Refactor c++ code and add github actions (#102)

.github/dependabot.yml

@@ -0,0 +1,27 @@
+version: 2
+
+updates:
+- package-ecosystem: docker
+  directory: "/"
+  schedule:
+    interval: "daily"
+  allow:
+      # Allow both direct and indirect updates for all packages
+      - dependency-type: "all"
+- package-ecosystem: github-actions
+  directory: "/"
+  schedule:
+    interval: "daily" 
+  allow:
+      # Allow both direct and indirect updates for all packages
+      - dependency-type: "all"
+
+- package-ecosystem: pip 
+  directory: "/" 
+  insecure-external-code-execution: allow
+  versioning-strategy: auto
+  schedule:
+    interval: "daily"
+  allow:
+      # Allow both direct and indirect updates for all packages
+      - dependency-type: "all"

.github/workflows/build_and_upolad.yaml

@@ -0,0 +1,179 @@
+name: Build&Upload
+
+on:
+  workflow_dispatch:
+  pull_request:
+  release:
+    types:
+      - released
+  push:
+    branches:
+      - feature/addGithubActions 
+
+env:
+  Python_Version: 3.9
+
+jobs:
+  build_sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: ${{env.Python_Version}}
+      - name: Build sdist
+        run: |
+          pip install -r requirements.txt
+          python setup.py sdist
+      - uses: actions/upload-artifact@v2
+        with:
+          name: artifact
+          path: dist/*.tar.gz
+          retention-days: 1
+
+  codecov:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: ${{env.Python_Version}}
+      - name: Install PyQUBO
+        run: |
+          python -m pip install .
+      - name: Generate Codecov Report
+        run: |
+          pip install -r requirements.txt
+          python -m coverage run -m unittest discover .
+      - name: Upload Codecov Report
+        run: |
+          codecov
+  
+  doctest:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: ${{env.Python_Version}}
+
+      - name: Install PyQUBO
+        run: |
+          python -m pip install .
+
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+          pip install -r requirements_doctest.txt
+          sphinx-build -W -b html docs docs/_build/html
+
+      - name: Run Doctest
+        run: |
+          make doctest
+  
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }} ${{matrix.arch}}
+    runs-on: ${{ matrix.os }}
+    env:
+      CIBW_DEPENDENCY_VERSIONS: pinned
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        arch: [x86_64, AMD64, i686, arm64]
+        python: [36, 37, 38, 39]
+        exclude:
+         - os: ubuntu-latest
+           arch: AMD64
+         - os: ubuntu-latest
+           arch: arm64
+
+         - os: macos-latest
+           arch: AMD64
+         - os: macos-latest
+           arch: i686
+         - os: macos-latest
+           arch: arm64
+           python: 36
+         - os: macos-latest
+           arch: arm64
+           python: 37
+
+         - os: windows-latest
+           arch: x86_64
+         - os: windows-latest
+           arch: i686
+         - os: windows-latest
+           arch: arm64
+
+        include:
+         - os: ubuntu-latest
+           CIBW_PLATFORM: linux
+           CIBW_BUILD: "cp3*-manylinux*"
+           CIBW_BEFORE_ALL: ""
+           CIBW_BEFORE_BUILD: "pip install scikit-build"
+           CIBW_REPAIR_WHEEL_COMMAND: "auditwheel repair -w {dest_dir} {wheel}"
+
+         - os: macos-latest
+           CIBW_PLATFORM: macos
+           CIBW_BUILD: "cp3*-macosx*"
+           CIBW_BEFORE_ALL: ""
+           CIBW_BEFORE_BUILD: "pip install git+https://github.com/scikit-build/scikit-build.git@master"
+           CIBW_REPAIR_WHEEL_COMMAND: "delocate-listdeps {wheel} && delocate-wheel --require-archs {delocate_archs} -w {dest_dir} {wheel}"
+
+
+         - os: windows-latest
+           CIBW_PLATFORM: windows
+           CIBW_BUILD: "cp3*-win_amd64*"
+           CIBW_BEFORE_ALL: ""
+           CIBW_BEFORE_BUILD: "pip install delvewheel scikit-build"
+           CIBW_REPAIR_WHEEL_COMMAND: "delvewheel repair -w {dest_dir} {wheel}"
+
+      fail-fast: false 
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: ${{env.Python_Version}}
+
+      - name: Build wheels on ${{ matrix.CIBW_PLATFORM }} ${{matrix.arch}}
+        uses: pypa/cibuildwheel@v1.12.0
+        env:
+          CIBW_PLATFORM:  ${{ matrix.CIBW_PLATFORM }}
+          CIBW_BUILD: cp${{matrix.python}}-*
+          CIBW_SKIP: "cp35-*"
+          CIBW_ENVIRONMENT:
+             CFLAGS="-flto -Ofast -pipe"
+             CXXFLAGS="-flto -Ofast -pipe"
+          CIBW_ARCHS: ${{matrix.arch}}
+          CIBW_BEFORE_TEST: "pip install -r requirements.txt"
+          CIBW_TEST_COMMAND: "python -m coverage run -m unittest discover {package}"
+          CIBW_DEPENDENCY_VERSIONS: ${{ env.CIBW_DEPENDENCY_VERSIONS }}
+          CIBW_BEFORE_BUILD: ${{matrix.CIBW_BEFORE_BUILD}}        
+          CIBW_BEFORE_ALL: ${{matrix.CIBW_BEFORE_ALL}}
+          CIBW_REPAIR_WHEEL_COMMAND: ${{matrix.CIBW_REPAIR_WHEEL_COMMAND}}
+          CIBW_BUILD_VERBOSITY: 3
+
+      - uses: actions/upload-artifact@v2
+        with:
+          name: artifact
+          path: ./wheelhouse/*.whl
+          retention-days: 1
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: artifact
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: ${{ secrets.PYPI_USERNAME }}
+          password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,71 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ master, main ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ master, main ]
+  schedule:
+    - cron: '31 12 * * 5'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'cpp', 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
+        # Learn more:
+        # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

