Merge pull request #6 from chinwobble/fix-test

Use SIMD for sequence::reversecomplement

.github/workflows/ci-cmake.yml

@@ -0,0 +1,116 @@
+# Copyright (c) 2021-2022-2023-2024 Luca Cappa
+# Released under the term specified in file LICENSE.txt
+# SPDX short identifier: MIT
+
+# A "pure" GitHub workflow using CMake, Ninja and vcpkg to build a C/C++ codebase.
+# It leverages both CMakePresets.json and vcpkg.json.
+# It is called "pure workflow" because it is an example which minimizes the usage of
+# custom GitHub Actions, but leverages directly the tools that could be easily run on
+# your development machines (i.e. CMake, vcpkg, Ninja) to ensure a perfectly identical
+# and reproducible local build (on your development machine) and a remote build on
+# build agents.
+name: ci-cmake
+on:
+  push:
+  workflow_dispatch:
+  pull_request:
+    branches:
+    - v11
+    - main
+
+jobs:
+  job:
+    name: ${{ matrix.os }}-${{ github.workflow }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-24.04, macos-13, macos-14, windows-2022]
+    env:
+      # Indicates the location of the vcpkg as a Git submodule of the project repository.
+      # Not using "VCPKG_ROOT" because a variable with the same name is defined in the VS's
+      # Developer Command Prompt environment in VS 2022 17.6, which would override this one
+      # if it had the same name.
+      _VCPKG_: ${{ github.workspace }}/vcpkg
+      # Tells vcpkg where binary packages are stored.
+      VCPKG_DEFAULT_BINARY_CACHE: ${{ github.workspace }}/vcpkg/bincache
+      # Let's use GitHub Action cache as storage for the vcpkg Binary Caching feature.
+      VCPKG_BINARY_SOURCES: 'clear;x-gha,readwrite'
+
+    steps:
+    # Set env vars needed for vcpkg to leverage the GitHub Action cache as a storage
+    # for Binary Caching.
+      - uses: actions/github-script@v7
+        with:
+          script: |
+            core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || '');
+            core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || '');
+
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+      - name: "Create directory '${{ env.VCPKG_DEFAULT_BINARY_CACHE }}'"
+        run: mkdir -p $VCPKG_DEFAULT_BINARY_CACHE
+        shell: bash
+
+      # Setup the build machine with the most recent versions of CMake and Ninja. Both are cached if not already: on subsequent runs both will be quickly restored from GitHub cache service.
+      - uses: lukka/get-cmake@latest
+
+      # Restore vcpkg from the GitHub Action cache service. Note that packages are restored by vcpkg's binary caching
+      # when it is being run afterwards by CMake.
+      - name: Restore vcpkg
+        uses: actions/cache@v4
+        with:
+          # The first path is the location of vcpkg: it contains the vcpkg executable and data files, as long as the
+          # built package archives (aka binary cache) which are located by VCPKG_DEFAULT_BINARY_CACHE env var.
+          # The other paths starting with '!' are exclusions: they contain termporary files generated during the build of the installed packages.
+          path: |
+            ${{ env._VCPKG_ }}
+            !${{ env._VCPKG_ }}/buildtrees
+            !${{ env._VCPKG_ }}/packages
+            !${{ env._VCPKG_ }}/downloads
+            !${{ env._VCPKG_ }}/installed
+          # The key is composed in a way that it gets properly invalidated whenever a different version of vcpkg is being used.
+          key: |
+            ${{ hashFiles( '.git/modules/vcpkg/HEAD' )}}
+
+      # On Windows runners, let's ensure to have the Developer Command Prompt environment setup correctly.
+      # As used here the Developer Command Prompt created is targeting x64 and using the default the Windows SDK.
+      - uses: ilammy/msvc-dev-cmd@v1
+
+      - name: install build dependencies (Ubuntu)
+        run: sudo apt update && sudo apt install -y libisal-dev
+        if: runner.os == 'Linux'
+      - name: install build dependencies (MacOS)
+        run: brew install isa-l
+        if: runner.os == 'macOS'
+      # Run CMake to generate Ninja project files, using the vcpkg's toolchain file to resolve and install
+      # the dependencies as specified in vcpkg.json. Note that the vcpkg's toolchain is specified
+      # in the CMakePresets.json file.
+      # This step also runs vcpkg with Binary Caching leveraging GitHub Action cache to
+      # store the built packages artifacts.
+      - name: Restore from cache the dependencies and generate project files
+        run: |
+          cmake --preset ninja-multi-vcpkg
+
+      # Build (Release configuration only) the whole project with Ninja (which is spawn by CMake).
+      #
+      # Note: if the preset misses the "configuration", it is possible to explicitly select the
+      # configuration with the `--config` flag, e.g.:
+      # run: cmake --build --preset ninja-vcpkg --config Release
+      - name: Build (Release configuration)
+        run: |
+          cmake --build --preset ninja-vcpkg-release
+
+      - name: run benchmarks
+        run: |
+          ./builds/ninja-multi-vcpkg/Release/fastplong_benchmarks
+        if: runner.os != 'Windows'
+
+      - name: run tests
+        run: |
+          ./builds/ninja-multi-vcpkg/Release/fastplong_tests
+      # Test the whole project with CTest, again Release configuration only.
+      # - name: Test (Release configuration)
+      #   run: |
+      #     ctest --preset test-release

