diff --git a/.github/workflows/build-larch.yml b/.github/workflows/build-larch.yml index 0c4dfea8..8adf1583 100644 --- a/.github/workflows/build-larch.yml +++ b/.github/workflows/build-larch.yml @@ -1,9 +1,17 @@ -name: Build and run tests +name: Build larch on linux and run tests + on: workflow_dispatch: + jobs: - test: + build-larch: runs-on: ubuntu-latest + + strategy: + matrix: + environment: [build-larch-debug, build-larch-release] + environment: ${{ matrix.environment }} + steps: - name: Check out code uses: actions/checkout@v2 @@ -12,34 +20,45 @@ jobs: - name: Prepare build environment run: | sudo apt-get update - sudo apt-get install build-essential cmake zlib1g-dev python3-pip python3-pytest + sudo apt-get install build-essential zlib1g-dev python3-pip python3-pytest git git-lfs - name: Install conda run: | curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh > Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/miniconda ~/miniconda/bin/conda update -n base -c defaults conda + mkdir build - name: Create conda env run: | source ~/miniconda/etc/profile.d/conda.sh - conda env create -f environment.yml + conda config --prepend channels conda-forge + conda config --prepend channels bioconda + conda config --show channels + conda env create -f environment-dev.yml - name: Build (cmake step) + env: + CMAKE_BUILD_TYPE: ${{ vars.CMAKE_BUILD_TYPE }} + CMAKE_NUM_THREADS: ${{ vars.CMAKE_NUM_THREADS }} + USE_USHER: ${{ vars.USE_USHER }} run: | source ~/miniconda/etc/profile.d/conda.sh conda activate larch-dev - mkdir build cd build - export CMAKE_NUM_THREADS="8" - cmake -DCMAKE_BUILD_TYPE=Debug .. + export CMAKE_NUM_THREADS=${CMAKE_NUM_THREADS} + cmake -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DUSE_USHER=${USE_USHER} .. - name: Build (make step) + env: + MAKE_NUM_THREADS: ${{ vars.MAKE_NUM_THREADS }} run: | source ~/miniconda/etc/profile.d/conda.sh conda activate larch-dev cd build - make -j20 - ln -s ../data + make VERBOSE=1 -j${MAKE_NUM_THREADS} - name: Run tests + env: + LARCH_TEST_FLAGS: ${{ vars.LARCH_TEST_FLAGS }} run: | source ~/miniconda/etc/profile.d/conda.sh conda activate larch-dev cd build - ./larch-test -tag slow + ln -s ../data + ./larch-test ${LARCH_TEST_FLAGS} diff --git a/.github/workflows/conda-publish.yml b/.github/workflows/conda-publish.yml new file mode 100644 index 00000000..2091ec20 --- /dev/null +++ b/.github/workflows/conda-publish.yml @@ -0,0 +1,43 @@ +name: Build larch on linux and publish to Anaconda Cloud + +on: + workflow_dispatch: + +jobs: + conda-publish: + runs-on: ubuntu-latest + environment: conda-publish + + steps: + - name: Check out code + uses: actions/checkout@v2 + with: + submodules: true + - name: Prepare build environment + run: | + sudo apt-get update + sudo apt-get install build-essential zlib1g-dev python3-pip python3-pytest git git-lfs + - name: Install conda + run: | + curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh > Miniconda3-latest-Linux-x86_64.sh + bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/miniconda + ~/miniconda/bin/conda update -n base -c defaults conda + - name: Create conda env + run: | + source ~/miniconda/etc/profile.d/conda.sh + conda config --prepend channels conda-forge + conda config --prepend channels bioconda + conda config --show channels + conda env create -f environment-dev.yml + - name: Build conda package and upload to Anaconda Cloud + env: + ANACONDA_USER: ${{ vars.ANACONDA_USER }} + ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} + ANACONDA_FLAGS: ${{ vars.ANACONDA_FLAGS }} + INCLUDE_TESTS: ${{ vars.INCLUDE_TESTS }} + run: | + source ~/miniconda/etc/profile.d/conda.sh + conda activate larch-dev + export LARCH_VERSION=$(cat ./VERSION) + export INCLUDE_TESTS=${INCLUDE_TESTS} + conda build . --user ${ANACONDA_USER} --token ${ANACONDA_TOKEN} ${ANACONDA_FLAGS} diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker-publish.yml similarity index 99% rename from .github/workflows/docker_publish.yml rename to .github/workflows/docker-publish.yml index 62ad9e6c..133f3eba 100644 --- a/.github/workflows/docker_publish.yml +++ b/.github/workflows/docker-publish.yml @@ -9,6 +9,7 @@ jobs: push_to_registry: name: Push Docker image to Docker Hub runs-on: ubuntu-latest + steps: - name: Check out the repo uses: actions/checkout@v4 diff --git a/.gitignore b/.gitignore index d586529b..09074a38 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,5 @@ tags .kak* cscope.* *.code-workspace + +tools/version.hpp diff --git a/CMakeLists.txt b/CMakeLists.txt index d2f10c1f..76a8e2a9 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,8 +1,6 @@ cmake_minimum_required(VERSION 3.16) project(larch) -option(USE_USHER "Use matOptimize" yes) - if(CMAKE_VERSION VERSION_GREATER_EQUAL "3.24.0") cmake_policy(SET CMP0135 NEW) endif() @@ -10,24 +8,40 @@ endif() set(CMAKE_INTERPROCEDURAL_OPTIMIZATION yes) set(CMAKE_EXPORT_COMPILE_COMMANDS yes) -include(FetchContent) +if(NOT CMAKE_BUILD_TYPE) + set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build (Debug, Release, RelWithDebInfo, MinSizeRel)" FORCE) +endif() +option(USE_USHER "Use matOptimize" yes) +if(USE_USHER) + set(TBB_VERSION "2019_U9") +else() + set(TBB_VERSION "v2021.11.0") +endif() + +message("cmake system architecture: ${CMAKE_SYSTEM_PROCESSOR}") +message("build type: ${CMAKE_BUILD_TYPE}") +message("using usher: ${USE_USHER}") + +include(FetchContent) if(USE_USHER) FetchContent_Declare(oneTBB-src GIT_REPOSITORY https://github.com/oneapi-src/oneTBB - GIT_TAG 2019_U9 + GIT_TAG ${TBB_VERSION} + GIT_PROGRESS true ) FetchContent_MakeAvailable(oneTBB-src) include(${onetbb-src_SOURCE_DIR}/cmake/TBBBuild.cmake) tbb_build(TBB_ROOT ${onetbb-src_SOURCE_DIR} CONFIG_DIR TBB_DIR MAKE_ARGS tbb_cpf=1 CFLAGS="-w") + find_package(TBB REQUIRED tbbmalloc tbbmalloc_proxy tbb_preview) find_package(MPI REQUIRED) include_directories(SYSTEM ${MPI_INCLUDE_PATH}) else() FetchContent_Declare(oneTBB GIT_REPOSITORY https://github.com/oneapi-src/oneTBB - GIT_TAG v2021.11.0 + GIT_TAG ${TBB_VERSION} GIT_SHALLOW true GIT_PROGRESS true UPDATE_DISCONNECTED true @@ -86,6 +100,12 @@ if(${USE_HTSLIB}) ) endif() +add_custom_target(generate_version_h ALL + COMMAND cd ${CMAKE_SOURCE_DIR} && ${CMAKE_COMMAND} -DBUILD_TYPE=${CMAKE_BUILD_TYPE} -P version.cmake + COMMENT "Generating version.hpp with version information" + VERBATIM +) + find_package(ZLIB) set(STRICT_WARNINGS -Werror -fno-common -Wno-unknown-warning-option -Wno-pragmas -Wall -Wextra -pedantic -Wold-style-cast -Wshadow -Wconversion -Wcast-align -Wcast-qual -Wlogical-op -Wlogical-not-parentheses -Wredundant-decls -Wunreachable-code -Wparentheses -Wno-dangling-reference -Wno-ignored-optimization-argument) @@ -181,6 +201,7 @@ function(larch_executable PRODUCT) target_compile_options(${PRODUCT} PRIVATE ${STRICT_WARNINGS}) larch_link_opts(${PRODUCT}) target_link_libraries(${PRODUCT} PUBLIC larch) + add_dependencies(${PRODUCT} generate_version_h) endfunction() add_library(larch @@ -271,11 +292,11 @@ if(${USE_USHER}) ) endif() -larch_executable(dag-util - tools/dag-util.cpp) +larch_executable(larch-dagutil + tools/larch-dagutil.cpp) -larch_executable(dag2dot - tools/dag2dot.cpp) +larch_executable(larch-dag2dot + tools/larch-dag2dot.cpp) if(${USE_USHER}) larch_executable(larch-usher diff --git a/LICENSE b/LICENSE new file mode 100644 index 00000000..f288702d --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md index 40bbc9b9..132afc4a 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ Requirements For Ubuntu 18.04 LTS the following commands installs the requirements: ```shell -sudo apt install --no-install-recommends git cmake make g++ mpi-default-dev libprotobuf-dev libboost-dev libboost-program-options-dev libboost-filesystem-dev libboost-iostreams-dev libboost-date-time-dev protobuf-compiler automake autoconf libtool nasm +sudo apt install --no-install-recommends git git-lfs cmake make g++ mpi-default-dev libprotobuf-dev libboost-dev libboost-program-options-dev libboost-filesystem-dev libboost-iostreams-dev libboost-date-time-dev protobuf-compiler automake autoconf libtool nasm ``` To get a recent cmake, download from `https://cmake.org/download/`, for example: @@ -33,19 +33,16 @@ singularity build larch-singularity.sif larch-singularity.def singularity shell larch-singularity.sif --net ``` -To setup a conda environment capable of building Larch, use: +To setup a conda environment capable of building Larch, create `larch` using the standard environment file provided: ```shell -conda create -n larch -conda activate larch -conda install --channel "conda-forge" --update-deps --override-channels cmake make cxx-compiler openmpi openmpi-mpicc openmpi-mpicxx boost-cpp automake autoconf libtool yasm ucx zlib +conda env create -f environment.yml ``` -To setup a conda environment capable of building Larch including development tools, create `larch-dev` using the environment -file provided: +To setup a conda environment capable of building Larch including development tools, create `larch-dev` using the development environment file provided: ```shell -conda env create -f environment.yml +conda env create -f environment-dev.yml ``` Building @@ -54,8 +51,8 @@ Building There are 4 executables that are built automatically as part of the larch package and provide various methods for exploring tree space and manipulating DAGs/trees: - `larch-test` is the suite of tests used to validate the various routines. - `larch-usher` is a tool that takes an input tree/DAG and explores tree space through SPR moves. -- `dag-util` is a utility that manipulates (e.g. merge, prune) or inspects DAGs/trees. -- `dag2dot` is a utility that writes a DAG to a DOT file format for easier viewing. +- `larch-dagutil` is a utility that manipulates (e.g. merge, prune) or inspects DAGs/trees. +- `larch-dag2dot` is a utility that writes a DAG to a DOT file format for easier viewing. Note: If you run against memory limitations during the cmake step, you can regulate number of parallel threads with `export CMAKE_NUM_THREADS="8"` (reduce number as necessary). diff --git a/VERSION b/VERSION new file mode 100644 index 00000000..fd05d675 --- /dev/null +++ b/VERSION @@ -0,0 +1 @@ +0.1.0_beta diff --git a/conda-recipes/build.sh b/conda-recipes/build.sh new file mode 100755 index 00000000..b4bb77f4 --- /dev/null +++ b/conda-recipes/build.sh @@ -0,0 +1,34 @@ +#!