Updating build infrastructure (#161)

* Updating build infrastructure

* cibuildwheel tag name

* skip all 32bit builds

Author: dfm

.github/workflows/tests.yml

@@ -14,16 +14,21 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: [ubuntu-latest]
+        include:
+          - python-version: "3.10"
+            os: macos-latest
+          - python-version: "3.10"
+            os: windows-latest
     steps:
       - name: Clone the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           submodules: recursive
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -38,12 +43,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Clone the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           submodules: recursive
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
       - name: Install dependencies
@@ -60,29 +65,29 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-10.15]
+        os: [ubuntu-latest, windows-latest, macos-latest]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: true
           fetch-depth: 0
-      - uses: pypa/cibuildwheel@2.5.0
+      - uses: pypa/cibuildwheel@v2.16.2
         env:
-          CIBW_SKIP: "*-win32 *-manylinux_i686"
+          CIBW_SKIP: "*-win32 *_i686"
           CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           path: ./wheelhouse/*.whl
 
   build_sdist:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: true
           fetch-depth: 0
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           python-version: "3.9"
@@ -91,7 +96,7 @@ jobs:
           python -m pip install -U pip
           python -m pip install -U build
           python -m build --sdist .
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           path: dist/*.tar.gz
 
@@ -100,12 +105,12 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist
 
-      - uses: pypa/gh-action-pypi-publish@v1.4.2
+      - uses: pypa/gh-action-pypi-publish@v1.8.10
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

CMakeLists.txt

@@ -0,0 +1,16 @@
+cmake_minimum_required(VERSION 3.15...3.26)
+project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
+
+set(PYBIND11_NEWPYTHON ON)
+find_package(pybind11 CONFIG REQUIRED)
+
+include_directories(
+  "src/george/include"
+  "vendor/eigen"
+)
+
+pybind11_add_module(kernel_interface "src/george/kernel_interface.cpp")
+install(TARGETS kernel_interface LIBRARY DESTINATION .)
+
+pybind11_add_module(_hodlr "src/george/solvers/_hodlr.cpp")
+install(TARGETS _hodlr LIBRARY DESTINATION ./solvers)

pyproject.toml

@@ -1,6 +1,24 @@
+[project]
+name = "george"
+description = "Blazingly fast Gaussian Processes for regression."
+readme = "README.rst"
+authors = [{ name = "Daniel Foreman-Mackey", email = "[email protected]" }]
+requires-python = ">=3.7"
+license = { file = "LICENSE" }
+urls = { Homepage = "https://github.com/dfm/george" }
+dependencies = ["numpy", "scipy"]
+dynamic = ["version"]
+
 [build-system]
-requires = ["setuptools>=40.6.0", "wheel", "setuptools_scm[toml]", "pybind11"]
-build-backend = "setuptools.build_meta"
+requires = ["scikit-build-core", "pybind11"]
+build-backend = "scikit_build_core.build"
+
+[tool.scikit-build]
+metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
+sdist.include = ["src/george/george_version.py"]
+wheel.install-dir = "george"
+minimum-version = "0.5"
+build-dir = "build/{wheel_tag}"
 
 [tool.setuptools_scm]
 write_to = "src/george/george_version.py"

scripts/compile_kernels.py

@@ -0,0 +1,39 @@
+import os
+
+import yaml
+from jinja2 import Template
+
+
+def compile_kernels(fns):
+    template_dir = "templates"
+    output_dir = os.path.join("src", "george")
+
+    with open(os.path.join(template_dir, "parser.h")) as f:
+        PARSER_TEMPLATE = Template(f.read())
+    with open(os.path.join(template_dir, "kernels.h")) as f:
+        CPP_TEMPLATE = Template(f.read())
+    with open(os.path.join(template_dir, "kernels.py")) as f:
+        PYTHON_TEMPLATE = Template(f.read())
+
+    specs = []
+    for i, fn in enumerate(fns):
+        with open(fn, "r") as f:
+            spec = yaml.load(f.read(), Loader=yaml.FullLoader)
+        print("Found kernel '{0}'".format(spec["name"]))
+        spec["index"] = i
+        spec["reparams"] = spec.get("reparams", {})
+        specs.append(spec)
+    print("Found {0} kernel specifications".format(len(specs)))
+
+    fn = os.path.join(output_dir, "include", "george", "parser.h")
+    with open(fn, "w") as f:
+        print("Saving parser to '{0}'".format(fn))
+        f.write(PARSER_TEMPLATE.render(specs=specs))
+    fn = os.path.join(output_dir, "include", "george", "kernels.h")
+    with open(fn, "w") as f:
+        print("Saving C++ kernels to '{0}'".format(fn))
+        f.write(CPP_TEMPLATE.render(specs=specs))
+    fn = os.path.join(output_dir, "kernels.py")
+    with open(fn, "w") as f:
+        print("Saving Python kernels to '{0}'".format(fn))
+        f.write(PYTHON_TEMPLATE.render(specs=specs))