Fix installation with pip

.github/workflows/python.yaml

@@ -0,0 +1,59 @@
+name: COBS Python
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  linux_build:
+    name: Build and test with Python ${{ matrix.python-version }} (Linux)
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+      fail-fast: false
+    steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Check out code for the build
+      uses: actions/checkout@v4
+      with:
+        submodules: recursive
+
+    - name: Build and test
+      run: |
+        pip install .
+        python -m unittest discover python/tests
+
+  mac_build_clang:
+    name: Build and test with Python ${{ matrix.python-version }} (macOS)
+    runs-on: macos-13
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+      fail-fast: false
+    steps:
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          brew install boost-python3
+
+      - name: Check out code for the build
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Build and test
+        run: |   
+          pip install .
+          python -m unittest discover python/tests

.gitignore

@@ -12,3 +12,7 @@ __pycache__
 cobs*.tar
 cobs*.tar.gz
 !tests/data/non_acgt_test/index.cobs_classic
+.devcontainer/
+cobs_index.egg-info
+*.so
+*.bin

.gitmodules

@@ -12,4 +12,5 @@
 	url = https://github.com/Cyan4973/xxHash.git
 [submodule "python/pybind11"]
 	path = python/pybind11
-	url = https://github.com/pybind/pybind11.git
+	url = ../../pybind/pybind11
+	branch = stable

CMakeLists.txt

@@ -65,8 +65,13 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
 if(NOOPENMP)
   message(WARNING "COMPILING WITHOUT OPENMP!")
 else()
-  set(CMAKE_C_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
+  find_package(OpenMP)
+  if(OpenMP_CXX_FOUND)
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+  else()
+    message(WARNING "OpenMP not found!")
+  endif()
 endif()
 
 # with run-time STL checks

README.md

@@ -48,13 +48,13 @@ COBS requires CMake, a C++17 compiler or the Boost.Filesystem library.
 
 To download and install COBS run:
 ```
-git clone --recursive https://github.com/bingmann/cobs.git
+git clone --recursive https://github.com/iqbal-lab-org/cobs.git
 mkdir cobs/build
 cd cobs/build
 cmake -DCMAKE_BUILD_TYPE=Release ..
 make -j4
 ```
-and optionally run `make test` to check the build.
+and optionally run `make test` to check the build. Note that to download submodules, `--recursive` has to be provided.
 
 ## OS X compilation
 

pyproject.toml

@@ -0,0 +1,5 @@
+[build-system]
+requires = ["setuptools==69.5.1", 
+      "cmake==3.29.2",
+]
+build-backend = "setuptools.build_meta"

setup.py

@@ -47,7 +47,7 @@ def build_extension(self, ext):
             build_args += ['--', '/m']
         else:
             cmake_args += ['-DCMAKE_BUILD_TYPE=' + cfg]
-            build_args += ['--', '-j2']
+            build_args += ['--']
 
         env = os.environ.copy()
         env['CXXFLAGS'] = '{} -DVERSION_INFO=\\"{}\\"'.format(