Merge branch 'cmake-build'

.github/workflows/requirements.txt

@@ -1,8 +1,6 @@
-coverage ~=6.0 ; sys_platform != 'win32'
+# coverage ~=7.0
 cython ~=3.0
-semantic-version ~=2.10
-wheel
-auditwheel
-setuptools >=46.4.0
+# semantic-version ~=2.10
+scikit-build-core
 importlib-resources ; python_version < '3.9'
-scoring-matrices ~=0.2.0
+scoring-matrices ~=0.3.0

.github/workflows/test.yml

@@ -8,7 +8,7 @@ jobs:
 
   test_linux:
     name: Test (Linux)
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     env:
       OS: Linux
     strategy:
@@ -27,12 +27,15 @@ jobs:
         - python-version: '3.10'
           python-release: v3.10
           python-impl: CPython
-        - python-version: '3.11'
+        - python-version: 3.11
           python-release: v3.11
           python-impl: CPython
-        - python-version: '3.12'
+        - python-version: 3.12
           python-release: v3.12
           python-impl: CPython
+        - python-version: 3.13
+          python-release: v3.13
+          python-impl: CPython
         - python-version: pypy-3.7
           python-release: v3.7
           python-impl: PyPy
@@ -54,26 +57,26 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install CI requirements
+    - name: Update pip
+      run: python -m pip install -U pip wheel setuptools
+    - name: Install Python requirements
       run: python -m pip install -r .github/workflows/requirements.txt
-    - name: Install test requirements
-      run: python -m pip install -r pyfamsa/tests/requirements.txt
-    - name: Build C extension in debug mode
-      run: python setup.py build_ext --inplace --debug
-    - name: Test with coverage
-      run: python -m coverage run -m unittest discover -vv
-    - name: Upload to Codecov
-      if: matrix.python-impl == 'CPython'
-      uses: codecov/codecov-action@v4
-      with:
-        flags: ${{ matrix.python-impl }},${{ matrix.python-release }},${{ env.OS }}
-        name: test-python-${{ matrix.python-version }}
-        fail_ci_if_error: false
-        token: ${{ secrets.CODECOV_TOKEN }}
+    - name: Build extension in debug mode
+      run: python -m pip install -v -e . --no-build-isolation
+    - name: Test extension
+      run: python -m unittest pyfamsa.tests -vv
+    # - name: Upload to Codecov
+    #   if: matrix.python-impl == 'CPython'
+    #   uses: codecov/codecov-action@v3
+    #   with:
+    #     flags: ${{ matrix.python-impl }},${{ matrix.python-release }},${{ env.OS }}
+    #     name: test-python-${{ matrix.python-version }}
+    #     fail_ci_if_error: true
+    #     token: ${{ secrets.CODECOV_TOKEN }}
 
   test_osx:
     name: Test (OSX)
-    runs-on: macos-12
+    runs-on: macos-13
     env:
       OS: OSX
     strategy:
@@ -98,6 +101,9 @@ jobs:
         - python-version: '3.12'
           python-release: v3.12
           python-impl: CPython
+        - python-version: '3.13'
+          python-release: v3.13
+          python-impl: CPython
         - python-version: pypy-3.7
           python-release: v3.7
           python-impl: PyPy
@@ -119,22 +125,26 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install CI requirements
+    - name: Setup deployment target
+      shell: bash
+      if: ${{ startsWith(matrix.python-version, 'pypy') || matrix.python-version == '3.11' || matrix.python-version == '3.12' }}
+      run: echo "MACOSX_DEPLOYMENT_TARGET=10.12" >> $GITHUB_ENV
+    - name: Update pip
+      run: python -m pip install -U pip wheel setuptools
+    - name: Install Python requirements
       run: python -m pip install -r .github/workflows/requirements.txt
-    - name: Install test requirements
-      run: python -m pip install -r pyfamsa/tests/requirements.txt
-    - name: Build C extension in debug mode
-      run: python setup.py build_ext --inplace --debug
-    - name: Test with coverage
-      run: python -m coverage run -m unittest discover -vv
-    - name: Upload to Codecov
-      if: matrix.python-impl == 'CPython'
-      uses: codecov/codecov-action@v4
-      with:
-        flags: ${{ matrix.python-impl }},${{ matrix.python-release }},${{ env.OS }}
-        name: test-python-${{ matrix.python-version }}
-        fail_ci_if_error: false
-        token: ${{ secrets.CODECOV_TOKEN }}
+    - name: Build extension in debug mode
+      run: python -m pip install -v -e . --no-build-isolation
+    - name: Test extension
+      run: python -m unittest pyfamsa.tests -vv
+    # - name: Upload to Codecov
+    #   if: matrix.python-impl == 'CPython'
+    #   uses: codecov/codecov-action@v3
+    #   with:
+    #     flags: ${{ matrix.python-impl }},${{ matrix.python-release }},${{ env.OS }}
+    #     name: test-python-${{ matrix.python-version }}
+    #     fail_ci_if_error: true
+    #     token: ${{ secrets.CODECOV_TOKEN }}
 
   test_windows:
     name: Test (Windows)
@@ -163,6 +173,9 @@ jobs:
         - python-version: '3.12'
           python-release: v3.12
           python-impl: CPython
+        - python-version: '3.13'
+          python-release: v3.13
+          python-impl: CPython
         - python-version: pypy-3.7
           python-release: v3.7
           python-impl: PyPy
@@ -185,9 +198,11 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
         architecture: x64
+    - name: Update pip
+      run: python -m pip install -U pip wheel setuptools
     - name: Install Python requirements
       run: python -m pip install -r .github/workflows/requirements.txt
-    - name: Build C extension
-      run: python setup.py build_ext --inplace
-    - name: Test without coverage
-      run: python -m unittest discover -vv
+    - name: Build extension in debug mode
+      run: python -m pip install -v . --no-build-isolation
+    - name: Test extension
+      run: python -m unittest pyfamsa.tests -vv

