Binary wheels on pip, build with github actions; v1.5.5

.github/workflows/build_wheels.yml

@@ -0,0 +1,155 @@
+name: Wheels
+
+on: [ push, pull_request ]
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    if: ${{ startsWith(github.ref, 'refs/tags/') || contains(github.event.head_commit.message, '[pypi]') }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ macos-11, macos-12, macos-13, flyci-macos-large-latest-m2, macos-14, ubuntu-latest, windows-latest ]
+
+    steps:
+      - uses: awvwgk/setup-fortran@main
+        if: matrix.os == 'windows-latest'
+        id: setup-fortran
+        with:
+          compiler: gcc
+          version: 11
+
+      - run: ln -s $(which gfortran-11) /usr/local/bin/gfortran
+        if: matrix.os != 'windows-latest'
+
+      - run: gfortran --version
+
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - uses: actions/setup-python@v5
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.18.1
+
+      - name: Build macos-13 wheels
+        if: matrix.os == 'macos-13' || matrix.os == 'macos-13-xlarge' || matrix.os == 'flyci-macos-large-latest-m2'
+        env:
+          MACOSX_DEPLOYMENT_TARGET: 13
+          CIBW_BUILD: cp311-*
+          CIBW_SKIP: pp*
+          CIBW_BUILD_VERBOSITY: 1
+        run: python -m cibuildwheel --output-dir wheelhouse
+
+      - name: Build macos-12 wheels
+        if: matrix.os == 'macos-12'
+        env:
+          MACOSX_DEPLOYMENT_TARGET: 12
+          CIBW_BUILD: cp311-*
+          CIBW_SKIP: pp*
+          CIBW_BUILD_VERBOSITY: 1
+        run: python -m cibuildwheel --output-dir wheelhouse
+
+      - name: Build macos-11 wheels
+        if: matrix.os == 'macos-11'
+        env:
+          # all cp3xx, since old macs seem to only use osx 11+ builds if this is set not "none"
+          # see consistency with get_tag() in setup.py
+          MACOSX_DEPLOYMENT_TARGET: 11
+          CIBW_SKIP: pp*
+          CIBW_BUILD_VERBOSITY: 1
+        run: python -m cibuildwheel --output-dir wheelhouse
+
+      - name: Build wheels
+        if: matrix.os == 'macos-14' || matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'
+        env:
+          MACOSX_DEPLOYMENT_TARGET: 14
+          CIBW_BUILD: cp311-*
+          CIBW_SKIP: pp* *-win32 *-manylinux_i686 *musllinux*
+          CIBW_BUILD_VERBOSITY: 1
+        run: python -m cibuildwheel --output-dir wheelhouse
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: |
+            wheelhouse/*.whl
+
+  build-sdist-and-upload:
+    runs-on: ubuntu-latest
+    needs: [ 'build_wheels' ]
+    environment: wheels
+    if: github.repository_owner == 'cmbant'
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          cache: pip
+          cache-dependency-path: "setup.py"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip
+          python -m pip install -U build twine
+
+      - name: Download wheels from build artifacts
+        uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          merge-multiple: true
+          path: dist-wheels/
+
+      - name: Build package
+        run: |
+          python -m build --sdist
+          twine check --strict dist/*
+          twine check --strict dist-wheels/*
+
+      - name: Publish wheels to PyPI Test
+        if: ${{ !startsWith(github.ref, 'refs/tags/') }}
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          packages-dir: dist-wheels/
+
+      - name: Publish sdist to PyPI Test
+        if: ${{ !startsWith(github.ref, 'refs/tags/') }}
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+      - name: Publish wheels to PyPI
+        if: ${{ startsWith(github.ref, 'refs/tags/') }}
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist-wheels/
+
+      - name: Publish sdist to PyPI
+        if: ${{ startsWith(github.ref, 'refs/tags/') }}
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  test_wheels:
+    name: Test wheels on ${{ matrix.os }}
+    if: contains(github.event.head_commit.message, '[testpypi]')
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ macos-11, macos-12, macos-13, flyci-macos-large-latest-m2, macos-14, ubuntu-latest, windows-latest ]
+
+    steps:
+      - uses: actions/setup-python@v5
+
+      - name: install
+        run: python -m pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ camb
+
+      - name: test
+        run: python -m unittest camb.tests.camb_test

