Faster and uglier implementation of the bidirectional algorithm for v…

…1.0 (#70) * Merge master into dev, Add boost docker image and example #65 * Clean up boost Dockerfile, disable boost-python * Add r_c_shortest_paths runner for Beasley benchmarks #65 * Update table with real comparison #65 * Refactor benchmark parsing * Add WIP * Change to wall clock time * Update python interface, fix timer * Spell checks, fix python example * Add unittest #69 * 'Refactored by Sourcery' (#71) Co-authored-by: Sourcery AI <> * Rework digraph to use LEMON - Changed internal handling of nodes from std::string to int. This requires converting nodes to integers before passing to the algorithm. Python interface unchanged - Add Bellman-Ford to preprocessing (still WIP) - Run benchmarks again for #65 and #66 * Add sudo to install script for linux * Add lemon include dir explicitly * Remove quotations for SWIG * Update README.md * Specify windows lemon installation dir * Add check step to lemon installation * Add explicit types for preprocessing, remove lemon check * Cast reverse digraph explicitly * Fix lambda expression to correct type * Remove unused member (indicator of primal bound) * Add lemon to test libraries * Link lemon with bidirectional * Add lemon license, makefile and update docker build * Fix #69, clean up tests * Update docs, fix #68 * Update docs and workflows * Add dev requirement Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com>
torressa · May 4, 2021 · 432ee0c · 432ee0c
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diff --git a/.dockerignore b/.dockerignore
@@ -1,4 +1,6 @@
-build/*
+build*/*
+examples/
+
 
 *.pyc
 *.sw*
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -11,28 +11,14 @@ assignees: ''
 A clear and concise description of what the bug is.
 
 **To Reproduce**
-Steps to reproduce the behavior:
-1. Go to '...'
-2. Click on '....'
-3. Scroll down to '....'
-4. See error
+Steps to reproduce the behavior. Include minimal working example if available.
 
 **Expected behavior**
 A clear and concise description of what you expected to happen.
 
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
-
 **Desktop (please complete the following information):**
- - OS: [e.g. iOS]
- - Browser [e.g. chrome, safari]
- - Version [e.g. 22]
-
-**Smartphone (please complete the following information):**
- - Device: [e.g. iPhone6]
- - OS: [e.g. iOS8.1]
- - Browser [e.g. stock browser, safari]
- - Version [e.g. 22]
+ - OS: [e.g. Linux, Windows, ...]
+ - Version [e.g. v1.0.0-alpha]
 
-**Additional context**
-Add any other context about the problem here.
+**Suggestions**
+How would you suggest the problem be fixed?
diff --git a/.github/workflows/macos_cpp.yml b/.github/workflows/macos_cpp.yml
@@ -7,6 +7,11 @@ jobs:
     runs-on: macos-latest
     steps:
     - uses: actions/checkout@v2
+    - name: Install LEMON
+      run: |
+        cp tools/docker/scripts/install_lemon .
+        chmod u+x install_lemon
+        ./install_lemon
     - name: Configure
       run: cmake -S . -Bbuild -DBUILD_TESTING=ON -DCMAKE_BUILD_TYPE=Release -DBUILD_PYTHON=OFF -DBUILD_SHARED_LIBS=OFF
     - name: Build

diff --git a/.github/workflows/macos_python.yml b/.github/workflows/macos_python.yml
@@ -12,6 +12,11 @@ jobs:
       - uses: actions/checkout@v2
       - name: Swig install
         run: brew install swig
+      - name: Install LEMON
+        run: |
+          cp tools/docker/scripts/install_lemon .
+          chmod u+x install_lemon
+          ./install_lemon
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -1,9 +1,9 @@
 name: PyPI Release
 
 on:
-  push:
-    branches:
-      - master
+  release:
+    types:
+      - published
 
