fix(moves)!: make Metropolis transitions reversible and reproducible

.github/CONTRIBUTING.md

@@ -2,7 +2,8 @@
 
 Thank you for helping improve CDT++.
 
-CDT++ is being prepared for one final C++23 release, v1.0.0, after which this repository will be archived. The project
+CDT++ v1.0.0-rc1 is the release candidate for the final C++23 release, v1.0.0, after which this repository will be
+archived. The project
 is maintained as a scientific reference implementation and regression oracle for
 [causal-triangulations](https://github.com/acgetchell/causal-triangulations), its supported Rust successor. The
 maintenance and archival scope is tracked by
@@ -46,9 +47,12 @@ substantial implementation so its maintenance value and scope can be agreed upon
    just ci
    ```
 
-   `just check` is the fast, non-mutating source and tooling gate. `just ci` adds the supported build and 22-test smoke
-   suite. When changing C++ behavior, also run `just clang-tidy` with the pinned LLVM 22 toolchain and review its
-   advisory diagnostics.
+   `just check` is the fast, non-mutating source and tooling gate, including the repository-owned Semgrep policy and
+   its fixtures. `just ci` adds the supported build and complete 21-entry CTest suite: all 83 doctest unit scenarios
+   and 20 CLI integration tests. When changing C++ behavior, also run
+   `just clang-tidy` with the pinned LLVM 22 toolchain and review its advisory diagnostics.
+   GitHub Actions runs the same `just ci` contract in its Ubuntu GCC, Ubuntu Clang, macOS AppleClang, and Windows
+   MSVC jobs. The Windows job continues to compile with native MSVC; LLVM tooling is used only for source formatting.
 
 6. Run the relevant Linux sanitizer configuration for changes involving memory, lifetime, undefined behavior, or
    concurrency:

.github/actions/setup-just/action.yml

@@ -36,6 +36,6 @@ runs:
         echo "version=$version" >> "$GITHUB_OUTPUT"
 
     - name: Install Just
-      uses: taiki-e/cache-cargo-install-action@417450f3c33ee20393705369577571770643d4c7  # v3.0.7
+      uses: taiki-e/install-action@43aecc8d72668fbcfe75c31400bc4f890f1c5853  # v2.83.2
       with:
         tool: just@${{ steps.resolve.outputs.version }}

.github/workflows/_sanitizer.yml

@@ -71,18 +71,8 @@ jobs:
       - name: Set up Just
         uses: ./.github/actions/setup-just
 
-      - name: Resolve LLVM version
-        id: llvm-version
-        shell: bash
-        run: echo "version=$(just --evaluate llvm_version)" >> "$GITHUB_OUTPUT"
-
-      - name: Set up Clang
+      - name: Set up pkgx
         uses: pkgxdev/setup@4d4ae97af87ccb39ab8be4e073dea697fef2c6f7  # v5.0.0
-        with:
-          +: llvm.org@${{ steps.llvm-version.outputs.version }}
-
-      - name: Report compiler version
-        run: clang --version
 
       - name: Restore artifacts or set up vcpkg
         uses: lukka/run-vcpkg@b1a0dd252f06b9e25b3c022a9a03bd7a427fb6a2  # v11.6

.github/workflows/ci.yml

@@ -44,69 +44,34 @@ jobs:
           - name: Windows MSVC
             os: windows-latest
             compiler_package: ""
-            cc: ""
-            cxx: ""
+            cc: cl
+            cxx: cl
 
     steps:
+      - name: Disable Git autocrlf on Windows
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          git config --global core.autocrlf false
+          git config --global core.eol lf
+
       - name: Check out repository
         uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0  # v7.0.0
         with:
           fetch-depth: 0
           persist-credentials: false
           submodules: true
 
-      - name: Set up Unix environment with pkgx
-        if: runner.os != 'Windows'
-        uses: pkgxdev/setup@4d4ae97af87ccb39ab8be4e073dea697fef2c6f7  # v5.0.0
-
       - name: Activate MSVC
         if: runner.os == 'Windows'
         uses: ilammy/msvc-dev-cmd@0b201ec74fa43914dc39ae48a89fd1d8cb592756  # v1.13.0
         with:
           arch: x64
 
-      - name: Select the Windows vcpkg triplet
-        if: runner.os == 'Windows'
-        shell: pwsh
-        run: Add-Content -Path $env:GITHUB_ENV -Value 'VCPKG_DEFAULT_TRIPLET=x64-windows'
-
-      - name: Restore artifacts or set up vcpkg
-        uses: lukka/run-vcpkg@b1a0dd252f06b9e25b3c022a9a03bd7a427fb6a2  # v11.6
-
-      - name: Build and test Unix
-        if: runner.os != 'Windows'
-        env:
-          CC: ${{ matrix.cc }}
-          CDT_PKGX_COMPILER_PACKAGE: ${{ matrix.compiler_package }}
-          CXX: ${{ matrix.cxx }}
-        run: ./scripts/pkgx-build.sh
-
-      - name: Configure Windows
-        if: runner.os == 'Windows'
-        run: cmake --preset reference -S .
-
-      - name: Build Windows
-        if: runner.os == 'Windows'
-        run: cmake --build --preset reference --parallel 2
-
-      - name: Test Windows
-        if: runner.os == 'Windows'
-        run: ctest --preset reference-smoke
-
-  quality:
-    name: Repository quality checks
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Check out repository
-        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0  # v7.0.0
-        with:
-          persist-credentials: false
-
       - name: Set up Just
         uses: ./.github/actions/setup-just
 
