Housekeeping: build with numpy 2.0; update JAX lowering syntax; etc. (#…

…129)

* update deps

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* disable unstable test

* Don't print

* Faster building; slower running

* fast run wheels

* building

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/python.yml

@@ -43,24 +43,13 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install -U pip
-          python -m pip install -U coveralls coverage[toml] nox
+          python -m pip install -U nox
 
       - name: Run tests
         run: |
           python -m nox --non-interactive --error-on-missing-interpreter \
             --session ${{ matrix.session }}-${{ matrix.python-version }}
 
-      - name: Combine and upload coverage
-        run: |
-          python -m coverage combine
-          python -m coverage xml -i
-          python -m coveralls --service=github
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_PARALLEL: true
-          COVERALLS_FLAG_NAME: ${{matrix.os}}-${{matrix.session}}-${{matrix.python-version}}
-
-
   tests-pymc:
     runs-on: ubuntu-latest
     defaults:
@@ -88,19 +77,3 @@ jobs:
         run: |
           python -m nox --non-interactive --error-on-missing-interpreter \
             --session pymc_mamba-3.10
-
-  coverage:
-    needs: tests
-    runs-on: ubuntu-latest
-    steps:
-      - name: Setup Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.9"
-      - name: Finish coverage collection
-        run: |
-          python -m pip install -U pip
-          python -m pip install -U coveralls
-          python -m coveralls --finish
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/wheels.yml

@@ -1,24 +1,34 @@
 name: Wheels
 on:
-  release:
-    types: [published]
+  push:
+    branches:
+      - main
+    tags:
+      - "*"
+  workflow_dispatch:
+    inputs:
+      prerelease:
+        description: "Run a pre-release, testing the build"
+        required: false
+        type: boolean
+        default: false
 
 jobs:
   build_wheels:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        os:
+          - "ubuntu-22.04"
+          - "macos-12"
+          - "macos-14"
+          - "windows-latest"
     steps:
       - uses: actions/checkout@v4
         with:
           submodules: true
           fetch-depth: 0
       - uses: pypa/[email protected]
-        env:
-          CIBW_SKIP: "pp* *-win32 *-manylinux_i686 *-musllinux*"
-          CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
-          CIBW_ARCHS_MACOS: "x86_64 universal2 arm64"
       - uses: actions/upload-artifact@v4
         with:
           name: binary-${{ matrix.os }}
@@ -34,28 +44,32 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: "3.9"
-      - name: Build sdist
+          python-version: "3.10"
+      - name: Install dependencies
         run: |
           python -m pip install -U pip
-          python -m pip install -U build
-          python -m build --sdist .
+          python -m pip install -U build twine
+      - name: Build sdist
+        run: python -m build --sdist .
+      - name: Check the sdist
+        run: python -m twine check dist/*.tar.gz
       - uses: actions/upload-artifact@v4
         with:
           name: sdist
           path: dist/*.tar.gz
 
   upload_pypi:
+    environment:
+      name: pypi
+      url: https://pypi.org/p/celerite2
+    permissions:
+      id-token: write
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
-    if: github.event_name == 'release' && github.event.action == 'published'
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
     steps:
       - uses: actions/download-artifact@v4
         with:
           path: dist
           merge-multiple: true
-
       - uses: pypa/[email protected]
-        with:
-          user: __token__
-          password: ${{ secrets.pypi_password }}

CMakeLists.txt

@@ -0,0 +1,25 @@
+cmake_minimum_required(VERSION 3.15...3.27)
+project(
+    ${SKBUILD_PROJECT_NAME}
+    VERSION ${SKBUILD_PROJECT_VERSION}
+    LANGUAGES CXX)
+
+set(PYBIND11_NEWPYTHON ON)
+find_package(pybind11 CONFIG REQUIRED)
+
+include_directories(
+    "c++/include"
+    "c++/vendor/eigen"
+    "python/celerite2")
+
+pybind11_add_module(driver "python/celerite2/driver.cpp")
+target_compile_features(driver PUBLIC cxx_std_14)
+install(TARGETS driver LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME})
+
+pybind11_add_module(backprop "python/celerite2/backprop.cpp")
+target_compile_features(backprop PUBLIC cxx_std_14)
+install(TARGETS backprop LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME})
+
+pybind11_add_module(xla_ops "python/celerite2/jax/xla_ops.cpp")
+target_compile_features(xla_ops PUBLIC cxx_std_14)
+install(TARGETS xla_ops LIBRARY DESTINATION "${SKBUILD_PROJECT_NAME}/jax")

noxfile.py

@@ -1,7 +1,7 @@
 import nox
 
 ALL_PYTHON_VS = ["3.8", "3.9", "3.10"]
-TEST_CMD = ["coverage", "run", "-m", "pytest", "-v"]
+TEST_CMD = ["python", "-m", "pytest", "-v"]
 
 
 def _session_run(session, path):

pyproject.toml

@@ -1,12 +1,61 @@
-[build-system]
-requires = [
-  "setuptools>=40.6.0",
-  "wheel",
-  "setuptools_scm",
-  "oldest-supported-numpy",
-  "pybind11>=2.4",
+[project]
+name = "celerite2"
+description = "Fast and scalable Gaussian Processes in 1D"
+authors = [{ name = "Dan Foreman-Mackey", email = "[email protected]" }]
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "MIT License" }
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: MIT License",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python",
+]
+dynamic = ["version"]
+dependencies = ["numpy"]
+
+[project.optional-dependencies]
+test = ["pytest", "scipy", "celerite"]
+pymc3 = ["pymc3>=3.9", "numpy<1.22", "xarray<2023.10.0"]
+theano = ["pymc3>=3.9", "numpy<1.22", "xarray<2023.10.0"]
+pymc = ["pymc>=5.9.2"]
+jax = ["jax"]
+docs = [
+  "sphinx",
+  "sphinx-material",
+  "sphinx_copybutton",
+  "breathe",
+  "myst-nb",
+  "matplotlib",
+  "scipy",
+  "emcee",
+  "pymc>=5",
+  "tqdm",
+  "numpyro",
 ]
-build-backend = "setuptools.build_meta"
+tutorials = ["matplotlib", "scipy", "emcee", "pymc>=5", "tqdm", "numpyro"]
+
+[project.urls]
+"Homepage" = "https://celerite2.readthedocs.io"
+"Source" = "https://github.com/exoplanet-dev/celerite2"
+"Bug Tracker" = "https://github.com/exoplanet-dev/celerite2/issues"
+
+[build-system]
+requires = ["scikit-build-core", "numpy", "pybind11"]
+build-backend = "scikit_build_core.build"
+
+[tool.scikit-build]
+sdist.exclude = []
+sdist.include = ["python/celerite2/celerite2_version.py"]
+metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
+
+[tool.setuptools_scm]
+write_to = "python/celerite2/celerite2_version.py"
+
+[tool.cibuildwheel]
+skip = "pp* *-win32 *-musllinux_* *-manylinux_i686"
 
 [tool.black]
 line-length = 79