Catch 2 v3

.appveyor.yml

@@ -5,7 +5,7 @@ skip_tags: true
 skip_branch_with_pr: true
 
 image:
-  - Visual Studio 2019
+  - Visual Studio 2022
 
 clone_folder: c:\projects\cdt-plusplus
 
@@ -19,9 +19,10 @@ clone_script:
       && git submodule update --init --recursive
 
 environment:
-  APPVEYOR_SAVE_CACHE_ON_ERROR : true
+  APPVEYOR_SAVE_CACHE_ON_ERROR: false
+  APPVEYOR_CACHE_SKIP_RESTORE: true
   VCPKG_DEFAULT_TRIPLET: x64-windows
-#  VCPKG_ROOT: c:\tools\vcpkg
+  VCPKG_ROOT: c:\tools\vcpkg
 
 cache:
   - c:\Users\appveyor\AppData\Local\vcpkg\archives\
@@ -30,29 +31,18 @@ cache:
 install:
   # Setup vcpkg
   - cd c:\tools\vcpkg
-#  - git clean -d -fx .
-  - git pull origin master --no-rebase
-#  - git reset --hard 56c0313
+  - git pull
   - .\bootstrap-vcpkg.bat
   - set PATH=%PATH%;%VCPKG_ROOT%
   - vcpkg integrate install
   - cmake --version
-  # Install required libraries in classic mode
-#  - set VCPKG_INSTALL_ROOT=%APPVEYOR_BUILD_FOLDER%\vcpkg_installed
-#  - vcpkg install --x-install-root=%VCPKG_INSTALL_ROOT% catch2 docopt date fmt ms-gsl eigen3 pcg tbb tl-expected
-  # CGAL requires GMP which requires yasm-tool:x86-windows, even if you are using x64-windows.
-#  - vcpkg install --x-install-root=%VCPKG_INSTALL_ROOT% --recurse yasm-tool:x86-windows
-#  - vcpkg install --x-install-root=%VCPKG_INSTALL_ROOT% cgal
-  # Upgrade required libraries
-#  - vcpkg upgrade --no-dry-run --x-install-root=%VCPKG_INSTALL_ROOT%
-#  - vcpkg list --x-install-root=%VCPKG_INSTALL_ROOT%
   # Setup Clang-cl
   - set PATH=%PATH%;"C:\Program Files\LLVM\bin"
   - clang-cl -v
   - set CC=clang-cl -mrtm
   - set CXX=clang-cl -mrtm
-  # Visual Studio 2019
-  - call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Auxiliary\Build\vcvars64.bat"
+  # Visual Studio 2022
+  - call "C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Auxiliary\Build\vcvars64.bat"
   - set CMAKE_CXX_COMPILER="C:\Program Files\LLVM\bin\clang-cl"
 
 platform:
@@ -63,17 +53,17 @@ configuration: Release
 build:
   verbosity: detailed
 
-before_build:
-  - cd %APPVEYOR_BUILD_FOLDER%
-  - vcpkg install --feature-flags=manifests
-
 build_script:
-  - cmake -G Ninja -D CMAKE_BUILD_TYPE=Release -D ENABLE_CACHE=OFF -D CMAKE_TOOLCHAIN_FILE=C:/Tools/vcpkg/scripts/buildsystems/vcpkg.cmake -S . -B build
+  - cd %APPVEYOR_BUILD_FOLDER%
+  - cmake --preset=appveyor
   - cmake --build build
 
-#on_success:
+#test_script:
 #  - cd build
-#  - ctest -VV
+#  - ctest --output-on-failure -j2 --output-junit test-results.xml
+#
+#after_test:
+#  - find "$APPVEYOR_BUILD_FOLDER" -type f -name 'test-results.xml' -print0 | xargs -0 -I '{}' curl -F 'file=@{}' "https://ci.appveyor.com/api/testresults/junit/$APPVEYOR_JOB_ID"
 
 notifications:
   - provider: Email

.clang-format

@@ -104,9 +104,10 @@ IndentCaseBlocks: false
 IndentGotoLabels: true
 IndentPPDirectives: None
 IndentExternBlock: AfterExternBlock
-IndentRequires:  false
+IndentRequiresClause:  true
 IndentWidth:     2
 IndentWrappedFunctionNames: false
+InsertBraces: true
 InsertTrailingCommas: None
 JavaScriptQuotes: Leave
 JavaScriptWrapImports: true
@@ -132,6 +133,15 @@ PenaltyReturnTypeOnItsOwnLine: 200
 PenaltyIndentedWhitespace: 0
 PointerAlignment: Left
 PPIndentWidth:   -1
+QualifierAlignment: Custom
+QualifierOrder:
+  - static
+  - inline
+  - type
+  - const
+  - constexpr
+  - volatile
+  - restrict
 RawStringFormats:
   - Language:        Cpp
     Delimiters:

