Work on support for numpy-2 and python-3.12 (#198)

* Work on support for numpy-2 and python-3.12

- Remove numpy-1 checks / constraints.

- Update wheel workflows and scripts.  Add dependabot workflow and
  combine wheel test / deploy workflows into one.  Remove python-3.8
  support.

- Update README instructions.

- Add pyproject.toml and remove unsupported distutils from setup.py

- Fix healpix_bare.c compiler warnings

- Add missing guard around omp.h inclusion

- Remove deprecated datetime functions

- Bump vendored boost to version 1.87 and compile our own libflac-1.5.0

- Build our own OpenBLAS for macos wheels

* Fix README typo

* Add note on the provenance and local modifications to the healpix_bare.c source

Author: tskisner

.github/dependabot.yml

@@ -0,0 +1,9 @@
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/deploy.yml

@@ -12,14 +12,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       # Fetch all history for all tags and branches
       with:
         fetch-depth: 0
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.8
 
     # Build
     - name: Build docker images

.github/workflows/official-docker-images.yml

@@ -2,8 +2,11 @@ name: Run Tests
 
 on:
   push:
-    branches-ignore: [ master ]
+    branches:
+      - master
   pull_request:
+    branches:
+      - master
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -15,11 +18,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.8
+      uses: actions/checkout@v4
 
     - name: Build docker images
       run: |

.github/workflows/pytest.yml

@@ -1,7 +1,10 @@
 
-name:  Test Binary Wheels
+name:  Binary Wheels
 
-on: workflow_dispatch
+on:
+  workflow_dispatch:
+  release:
+    types: [ published ]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -18,10 +21,6 @@ jobs:
       matrix:
         include:
           # Linux 64 bit manylinux
-          - os: ubuntu-latest
-            arch: x86_64
-            python: 38
-            builder: manylinux
           - os: ubuntu-latest
             arch: x86_64
             python: 39
@@ -34,6 +33,14 @@ jobs:
             arch: x86_64
             python: 311
             builder: manylinux
+          - os: ubuntu-latest
+            arch: x86_64
+            python: 312
+            builder: manylinux
+          # - os: ubuntu-latest
+          #   arch: x86_64
+          #   python: 313
+          #   builder: manylinux
 
           # MacOS x86_64.  The macos-13 runner is the last
           # Intel-based runner version.  At some point we'll
@@ -42,27 +49,80 @@ jobs:
             arch: x86_64
             python: 39
             builder: macosx
+            deploy: 13.0
           - os: macos-13
             arch: x86_64
             python: 310
             builder: macosx
+            deploy: 13.0
           - os: macos-13
             arch: x86_64
             python: 311
             builder: macosx
+            deploy: 13.0
+          - os: macos-13
+            arch: x86_64
+            python: 312
+            builder: macosx
+            deploy: 13.0
+          # - os: macos-13
+          #   arch: x86_64
+          #   python: 313
+          #   builder: macosx
+          #   deploy: 13.0
+
+          # MacOS arm64
+          - os: macos-latest
+            arch: arm64
+            python: 310
+            builder: macosx
+            deploy: 14.0
+          - os: macos-latest
+            arch: arm64
+            python: 311
+            builder: macosx
+            deploy: 14.0
+          - os: macos-latest
+            arch: arm64
+            python: 312
+            builder: macosx
+            deploy: 14.0
+          # - os: macos-latest
+          #   arch: arm64
+          #   python: 313
+          #   builder: macosx
+          #   deploy: 14.0
     env:
       CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.builder }}_${{ matrix.arch }}
       CIBW_MANYLINUX_X86_64_IMAGE: ${{ matrix.builder }}2014
       CIBW_MANYLINUX_I686_IMAGE: ${{ matrix.builder }}2014
       CIBW_BUILD_VERBOSITY: 3
-      CIBW_ENVIRONMENT_LINUX: "CC=gcc CXX=g++ CFLAGS='-O3 -fPIC' CXXFLAGS='-O3 -fPIC -std=c++14' BOOST_ROOT=/usr/local"
-      CIBW_ENVIRONMENT_MACOS: "MACOSX_DEPLOYMENT_TARGET=13.0 CC=gcc-14 CXX=g++-14 CFLAGS='-O3 -fPIC' CXXFLAGS='-O3 -fPIC -std=c++14' BOOST_ROOT=/usr/local FLAC_ROOT=/usr/local BLAS_LIBRARIES=/usr/local/lib/libscipy_openblas.dylib"
+      CIBW_ENVIRONMENT_LINUX: >
+        CC=gcc
+        CXX=g++
+        CFLAGS='-O3 -fPIC'
+        CXXFLAGS='-O3 -fPIC -std=c++14'
+        BOOST_ROOT=/usr/local
+        FLAC_ROOT=/usr/local
+        SO3G_BUILD_BLAS_LIBRARIES='-L/usr/local/lib -lopenblas -fopenmp -lm -lgfortran'
+      CIBW_ENVIRONMENT_MACOS: >
+        MACOSX_DEPLOYMENT_TARGET=${{ matrix.deploy }}
+        CC=gcc-14
+        CXX=g++-14
+        CFLAGS='-O3 -fPIC'
+        CXXFLAGS='-O3 -fPIC -std=c++14'
+        CPATH='/usr/local/include'
+        BOOST_ROOT=/usr/local
+        FLAC_ROOT=/usr/local
+        SO3G_BUILD_BLAS_LIBRARIES='/usr/local/lib/libopenblas.dylib'
       CIBW_BEFORE_BUILD_LINUX: ./wheels/install_deps_linux.sh
-      CIBW_BEFORE_BUILD_MACOS: ./wheels/install_deps_osx.sh ${{ matrix.builder }}_${{ matrix.arch }}
+      CIBW_BEFORE_BUILD_MACOS: >
+        ln -s $(dirname $(readlink -f $(which python3)))/python3-config $(dirname $(which python3))/python3-config &&
+        ./wheels/install_deps_osx.sh
       CIBW_REPAIR_WHEEL_COMMAND_LINUX: ./wheels/repair_wheel_linux.sh {dest_dir} {wheel}
       CIBW_REPAIR_WHEEL_COMMAND_MACOS: ./wheels/repair_wheel_macos.sh {dest_dir} {wheel} {delocate_archs}
       CIBW_BEFORE_TEST: export OMP_NUM_THREADS=2
-      CIBW_TEST_REQUIRES: pytest
+      CIBW_TEST_REQUIRES: pytest pixell
       CIBW_TEST_COMMAND: >
         python -c 'import so3g.smurf.reader; from spt3g import core' &&
         python -m pytest {package}/test
@@ -73,17 +133,36 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: '3.10'
+          python-version: '3.12'
 
       - name: Install cibuildwheel
         run: |
-          python -m pip install cibuildwheel==2.20.0
+          python -m pip install cibuildwheel==2.22.0
 
       - name: Build wheel
         run: |
           python -m cibuildwheel --output-dir wheelhouse
 
       - uses: actions/upload-artifact@v4
         with:
-          name: wheels_cp${{ matrix.python }}-${{ matrix.builder }}
-          path: ./wheelhouse/so3g*cp${{ matrix.python }}-${{ matrix.builder }}*.whl
+          name: wheels_cp${{ matrix.python }}-${{ matrix.builder }}_${{ matrix.arch }}
+          path: ./wheelhouse/so3g*cp${{ matrix.python }}-${{ matrix.builder }}*${{ matrix.arch }}*.whl
+
+  upload_pypi:
+    needs: build_wheels
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          # unpacks all CIBW artifacts into dist/
+          pattern: wheels_*
+          path: dist
+          merge-multiple: true
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1