 
 #  TODO add windows as per:
@@ -21,6 +21,11 @@ jobs:
       - uses: actions/checkout@v2
       - name: Swig install
         run: brew install swig
+      - name: Install LEMON
+        run: |
+          cp tools/docker/scripts/install_lemon .
+          chmod u+x install_lemon
+          ./install_lemon
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
@@ -68,6 +73,14 @@ jobs:
           echo "$((Get-Item .).FullName)/swigwin-4.0.2" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
       - name: Check swig
         run: swig -version
+      - name: Install LEMON 1.3.1
+        run: |
+          (New-Object System.Net.WebClient).DownloadFile("http://lemon.cs.elte.hu/pub/sources/lemon-1.3.1.zip","lemon-1.3.1.zip");
+          Expand-Archive .\lemon-1.3.1.zip .;
+          cd lemon-1.3.1;
+          cmake -S. -Bbuild -G "Visual Studio 16 2019" -DCMAKE_BUILD_TYPE=Release -DLEMON_ENABLE_GLPK=NO -DLEMON_ENABLE_COIN=NO -DLEMON_ENABLE_ILOG=NO;
+          cmake --build build --config Release --target ALL_BUILD -- /verbosity:normal /maxcpucounte;
+          cmake --build build --config Release --target INSTALL -- /verbosity:normal /maxcpucount
       - name: Configure
         run: cmake -S. -Bbuild -G "Visual Studio 16 2019" -DCMAKE_BUILD_TYPE=Release -DBUILD_PYTHON=ON -DBUILD_TESTING=ON -DPython3_ROOT_DIR=$env:pythonLocation -DPython_ROOT_DIR=$env:pythonLocation -DPython3_FIND_STRATEGY=LOCATION -DPython3_FIND_REGISTRY=LAST
       - name: Build

diff --git a/.github/workflows/ubuntu_cpp.yml b/.github/workflows/ubuntu_cpp.yml
@@ -7,6 +7,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
+    - name: Install LEMON
+      run: |
+        cp tools/docker/scripts/install_lemon .
+        chmod u+x install_lemon
+        sudo ./install_lemon
     - name: Configure
       run: cmake -S . -Bbuild -DBUILD_TESTING=ON -DCMAKE_BUILD_TYPE=Release -DBUILD_PYTHON=OFF -DBUILD_SHARED_LIBS=OFF
     - name: Build

diff --git a/.github/workflows/ubuntu_docs.yml b/.github/workflows/ubuntu_docs.yml
@@ -20,7 +20,11 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: 3.8
-
+      - name: Install LEMON
+        run: |
+          cp tools/docker/scripts/install_lemon .
+          chmod u+x install_lemon
+          sudo ./install_lemon
       - name: Configure
         run: cmake -S . -Bbuild -DBUILD_TESTING=ON -DBUILD_PYTHON=ON -DBUILD_SHARED_LIBS=ON
       - name: Install rtds-action

diff --git a/.github/workflows/ubuntu_python.yml b/.github/workflows/ubuntu_python.yml
@@ -14,6 +14,11 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Install LEMON
+        run: |
+          cp tools/docker/scripts/install_lemon .
+          chmod u+x install_lemon
+          sudo ./install_lemon
       - name: Configure
         run: |
           echo $pythonLocation

diff --git a/.github/workflows/windows_cpp.yml b/.github/workflows/windows_cpp.yml
@@ -13,6 +13,14 @@ jobs:
         (New-Object System.Net.WebClient).DownloadFile("http://prdownloads.sourceforge.net/swig/swigwin-4.0.2.zip","swigwin-4.0.2.zip");
         Expand-Archive .\swigwin-4.0.2.zip .;
         echo "$((Get-Item .).FullName)/swigwin-4.0.2" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+    - name: Install LEMON 1.3.1
+      run: |
+        (New-Object System.Net.WebClient).DownloadFile("http://lemon.cs.elte.hu/pub/sources/lemon-1.3.1.zip","lemon-1.3.1.zip");
+        Expand-Archive .\lemon-1.3.1.zip .;
+        cd lemon-1.3.1;
+        cmake -S. -Bbuild -G "Visual Studio 16 2019" -DCMAKE_BUILD_TYPE=Release -DLEMON_ENABLE_GLPK=NO -DLEMON_ENABLE_COIN=NO -DLEMON_ENABLE_ILOG=NO;
+        cmake --build build --config Release --target ALL_BUILD -- /verbosity:normal /maxcpucounte;
+        cmake --build build --config Release --target INSTALL -- /verbosity:normal /maxcpucount
     - name: Check swig
       run: swig -version
     - name: Check cmake