.cmake-format.yaml

@@ -16,3 +16,6 @@ max_pargs_hwrap: 3
 separate_ctrl_name_with_space: false
 separate_fn_name_with_space: false
 tab_size: 2
+
+markup:
+  enable_markup: false

.codecov.yml

@@ -12,8 +12,8 @@ coverage:
     project:
       default:
         threshold: 3%
-    patch: no
-    changes: no
+    patch: off
+    changes: false
 
   notify:
       gitter:

.coderabbit.yaml

@@ -0,0 +1,77 @@
+language: en-US
+tone_instructions: 'Be constructive and professional. Focus on technical accuracy while maintaining a friendly tone.'
+early_access: true
+enable_free_tier: true
+reviews:
+  profile: assertive
+  request_changes_workflow: true
+  high_level_summary: true
+  high_level_summary_placeholder: '@coderabbitai summary'
+  auto_title_placeholder: '@coderabbitai'
+  review_status: true
+  commit_status: true
+  poem: true
+  collapse_walkthrough: false
+  sequence_diagrams: true
+  changed_files_summary: true
+  labeling_instructions: []
+  path_filters: []
+  path_instructions:
+    - path: 'src/**/*.cpp'
+      instructions: 'Focus on performance, memory management, and RAII principles'
+    - path: 'include/**/*.hpp'
+      instructions: 'Focus on design patterns, interfaces, and encapsulation'
+    - path: 'test/**/*.cpp'
+      instructions: |
+        Review the following unit test code written using doctest. Ensure the following:
+          - Comprehensive test coverage and proper test organization.
+          - The code adheres to best practices using doctest.
+          - Descriptive test names are used to clearly convey the intent of each test.
+  abort_on_close: true
+  auto_review:
+    enabled: true
+    auto_incremental_review: true
+    ignore_title_keywords: []
+    labels: []
+    drafts: true
+    base_branches: []
+  tools:
+    shellcheck:
+      enabled: true
+    markdownlint:
+      enabled: true
+    github-checks:
+      enabled: true
+      timeout_ms: 90000
+    gitleaks:
+      enabled: true
+    cppcheck:
+      enabled: true
+    languagetool:
+      enabled: true
+      enabled_only: false
+      level: default
+    hadolint:
+      enabled: true
+    yamllint:
+      enabled: true
+    actionlint:
+      enabled: true
+    pmd:
+      enabled: true
+    semgrep:
+      enabled: true
+chat:
+  auto_reply: true
+knowledge_base:
+  opt_out: false
+  learnings:
+    scope: auto
+  issues:
+    scope: auto
+  jira:
+    project_keys: []
+  linear:
+    team_keys: []
+  pull_requests:
+    scope: auto

.github/CONTRIBUTING.md

@@ -2,9 +2,9 @@
 
 First, thank you!
 
-Writing esoteric scientific software can be it's own reward, but it's not for the faint of heart.
+Writing esoteric scientific software can be its 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 the [Wiki], or my talk
+If you want a general overview as to why this software package exists, please look at the [Wiki] or my talk
 [Causal Dynamical Triangulations with CGAL][slides].
 
 Second, here are some simple guidelines that will make it easier on me to process and accept your contributions.
@@ -16,16 +16,16 @@ New [releases] are periodically made from [develop], then merged back into [mast
 which is the stable work history. [Tagged] versions are [releases] at a point in time, citable via [ORCID].
 for reproducibility.
 
-3. Familiarize yourself with [Catch] and the [Gherkin] syntax.
+3. Familiarize yourself with [doctest] and the [Gherkin] syntax.
 
 4. Write a unit test for your proposed contribution. Unit tests go in the `tests` directory and are named
-\{YourContribution\}_test.cpp, so that they can be automatically built.
+\{YourContribution\}_test.cpp, don't forget to add to `/tests/CMakeLists.txt`.
 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.
+Consult the [doctest test cases] if you are unsure, or consult existing tests for examples.
 
 5. 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.
+[Test-Driven Development] (and [BDD]) has saved me quite a bit from various mistakes.
 
 6. Project source files go into the `src` directory; header files go into `include`.
 This makes integration into various tests and the main program easy and modular, and follows convention.
@@ -43,12 +43,15 @@ Consult existing code for examples.
 11. Run `clang-tidy` using the project's [clang-tidy.sh].
 
 12. 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 18.04) and MacOS with clang and gcc.
-[AppVeyor] will test it against Visual Studio 2017 with `clang-cl` (version 9). Ensure that
+[Travis-CI] will test it against combinations of Linux (Ubuntu 22.04) with clang and gcc. [GitHub Actions] will test
+against macOS and run various other checks.
+[AppVeyor] will test it against Visual Studio 2019 with `clang-cl` (version 14.0.6). Ensure that
 your code compiles on Windows, macOS, and Linux with `msvc`, `gcc`, and `clang`.
 
