Merge pull request #6 from Battery-Intelligence-Lab/develop

Version 1.0.0-rc0

.github/dependabot.yml

@@ -0,0 +1,9 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/documentation.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout current branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Setup Pages
         uses: actions/configure-pages@v2
       - name: Build master with Jekyll

.github/workflows/draft-pdf.yml

@@ -13,7 +13,7 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Build draft PDF
         uses: openjournals/openjournals-draft-action@master
         with:

.github/workflows/macos-unit.yml

@@ -3,35 +3,38 @@ name: macOS unit
 on:
   push:
     branches:
-    #  - main
+      # - main
       - develop
   pull_request:
     branches:
       - '**'
 
 jobs:
-
   build-and-test:
     name: macOS unit
     runs-on: macos-latest
 
     steps:
-      - uses: actions/checkout@v3
-
-      - name: install openmp
-        run: brew reinstall libomp & brew link libomp --force
+      - uses: actions/checkout@v4
 
-      - name: make build directory
+      - name: Install libomp without linking
+        run: |
+          brew install libomp llvm && brew link --force libomp
+
+      - name: Make build directory
         run: mkdir build_dir
 
-      - name: cmake configure
-        run: cmake .. -DCMAKE_BUILD_TYPE=Debug -DDTWC_BUILD_TESTING=ON
+      - name: CMake configure
+        run: |
+          cmake .. -DCMAKE_BUILD_TYPE=Debug -DDTWC_BUILD_TESTING=ON
         working-directory: build_dir
 
-      - name: cmake build
-        run: cmake --build . --parallel 2
+      - name: CMake build
+        run: |
+          cmake --build . --parallel 2
         working-directory: build_dir
 
-      - name: cmake test
-        run: ctest -j2 -C Debug --output-on-failure
-        working-directory: build_dir
+      - name: CMake test
+        run: |
+          ctest -j2 -C Debug --output-on-failure
+        working-directory: build_dir

.github/workflows/ubuntu-unit.yml

@@ -1,16 +1,14 @@
-name: Ubuntu unit
-# adapted from: https://github.com/trase-cpp/trase/tree/master/.github/workflows
+name: Ubuntu unit # adapted from: https://github.com/trase-cpp/trase/tree/master/.github/workflows
 on:
   push:
     branches:
-   #   - main
+      # - main
       - develop
   pull_request:
     branches:
       - '**'
 
 jobs:
-
   build-and-test:
     name: Ubuntu unit ${{matrix.CC}}
     runs-on: ubuntu-latest
@@ -42,18 +40,25 @@ jobs:
           - CC: clang-15
             CXX: clang++-15
             compiler: clang-15 libomp-15-dev
-          # - CC: clang-16  -> we don't have these as package. 
-          #   CXX: clang++-16
-          #   compiler: clang-16
-          # - CC: clang-17
-          #   CXX: clang++-17
-          #   compiler: clang-17
+          - CC: clang-16
+            CXX: clang++-16
+            compiler: clang-16 libomp-16-dev
+          - CC: clang-17
+            CXX: clang++-17
+            compiler: clang-17 libomp-17-dev
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: update
         run: sudo apt update
 
+      - name: Install Clang 16 or 17
+        if: matrix.CC == 'clang-16' || matrix.CC == 'clang-17'
+        run: |
+          wget https://apt.llvm.org/llvm.sh
+          chmod +x llvm.sh
+          sudo ./llvm.sh $(echo "${{ matrix.CC }}" | cut -d '-' -f 2)
+
       - name: install compiler
         run: sudo apt install ${{matrix.compiler}}
 

.github/workflows/windows-unit.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: windows-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: make build directory
         run: mkdir build_dir

.gitignore

@@ -49,3 +49,4 @@ cmake-build-debug/*
 cmake-build-relwithdebinfo/*
 build/*
 bin/*
+*.egg-info/*

CHANGELOG.md

@@ -6,13 +6,12 @@ This changelog contains a non-exhaustive list of new features and notable bug-fi
 
 
 <br/><br/>
-# DTWC v0.1.0
+# DTWC v1.0.0
 
 ## New features
-* HiGHS solver is added for open-source alternative to Gurobi. 
+* HiGHS solver is added for open-source alternative to Gurobi (which is now not necessary for compilation and can be enabled by necessary flags). 
 * Command line interface is added. 
-* Documentation is improved.
-
+* Documentation is improved (Doxygen website).
 
 
 ## Notable Bug-fixes
@@ -27,9 +26,10 @@ This changelog contains a non-exhaustive list of new features and notable bug-fi
 
 ## Developer updates: 
 * The software is now being tested via Catch2 library. 
+* Dependabot is added. 
 
 <br/><br/>
-# DTWC v0.0.3
+# DTWC v0.3.0
 
 ## New features
 * UCR_test_2018 data integration for benchmarking. 
@@ -44,9 +44,9 @@ This changelog contains a non-exhaustive list of new features and notable bug-fi
 * `std::filesystem::path operator+` was unnecessary and removed. 
 
 <br/><br/>
-# DTWC v0.0.2
+# DTWC v0.2.0
 
-DTWC with a better interface for other people's use. 
+A user interface is created for other people's use. 
 
