PullRequest Full Project Review Comments [2020-01-09]

AUTHORS.rst

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+Authors
+=======
+
+The DAGMC project began as the CAD-MCNPX project in 2003, and since then has
+included contributions from the following:
+
+* Andrew Davis
+* Kerry L. Dunn
+* Moataz Harb
+* Steve Jackson
+* Brian Kiedrowski
+* Kalin Kiesling
+* Jason Kraftcheck
+* Lucas Jacobson
+* Eric Relson
+* Patrick Shriwise
+* Rachel N. Slaybaugh
+* Brandon Smith
+* Tim Tautges
+* Meng-Kuo Wang
+* Zach Welch
+* Paul P.H. Wilson
+* Julie C. Zachman
+
+The DAGMC project also relies heavily on the MOAB_ project and the Trelis_
+software package.
+
+.. _MOAB: http://sigma.mcs.anl.gov/moab-library
+.. _Trelis: http://www.csimsoft.com/trelis.jsp

CMakeLists.txt

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+project(DAGMC)
+cmake_minimum_required(VERSION 3.1)
+enable_language(Fortran)
+
+# Set DAGMC version
+set(DAGMC_MAJOR_VERSION 3)
+set(DAGMC_MINOR_VERSION 1)
+set(DAGMC_PATCH_VERSION 0)
+set(DAGMC_VERSION ${DAGMC_MAJOR_VERSION}.${DAGMC_MINOR_VERSION}.${DAGMC_PATCH_VERSION})
+
+# Make the scripts in the "cmake" directory available to CMake
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake)
+include(DAGMC_macros)
+
+dagmc_setup_build()
+
+dagmc_setup_options()
+
+find_package(MOAB REQUIRED)
+find_package(OpenMP)
+
+dagmc_setup_flags()
+
+if (BUILD_TESTS)
+  enable_testing()
+endif ()
+
+add_subdirectory(src)
+
+dagmc_make_configure_file()
+
+message("")

CODE_OF_CONDUCT.md

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+Contributor Code of Conduct
+===========================
+
+Our Pledge
+----------
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers of the Svalinn software suite, including DAGMC,
+pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+Our Standards
+-------------
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Showing empathy towards other community members
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+Our Responsibilities
+--------------------
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+Scope
+-----
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+Enforcement
+-----------
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the research staff at [email protected]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The research staff is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+Attribution
+-----------
+
+This Code of Conduct is adapted from the Contributor Covenant, version 1.4,
+available [here](https://www.contributor-covenant.org/version/1/4/code-of-conduct.html).
+
+For answers to common questions about this code of conduct, see [here](https://www.contributor-covenant.org/faq).

CONTRIBUTING.md

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+Contributing to DAGMC
+=====================
+
+The following is a guide to contributing to the DAGMC repository.
+Please note there is a [Code of Conduct](https://github.com/svalinn/DAGMC/blob/develop/CODE_OF_CONDUCT.md)
+and make sure to follow it in all interactions with this project.
+
+Creating a Pull Request
+-----------------------
+1. Fork this repository from `develop` and create a branch for new code.
+2. Add or update any applicaple tests for the new code.
+3. If applicable, update the [README documentation](https://github.com/svalinn/DAGMC/blob/develop/README.rst) or [website documentation](https://github.com/svalinn/DAGMC/tree/develop/doc).
+4. Issue a pull request using the pull request template. All pull requests must be accompanied by a news update.
+
+Reporting an Issue
+------------------
+* If you wish to report a bug, use the bug report template.
+* If you wish to suggest an improvement, use the feature request template.
+* If you have any other issue, be clear and concise in its description and label it accordingly.
+
+Important Resources
+-------------------
+* [Pull Request Template](https://github.com/svalinn/DAGMC/blob/develop/PULL_REQUEST_TEMPLATE.md)
+* [Bug Report Template](https://github.com/svalinn/DAGMC/blob/develop/.github/ISSUE_TEMPLATE/bug-report.md)
+* [Feature Request Template](https://github.com/svalinn/DAGMC/blob/develop/.github/ISSUE_TEMPLATE/feature-request.md)
+
+License
+-------
+By contributing, you agree that your contributions will be licensed under the
+[Simplified BSD License](https://github.com/svalinn/DAGMC/blob/develop/LICENSE.txt).
+
+References
+----------
+These guidelines were adapted from [here](https://gist.github.com/briandk/3d2e8b3ec8daf5a27a62) and [here](https://github.com/drush-ops/drush/blob/master/CONTRIBUTING.md).