/bin/bash + +rm -rf build +mkdir build +cd build + +CMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE:-"Release"} +USE_USHER=${USE_USHER:-"ON"} +CMAKE_NUM_THREADS=${CMAKE_NUM_THREADS:-"4"} +MAKE_NUM_THREADS=${MAKE_NUM_THREADS:-"20"} +INCLUDE_LARCH_TEST=${INCLUDE_LARCH_TEST:-"false"} + +echo "INCLUDE_LARCH_TEST: ${INCLUDE_LARCH_TEST}" +echo "CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}" +echo "USE_USHER: ${USE_USHER}" +echo "CMAKE_NUM_THREADS: ${CMAKE_NUM_THREADS}" +echo "MAKE_NUM_THREADS: ${MAKE_NUM_THREADS}" + +export CMAKE_NUM_THREADS=${CMAKE_NUM_THREADS} +cmake -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DUSE_USHER=${USE_USHER} .. +make -j${MAKE_NUM_THREADS} + +mkdir -p $PREFIX/lib +cp $(find . -name *.so*) $PREFIX/lib/ + +mkdir -p $PREFIX/bin +cp larch-usher $PREFIX/bin/larch-usher +cp larch-dagutil $PREFIX/bin/larch-dagutil +cp larch-dag2dot $PREFIX/bin/larch-dag2dot + +if [[ ${INCLUDE_LARCH_TEST} == true ]]; then + cp larch-test $PREFIX/bin/larch-test +fi + diff --git a/conda-recipes/conda_build_config.yaml b/conda-recipes/conda_build_config.yaml new file mode 100644 index 00000000..bcd3a8b1 --- /dev/null +++ b/conda-recipes/conda_build_config.yaml @@ -0,0 +1,4 @@ +channels: + - conda-forge + - bioconda + - defaults diff --git a/conda-recipes/meta.yaml b/conda-recipes/meta.yaml new file mode 100644 index 00000000..27d839d4 --- /dev/null +++ b/conda-recipes/meta.yaml @@ -0,0 +1,98 @@ +{% set name = "larch-phylo" %} +{% set version = environ.get('LARCH_VERSION', '0.0.0') %} +{% set git_commit = environ.get('LARCH_COMMIT', 'main') %} +{% set git_src = environ.get('LARCH_SRC', 'local') %} + +package: + name: {{ name }} + version: {{ version }} + +source: + {% if git_src == 'local' %} + # method 1: use local repo + path: ../ + {% else %} + # method 2: use online repo + git_url: https://github.com/matsengrp/larch.git + git_rev: {{ git_commit }} + git_submodules: true + {% endif %} + +build: + number: 0 + skip: true # [win] + +requirements: + build: + - cmake=3.19.6 + - make + - openmpi + - openmpi-mpicc + - openmpi-mpicxx + - boost-cpp=1.76 + - automake + - autoconf + - libtool + - yasm + - ucx + - zlib + - git-lfs + + - gcc + - gxx + - binutils + - binutils_impl_linux-64 + - binutils_linux-64 + - gdb + - libstdcxx-ng + - libgcc-ng + - libgomp + - libgfortran-ng + - libgfortran5 + - libedit + - libffi + - expat + - libuuid + - libiconv + - libzlib + - perl + - gettext + - libasprintf + - libtool + - kernel-headers_linux-64 + - rdma-core + - openssl + - keyutils + + run: + - openmpi + - openmpi-mpicc + - openmpi-mpicxx + - boost-cpp=1.76 + - ucx + - zlib + + host: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + +test: + commands: + - larch-usher --version + +extra: + system: + apt: + - git + - git-lfs + +about: + home: https://github.com/matsengrp/larch + license: GNU General Public License + license_family: GPL + license_file: LICENSE + summary: 'Tool for exploring tree space of DAG/tree through SPR moves' + description: | + Tool for exploring tree space of DAG/tree through SPR moves + doc_url: https://github.com/matsengrp/larch/blob/main/README.md + dev_url: https://github.com/matsengrp/larch diff --git a/data/sample_dag/sample_dag.dagbin b/data/sample_dag/sample_dag.dagbin new file mode 100644 index 00000000..da71bb2f Binary files /dev/null and b/data/sample_dag/sample_dag.dagbin differ diff --git a/data/sample_dag/sample_dag.pb b/data/sample_dag/sample_dag.pb new file mode 100644 index 00000000..126ad85e Binary files /dev/null and b/data/sample_dag/sample_dag.pb differ diff --git a/environment-dev.yml b/environment-dev.yml new file mode 100644 index 00000000..0197e99f --- /dev/null +++ b/environment-dev.yml @@ -0,0 +1,37 @@ +name: larch-dev +channels: + - conda-forge + - bioconda + - defaults +dependencies: + # larch + - cmake=3.19.6 + - make + - cxx-compiler + - openmpi + - openmpi-mpicc + - openmpi-mpicxx + - boost-cpp=1.76 + - automake + - autoconf + - libtool + - yasm + - zlib + - ucx + - cuda-cudart + - git-lfs + # development + - git + - mafft + - python + - rsync + - wget + - openssh + - gdb + - bzip2 + - backports.lzma + - protobuf=3.12.3 + # conda packaging + - conda-build + - conda-verify + - anaconda-client diff --git a/environment.yml b/environment.yml index 0f334a93..7db75028 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: larch-dev +name: larch channels: - conda-forge - bioconda @@ -10,21 +10,10 @@ dependencies: - openmpi - openmpi-mpicc - openmpi-mpicxx - - boost-cpp + - boost-cpp=1.76 - automake - autoconf - libtool - yasm - - ucx - zlib - - - git - - mafft - - python - - rsync - - wget - - openssh - - gdb - - bzip2 - - backports.lzma - - protobuf=3.12.3 + - ucx diff --git a/include/larch/dagbin_fileio.hpp b/include/larch/dagbin_fileio.hpp index 0c497948..260878c3 100644 --- a/include/larch/dagbin_fileio.hpp +++ b/include/larch/dagbin_fileio.hpp @@ -68,7 +68,7 @@ class DagbinFileIO { const std::vector &offsets); template - inline static bool CheckMagicNumber(iostream &infile); + inline static bool CheckMagicNumber(iostream &infile, bool do_assert = true); template inline static void WriteMagicNumber(iostream &outfile); diff --git a/include/larch/impl/dag/connections_impl.hpp b/include/larch/impl/dag/connections_impl.hpp index 39e2c583..4e041247 100644 --- a/include/larch/impl/dag/connections_impl.hpp +++ b/include/larch/impl/dag/connections_impl.hpp @@ -136,7 +136,7 @@ void FeatureMutableView::MakeComplete() const { size_t taxon_count = dag.GetLeafsCount(); dag.ClearConnections(); // Connect rootsplit nodes. - bool rootsplits_found = false; + [[maybe_unused]] bool rootsplits_found = false; for (auto& [clade_union, node_ids] : clade_union_map) { if (clade_union.size() == taxon_count) { for (auto node_id : node_ids) { diff --git a/include/larch/impl/dagbin_fileio_impl.hpp b/include/larch/impl/dagbin_fileio_impl.hpp index 00252006..c758dc9b 100644 --- a/include/larch/impl/dagbin_fileio_impl.hpp +++ b/include/larch/impl/dagbin_fileio_impl.hpp @@ -2,7 +2,7 @@ bool DagbinFileIO::IsFileDagbinFormat(std::string_view path) { std::ifstream infile; infile.open(std::string{path}, std::ios::binary); - auto is_dagbin_file = CheckMagicNumber(infile); + auto is_dagbin_file = CheckMagicNumber(infile, false); infile.close(); return is_dagbin_file; } @@ -32,18 +32,20 @@ MADAGStorage<> DagbinFileIO::ReadDAG(std::string_view path) { ReadEdges(infile, dag); break; default: - Assert(false && "ERROR: Invalid section_id"); + assert(false && "ERROR: Invalid section_id"); } }; infile.open(std::string{path}, std::ios::binary); - Assert(CheckMagicNumber(infile)); + CheckMagicNumber(infile); for (auto [section_begpos, section_id] : labeled_linked_list) { - Assert(section_id == ReadData(infile)); + [[maybe_unused]] auto true_section_id = ReadData(infile); + Assert(section_id == true_section_id); auto section_endpos = ReadData(infile); read_section(section_id); - Assert(section_endpos == infile.tellg()); + [[maybe_unused]] auto true_section_endpos = infile.tellg(); + Assert(section_endpos == true_section_endpos); } infile.close(); @@ -115,7 +117,7 @@ void DagbinFileIO::AppendDAG(DAG dag, std::string_view path) { // Read old header file.seekg(0, std::ios::beg); - Assert(CheckMagicNumber(file)); + CheckMagicNumber(file); auto section_id = ReadData(file); auto section_offset = ReadData(file); Assert(section_id == SectionId::Header); @@ -190,7 +192,7 @@ DagbinFileIO::ReadLabeledLinkedList(iostream &infile) { SectionId section_id; std::streampos section_offset; infile.seekg(0, std::ios::beg); - Assert(CheckMagicNumber(infile)); + CheckMagicNumber(infile); section_offset = infile.tellg(); while (!infile.eof()) { infile.seekg(section_offset); @@ -213,7 +215,7 @@ std::vector DagbinFileIO::ReadLinkedList(iostream &infile) { std::streampos section_offset; infile.seekg(0, std::ios::beg); - Assert(CheckMagicNumber(infile)); + CheckMagicNumber(infile); section_offset = infile.tellg(); while (!infile.eof()) { offsets.push_back(section_offset); @@ -241,9 +243,10 @@ void DagbinFileIO::WriteLinkedList(iostream &outfile, } template -bool DagbinFileIO::CheckMagicNumber(iostream &infile) { +bool DagbinFileIO::CheckMagicNumber(iostream &infile, bool do_assert) { std::vector magic_number(MAGIC_NUMBER.size()); infile.read(reinterpret_cast(magic_number.data()), MAGIC_NUMBER.size()); + if (do_assert) Assert(magic_number == MAGIC_NUMBER) return (magic_number == MAGIC_NUMBER); } diff --git a/protobuf.cmake b/protobuf.cmake index 1f4c7ef5..b8fb3f56 100644 --- a/protobuf.cmake +++ b/protobuf.cmake @@ -4,7 +4,7 @@ set(Protobuf_USE_STATIC_LIBS ON) cmake_policy(SET CMP0026 OLD) if(NOT DEFINED CMAKE_NUM_THREADS) - set(CMAKE_NUM_THREADS "16") + set(CMAKE_NUM_THREADS "8") endif() FetchContent_Declare( diff --git a/test/main.cpp b/test/main.cpp index 8ca4bced..917daac6 100644 --- a/test/main.cpp +++ b/test/main.cpp @@ -4,6 +4,8 @@ #include #include #include +#include +#include #ifdef USE_USHER #include @@ -83,6 +85,8 @@ int main(int argc, char* argv[]) { bool opt_list_names = false; bool opt_test_range = false; + assert(std::filesystem::exists("./data/") && "Test data folder not found."); + std::set range; std::regex regex{".*"}; std::set include_tags; @@ -90,6 +94,8 @@ int main(int argc, char* argv[]) { for (int i = 1; i < argc; ++i) { if (std::string("-h") == argv[i]) { get_usage(); + } else if (std::string("--version") == argv[i]) { + Version("larch-test"); } else if (std::string("nocatch") == argv[i]) { no_catch = true; } else if (std::string("--list") == argv[i]) { diff --git a/test/test_fileio_dagbin.cpp b/test/test_fileio_dagbin.cpp index 631a2189..45f3d64a 100644 --- a/test/test_fileio_dagbin.cpp +++ b/test/test_fileio_dagbin.cpp @@ -25,6 +25,32 @@ return true; } +[[maybe_unused]] static void read_dagbin_sample_dag() { + std::string protobuf_path = "data/sample_dag/sample_dag.pb"; + std::string dagbin_path = "data/sample_dag/sample_dag.dagbin"; + + auto sample_dag = make_sample_dag(); + dag_info(sample_dag); + + // Compare read/write dag protobuf vs dagbin + auto sample_dag_from_protobuf = LoadDAGFromProtobuf(protobuf_path); + auto sample_dag_from_dagbin = LoadDAGFromDagbin(dagbin_path); + dag_info(sample_dag_from_protobuf); + dag_info(sample_dag_from_dagbin); + TestAssert(compare_treedags(sample_dag_from_dagbin.View(), + sample_dag_from_protobuf.View()) && + "Loading Sample DAG via Protobuf and Dagbin do not have the same result."); + + // Compare dag to sample dag. + sample_dag_from_protobuf.View().RecomputeCompactGenomes(); + TestAssert(compare_treedags(sample_dag_from_protobuf.View(), sample_dag.View()) && + "Loaded Protobuf DAG does not match Sample DAG."); + sample_dag_from_dagbin.View().RecomputeCompactGenomes(); + TestAssert(compare_treedags(sample_dag_from_dagbin.View(), sample_dag.View()) && + "Loaded Dagbin DAG does not match Sample DAG."); +} + + [[maybe_unused]] static void test_dagbin_sample_dag() { std::string