Merge branch 'release/0.1.5'

.appveyor.yml

@@ -41,7 +41,7 @@ install:
   # Install TBB
   - conda install -c conda-forge tbb -y
   # Install Boost
-  - conda install -c conda-forge boost -y
+  # - conda install -c conda-forge boost -y
   # Install MPFR
   - conda install -c conda-forge mpfr -y
   # Install CGAL
@@ -53,8 +53,6 @@ install:
 #  - cmake -G "Visual Studio 14 2015 Win64" ..
 #  - cmake --build .
   - nuget install rmt_curl -Version 7.51.0
-  # Install gtest
-#  - conda install -c conda-forge gtest -y
 
 before_build:
   - cd C:\projects\CDT-plusplus

.codecov.yml

@@ -0,0 +1,33 @@
+codecov:
+  max_report_age: off
+  notify:
+    require_ci_to_pass: no
+
+coverage:
+  precision: 2
+  round: down
+  range: "30...100"  # Figure out how to exclude or test included subrepos
+
+  status:
+    project: yes
+    patch: yes
+    changes: no
+
+  notify:
+      gitter:
+        default:
+          url: https://webhooks.gitter.im/e/c70e4d2749931f601747
+          threshold: 1%
+
+parsers:
+  gcov:
+    branch_detection:
+      conditional: yes
+      loop: yes
+      method: no
+      macro: no
+
+comment:
+  layout: "reach, diff, flags, files, footer"
+  behavior: default
+  require_changes: no

.github/CONTRIBUTING.md

@@ -0,0 +1,65 @@
+# How to Contribute
+
+First, thank you!
+
+Writing esoteric scientific software can be it's own reward, but it's not for the faint of heart.
+
+If you want a general overview as to why this software package exists, please look at my talk [Causal Dynamical Triangulations with CGAL][slides], or the [Wiki].
+
+Second, here are some simple guidelines that will make it easier on me to process and accept your contributions.
+
+1. Fork the repository.
+2. Familiarize yourself with [Catch] and in particular, the [Gherkin] syntax.
+3. Write a unit test for your proposed contribution. Unit tests go in the `test` directory and are named \{YourContribution\}Test.cpp, so that they can be automatically built.
+All proposed features of your contribution should have a corresponding test in \{YourContribution\}Test.cpp.
+Consult the [Catch Test cases and sections] if you are unsure, or consult existing tests for examples.
+4. I highly recommend writing your tests first, before your contribution, as this helps to think about how the rest of the program will use your functions and/or classes.
+[Test-Driven Development] (and [BDD]) has saved me quite a lot from various mistakes.
+5. Project source files go into the `src` directory; header files go into `include`.
+This makes integration into tests and the main program easy and modular, and follows convention.
+6. Don't forget documentation! It's helpful if you state explicitly what your functions and classes do.
+I use [Doxygen] to automatically build documentation, so using `/// @brief` and `/// @param` is helpful and easy.
+Consult existing code for examples.
+7. Commit your changes with a clear, [well-written commit message].
+*I am guilty of not always writing the clearest commit messages in this project, and will do better.
+For the longest time, however, no one but me actually read them.
+When I contribute to other projects, I definitely try to have useful, clear commit messages and you should, too.*
+8. Run `clang-format` using the project's [.clang-format].
+9. Open a pull request against the develop branch of the main repository (which is the default).
+[Travis-CI] will test it against combinations of Linux (Ubuntu 14.04), MacOS, clang, and gcc, so ensure that your code compiles on both platforms with both compilers.
+10. All pull requests must pass [Travis-CI] and [AppVeyor] to be accepted.
+In particular, look at results from git whitespace checks (`git diff --check HEAD^`), [ClangFormat], [ClangTidy], [Valgrind], [Coverity], and [Codecov] .
+11. I will get to your change as soon as I can.
+Feel free to ping me on [Gitter] with any questions.
+You will receive proper credit for your contributions both in the code and any resulting scientific papers using the output of `git log --format='%aN | sort -u`.
+
+# Style Guide
+
+This project generally follows [Stroustrup formatting with Allman brackets][1], enforced by [ClangFormat].
+The [C++ Core Guidelines][cpp-core] are checked using [ClangTidy].
+Running [clang-tidy.sh] changes the code (using `-fix`), so compare results and run unit tests before you commit.
+Especially since some of ClangTidy's fixes break the codebase (the script runs just the tests that don't).
+
+Most editors/IDEs have plugins for `clang-format` and `clang-tidy`.
+
+[Wiki]: https://github.com/acgetchell/CDT-plusplus/wiki
+[Test-Driven Development]: http://alexott.net/en/cpp/CppTestingIntro.html
+[Doxygen]: http://doxygen.org
+[well-written commit message]: https://chris.beams.io/posts/git-commit/
+[Travis-CI]: https://travis-ci.org/acgetchell/CDT-plusplus
+[1]: https://isocpp.org/wiki/faq/coding-standards
+[2]: http://llvm.org/releases/4.0.0/tools/clang/docs/ClangFormatStyleOptions.html
+[ClangFormat]: https://github.com/acgetchell/CDT-plusplus/blob/master/.clang-format
+[slides]: http://slides.com/acgetchell/causal-dynamical-triangulations-3
+[Valgrind]: http://valgrind.org/docs/manual/quick-start.html#quick-start.mcrun
+[cpp-core]: https://github.com/isocpp/CppCoreGuidelines/blob/master/CppCoreGuidelines.md
+[clang-tidy.sh]: https://github.com/acgetchell/CDT-plusplus/blob/master/clang-tidy.sh
+[AppVeyor]: https://ci.appveyor.com/project/acgetchell/cdt-plusplus
+[Catch]: https://github.com/catchorg/Catch2/blob/master/docs/Readme.md
+[Gherkin]: https://www.tutorialspoint.com/behavior_driven_development/behavior_driven_development_gherkin.htm
+[BDD]: https://en.wikipedia.org/wiki/Behavior-driven_development
+[Catch Test cases and sections]: https://github.com/catchorg/Catch2/blob/master/docs/test-cases-and-sections.md
+[Codecov]: https://codecov.io/support
+[Gitter]: https://gitter.im/acgetchell/CDT-plusplus
+[ClangTidy]: http://clang.llvm.org/extra/clang-tidy/index.html
+[Coverity]: https://scan.coverity.com/projects/acgetchell-cdt-plusplus

.github/issue_template.md

@@ -0,0 +1,7 @@
+### Expected behavior
+
+
+### Actual behavior
+
+
+### Steps to reproduce the behavior

.gitignore

@@ -24,8 +24,8 @@ profile
 # Build, Doc, and Testing dirs
 build/*
 html/
-googletest/
 cov-int
+Testing
 
 # Editor files
 .clang_complete
@@ -38,12 +38,12 @@ cdt_tests
 grid_d
 
 # Output files
-output
+output*
 errors
 *.off
-*.log
 *.dat
 slurm-*.out
+*.tmp
 
 # Instrumentation
 *.trace