-      - name: Resolve tool versions
+      - name: Resolve CI tool versions
         id: tool-versions
         shell: bash
         run: |
@@ -116,7 +81,8 @@ jobs:
             echo "zizmor=$(just --evaluate zizmor_version)"
           } >> "$GITHUB_OUTPUT"
 
-      - name: Set up repository tools with pkgx
+      - name: Set up canonical CI environment with pkgx
+        if: runner.os != 'Windows'
         uses: pkgxdev/setup@4d4ae97af87ccb39ab8be4e073dea697fef2c6f7  # v5.0.0
         with:
           +: llvm.org@${{ steps.tool-versions.outputs.llvm }}
@@ -135,26 +101,48 @@ jobs:
         run: uv sync --locked --group dev
 
       - name: Install zizmor
-        uses: taiki-e/cache-cargo-install-action@417450f3c33ee20393705369577571770643d4c7  # v3.0.7
+        uses: taiki-e/install-action@43aecc8d72668fbcfe75c31400bc4f890f1c5853  # v2.83.2
         with:
           tool: zizmor@${{ steps.tool-versions.outputs.zizmor }}
 
-      - name: Check repository quality
-        run: just check
+      - name: Install pinact on Windows
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          $installDirectory = Join-Path $env:RUNNER_TEMP 'pinact-bin'
+          New-Item -ItemType Directory -Force -Path $installDirectory | Out-Null
+          $env:GOBIN = $installDirectory
+          $pinactModule = just --evaluate pinact_module
+          go install $pinactModule
+          $installDirectory >> $env:GITHUB_PATH
+
+      - name: Select the Windows vcpkg triplet
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: Add-Content -Path $env:GITHUB_ENV -Value 'VCPKG_DEFAULT_TRIPLET=x64-windows'
+
+      - name: Restore artifacts or set up vcpkg
+        uses: lukka/run-vcpkg@b1a0dd252f06b9e25b3c022a9a03bd7a427fb6a2  # v11.6
+        with:
+          vcpkgDirectory: ${{ github.workspace }}/.cache/vcpkg
+
+      - name: Run the canonical local CI contract
+        env:
+          CC: ${{ matrix.cc }}
+          CDT_PKGX_COMPILER_PACKAGE: ${{ matrix.compiler_package }}
+          CXX: ${{ matrix.cxx }}
+        run: just ci
 
   build:
     name: build
     if: ${{ always() }}
     needs:
       - platform
-      - quality
     runs-on: ubuntu-latest
 
     steps:
       - name: Verify platform matrix
         env:
           PLATFORM_RESULT: ${{ needs.platform.result }}
-          QUALITY_RESULT: ${{ needs.quality.result }}
         run: |
           test "${PLATFORM_RESULT}" = success
-          test "${QUALITY_RESULT}" = success

.github/workflows/codeql.yml

@@ -64,6 +64,10 @@ jobs:
         with:
           persist-credentials: false
 
+      - name: Set up Just
+        if: matrix.language == 'c-cpp'
+        uses: ./.github/actions/setup-just
+
       - name: Set up C++ environment with pkgx
         if: matrix.language == 'c-cpp'
         uses: pkgxdev/setup@4d4ae97af87ccb39ab8be4e073dea697fef2c6f7  # v5.0.0
@@ -72,6 +76,14 @@ jobs:
         if: matrix.language == 'c-cpp'
         uses: lukka/run-vcpkg@b1a0dd252f06b9e25b3c022a9a03bd7a427fb6a2  # v11.6
 
+      - name: Prepare C++ dependencies outside CodeQL tracing
+        if: matrix.language == 'c-cpp'
+        env:
+          CC: gcc
+          CDT_PKGX_COMPILER_PACKAGE: gnu.org/gcc@16
+          CXX: g++
+        run: just codeql-prepare
+
       - name: Initialize CodeQL
         uses: github/codeql-action/init@99df26d4f13ea111d4ec1a7dddef6063f76b97e9  # v4.37.0
         with:
@@ -84,7 +96,7 @@ jobs:
           CC: gcc
           CDT_PKGX_COMPILER_PACKAGE: gnu.org/gcc@16
           CXX: g++
-        run: ./scripts/pkgx-build.sh
+        run: just codeql-build
 
       - name: Perform CodeQL Analysis
         uses: github/codeql-action/analyze@99df26d4f13ea111d4ec1a7dddef6063f76b97e9  # v4.37.0

