Move SR2ML from GitLab Repo to GitHub Repo

.gitignore

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+.libs
+*.dylib
+*.la
+*.lo
+*.d
+*.o
+*.a
+*-opt
+*-dbg
+*-oprof
+*-devel
+*.e
+*.csv
+*.so
+*~
+*.ctf
+*.png
+*.toc
+*.log
+*.out
+*.aux
+*.pdf
+*.bbl
+*.blg
+
+# eclipse
+.project
+.cproject
+
+#osx
+.DS_Store
+
+# python
+*.pyc
+*.pyo
+
+# vim
+*~
+*.swp
+

.gitlab-ci.yml

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+before_script:
+      # Print out python version for debugging
+    - python -V
+      # clone raven
+    - git clone https://github.com/idaholab/raven.git
+    - cd raven
+      # we technically still need moose for running the tests, currently
+    - git checkout master
+    - git clean -xfd
+    - if which conda 2> /dev/null; then
+        echo "Conda found!";
+        conda update conda;
+      else
+        echo "ERROR Conda not found!";
+        exit 404;
+      fi
+      # create libraries or create them
+    - ./scripts/establish_conda_env.sh --install --conda-defs $HOME/miniconda2/etc/profile.d/conda.sh
+    - ./build_raven
+      # Install plugin branch ...
+    - cd scripts
+    - python install_plugins.py -s `pwd`/../../
+      # return to project path main dir
+    - cd ../..
+
+user_manual:
+  script:
+    - cd doc/user_manual/
+    - make
+    - cd ../../
+  artifacts:
+    paths:
+    - doc/user_manual/user_manual.pdf
+
+sqa:
+  script:
+    - cd doc/sqa/
+    - ./make_docs.sh
+    - cd ../../
+  artifacts:
+    paths:
+    - doc/sqa/sqa_built_documents/
+
+test:
+    script:
+      - echo PATH $PATH
+      - cd raven
+      - ./run_tests --library-report
+      - ./run_tests -j4 --plugins

.gitlab/issue_templates/ISSUE_TEMPLATE.md

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+--------
+Issue Description
+--------
+##### Please describe your issue here.
+
+
+
+
+----------------
+For Change Control Board: Issue Review
+----------------
+This review should occur before any development is performed as a response to this issue.
+- [ ] 1. Is it tagged with a type: defect or task?
+- [ ] 2. Is it tagged with a priority: critical, normal or minor?
+- [ ] 3. If it is a defect, can it cause wrong results for users? If so a detailed description should be provided.
+- [ ] 4. Is a rationale provided? (Such as explaining why the task is needed or why current code is wrong.)
+
+-------
+For Change Control Board: Issue Closure
+-------
+This review should occur when the issue is imminently going to be closed.
+- [ ] 1. If the issue is a defect, is the defect fixed?
+- [ ] 2. If the issue is a defect, is the defect tested for in the regression test system?  (If not explain why not.)
+- [ ] 3. If the issue can impact users, has the detailed description been written?
+- [ ] 4. If the issue is being closed without a merge request, has an explanation of why it is being closed been provided?

.gitlab/merge_request_templates/PULL_REQUEST_TEMPLATE.md

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+--------
+Pull Request Description
+--------
+##### What issue does this change request address? (Use "#" before the issue to link it, i.e., #42.)
+
+
+##### What are the significant changes in functionality due to this change request?
+
+
+----------------
+For Change Control Board: Change Request Review
+----------------
+The following review must be completed by an authorized member of the Change Control Board.
+- [ ] 1. Review all computer code.
+- [ ] 2. If any changes occur to the input syntax, there must be an accompanying change to the user manual.
+- [ ] 3. Make sure the Python code and commenting standards are respected (camelBack, etc.) - See on the [wiki](https://github.com/idaholab/raven/wiki/RAVEN-Code-Standards#python) for details.
+- [ ] 4. Regression tests have to complete successfully.
+- [ ] 5. If significant functionality is added, there must be tests added to check this. Tests should cover all possible options.  Multiple short tests are preferred over one large test.
+- [ ] 6. The merge request must reference an issue.  If the issue is closed, the issue close checklist shall be done.