CMakeLists.txt

@@ -1,24 +1,30 @@
-cmake_minimum_required(VERSION 3.11)
+cmake_minimum_required(VERSION 3.20)
 
 project(cpp_pyqubo)
 
-set(CMAKE_INTERPROCEDURAL_OPTIMIZATION True)
-
-set(CXX_STANDARD_REQUIRED TRUE)
-set(CMAKE_VERBOSE_MAKEFILE TRUE)
-
-set(CMAKE_CXX_STANDARD 14)
-#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-declarations")
-set(CMAKE_C_FLAGS "-Ofast -pipe" )
-set(CMAKE_CXX_FLAGS "-Ofast -pipe")
-set(CMAKE_C_FLAGS_RELEASE "-Ofast -pipe")
-set(CMAKE_CXX_FLAGS_RELEASE "-Ofast -pipe")
-
+include(external/boost_assert.cmake)
+include(external/boost_config.cmake)
+include(external/boost_container.cmake)
+include(external/boost_container_hash.cmake)
+include(external/boost_core.cmake)
+include(external/boost_detail.cmake)
+include(external/boost_integer.cmake)
+include(external/boost_intrusive.cmake)
+include(external/boost_move.cmake)
+include(external/boost_static_assert.cmake)
+include(external/boost_type_traits.cmake)
+include(external/cimod.cmake)
+include(external/eigen.cmake)
 include(external/pybind11.cmake)
-include_directories(cpp_dimod)
-add_subdirectory(src)
-
-
-
-include(external/googletest.cmake)
-add_subdirectory(tests)
+include(external/robin_hood.cmake)
+
+pybind11_add_module(cpp_pyqubo src/main.cpp)
+
+target_compile_definitions(cpp_pyqubo PRIVATE VERSION_INFO=${PYQUBO_VERSION_INFO})
+target_compile_features(cpp_pyqubo PRIVATE cxx_std_17)
+target_compile_options(cpp_pyqubo PRIVATE
+    $<$<CXX_COMPILER_ID:GNU>: -Ofast -Wall -Wno-terminate>
+    $<$<CXX_COMPILER_ID:AppleClang>: -Ofast -Wno-exceptions>
+    $<$<CXX_COMPILER_ID:MSVC>: /O2 /wd4297>
+)
+target_include_directories(cpp_pyqubo PRIVATE ${Boost_INCLUDE_DIRS})

MANIFEST.in

@@ -10,5 +10,3 @@ recursive-include pyqubo *
 recursive-include tests *
 recursive-include src *
 recursive-include external *
-recursive-include include *
-recursive-include cpp_dimod *

README.rst

@@ -47,13 +47,13 @@ By calling ``model.to_qubo()``, we get the resulting QUBO.
 >>> pprint(qubo)
 {('s1', 's1'): -160.0,
 ('s1', 's2'): 64.0,
+('s1', 's3'): 224.0,
+('s1', 's4'): 32.0,
 ('s2', 's2'): -96.0,
-('s3', 's1'): 224.0,
-('s3', 's2'): 112.0,
+('s2', 's3'): 112.0,
+('s2', 's4'): 16.0,
 ('s3', 's3'): -196.0,
-('s4', 's1'): 32.0,
-('s4', 's2'): 16.0,
-('s4', 's3'): 56.0,
+('s3', 's4'): 56.0,
 ('s4', 's4'): -52.0}
 
 .. _integration:
@@ -108,12 +108,12 @@ or
 
 .. code-block:: shell
 
-    python setup.py install
+    python -m pip install .
 
 Supported Python Versions
 -------------------------
 
-Python 3.5, 3.6, 3.7, 3.8 and 3.9 are supported.
+Python 3.7, 3.8 and 3.9 are supported.
 
 Supported Operating Systems
 ---------------------------
@@ -131,12 +131,14 @@ Run all tests.
 
 .. code-block:: shell
 
+    export USE_TEST=1
     python -m unittest discover test
 
 Show coverage report.
 
 .. code-block:: shell
 
+    export USE_TEST=1
     coverage run -m unittest discover
     coverage html
 

codecov.yml

@@ -0,0 +1,2 @@
+fixes:
+  - "/home/runner/work/pyqubo/pyqubo/::"