protobuf_path = test_output_folder + "/sample_dag.pb"; std::string dagbin_path = test_output_folder + "/sample_dag.dagbin"; @@ -37,6 +63,8 @@ StoreDAGToDagbin(sample_dag.View(), dagbin_path); auto sample_dag_from_protobuf = LoadDAGFromProtobuf(protobuf_path); auto sample_dag_from_dagbin = LoadDAGFromDagbin(dagbin_path); + dag_info(sample_dag_from_protobuf); + dag_info(sample_dag_from_dagbin); TestAssert(compare_treedags(sample_dag_from_dagbin.View(), sample_dag_from_protobuf.View()) && "Loading Sample DAG via Protobuf and Dagbin do not have the same result."); @@ -164,23 +192,25 @@ } [[maybe_unused]] static const auto test_added0 = + add_test({read_dagbin_sample_dag, "Load dagbin: Sample DAG (Read-only)"}); +[[maybe_unused]] static const auto test_added1 = add_test({test_dagbin_sample_dag, "Load dagbin: Sample DAG"}); const std::string input_dag_path = "data/test_5_trees/full_dag.pb.gz"; -[[maybe_unused]] static const auto test_added1 = +[[maybe_unused]] static const auto test_added2 = add_test({[] { test_dagbin(input_dag_path, FileFormat::ProtobufDAG); }, "Load dagbin: test_5_trees"}); -[[maybe_unused]] static const auto test_added2 = +[[maybe_unused]] static const auto test_added3 = add_test({[] { test_dagbin_via_larchusher(input_dag_path, 3, true, true); }, "Load dagbin: test_5_trees, 3 iters, simultaneous write"}); -[[maybe_unused]] static const auto test_added3 = +[[maybe_unused]] static const auto test_added4 = add_test({[] { test_dagbin_via_larchusher(input_dag_path, 3, true, false); }, "Load dagbin: test_5_trees, 3 iters, seeded"}); const std::string big_input_dag_path = "data/big_test/big_test.pb.gz"; -[[maybe_unused]] static const auto test_added4 = +[[maybe_unused]] static const auto test_added5 = add_test({[] { test_dagbin(big_input_dag_path, FileFormat::ProtobufDAG); }, "Load dagbin: big_test", {"slow"}}); diff --git a/test/test_rf_distance.cpp b/test/test_rf_distance.cpp index e8838c88..0d0d2c16 100644 --- a/test/test_rf_distance.cpp +++ b/test/test_rf_distance.cpp @@ -127,7 +127,7 @@ static void test_rf_distance_hand_computed_example() { merge1.AddDAGs(std::vector{dag1}); Merge merge2(dag1.GetReferenceSequence()); merge2.AddDAGs(std::vector{dag1, dag2}); - auto true_dist = dag1.GetEdgesCount() + dag2.GetEdgesCount() - + [[maybe_unused]] auto true_dist = dag1.GetEdgesCount() + dag2.GetEdgesCount() - dag1.GetLeafs().size() - dag2.GetLeafs().size() - 2; Assert(get_rf_distance(merge1, merge2) == true_dist); @@ -169,7 +169,7 @@ static void test_rf_distance_different_weight_ops() { true_dist_map[{2, 3}] = true_dist_map[{3, 2}] = 7; // Use hand-computed distances to find rf-distance types on merged MADAGs. - auto compute_true_dist = [&](std::vector compute_ids, std::vector ref_ids, + [[maybe_unused]] auto compute_true_dist = [&](std::vector compute_ids, std::vector ref_ids, RFDistanceType rf_dist_type, bool do_print = false) { ArbitraryInt total = 0; std::vector vec; diff --git a/tools/dag2dot.cpp b/tools/larch-dag2dot.cpp similarity index 98% rename from tools/dag2dot.cpp rename to tools/larch-dag2dot.cpp index 6ece0cad..acb04ad0 100644 --- a/tools/dag2dot.cpp +++ b/tools/larch-dag2dot.cpp @@ -34,6 +34,8 @@ int main(int argc, char** argv) try { for (auto [name, params] : args) { if (name == "-h" or name == "--help") { Usage(); + } else if (name == "--version") { + Version(); } else if (name == "-i" or name == "--input") { ParseOption(name, params, input_path, 1); } else if (name == "-o" or name == "--output") { diff --git a/tools/dag-util.cpp b/tools/larch-dagutil.cpp similarity