NOTICE.txt

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+This project contains code from Idaho National Laboratory's SR2ML Project
+Github URL :  idaholab/SR2ML
+
+Licensed under Apache License.
+
+
+© 2020 Battelle Energy Alliance, LLC
+ALL RIGHTS RESERVED
+
+Prepared by Battelle Energy Alliance, LLC
+Under Contract No. DE-AC07-05ID14517
+With the U. S. Department of Energy
+
+NOTICE:  This computer software was prepared by Battelle Energy
+Alliance, LLC, hereinafter the Contractor, under Contract
+No. AC07-05ID14517 with the United States (U. S.) Department of
+Energy (DOE).  The Government is granted for itself and others acting on
+its behalf a nonexclusive, paid-up, irrevocable worldwide license in this
+data to reproduce, prepare derivative works, and perform publicly and
+display publicly, by or on behalf of the Government. There is provision for
+the possible extension of the term of this license.  Subsequent to that
+period or any extension granted, the Government is granted for itself and
+others acting on its behalf a nonexclusive, paid-up, irrevocable worldwide
+license in this data to reproduce, prepare derivative works, distribute
+copies to the public, perform publicly and display publicly, and to permit
+others to do so.  The specific term of the license can be identified by
+inquiry made to Contractor or DOE.  NEITHER THE UNITED STATES NOR THE UNITED
+STATES DEPARTMENT OF ENERGY, NOR CONTRACTOR MAKES ANY WARRANTY, EXPRESS OR
+IMPLIED, OR ASSUMES ANY LIABILITY OR RESPONSIBILITY FOR THE USE, ACCURACY,
+COMPLETENESS, OR USEFULNESS OR ANY INFORMATION, APPARATUS, PRODUCT, OR
+PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE WOULD NOT INFRINGE PRIVATELY
+OWNED RIGHTS.
+
+Authors:
+Diego Mandelli
+Congjian Wang
+

README.md

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+# SR2ML: Safety Risk and Reliability Model Library
+
+SR2ML is a software package which contains a set of safety and reliability models
+designed to be interfaced with the INL developed RAVEN code. These models can be
+employed to perform both static and dynamic system risk analysis and determine risk
+importance of specific elements of the considered system. Two classes of reliability
+models have been developed; the first class includes all classical reliability models
+(Fault-Trees, Event-Trees, Markov models and Reliability Block Diagrams) which have
+been extended to deal not only with Boolean logic values but also time dependent
+values. The second class includes several components aging models. Models of these
+two classes are designed to be included in a RAVEN ensemble model to perform time
+dependent system reliability analysis (dynamic analysis). Similarly, these models
+can be interfaced with system analysis codes to determine failure time of systems
+and evaluate accident progression (static analysis).
+
+
+## Available Safety Risk and Reliability Models
+- Event Tree (ET) Model
+- Fault Tree (FT) Model
+- Markov Model
+- Reliability Block Diagram (RBD) Model
+- Data Classifier
+- Event Tree Data Importer
+- Fault Tree Data Importer
+- Reliability models with time dependent failure rates
+
+## Installation and How to Use?
+
+Please check: https://github.com/idaholab/raven/wiki/Plugins
+
+### Other Software
+Idaho National Laboratory is a cutting edge research facility which is a constantly producing high quality research and software. Feel free to take a look at our other software and scientific offerings at:
+
+[Primary Technology Offerings Page](https://www.inl.gov/inl-initiatives/technology-deployment)
+
+[Supported Open Source Software](https://github.com/idaholab)
+
+[Raw Experiment Open Source Software](https://github.com/IdahoLabResearch)
+
+[Unsupported Open Source Software](https://github.com/IdahoLabCuttingBoard)
+
+
+### Licensing
+-----
+This software is licensed under the terms you may find in the file named "LICENSE" in this directory.
+
+### Developers
+-----
+By contributing to this software project, you are agreeing to the following terms and conditions for your contributions:
+
+You agree your contributions are submitted under the Apache license. You represent you are authorized to make the contributions and grant the license. If your employer has rights to intellectual property that includes your contributions, you represent that you have received permission to make contributions and grant the required license on behalf of that employer.

__init__.py

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+# Copyright 2020, Battelle Energy Alliance, LLC
+# ALL RIGHTS RESERVED
+from SR2ML.src import ETModel
+from SR2ML.src import FTModel
+from SR2ML.src import GraphModel
+from SR2ML.src import MarkovModel
+# from SR2ML.src import TDFailureRateReliabilityModel
+from SR2ML.src import ReliabilityModel
+from SR2ML.src import MaintenanceModel