.travis.yml

@@ -88,16 +88,3 @@ script:
 after_failure:
   - test $TRAVIS_PULL_REQUEST == "false" && test $PYPI_DIST == "true" && test $TRAVIS_REPO_SLUG == "cmbant/CAMB" && [ -d fortran/testfiles ] && bash fortran/tests/upload_tests.sh
 
-before_deploy:
-  - pushd fortran; make clean delete; popd
-
-deploy:
-  - provider: pypi
-    distributions: sdist
-    username: "__token__"
-    password: $PYPI_PASSWORD
-    on:
-      branch: master
-      repo: cmbant/CAMB
-      tags: true
-      condition: $PYPI_DIST = true

README.rst

@@ -39,9 +39,9 @@ Then install using::
 
     pip install -e ./CAMB [--user]
 
-You will need gfortran 6 or higher installed to compile. Binary files for Windows are also provided, so these are used instead if no
-gfortran installation is found on Windows machines. If you have gfortran installed, "python setup.py make"
-(and other standard setup commands) will build the Fortran library on all systems (including Windows without directly using a Makefile).
+You will need gfortran 6 or higher installed to compile (usually included with gcc by default).
+If you have gfortran installed, "python setup.py make" (and other standard setup commands) will build the Fortran
+library on all systems (including Windows without directly using a Makefile).
 
 The python wrapper provides a module called "camb" documented in the Python `CAMB documentation <https://camb.readthedocs.io/en/latest/>`_.
 

camb/__init__.py

@@ -7,7 +7,7 @@
 __author__ = "Antony Lewis"
 __contact__ = "antony at cosmologist dot info"
 __url__ = "https://camb.readthedocs.io"
-__version__ = "1.5.4"
+__version__ = "1.5.5"
 
 from . import baseconfig
 

camb/sources.py

@@ -57,7 +57,7 @@ def set_table(self, z, W, bias_z=None, k_bias=None, bias_kz=None):
         :param z: array of redshift values (monotonically increasing)
         :param W: array of window function values. It must be well enough sampled to smoothly cubic-spline interpolate
         :param bias_z: optional array of bias values at each z for scale-independent bias
-        :param k_bias: optional array of k values for bias
+        :param k_bias: optional array of k values for bias (Mpc^-1)
         :param bias_kz: optional 2D contiguous array for space-dependent bias(k, z).
                         Must ensure range of k is large enough to cover required values.
 

camb/tests/camb_test.py

@@ -13,7 +13,7 @@
 from camb import model, correlations, bbn, dark_energy, initialpower
 from camb.baseconfig import CAMBParamRangeError, CAMBValueError
 
-fast = 'ci fast' in os.getenv("TRAVIS_COMMIT_MESSAGE", "")
+fast = 'ci fast' in os.getenv("TRAVIS_COMMIT_MESSAGE", "") or os.getenv("GITHUB_ACTIONS")
 
 
 class CambTest(unittest.TestCase):

docs/source/fortran_compilers.rst

@@ -45,7 +45,7 @@ This includes in Jupyter notebooks; just re-start the kernel or use::
     import IPython
     IPython.Application.instance().kernel.do_shutdown(True)
 
-If you want to automamatically rebuild the library from Jupyter you can do something like this::
+If you want to automatically rebuild the library from Jupyter you can do something like this::
 
     import subprocess
     import sys

docs/source/index.rst

@@ -21,17 +21,17 @@ If you want to work on the code from `GitHub <https://github.com/cmbant/camb>`_,
     pip install -e ./CAMB [--user]
 
 You will need ifort or gfortran 6 or higher installed (and on your path) to compile; see :ref:`fortran-compilers` for
-compiler installation details if needed. A compiled library for Windows is also provided, and is used if no
-gfortran installation is found on Windows machines. If you have gfortran installed, "python setup.py make" will build
+compiler installation details if needed. If you have gfortran installed, "python setup.py make" will build
 the Fortran library on all systems (including Windows without directly using a Makefile), and can be used to update
 a source installation after changes or pulling an updated version.
 