diff --git a/.github/workflows/windows_python.yml b/.github/workflows/windows_python.yml
@@ -24,6 +24,14 @@ jobs:
         echo "$((Get-Item .).FullName)/swigwin-4.0.2" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
     - name: Check swig
       run: swig -version
+    - name: Install LEMON 1.3.1
+      run: |
+        (New-Object System.Net.WebClient).DownloadFile("http://lemon.cs.elte.hu/pub/sources/lemon-1.3.1.zip","lemon-1.3.1.zip");
+        Expand-Archive .\lemon-1.3.1.zip .;
+        cd lemon-1.3.1;
+        cmake -S. -Bbuild -G "Visual Studio 16 2019" -DCMAKE_BUILD_TYPE=Release -DLEMON_ENABLE_GLPK=NO -DLEMON_ENABLE_COIN=NO -DLEMON_ENABLE_ILOG=NO;
+        cmake --build build --config Release --target ALL_BUILD -- /verbosity:normal /maxcpucounte;
+        cmake --build build --config Release --target INSTALL -- /verbosity:normal /maxcpucount
     - name: Configure
       run: cmake -S. -Bbuild -G "Visual Studio 16 2019" -DCMAKE_BUILD_TYPE=Release -DBUILD_PYTHON=ON -DBUILD_TESTING=ON -DPython3_ROOT_DIR=$env:pythonLocation -DPython_ROOT_DIR=$env:pythonLocation -DPython3_FIND_STRATEGY=LOCATION -DPython3_FIND_REGISTRY=LAST
     - name: Build

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -3,7 +3,7 @@ version: 2
 python:
   version: 3.7
   install:
-    - requirements: docs/requirements.txt
+    - requirements: docs/requirements.dev.txt
 
 submodules:
   exclude: all
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [unreleased]
 
+## [v1.0.0]
+
+### Changed
+
+ - Graph implementation replaced with [LEMON](https://lemon.cs.elte.hu/trac/lemon). This brings significant improvement.
+
+### Added
+ - Benchmarks against boost's r_c_shortest_paths (#65)
+
+### Fixed
+ - Issues #66, #68, #69, #72
+
+## [v1.0.0-alpha]
+
 ### Changed
 
 Rewrite of the bidirectional algorithm in C++ interfaced with Python using SWIG.
@@ -236,7 +250,9 @@ path using `networkx.shortest_simple_paths`.
 - Docstring modifications to include maths.
 - Updated README.
 
-[unreleased]: https://github.com/torressa/cspy/compare/v0.1.2...HEAD
+[unreleased]: https://github.com/torressa/cspy/compare/v1.0.0...HEAD
+[v1.0.0]: https://github.com/torressa/cspy/compare/v1.0.0-alpha...v1.0.0
+[v1.0.0-alpha]: https://github.com/torressa/cspy/compare/v0.1.2...v1.0.0-alpha
 [v0.1.2]: https://github.com/torressa/cspy/compare/v0.1.1...v0.1.2
 [v0.1.1]: https://github.com/torressa/cspy/compare/v0.1.0...v0.1.1
 [v0.1.0]: https://github.com/torressa/cspy/compare/v0.0.14...v0.1.0

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -43,7 +43,6 @@ endif()
 project(
   cspy
   VERSION 1.0.0
-  DESCRIPTION alpha
   LANGUAGES CXX)
 message(STATUS "project: ${PROJECT_NAME}")
 message(STATUS "version: ${PROJECT_VERSION}")
@@ -112,6 +111,19 @@ message(STATUS "Build Python: ${BUILD_PYTHON}")
 # option(BUILD_DOTNET "Build .NET Library" OFF) message(STATUS "Build Java:
 # ${BUILD_JAVA}") message(STATUS "Build .Net: ${BUILD_DOTNET}")
 
