Conda packaging (#88)

- Adds meta data and build scripts for conda packaging - Adds github action CI for conda packaging - Adds GPL license file - Adds VERSION file - Adds version info that gives git-hash and date of current build
matsengrp · Sep 18, 2024 · fb4ebd8 · fb4ebd8
1 parent b3672b8
commit fb4ebd8
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diff --git 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
@@ -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 → .github/workflows/docker-publish.yml b/.github/workflows/docker_publish.yml → .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
@@ -7,3 +7,5 @@ tags
 .kak*
 cscope.*
 *.code-workspace
+
+tools/version.hpp
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,33 +1,47 @@
 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()
 
 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