+The standard pip installation includes binary pre-compiled code, so no need for a Fortran compiler
+(unless you want to use custom sources/symbolic compilation features).
 Anaconda users can also install from conda-forge, best making a new clean environment using::
 
-  conda create -n camb -c conda-forge python=3.9 camb
+  conda create -n camb -c conda-forge python=3.11 camb
   activate camb
 
-with no need for a Fortran compiler (unless you want to use custom sources/symbolic compilation features).
 Check that conda installs the latest version, if not try installing
 in a new clean conda environment as above.
 

fortran/config.f90

@@ -3,7 +3,7 @@ module config
     use constants, only: const_twopi
     implicit none
 
-    character(LEN=*), parameter :: version = '1.5.4'
+    character(LEN=*), parameter :: version = '1.5.5'
 
     integer :: FeedbackLevel = 0 !if >0 print out useful information about the model
 

pyproject.toml

@@ -8,19 +8,18 @@ authors = [
     { name = "Antony Lewis" },
 ]
 description = "Code for Anisotropies in the Microwave Background"
-keywords= ['cosmology', 'CAMB', 'CMB']
+keywords = ['cosmology', 'CAMB', 'CMB']
 readme = "docs/README_pypi.rst"
 license = { file = "LICENCE.txt" }
 dynamic = ["version"]
-requires-python = ">=3.6.0"
+requires-python = ">=3.7.0"
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Operating System :: OS Independent",
     "Environment :: Console",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Astronomy",
     "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
-    "Programming Language :: Python :: 3.6",
     "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
@@ -46,4 +45,4 @@ Tracker = "https://github.com/cmbant/camb/issues"
 Licensing = "https://github.com/cmbant/camb/blob/master/LICENCE.txt"
 
 [tool.setuptools.dynamic]
-version = {attr = "camb.__version__"}
+version = { attr = "camb.__version__" }

setup.py

@@ -3,10 +3,12 @@
 import os
 import shutil
 from typing import Any
-from setuptools import setup
+from setuptools import setup, Command, Extension
+from setuptools.command.build_ext import build_ext
 from setuptools.command.build_py import build_py
 from setuptools.command.develop import develop
-from setuptools import Command
+from setuptools.command.install import install
+from wheel.bdist_wheel import bdist_wheel as _bdist_wheel
 
 file_dir = os.path.abspath(os.path.dirname(__file__))
 os.chdir(file_dir)
@@ -19,6 +21,7 @@
 else:
     DLLNAME = 'camblib.so'
 
+
 def get_forutils():
     fpath = os.getenv('FORUTILSPATH')
 
@@ -177,7 +180,7 @@ def make_library(cluster=False):
         get_forutils()
         print("Compiling source...")
         subprocess.call("make python PYCAMB_OUTPUT_DIR=%s/camb/ CLUSTER_SAFE=%d" %
-                        (pycamb_path, int(cluster)), shell=True)
+                        (pycamb_path, int(cluster if not os.getenv("GITHUB_ACTIONS") else 1)), shell=True)
         subprocess.call("chmod 755 %s" % lib_file, shell=True)
 
     if not os.path.isfile(os.path.join(pycamb_path, 'camb', DLLNAME)):
@@ -246,12 +249,41 @@ def run(self):
             subprocess.call("make clean", shell=True, cwd=os.path.join(file_dir, 'fortran'))
 
 
+class BDistWheelNonPure(_bdist_wheel):
+    def finalize_options(self):
+        super().finalize_options()
+        self.root_is_pure = False
+
+    def get_tag(self):
+        _, _, plat = super().get_tag()
+        if "osx_11" in plat:
+            return _, _, plat
+        return "py3", "none", plat
+
+
+class InstallPlatlib(install):
+    def finalize_options(self):
+        super().finalize_options()
+        if self.distribution.has_ext_modules():
+            self.install_lib = self.install_platlib
+
+
+class BuildExtCommand(build_ext):
+    """Ensure built extensions are added to the correct path in the wheel."""
+
+    def run(self):
+        pass
+
+
 if __name__ == "__main__":
     setup(name=os.getenv('CAMB_PACKAGE_NAME', 'camb'),
           zip_safe=False,
           cmdclass={'build_py': SharedLibrary, 'build_cluster': SharedLibraryCluster,
                     'make': MakeLibrary, 'make_cluster': MakeLibraryCluster, 'clean': CleanLibrary,
-                    'develop': DevelopLibrary, 'develop_cluster': DevelopLibraryCluster},
+                    'develop': DevelopLibrary, 'develop_cluster': DevelopLibraryCluster,
+                    'bdist_wheel': BDistWheelNonPure, 'install': InstallPlatlib,
+                    "build_ext": BuildExtCommand},
+          ext_modules=[Extension("camb.camblib", [])],
           packages=['camb', 'camb.tests'],
           platforms="any",
           package_data={'camb': [DLLNAME, 'HighLExtrapTemplate_lenspotentialCls.dat',