 ## New features / updates
 - Scores file with silhouette score is added. 
@@ -68,7 +68,7 @@ DTWC with a better interface for other people's use.
   * Required C++ standard is upgraded from C++17 to C++20. 
 
 <br/><br/>
-# DTWC v0.0.1
+# DTWC v0.1.0
 
 This is the initial release of DTWC. 
 

CMakeLists.txt

@@ -6,7 +6,7 @@ cmake_minimum_required(VERSION 3.21)
 # so that it works well with tools like CPM or other
 # manual dependency management
 
-project(DTWC++ VERSION "0.1.0"
+project(DTWC++ VERSION "1.0.0"
   DESCRIPTION "A C++ library for fast Dynamic Time Wrapping Clustering"
   HOMEPAGE_URL https://battery-intelligence-lab.github.io/dtw-cpp/
   LANGUAGES CXX C)
@@ -78,4 +78,15 @@ endif()
 
 if(BUILD_BENCHMARK)
   add_subdirectory(benchmark)
+endif()
+
+find_package(pybind11 QUIET)
+
+if(pybind11_FOUND)
+    pybind11_add_module(dtwcpp 
+            python/py_main.cpp)
+
+    target_link_libraries(dtwcpp PRIVATE dtwc++ project_warnings project_options armadillo)
+else()
+    message(STATUS "pybind11 not found. Skipping the dtwcpp module.")
 endif()

benchmark/UCR_dtwc.cpp

@@ -97,6 +97,9 @@ inline void UCR_2018()
     //(settings::root_folder / "data/benchmark/UCRArchive_2018/AllGestureWiimoteZ/AllGestureWiimoteZ_TEST.tsv")
 
   };
+
+  dataofInterest = UCR_list; // Comment this out to do an individual testing.
+
   size_t solved = 0;
   for (auto &file_path : dataofInterest) {
     dl.path(file_path);
@@ -108,10 +111,8 @@ inline void UCR_2018()
 
     std::cout << "Now, number " << solved << " " << file_path << " is being solved.\n";
     solved++;
-    // if (solved < 25) // We already calculated this part
-    //   continue;
 
-    if (prob.data.size() > 1000) // DOnt calculate large data it is not good. For example Crop.
+    if (prob.data.size() > 1000) // Don't calculate large data it is not good. For example Crop.
       continue;
 
     prob.set_numberOfClusters(Nc); // Nc = number of clusters.

cmake/Dependencies.cmake

@@ -55,5 +55,4 @@ function(dtwc_setup_dependencies)
     OPTIONS
     "BUILD_SMOKE_TEST OFF"
   )
-
 endfunction()

develop/TODO.md

@@ -8,13 +8,15 @@
 
 ### Current priority: 
 
+- [ ] Numpy-like arrays for multi-dimensional DTW.
 - [ ] If you accidentally compile with amd64_x86 you get bad_alloc due to the insufficient RAM in 32-bit computer. So, put a warning for that. 
 - [ ] Modernise `*.csv` reading interface, allow for rowwise or columnwise data. 
 - [x] CMake files arranging:
   - [x] HiGHS 1.6.0 does not always work. Also it does not work in debug mode due to iterator level. 
 - [ ] Commenting
 - [ ] MATLAB / Python integration
-- [ ] JOSS paper  
+ - [ ] Pybind11 usage for Python integration.
+- [x] JOSS paper  
 - [ ] Speed up the code
 - [ ] GPU programming 
 - [ ] Lighter and faster DTW cost calculation + make the band from long side so it is more accurate. 
@@ -26,8 +28,8 @@
 - [ ] Give error message if data could not be loaded. 
 - Benchmarking:
   - [x] UCR_test_2018 is continuing. 
-  - [ ] USR_dtai.py
-  - [ ] TSlearn 
+  - [x] USR_dtai.py
+  - [x] TSlearn 
   - [ ] dtwclust in R
 - [ ] Encapsulating Data and related functions in one folder. 
 - [ ] Open-source solver addition. 
@@ -38,7 +40,7 @@
 - [x] Doxygen website? 
 - [x] Remove unnecessary warping functions. 
 - [ ] Fix warnings. Especially, we should not get warnings from external libraries. 
-- [ ] Make Gurobi dependency optional. (Now it cannot be disabled. )
+- [x] Make Gurobi dependency optional. (Now it cannot be disabled. )
 - [x] Consider including Eigen library for matrix operations / linear system solution. 
 - [ ] w based DTW. 
 - [ ] Reading memoisation matrix distMat from file instead of re-calculating DTW every time. 

develop/conventions.md

@@ -3,6 +3,15 @@
 - Do not use "using" in global namespace.
 - First include standard headers then our headers.
 
+## Versioning: 
+
+We use semantic versioning with MAJOR.MINOR.PATCH where:
+
+- PATCH: Backwards compatible bug fix without introducing a new feature. 
+- MINOR: Backwards compatible new feature. 
+- MAJOR: Incompatible changes, especially on API. 
+
+See [this link](https://www.youtube.com/watch?v=xvPiZyx0cDc) for a detailed tutorial on versioning. 
 
 ### Commenting: 
 

docs/Doxyfile

@@ -48,7 +48,7 @@ PROJECT_NAME           = DTWC++
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 0.1.0
+PROJECT_NUMBER         = 1.0.0-rc0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a