LICENSE.txt

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+DAGMC is licensed under the Simplified BSD License. This license applies to all
+files in the DAGMC repository except those in the pyne/ and tally/lapack/
+directories.
+
+Copyright (c) 2003-2018, the DAGMC development team
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are
+permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, this list of
+      conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, this list
+      of conditions and the following disclaimer in the documentation and/or other materials
+      provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE DAGMC DEVELOPMENT TEAM "AS IS" AND ANY EXPRESS OR IMPLIED
+WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE DAGMC DEVELOPMENT TEAM OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+The views and conclusions contained in the software and documentation are those of the
+authors and should not be interpreted as representing official policies, either expressed
+or implied, of the stakeholders of the DAGMC project or the employers of DAGMC developers.
+
+--------------------------------------------------------------------------------
+
+The files located in the pyne/ directory are from the PyNE project and are
+licensed under the Simplified BSD License.
+
+Copyright 2011-2015, the PyNE Development Team. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are
+permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, this list of
+      conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, this list
+      of conditions and the following disclaimer in the documentation and/or other materials
+      provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE PYNE DEVELOPMENT TEAM ``AS IS'' AND ANY EXPRESS OR IMPLIED
+WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+The views and conclusions contained in the software and documentation are those of the
+authors and should not be interpreted as representing official policies, either expressed
+or implied, of the stakeholders of the PyNE project or the employers of PyNE developers.

Makefile

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+# Makefile for Sphinx documentation
+
+# Top-level directory of all the ReST source files
+GH_SOURCE_DIR     = doc
+# Repository branch that contains the source
+GH_SOURCE_BRANCH  = develop
+# Repository branch that contains the rendered HTML
+GH_PUBLISH_BRANCH = gh-pages
+# Repository that contains the rendered HTML
+GH_UPSTREAM_URL   = https://github.com/svalinn/DAGMC
+# Directory that contains the rendered HTML
+BUILDDIR          = gh-build
+# Sphinx executable
+SPHINXBUILD       = sphinx-build
+# Sphinx options
+SPHINXOPTS        =
+
+ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) $(GH_SOURCE_DIR)
+
+help:
+	@echo "Please use \"make <target\" where <target> is one of"
+	@echo "  html     to build HTML in directory \"$(BUILDDIR)\" for testing"
+	@echo "  clean    to cleanup HTML build in directory \"$(BUILDDIR)\" after testing"
+	@echo "  publish  final build and push from \"$(GH_SOURCE_BRANCH)\" branch to \"$(GH_PUBLISH_BRANCH)\" branch"
+
+clean:
+	-rm -rf $(BUILDDIR)
+
+html:
+	$(SPHINXBUILD) -nvW -b html $(ALLSPHINXOPTS) $(BUILDDIR)
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)."
+
+check_ready_for_publish:
+	$(eval CURRENT_BRANCH = $(shell git rev-parse --abbrev-ref --symbolic-full-name @{u}))
+	@if [ $(CURRENT_BRANCH) != origin/$(GH_SOURCE_BRANCH) ]; then \
+	   echo "On branch \"$(CURRENT_BRANCH)\"; must be on branch \"origin/$(GH_SOURCE_BRANCH)\". Cannot publish."; \
+	   exit 1; \
+	 fi
+	$(eval CURRENT_URL = $(shell git config --get remote.origin.url))
+	@if [ $(CURRENT_URL) != $(GH_UPSTREAM_URL) ]; then \
+	   echo "The origin remote points to \"$(CURRENT_URL)\"; must point to \"$(GH_UPSTREAM_URL)\". Cannot publish."; \
+	   exit 1; \
+	 fi
+	$(eval EXTRA_COMMITS = $(shell git rev-list $(CURRENT_BRANCH)...origin/$(GH_SOURCE_BRANCH)))
+	@if [ "$(EXTRA_COMMITS)" != "" ]; then \
+	   echo "Current branch \"$(CURRENT_BRANCH)\" is not up-to-date with \"origin/$(GH_SOURCE_BRANCH)\". Cannot publish."; \
+	   exit 1; \
+	 fi
+	$(eval UNSTAGED_CHANGES = $(shell git status --porcelain))
+	@if [ "$(UNSTAGED_CHANGES)" != "" ]; then \
+	   echo "There are changes not staged for commit. Cannot publish."; \
+	   exit 1; \
+	 fi
+
+publish: check_ready_for_publish
+	git checkout $(GH_PUBLISH_BRANCH) && \
+	git rm -rf * && \
+	git checkout $(GH_SOURCE_BRANCH) -- $(GH_SOURCE_DIR) Makefile && \
+	git reset HEAD && \
+	make clean && \
+	make html && \
+	rsync -a $(BUILDDIR)/* . && \
+	rsync -a $(BUILDDIR)/.* . && \
+	rm -rf $(GH_SOURCE_DIR) $(BUILDDIR) && \
+	git add . && \
+	git commit -m "Generated $(GH_PUBLISH_BRANCH) for `git log $(GH_SOURCE_BRANCH) -1 --pretty=short --abbrev-commit`" && \
+	git push $(GH_UPSTREAM_URL) $(GH_PUBLISH_BRANCH) && \
+	git checkout $(GH_SOURCE_BRANCH)

