Initial version of Chromobius, at time of arXiv preprint

.clang-format

@@ -0,0 +1,22 @@
+---
+Language: Cpp
+BasedOnStyle: Google
+IndentWidth: 4
+ColumnLimit: 120
+AlignAfterOpenBracket: AlwaysBreak
+AllowShortBlocksOnASingleLine: Never
+AllowShortFunctionsOnASingleLine: None
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLoopsOnASingleLine: false
+AllowShortLambdasOnASingleLine: None
+BinPackArguments: false
+BinPackParameters: false
+
+IncludeCategories:
+  - Regex:           '^<.*>$'
+    Priority:        1
+  - Regex:           '^"gtest/.*"$'
+    Priority:        2
+  - Regex:           '^".*"$'
+    Priority:        3
+...

.github/workflows/ci.yml

@@ -0,0 +1,177 @@
+# Copyright 2021 Google LLC
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+name: ci
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - v*
+  pull_request:
+    branches:
+      - main
+jobs:
+  build_dist:
+    runs-on: ${{ matrix.os_dist.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os_dist: [
+          {os: ubuntu-latest, dist: cp310-manylinux_x86_64},
+          {os: ubuntu-latest, dist: cp311-manylinux_x86_64},
+          {os: ubuntu-latest, dist: cp312-manylinux_x86_64},
+
+          {os: macos-latest, dist: cp310-macosx_x86_64, macosarch: x86_64},
+          {os: macos-latest, dist: cp311-macosx_x86_64, macosarch: x86_64},
+          {os: macos-latest, dist: cp312-macosx_x86_64, macosarch: x86_64},
+
+          {os: macos-latest, dist: cp310-macosx_arm64, macosarch: arm64},
+          {os: macos-latest, dist: cp311-macosx_arm64, macosarch: arm64},
+          {os: macos-latest, dist: cp312-macosx_arm64, macosarch: arm64},
+
+          # Currently disabled because in CI it gives "DLL load failed" errors I don't understand when testing the wheel.
+          # {os: windows-latest, dist: cp310-win_amd64},
+          # {os: windows-latest, dist: cp311-win_amd64},
+          # {os: windows-latest, dist: cp312-win_amd64},
+        ]
+    env:
+      MACOSX_DEPLOYMENT_TARGET: "10.15"
+      CIBW_BUILD: "${{ matrix.os_dist.dist }}"
+      CIBW_ARCHS_MACOS: "${{ matrix.os_dist.macosarch }}"
+      CIBW_TEST_REQUIRES: pytest stim sinter pygltflib
+      CIBW_TEST_COMMAND: pytest {project}/src
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - run: python tools/overwrite_dev_versions_with_date.py
+      - run: mkdir -p output/stim
+      - run: mkdir -p output/stimcirq
+      - run: mkdir -p output/sinter
+      - run: python -m pip install pybind11~=2.11.1 cibuildwheel~=2.16.2 setuptools
+      - run: python -m cibuildwheel --print-build-identifiers
+      - run: python -m cibuildwheel --output-dir output/chromobius
+      - run: python setup.py sdist
+      - run: mv dist/* output/chromobius
+      - uses: actions/upload-artifact@v3
+        with:
+          name: dist
+          path: |
+            ./output/chromobius/*
+  check_sdist_installs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - run: python -m pip install pybind11~=2.11.1 cibuildwheel~=2.16.2 setuptools
+      - run: python setup.py sdist
+      - run: pip install dist/*.tar.gz
+  run_main:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - run: cmake .
+    - run: make chromobius -j 2
+    - run: out/chromobius --help
+  build_bazel:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - uses: bazelbuild/setup-bazelisk@v1
+    - run: bazel build :all
+    - run: bazel test :chromobius_test
+  build_clang:
+    runs-on: ubuntu-20.04
+    steps:
+    - uses: actions/checkout@v1
+    - run: |
+        cd ..
+        git clone https://github.com/google/googletest.git -b release-1.12.1
+        mkdir googletest/build && cd googletest/build
+        cmake .. -DBUILD_GMOCK=OFF
+        make
+        sudo make install
+    - uses: egor-tensin/setup-clang@v1
+      with:
+        version: latest
+        platform: x64
+    - run: cmake . -DCMAKE_C_COMPILER=cc -DCMAKE_CXX_COMPILER=c++
+    - run: cmake --build . --target chromobius chromobius_test chromobius_perf
+    - run: out/chromobius --help
+  perf:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - run: cmake .
+    - run: make chromobius_perf -j 2
+    - run: out/chromobius_perf
+  test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - run: |
+        cd ..
+        git clone https://github.com/google/googletest.git -b release-1.12.1
+        mkdir googletest/build && cd googletest/build
+        cmake .. -DBUILD_GMOCK=OFF
+        make
+        sudo make install
+    - run: cmake .
+    - run: make chromobius_test -j 2
+    - run: out/chromobius_test
+  test_o3:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - run: |
+        cd ..
+        git clone https://github.com/google/googletest.git -b release-1.12.1
+        mkdir googletest/build && cd googletest/build
+        cmake .. -DBUILD_GMOCK=OFF
+        make
+        sudo make install
+    - run: cmake . -DSIMD_WIDTH=256
+    - run: make chromobius_test_o3 -j 2
+    - run: out/chromobius_test_o3
+  test_generated_docs_are_fresh:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - uses: bazelbuild/setup-bazelisk@v1
+      - run: bazel build :chromobius_dev_wheel
+      - run: pip install bazel-bin/chromobius-0.0.dev0-py3-none-any.whl
+      - run: diff <(python tools/gen_chromobius_api_reference.py -dev) doc/chromobius_api_reference.md
+      - run: diff <(python tools/gen_chromobius_stub_file.py -dev) doc/chromobius.pyi
+      - run: python doc/chromobius.pyi
+  test_generated_file_lists_are_fresh:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - run: tools/regen_file_lists.sh /tmp
+      - run: diff /tmp/perf_files file_lists/perf_files
+      - run: diff /tmp/pybind_files file_lists/pybind_files
+      - run: diff /tmp/source_files_no_main file_lists/source_files_no_main
+      - run: diff /tmp/test_files file_lists/test_files
+  test_pybind:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - uses: bazelbuild/setup-bazelisk@v1
+      - run: bazel build :chromobius_dev_wheel
+      - run: pip install bazel-bin/chromobius-0.0.dev0-py3-none-any.whl
+      - run: pip install pytest stim sinter pygltflib
+      - run: pytest src
+      - run: tools/doctest_proper.py --module chromobius

