Merge branch 'cmake-build'

.github/workflows/package.yml

@@ -257,22 +257,22 @@ jobs:
       uses: actions/checkout@v4
       with:
         submodules: true
-    - name: Set up Python 3.10
+    - name: Set up Python 3.12
       uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: 3.12
     - name: Download source distribution
       uses: actions/download-artifact@v4
       with:
         name: sdist
         path: dist/
         merge-multiple: true
     - name: Extract package version
-      run: "echo PKGVER=$(python setup.py --version) >> $GITHUB_ENV"
+      run: "echo PKGVER=$( grep 'version =' pyproject.toml | cut -d\\\" -f2 ) >> $GITHUB_ENV"
     - name: Compute SHA256 of source distribution
       run: "echo SHA256=$(sha256sum dist/pyhmmer-${{ env.PKGVER }}.tar.gz | cut -f1 -d' ') >> $GITHUB_ENV"
     - name: Generate PKGBUILD
-      run: 'sed -e "s/%pkgver/${{ env.PKGVER }}/g" -e "s/%sha256sum/${{ env.SHA256 }}/g" pkg/aur/PKGBUILD.in > pkg/aur/PKGBUILD'
+      run: 'sed -e "s/%pkgver/${{ github.ref }}/g" -e "s/%sha256sum/${{ env.SHA256 }}/g" pkg/aur/PKGBUILD.in > pkg/aur/PKGBUILD'
     - name: Update package
       uses: KSXGitHub/github-actions-deploy-aur@v2.7.2
       with:

.github/workflows/requirements.txt

@@ -1,7 +1,7 @@
 # build dependencies
-setuptools >=46.4
-wheel >=0.34.0
 cython ~=3.0
+scikit-build-core
+ninja
 
 # run dependencies
 psutil ~=5.0

.github/workflows/test.yml

@@ -60,11 +60,11 @@ jobs:
     - 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 --debug -j0
+      run: pip install -vv -e . --no-build-isolation
     - name: Install test requirements
-      run: python -m pip install -r pyhmmer/tests/requirements.txt
+      run: python -m pip install -r src/pyhmmer/tests/requirements.txt
     - name: Test with coverage
-      run: python -m coverage run -m unittest discover -vv
+      run: python -m coverage run -m unittest pyhmmer.tests -vv
     - name: Upload to Codecov
       if: matrix.python-impl == 'CPython'
       uses: codecov/codecov-action@v3
@@ -164,12 +164,12 @@ jobs:
     - name: Install Python requirements
       run: python -m pip install -r .github/workflows/requirements.txt
     - name: Build C extension
-      run: arch -x86_64 python setup.py build_ext --inplace --debug
+      run: arch -x86_64 pip install -vv -e . --no-build-isolation
     - name: Install test requirements
-      run: python -m pip install -r pyhmmer/tests/requirements.txt
+      run: python -m pip install -r src/pyhmmer/tests/requirements.txt
       if: matrix.python-impl == 'CPython'
     - name: Test with coverage
-      run: python -m coverage run -m unittest discover -vv
+      run: python -m coverage run -m unittest pyhmmer.tests -vv
     - name: Upload to Codecov
       uses: codecov/codecov-action@v4
       if: matrix.python-impl == 'CPython'

.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 +1,52 @@
+cmake_minimum_required(VERSION 3.20)
+project(${SKBUILD_PROJECT_NAME} VERSION ${SKBUILD_PROJECT_VERSION} LANGUAGES C)
+
+set(BUILD_SHARED_LIBS OFF)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+set_property(GLOBAL PROPERTY PYTHON_EXTENSIONS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
+
+# --- Detect SIMD --------------------------------------------------------------
+
+include("src/scripts/cmake/FindNEON.cmake")
+include("src/scripts/cmake/FindSSE2.cmake")
+include("src/scripts/cmake/FindSSE4.cmake")
+include("src/scripts/cmake/FindVMX.cmake")
+include("src/scripts/cmake/Destatic.cmake")
+include("src/scripts/cmake/CythonExtension.cmake")
+
+if(HAVE_SSE4)
+    set(eslENABLE_SSE4 true)
+    string(STRIP "${SSE4_C_FLAGS}" IMPL_FLAGS)
+    if(IMPL_FLAGS)
+        add_compile_options(${IMPL_FLAGS})
+    endif()
+endif()
+
+if(HAVE_SSE2)
+    set(eslENABLE_SSE true)
+    set(HMMER_IMPL "SSE")
+    string(STRIP "${SSE2_C_FLAGS}" IMPL_FLAGS)
+elseif(HAVE_NEON)
+    set(eslENABLE_NEON true)
+    set(HMMER_IMPL "NEON")
+    string(STRIP "${NEON_C_FLAGS}" IMPL_FLAGS)
+elseif(HAVE_VMX)
+    set(eslENABLE_VMX true)
+    set(HMMER_IMPL "VMX")
+    string(STRIP "${VMX_C_FLAGS}" IMPL_FLAGS)
+else()
+    message(FATAL_ERROR "Unsupported platform, none of SSE2, NEON or AltiVec available.")
+endif()
+
+if(IMPL_FLAGS)
+    add_compile_options(${IMPL_FLAGS})
+endif()
+
+# --- Setup include folders ----------------------------------------------------
+
+set(CYTHON_HEADERS_DIR ${CMAKE_CURRENT_LIST_DIR}/include)
+
+# --- Compile source code ------------------------------------------------------
+
+add_subdirectory("src")