doc/sqa/make_docs.sh

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+#!/bin/bash
+
+SCRIPT_NAME=`readlink $0`
+if test -x "$SCRIPT_NAME";
+then
+    SCRIPT_DIRNAME=`dirname $SCRIPT_NAME`
+else
+    SCRIPT_DIRNAME=`dirname $0`
+fi
+SCRIPT_DIR=`(cd $SCRIPT_DIRNAME; pwd)`
+cd $SCRIPT_DIR
+
+VERB=0
+for i in "$@"
+do
+  if [[ $i == "--verbose" ]]
+  then
+    VERB=1
+    echo Entering verbose mode...
+  fi
+done
+
+rm -Rvf sqa_built_documents
+mkdir sqa_built_documents
+# load raven libraries; use utils to do this.
+RAVEN_PATH=$(python $(pwd)/../../src/_utils.py get_raven_loc)
+source $RAVEN_PATH/../scripts/establish_conda_env.sh --load --quiet
+
+# add custom, collective inputs to TEXINPUTS
+#
+# Since on Windows we use MikTeX (which is a native Windows program), the TEXTINPUTS variable used i
+#   to tell the LaTeX processor where to look for .sty files must be set using Windows-style paths
+#   (not the Unix-style ones used on other platforms).  This also means semi-colons need to be used
+#   to separate terms instead of the Unix colon.
+#
+if [ "$(uname)" == "Darwin" ] || [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]
+then
+  export TEXINPUTS=.:$SCRIPT_DIR/tex_inputs/:$TEXINPUTS
+elif [ "$(expr substr $(uname -s) 1 5)" == "MINGW" ]  || [  "$(expr substr $(uname -s) 1 4)" == "MSYS" ]
+then
+  export TEXINPUTS=.\;`cygpath -w $SCRIPT_DIR/tex_inputs`\;$TEXINPUTS
+fi
+# copy files that are not built
+# Configuration Item list
+cp CIlist/*.docx sqa_built_documents/
+# FIXME: CR_scheme #TODO current use RAVEN CR scheme
+cp CR_scheme.pptx sqa_built_documents/
+# Dashboard
+cp SR2ML_SQA_Status_Dashboard.pptx sqa_built_documents/
+
+if git describe
+then
+    git describe | sed 's/_/\\_/g' > ../new_version.tex
+    echo "\\\\" >> ../new_version.tex
+    git log -1 --format="%H %an\\\\%aD" . >> ../new_version.tex
+    if diff ../new_version.tex ../version.tex
+    then
+        echo No change in ../version.tex
+    else
+        mv ../new_version.tex ../version.tex
+    fi
+fi
+
+for DIR in  sdd rtr srs srs_rtr_combined; do
+    cd $DIR
+    echo Building in $DIR...
+    if [ "$(uname)" == "Darwin" ] || [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]
+    then
+      if [[ 1 -eq $VERB ]]
+      then
+        make; MADE=$?
+      else
+        make > /dev/null; MADE=$?
+      fi
+    elif [ "$(expr substr $(uname -s) 1 5)" == "MINGW" ]  || [  "$(expr substr $(uname -s) 1 4)" == "MSYS" ]
+    then
+      if [[ 1 -eq $VERB ]]
+      then
+        bash.exe make_win.sh; MADE=$?
+      else
+        bash.exe make_win.sh > /dev/null; MADE=$?
+      fi
+    fi
+    if [[ 0 -eq $MADE ]]; then
+        echo ...Successfully made docs in $DIR
+        cp *.pdf ../sqa_built_documents
+    else
+        echo ...Failed to make docs in $DIR
+        exit -1
+    fi
+    cd $SCRIPT_DIR
+done

doc/sqa/rtr/Makefile

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+LATEX_FLAGS=-interaction=nonstopmode
+
+all: default sr2ml_requirements_traceability_matrix.pdf
+
+sr2ml_requirements_traceability_matrix.pdf : sr2ml_requirements_traceability_matrix.tex sr2ml_requirements_traceability_matrix.bib intro.tex ../../version.tex ../sdd/sr2mlDepAndLimitations.tex
+	pdflatex $(LATEX_FLAGS) sr2ml_requirements_traceability_matrix.tex
+	pdflatex $(LATEX_FLAGS) sr2ml_requirements_traceability_matrix.tex
+	pdflatex $(LATEX_FLAGS) sr2ml_requirements_traceability_matrix.tex
+
+../../version.tex : *.tex
+	git log -1 --format="%H %an %aD" .. > ../../version.tex
+
+default: *.tex
+	python createSQAtracebilityMatrix.py -i ../srs/requirements_list.xml -o traceability_matrix.tex
+	git log -1 --format="%H %an %aD" .. > ../../version.tex
+
+.PHONY: clean
+
+clean:
+	@rm -f *~ *.aux *.bbl *.blg *.log *.out *.toc *.lot *.lof sr2ml_requirements_traceability_matrix.pdf