index 99% rename from tools/dag-util.cpp rename to tools/larch-dagutil.cpp index 916d057e..c053d3c1 100644 --- a/tools/dag-util.cpp +++ b/tools/larch-dagutil.cpp @@ -207,6 +207,8 @@ int main(int argc, char** argv) try { for (auto [name, params] : args) { if (name == "-h" or name == "--help") { Usage(); + } else if (name == "--version") { + Version(); } else if (name == "-i" or name == "--input") { ParseOption(name, params, input_paths, -1); ranges::actions::push_back(input_paths, params); diff --git a/tools/larch-usher.cpp b/tools/larch-usher.cpp index df46e2dc..6960dc4b 100644 --- a/tools/larch-usher.cpp +++ b/tools/larch-usher.cpp @@ -583,6 +583,8 @@ int main(int argc, char** argv) { // NOLINT(bugprone-exception-escape) for (auto [name, params] : args) { if (name == "-h" or name == "--help") { Usage(); + } else if (name == "--version") { + Version(); } else if (name == "-i" or name == "--input") { ParseOption(name, params, input_dag_path, 1); } else if (name == "-o" or name == "--output") { diff --git a/tools/tools_common.hpp b/tools/tools_common.hpp index 711e8fd9..6866fa27 100644 --- a/tools/tools_common.hpp +++ b/tools/tools_common.hpp @@ -5,6 +5,7 @@ #include #include +#include "version.hpp" #include "larch/common.hpp" [[noreturn]] inline static void Fail() { @@ -13,6 +14,15 @@ std::exit(EXIT_FAILURE); } +inline static void Version(std::string program_name = "larch-usher") { + std::cout << program_name << "\n"; + std::cout << "Build version: " << VERSION_NUMBER << "\n"; + std::cout << "Build date: " << GIT_COMMIT_DATE << "\n"; + std::cout << "Build commit: " << GIT_COMMIT_HASH << "\n"; + + exit(EXIT_SUCCESS); +} + ////////////////////////////////////////////////////////////////////////////////////// // Commandline Parsers diff --git a/tools/version.hpp.in b/tools/version.hpp.in new file mode 100644 index 00000000..b4506808 --- /dev/null +++ b/tools/version.hpp.in @@ -0,0 +1,6 @@ +#pragma once + +#define VERSION_NUMBER "@VERSION_NUMBER@" +#define GIT_COMMIT_HASH "@GIT_COMMIT_HASH@" +#define GIT_COMMIT_DATE "@GIT_COMMIT_DATE@" +#define BUILD_TYPE "@BUILD_TYPE@" diff --git a/version.cmake b/version.cmake new file mode 100644 index 00000000..4945a222 --- /dev/null +++ b/version.cmake @@ -0,0 +1,49 @@ +# set the version from VERSION file, and the build commit and date from git repo + +# get git version tag +execute_process( + COMMAND git describe --tags --abbrev=0 + WORKING_DIRECTORY ${CMAKE_SOURCE_DIR} + OUTPUT_VARIABLE GIT_TAG_VERSION + OUTPUT_STRIP_TRAILING_WHITESPACE + ERROR_QUIET +) + +# get version from git tag if available, else fall back to VERSION file +if(GIT_TAG_VERSION) + set(VERSION_NUMBER ${GIT_TAG_VERSION}) + message("using version from git tag: ${VERSION_NUMBER}") +else() + file(READ "${CMAKE_SOURCE_DIR}/VERSION" VERSION_NUMBER) + string(STRIP "${VERSION_NUMBER}" VERSION_NUMBER) + set(VERSION_NUMBER "v${VERSION_NUMBER}") + message("using version from VERSION file: ${VERSION_NUMBER}") +endif() + +# get git hash +execute_process( + COMMAND git rev-parse --short HEAD + WORKING_DIRECTORY ${CMAKE_SOURCE_DIR} + OUTPUT_VARIABLE GIT_COMMIT_HASH + OUTPUT_STRIP_TRAILING_WHITESPACE +) + +# get git date +execute_process( + COMMAND git log -1 --format=%cd --date=short + WORKING_DIRECTORY ${CMAKE_SOURCE_DIR} + OUTPUT_VARIABLE GIT_COMMIT_DATE + OUTPUT_STRIP_TRAILING_WHITESPACE +) + +if (NOT BUILD_TYPE) + set(BUILD_TYPE "Unknown") +endif() +message("BUILD_TYPE: ${BUILD_TYPE}") + +# output version details to file +configure_file( + "tools/version.hpp.in" + "tools/version.hpp" + @ONLY +)