.gitignore

@@ -97,7 +97,6 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
-pyproject.toml
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

CMakeLists.txt

@@ -0,0 +1,45 @@
+cmake_minimum_required(VERSION 3.20)
+project(${SKBUILD_PROJECT_NAME} VERSION ${SKBUILD_PROJECT_VERSION} LANGUAGES C CXX)
+
+set(BUILD_SHARED_LIBS OFF)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED TRUE)
+
+message(STATUS "Building ${SKBUILD_PROJECT_NAME} for ${CMAKE_SYSTEM_PROCESSOR}")
+
+# --- Setup include folders ----------------------------------------------------
+
+set_property(GLOBAL PROPERTY PYTHON_EXTENSIONS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
+set(CYTHON_HEADERS_DIR ${CMAKE_CURRENT_LIST_DIR}/include)
+
+# --- Add global C++ flags -----------------------------------------------------
+
+include(CheckCXXCompilerFlag)
+
+check_cxx_compiler_flag(-funroll-loops HAVE_UNROLL_LOOPS)
+if(HAVE_UNROLL_LOOPS)
+    add_compile_options(-funroll-loops)
+endif()
+
+add_definitions(-DOLD_ATOMIC_FLAG -DNO_PROFILE_PAR)
+
+if(WIN32)
+    add_definitions(-D_WIN32)
+endif()
+
+# --- Add scripts for Cython ---------------------------------------------------
+
+include("src/scripts/cmake/FindAVX1.cmake")
+include("src/scripts/cmake/FindAVX2.cmake")
+# include("src/scripts/cmake/FindAVX512.cmake")
+include("src/scripts/cmake/FindNEON.cmake")
+include("src/scripts/cmake/FindPOPCNT.cmake")
+include("src/scripts/cmake/FindSSE2.cmake")
+include("src/scripts/cmake/FindSSE4.cmake")
+include("src/scripts/cmake/CythonExtension.cmake")
+
+# --- Compile code -------------------------------------------------------------
+
+add_subdirectory("src")

CONTRIBUTING.md

@@ -20,13 +20,13 @@ the standard library. Running them requires the extension to be built
 locally:
 
 ```console
-$ python setup.py build_ext --debug --inplace
+$ python -m pip install -v -e . --no-build-isolation
 $ python -m unittest discover -vv
 ```
 
 ## Coding guidelines
 
-This project targets Python 3.6 or later.
+This project targets Python 3.7 or later.
 
 Python objects should be typed; since it is not supported by Cython,
 you must manually declare types in type stubs (`.pyi` files). In Python

README.md

@@ -43,16 +43,16 @@ the following advantages:
 - **friendly interface**: The different guide tree build methods and
   heuristics can be selected from the Python code with a simple keyword
   argument when configuring a new [`Aligner`](https://pyfamsa.readthedocs.io/en/stable/api/aligner.html#pyfamsa.Aligner).
-- **custom scoring matrices**: You can use any custom scoring matrix from 
+- **custom scoring matrices**: You can use any custom scoring matrix from
   the [`scoring-matrices`](https://pypi.org/project/scoring-matrices) library
-  in addition to the default MIQS to score the alignment. 
+  in addition to the default MIQS to score the alignment.
 
 ## 🔧 Installing
 
 PyFAMSA can be installed directly from [PyPI](https://pypi.org/project/pyfamsa/),
-which hosts some pre-built wheels for the x86-64 architecture (Linux/OSX)
-and the Aarch64 architecture (Linux only), as well as the code required to
-compile from source with Cython:
+which hosts some pre-built wheels for the x86-64 and Aarch architectures
+for Linux, MacOS and Windows, as well as the code required to compile from
+source with Cython:
 ```console
 $ pip install pyfamsa
 ```
@@ -63,7 +63,7 @@ package:
 $ conda install -c bioconda pyfamsa
 ```
 
-Otherwise, have a look at the [Installation page](https://pyfamsa.readthedocs.io/en/stable/install.html) of the [online documentation](https://pyfamsa.readthedocs.io/)
+Otherwise, have a look at the [Installation page](https://pyfamsa.readthedocs.io/en/stable/guide/install.html) of the [online documentation](https://pyfamsa.readthedocs.io/)
 
 ## 💡 Example
 

patches/sequence.cpp.patch

@@ -1,7 +1,3 @@
-diff --git a/src/core/sequence.cpp b/src/core/sequence.cpp
-index 54401be..83d0f2f 100644
---- a/src/core/sequence.cpp
-+++ b/src/core/sequence.cpp
 @@ -19,6 +19,18 @@ char CGappedSequence::mapping_table[25] = "ARNDCQEGHILKMFPSTWYVBZX*";
 
 

patches/sequence.h.patch

@@ -1,7 +1,3 @@
-diff --git a/src/core/sequence.h b/src/core/sequence.h
-index ac37942..e17620e 100644
---- a/src/core/sequence.h
-+++ b/src/core/sequence.h
 @@ -32,7 +32,7 @@ public:
  	bit_vec_t *p_bit_masks;
  	uint32_t p_bv_len;