.gitignore

@@ -0,0 +1,31 @@
+.idea
+.pytest_cache
+out
+__pycache__
+cmake-build-debug
+.cmake
+CMakeFiles
+CMakeCache.txt
+.ninja_deps
+.ninja_log
+Testing
+_deps
+build.ninja
+cmake_install.cmake
+perf.data
+perf.data.old
+lib
+bazel-bin
+bazel-out
+bazel-testlogs
+bazel-*
+python_build_chromobius
+chromobius.egg-info
+.clwb
+wheelhouse
+build
+package_data
+.eggs
+dist
+MODULE.bazel
+MODULE.bazel.lock

BUILD

@@ -0,0 +1,127 @@
+package(default_visibility = ["//visibility:public"])
+
+load("@rules_python//python:packaging.bzl", "py_wheel")
+
+SOURCE_FILES_NO_MAIN = glob(
+    [
+        "src/**/*.cc",
+        "src/**/*.h",
+        "src/**/*.inl",
+    ],
+    exclude = glob([
+        "src/**/*.test.cc",
+        "src/**/*.test.h",
+        "src/**/*.perf.cc",
+        "src/**/*.perf.h",
+        "src/**/*.pybind.cc",
+        "src/**/*.pybind.h",
+        "src/**/main.cc",
+    ]),
+)
+
+TEST_FILES = glob(
+    [
+        "src/**/*.test.cc",
+        "src/**/*.test.h",
+    ],
+)
+
+PERF_FILES = glob(
+    [
+        "src/**/*.perf.cc",
+        "src/**/*.perf.h",
+    ],
+)
+
+PYBIND_FILES = glob(
+    [
+        "src/**/*.pybind.cc",
+        "src/**/*.pybind.h",
+    ],
+)
+
+cc_binary(
+    name = "chromobius",
+    srcs = SOURCE_FILES_NO_MAIN + glob(["src/**/main.cc"]),
+    copts = [
+        "-std=c++20",
+        "-O3",
+        "-DNDEBUG",
+    ],
+    includes = ["src/"],
+    deps = [
+        "@pymatching//:libpymatching",
+        "@stim//:stim_lib",
+    ],
+)
+
+cc_binary(
+    name = "chromobius_perf",
+    srcs = SOURCE_FILES_NO_MAIN + PERF_FILES,
+    copts = [
+        "-O3",
+        "-std=c++20",
+        "-DNDEBUG",
+    ],
+    data = glob(["test_data/**"]),
+    includes = ["src/"],
+    deps = [
+        "@pymatching//:libpymatching",
+        "@stim//:stim_lib",
+    ],
+)
+
+cc_test(
+    name = "chromobius_test",
+    srcs = SOURCE_FILES_NO_MAIN + TEST_FILES,
+    copts = [
+        "-std=c++20",
+    ],
+    data = glob(["test_data/**"]),
+    includes = ["src/"],
+    deps = [
+        "@gtest",
+        "@gtest//:gtest_main",
+        "@pymatching//:libpymatching",
+        "@stim//:stim_lib",
+    ],
+)
+
+cc_binary(
+    name = "chromobius.so",
+    srcs = SOURCE_FILES_NO_MAIN + PYBIND_FILES,
+    copts = [
+        "-O3",
+        "-std=c++20",
+        "-fvisibility=hidden",
+        "-DNDEBUG",
+    ],
+    includes = ["src/"],
+    linkshared = 1,
+    deps = [
+        "@pybind11",
+        "@pymatching//:libpymatching",
+        "@stim//:stim_lib",
+    ],
+)
+
+genrule(
+    name = "chromobius_wheel_files",
+    srcs = ["doc/chromobius.pyi"],
+    outs = ["chromobius.pyi"],
+    cmd = "cp $(location doc/chromobius.pyi) $@",
+)
+
+py_wheel(
+    name = "chromobius_dev_wheel",
+    distribution = "chromobius",
+    requires = [
+        "numpy",
+        "stim",
+    ],
+    version = "0.0.dev0",
+    deps = [
+        ":chromobius.so",
+        ":chromobius_wheel_files",
+    ],
+)