pkg/aur/PKGBUILD.in

@@ -8,7 +8,7 @@ pkgdesc="Cython bindings and Python interface to HMMER3"
 url="https://github.com/althonos/pyhmmer"
 arch=('i686' 'pentium4' 'x86_64' 'armv7h' 'aarch64')
 license=("MIT")
-makedepends=('python-setuptools' 'cython' 'python-build' 'python-installer')
+makedepends=('cython' 'python-build' 'python-installer')
 depends=('python' 'python-psutil')
 source=("https://files.pythonhosted.org/packages/source/${_name::1}/$_name/$_name-$pkgver.tar.gz")
 sha256sums=(%sha256sum)

pyproject.toml

@@ -0,0 +1,112 @@
+[build-system]
+requires = ["scikit-build-core", "cython >= 3.0"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "pyhmmer"
+version = "0.10.15"
+description = "Cython bindings and Python interface to HMMER3."
+readme = "README.md"
+requires-python = ">=3.7"
+license = { file = "COPYING" }
+authors = [
+  { name = "Martin Larralde", email = "martin.larralde@embl.de" },
+]
+# platform = "posix"
+keywords = ["bioinformatics", "profile", "HMM", "sequence", "pfam"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: POSIX",
+    "Programming Language :: C",
+    "Programming Language :: Cython",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+    "Typing :: Typed",
+]
+dependencies = [
+    "psutil ~=6.0"
+]
+
+[project.urls]
+"Documentation" = "https://pyhmmer.readthedocs.io/en/stable/"
+"Bug Tracker" = "https://github.com/althonos/pyhmmer/issues"
+"Changelog" = "https://github.com/althonos/pyhmmer/blob/master/CHANGELOG.md"
+"Coverage" = "https://codecov.io/gh/althonos/pyhmmer/"
+"Builds" = "https://github.com/althonos/pyhmmer/actions"
+"Paper" = "https://doi.org/10.1093/bioinformatics/btad214"
+"PyPI" = "https://pypi.org/project/pyhmmer"
+
+[project.optional-dependencies]
+test = ["importlib-resources ; python_version < '3.9'"]
+
+[tool.scikit-build]
+build-dir = "build/{build_type}"
+editable.rebuild = true
+editable.verbose = false
+
+[[tool.scikit-build.generate]]
+path = "src/pyhmmer/_version.py"
+template = '__version__ = "${version}"'
+location = 'source'
+
+[[tool.scikit-build.overrides]]
+if.state = "editable"
+cmake.build-type = "Debug"
+
+[[tool.scikit-build-overrides]]
+if.env.SCCACHE = true
+cmake.define.CMAKE_C_COMPILER_LAUNCHER = "sccache"
+cmake.define.CMAKE_CXX_COMPILER_LAUNCHER = "sccache"
+
+[[tool.scikit-build-overrides]]
+if.env.MOLD = true
+cmake.define.CMAKE_LINKER_TYPE = "mold"
+
+#[tool.coverage.run]
+#plugins = ["Cython.Coverage"]
+
+[tool.coverage.report]
+include = ["src/pyhmmer/*"]
+omit = ["src/pyhmmer/tests/*"]
+show_missing = true
+exclude_lines = [
+    "pragma: no cover",
+    "if typing.TYPE_CHECKING:",
+    "@abc.abstractmethod",
+    "@abc.abstractproperty",
+    "raise NotImplementedError",
+    "return NotImplemented",
+    "raise UnexpectedError",
+    "raise AllocationError",
+]
+
+[tool.coverage.paths]
+source = [
+    "src/pyhmmer/",
+    "build/Debug/src/pyhmmer/",
+]
+
+[tool.mypy]
+disallow_any_decorated = true
+disallow_any_generics = true
+disallow_any_unimported = false
+disallow_subclassing_any = false
+disallow_untyped_calls = true
+disallow_untyped_defs = true
+ignore_missing_imports = true
+warn_unused_ignores = true
+warn_return_any = true
+
+["tool.mypy-pyhmmer.tests.*"]
+ignore_errors = true