PULL_REQUEST_TEMPLATE.md

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+Please follow these guidelines when making a Pull Request.
+This template was adapted from [here](https://github.com/stevemao/github-issue-templates/edit/master/questions-answers/PULL_REQUEST_TEMPLATE.md) and [here](https://github.com/stevemao/github-issue-templates/edit/master/conversational/PULL_REQUEST_TEMPLATE.md).
+
+## Description
+Describe your changes in detail.
+
+## Motivation and Context
+Why is this change required? What problem does it solve?
+If it fixes an open issue, please link to the issue here.
+
+## Changes
+What kind of change does this PR introduce? (Bug fix, feature, documentation update...)
+
+## Behavior
+What is the current behavior? What is the new behavior?
+
+## Other Information
+Other relevant information to this pull request.
+
+## News file
+All pull requests are required to include an updated news file with the PR.
+The file should be located at the `/news/PR-<#>.rst` where `<#>` should be replaced with the appropriate PR number.
+Please see [here](https://github.com/svalinn/DAGMC/blob/develop/news/TEMPLATE.rst) for the news file template.

README.rst

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+DAGMC: Direct Accelerated Geometry Monte Carlo
+==============================================
+
+..  image:: https://travis-ci.org/svalinn/DAGMC.svg?branch=develop
+    :target: https://travis-ci.org/svalinn/DAGMC
+
+Direct Accelerated Geometry Monte Carlo (DAGMC) is a software package that
+allows users to perform Monte Carlo radiation transport directly on CAD models.
+
+DAGMC has been integrated into a variety of Monte Carlo radiation codes
+including MCNP5_, MCNP6_, Geant4_, FLUKA_, Tripoli4_, and Shift_. There are also
+efforts planned to integrate DAGMC into other codes such as Serpent2_, OpenMC_,
+Phits_, and Frensie.
+
+DAGMC currently relies on using the solid modeling software Cubit_ or its
+commercial counterpart, Trelis_, to prepare solid models. These packages can be
+used to import CAD models from other tools such as SolidWorks, CATIA, etc., or
+to create geometry from scratch. DAGMC also relies on Trelis/Cubit to assign
+materials and other geometry-related information.
+
+For more information, please visit the `DAGMC website <DAGMC_>`_.
+
+Quick links:
+
+* `Install guide <http://svalinn.github.io/DAGMC/install/index.html>`_
+* `Users guide <http://svalinn.github.io/DAGMC/usersguide/index.html>`_
+* `Contributors guide <http://svalinn.github.io/DAGMC/contribute/index.html>`_
+
+..  _DAGMC: http://svalinn.github.io/DAGMC
+..  _Cubit: https://cubit.sandia.gov
+..  _Trelis: http://www.csimsoft.com/trelis
+..  _MCNP5: https://mcnp.lanl.gov
+..  _MCNP6: https://mcnp.lanl.gov
+..  _Geant4: http://geant4.cern.ch
+..  _FLUKA: http://www.fluka.org/fluka.php
+..  _Tripoli4: https://rsicc.ornl.gov/codes/ccc/ccc8/ccc-806.html
+..  _Shift: http://web.ornl.gov/sci/nsed/rnsd/rt
+..  _Serpent2: http://montecarlo.vtt.fi
+..  _OpenMC: https://mit-crpg.github.io/openmc
+..  _Phits: http://phits.jaea.go.jp