 13. All pull requests must pass [Travis-CI] and [AppVeyor] to be accepted.
-In particular, look at results from [Cppcheck], [Valgrind], [ASAN], [MSAN], [ClangTidy], , and [LGTM].
+In particular, look at results from [Cppcheck], [Valgrind], [ASAN], [LSAN], [MSAN], and [TSAN], because simulations may
+run for a long time so memory leaks will be eventually fatal.
+[GitHub Actions] also has a lot of useful checks that will help fix your code.
 
 14. I will get to your change as soon as I can.
 Feel free to ping me on [Gitter] with any questions.
@@ -77,10 +80,10 @@ Most editors/IDEs have plugins for `clang-format` and `clang-tidy`.
 [cpp-core]: https://github.com/isocpp/CppCoreGuidelines/blob/master/CppCoreGuidelines.md
 [clang-tidy.sh]: https://github.com/acgetchell/CDT-plusplus/blob/develop/clang-tidy.sh
 [AppVeyor]: https://ci.appveyor.com/project/acgetchell/cdt-plusplus
-[Catch]: https://github.com/catchorg/Catch2/blob/master/docs/Readme.md
+[doctest]: https://github.com/doctest/doctest
 [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
+[doctest test cases]: https://github.com/doctest/doctest/blob/master/doc/markdown/testcases.md
 [Gitter]: https://gitter.im/acgetchell/CDT-plusplus
 [ClangTidy]: https://releases.llvm.org/6.0.1/tools/clang/tools/extra/docs/clang-tidy/index.html
 [LGTM]: https://lgtm.com/projects/g/acgetchell/CDT-plusplus/
@@ -94,4 +97,7 @@ Most editors/IDEs have plugins for `clang-format` and `clang-tidy`.
 [ORCID]: https://orcid.org/
 [Cppcheck]: http://cppcheck.sourceforge.net
 [ASAN]: https://github.com/google/sanitizers/wiki/AddressSanitizer
-[MSAN]: https://github.com/google/sanitizers/wiki/MemorySanitizer
+[MSAN]: https://github.com/google/sanitizers/wiki/MemorySanitizer
+[GitHub Actions]: https://github.com/acgetchell/CDT-plusplus/actions
+[LSAN]: https://github.com/google/sanitizers/wiki/AddressSanitizerLeakSanitizer
+[TSAN]: https://github.com/google/sanitizers/wiki/ThreadSanitizerCppManual

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/asan.yml

@@ -0,0 +1,68 @@
+name: Address Sanitizer
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - develop
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: true
+
+      - name: Setup
+        run: |
+          sudo apt update
+          sudo apt-get install build-essential automake autoconf autoconf-archive texinfo libtool-bin yasm ninja-build ccache
+
+      - name: Setup Clang
+        uses: pkgxdev/setup@v4
+        with:
+          +: clang@20
+
+      -  run: clang --version
+
+      - name: Restore artifacts or setup vcpkg
+        uses: lukka/run-vcpkg@v11
+        with:
+          vcpkgGitCommitId: ${{ vars.VCPKG_GIT_COMMIT_ID }}
+
+      - name: Configure
+        run: cmake --preset=asan
+
+      - name: Build
+        run: cmake --build build -j 2
+
+      - name: Run tests
+        working-directory: build
+        continue-on-error: true
+        run: ctest -VV
+
+      - name: Run ASAN on initialize
+        working-directory: build/src
+        continue-on-error: true
+        run: ./initialize --s -n32000 -t11 -o
+
+      - name: Run ASAN on cdt-opt
+        working-directory: build/src
+        continue-on-error: true
+        run: ./cdt-opt
+
+      - name: Run ASAN on cdt
+        working-directory: build/src
+        continue-on-error: true
+        run: ./cdt --s -n64 -t3 -a.6 -k1.1 -l.1 -p10

.github/workflows/clang-format-check.yml

@@ -1,5 +1,14 @@
 name: clang-format Check
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - develop
+  workflow_dispatch:
+
 jobs:
   formatting-check:
     name: Formatting Check
@@ -10,10 +19,10 @@ jobs:
           - 'src'
           - 'include'
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Run clang-format style check for C/C++/Protobuf programs.
-        uses: jidicula/clang-format-action@v4.5.0
+        uses: jidicula/clang-format-action@v4.15.0
         with:
-          clang-format-version: '14'
+          clang-format-version: '18'
           check-path: ${{ matrix.path }}
           fallback-style: 'Google' # optional