.gitignore

@@ -31,3 +31,4 @@
 *.out
 *.app
 bin
+builds

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "vcpkg"]
+	path = vcpkg
+	url = https://github.com/microsoft/vcpkg

.vscode/extensions.json

@@ -0,0 +1,14 @@
+{
+	// See https://go.microsoft.com/fwlink/?LinkId=827846 to learn about workspace recommendations.
+	// Extension identifier format: ${publisher}.${name}. Example: vscode.csharp
+
+	// List of extensions which should be recommended for users of this workspace.
+	"recommendations": [
+		"ms-vscode.cpptools",
+		"ms-vscode.cmake-tools"
+	],
+	// List of extensions recommended by VS Code that should not be recommended for users of this workspace.
+	"unwantedRecommendations": [
+
+	]
+}

CMakeLists.txt

@@ -0,0 +1,121 @@
+# CMakeLists.txt
+cmake_minimum_required(VERSION 3.21)
+project(fastplong VERSION 0.2.1)
+set(CMAKE_CXX_STANDARD 23)
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
+# Find dependencies provided by vcpkg (via vcpkg.cmake)
+find_package(hwy CONFIG REQUIRED)
+find_package(benchmark CONFIG REQUIRED)
+find_package(libdeflate CONFIG REQUIRED)
+
+if (MSVC)
+find_package(unofficial-isal CONFIG REQUIRED)
+set(
+    FASTPLONG_LIBS
+    hwy::hwy
+    unofficial::isal::isal
+    $<IF:$<TARGET_EXISTS:libdeflate::libdeflate_shared>,libdeflate::libdeflate_shared,libdeflate::libdeflate_static>
+)
+else()
+set(
+    FASTPLONG_LIBS
+    hwy::hwy
+    $<IF:$<TARGET_EXISTS:libdeflate::libdeflate_shared>,libdeflate::libdeflate_shared,libdeflate::libdeflate_static>
+    -lisal
+)
+endif()
+
+if (CMAKE_CXX_COMPILER_ARCHITECTURE_ID MATCHES "x86_64")
+    add_compile_options(-march=haswell -maes)
+    ## HWY_AVX3 which is 512
+    # SET(GCC_COVERAGE_COMPILE_FLAGS "-march=sapphirerapids")
+endif()
+if (MSVC)
+    add_compile_options(/arch:AVX2)
+endif()
+
+set(
+    FASTPLONG_SOURCES
+    src/adaptertrimmer.cpp
+    src/editdistance.cpp
+    src/evaluator.cpp
+    src/fastareader.cpp
+    src/fastqreader.cpp
+    src/filter.cpp
+    src/filterresult.cpp
+    src/jsonreporter.cpp
+    src/htmlreporter.cpp
+    src/nucleotidetree.cpp
+    src/options.cpp
+    src/polyx.cpp
+    src/processor.cpp
+    src/read.cpp
+    src/readpool.cpp
+    src/seprocessor.cpp
+    src/sequence.cpp
+    src/stats.cpp
+    src/threadconfig.cpp
+    src/writer.cpp
+    src/writerthread.cpp
+)
+
+set(
+    FASTPLONG_TEST_SOURCES
+    test/adaptertrimmer_test.cpp
+    test/fastareader_test.cpp
+    test/filter_test.cpp
+    test/nucleotidetree_test.cpp
+    test/read_test.cpp
+    test/evaluator_test.cpp
+    test/fastqreader_test.cpp
+    test/globals.cpp
+    test/polyx_test.cpp
+    test/sequence_test.cpp
+)
+include_directories(
+    /usr/local/include
+    # arm64 mac install location
+    /opt/homebrew/include
+)
+link_directories(
+    /usr/local/lib
+    # arm64 mac install location
+    /opt/homebrew/lib
+)
+
+
+if (NOT MSVC)
+    # benchmark target
+    add_executable(fastplong_benchmarks)
+    target_sources(
+        fastplong_benchmarks PRIVATE
+        benchmarks/sequence_benchmark.cpp
+        test/globals.cpp
+        ${FASTPLONG_SOURCES}
+    )
+    target_link_libraries(
+        fastplong_benchmarks PRIVATE
+        ${FASTPLONG_LIBS}
+        benchmark::benchmark
+        benchmark::benchmark_main
+    )
+endif()
+# main target
+add_executable(fastplong src/main.cpp ${FASTPLONG_SOURCES})
+target_link_libraries(
+    fastplong PUBLIC
+    ${FASTPLONG_LIBS}
+)
+# tests target
+enable_testing()
+find_package(GTest CONFIG REQUIRED)
+add_executable(fastplong_tests ${FASTPLONG_SOURCES} ${FASTPLONG_TEST_SOURCES})
+target_link_libraries(
+    fastplong_tests PRIVATE
+    ${FASTPLONG_LIBS}
+    GTest::gtest
+    GTest::gtest_main
+    -lpthread
+)
+add_test(fastplong_tests fastplong_tests)