/template_TT_ICE_documentation.py → src/TTICE/template_TT_ICE_documentation.py