.github/workflows/doxygen.yml

@@ -20,9 +20,23 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: DenverCoder1/doxygen-github-pages-action@a30f9538f8ef1305aeceb563018f452c7a62d200  # v2.0.0
+      - name: Check out repository
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0  # v7.0.0
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
+          persist-credentials: false
+
+      - name: Set up Just
+        uses: ./.github/actions/setup-just
+
+      - name: Set up pkgx
+        uses: pkgxdev/setup@4d4ae97af87ccb39ab8be4e073dea697fef2c6f7  # v5.0.0
+
+      - name: Build documentation
+        run: just docs
+
+      - name: Publish documentation
+        uses: JamesIves/github-pages-deploy-action@d92aa235d04922e8f08b40ce78cc5442fcfbfa2f  # v4.8.0
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
           branch: gh-pages
           folder: docs/html
-          config_file: docs/Doxyfile

.semgrepignore

@@ -0,0 +1,6 @@
+# CDT++ intentionally scans tests/; Semgrep's built-in defaults do not.
+.git/
+.cache/
+.venv/
+out/
+vcpkg_installed/

CITATION.cff

@@ -0,0 +1,24 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+type: software
+title: "CDT-plusplus: Causal Dynamical Triangulations in C++"
+abstract: >-
+  A C++23 scientific reference implementation of 2+1-dimensional causal
+  dynamical triangulations, including foliated triangulation construction,
+  Pachner moves, the Regge action, and Metropolis-Hastings evolution.
+authors:
+  - family-names: "Getchell"
+    given-names: "Adam"
+    email: "adam@adamgetchell.org"
+    orcid: "https://orcid.org/0000-0002-0797-0021"
+version: "1.0.0-rc1"
+date-released: "2026-07-20"
+repository-code: "https://github.com/acgetchell/CDT-plusplus"
+url: "https://github.com/acgetchell/CDT-plusplus"
+license: BSD-3-Clause
+keywords:
+  - "causal-dynamical-triangulations"
+  - "computational-geometry"
+  - "metropolis-hastings"
+  - "quantum-gravity"
+  - "regge-calculus"

CMakeLists.txt

@@ -22,10 +22,16 @@ unset(_vcpkg_install_options)
 
 project(
   CDT-plusplus
-  VERSION 0.1.8
+  VERSION 1.0.0
   DESCRIPTION "Fast Causal Dynamical Triangulations in C++"
   LANGUAGES CXX)
 
+# CMake project versions are numeric, so keep the release-candidate suffix in
+# the product version used by executables and release metadata.
+set(CDT_VERSION_SUFFIX "-rc1")
+set(CDT_VERSION "${PROJECT_VERSION}${CDT_VERSION_SUFFIX}")
+configure_file(cmake/Version.hpp.in "${PROJECT_BINARY_DIR}/Version.hpp" @ONLY)
+
 # Project settings
 include(cmake/StandardProjectSettings.cmake)
 
@@ -114,7 +120,8 @@ find_package(fmt CONFIG REQUIRED)
 find_package(Microsoft.GSL CONFIG REQUIRED)
 
 # https://www.pcg-random.org
-find_path(PCG_INCLUDE_DIRS "pcg_extras.hpp")
+find_path(PCG_INCLUDE_DIRS "pcg_extras.hpp" REQUIRED)
+target_include_directories(project_options SYSTEM INTERFACE "${PCG_INCLUDE_DIRS}")
 
 find_package(Boost CONFIG REQUIRED COMPONENTS compat program_options)
 target_link_libraries(project_options INTERFACE Boost::compat)
@@ -126,14 +133,12 @@ find_package(spdlog CONFIG REQUIRED)
 find_package(TBB CONFIG REQUIRED)
 
 # Header files
-include_directories(BEFORE ${PROJECT_SOURCE_DIR}/include)
+include_directories(BEFORE ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}/include)
 
 # doctest
 if(ENABLE_TESTING)
   enable_testing()
-  message(STATUS "Building tests. Look at /tests for unit tests.")
-  message(STATUS "Look at /tests/logs for spdlog results from unit tests.")
-  message(NOTICE "These logs can get quite big in DEBUG mode if you run all tests.")
+  message(STATUS "Building tests.")
   add_subdirectory(tests)
 endif()
 

CMakePresets.json

@@ -102,18 +102,12 @@
   "testPresets": [
     {
       "name": "reference-smoke",
-      "displayName": "Run the supported reference smoke tests",
-      "description": "Exclude the full and duplicate unit-test registrations",
+      "displayName": "Run the complete unit and integration suite",
+      "description": "Run all registered unit and integration tests",
       "configurePreset": "reference",
       "output": {
         "outputOnFailure": true
       },
-      "filter": {
-        "exclude": {
-          "name": "^(cdt-unit-tests|cdt-utilities-tests)$",
-          "label": "reference-smoke-exclude"
-        }
-      },
       "execution": {
         "noTestsAction": "error",
         "stopOnFailure": false