+include(FetchContent)
+set(FETCHCONTENT_QUIET OFF)
+
+# TODO: download and install lemon with FetchContent
+
+# FetchContent_Declare(lemon URL
+# http://lemon.cs.elte.hu/pub/sources/lemon-1.3.1.tar.gz)
+# option(LEMON_ENABLE_GLPK NO) option(LEMON_ENABLE_COIN NO)
+# option(LEMON_ENABLE_ILOG NO) option(LEMON_ENABLE_SOPLEX NO)
+# FetchContent_MakeAvailable(lemon)
+
+find_package(LEMON REQUIRED)
+
 enable_testing()
 include(cpp)
 
@@ -127,12 +139,11 @@ endif()
 include(python)
 
 if(NOT BUILD_PYTHON)
-  # Prevent overriding the parent project's compiler/linker settings on Windows
   set(FETCHCONTENT_QUIET OFF)
+  # Prevent overriding the parent project's compiler/linker settings on Windows
   set(gtest_force_shared_crt
       ON
       CACHE BOOL "" FORCE)
-  include(FetchContent)
   FetchContent_Declare(
     googletest
     GIT_REPOSITORY https://github.com/google/googletest.git

diff --git a/Makefile b/Makefile
@@ -0,0 +1,29 @@
+# Run unit tests
+all:
+	cmake -S . -Bbuild -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=ON
+	cmake --build build --config Release --target all -v
+	cd build && ctest --verbose
+
+# Run benchmarks
+benchmark:
+	cmake -S . -Bbuild -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=ON \
+				-DBENCHMARK_TESTS=ON
+	cmake --build build --config Release --target all -v
+	cd build && ctest --verbose
+
+# Build and test python interface
+python:
+	cmake -S . -Bbuild -DCMAKE_BUILD_TYPE=Release  -DBUILD_TESTING=ON \
+    -DBUILD_PYTHON=ON -DBUILD_SHARED_LIBS=ON
+	cmake --build build --config Release --target all -v
+	cd build && ctest --verbose -R python_unittest
+
+# Run benchmarks using boost (as well as cspy)
+benchmarks_boost:
+	cmake -S . -Bbuild -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=ON \
+    -DBENCHMARK_TESTS=ON -DBENCHMARK_BOOST=ON -DBUILD_SHARED_LIBS=OFF
+	cmake --build build --config Release --target all -v
+	cd build && ctest --verbose
+
+clean:
+	rm -rf build
diff --git a/README.md b/README.md
@@ -153,31 +153,43 @@ void wrap() {
 - [`jpath`](examples/jpath) : Simple example showing the necessary graph adptations and the use of custom resource extension functions.
 
 
-## Running the tests
+## Building
 
-### Prerequisites
+### Docker
 
-- Docker, docker-compose
+Using docker, docker-compose is the easiest way.
 
 To run the tests first, clone the repository into a path in your machine `~/path/newfolder` by running
 
 ```none
 git clone https://github.com/torressa/cspy.git ~/path/newfolder
 ```
-### Running the Cpp tests
+
+#### Running the Cpp tests
 
 ```
 cd ~/path/newfolder/tools/dev
 ./build
 ```
 
-### Running the Python tests
+#### Running the Python tests
 
 ```
 cd ~/path/newfolder/tools/dev
 ./build -c -p
 ```
 
+### Locally
+
+Requirements:
+
+- CMake (>=v3.14)
+- Standard C++ toolchain
+- [LEMON](https://lemon.cs.elte.hu/trac/lemon) installed (see [`tools/docker/scripts/install_lemon`](tools/docker/scripts/install_lemon))
+- Python (>=3.6)
+
+Then use the [`Makefile`] e.g. `make` in the root dir runs the unit tests
+
 ## License
 
 This project is licensed under the MIT License - see the [LICENSE.txt](LICENSE.txt) file for details.
@@ -203,7 +215,7 @@ After that feel free to send a pull request.
 
 If you have a question or need help, feel free to raise an issue explaining it.
 
-Alternatively, email me at `[email protected]`.
+Alternatively, email me at `[email protected]`.
 
 ## Citing