Merge pull request #100 from simonsobs/feature-mesonpy

Feature mesonpy

Author: thibautlouis

.github/workflows/testing.yml

@@ -9,14 +9,20 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+env:
+  FC: gfortran-12
+  CC: gcc-12
+  CXX: gcc-12
+
 jobs:
+
   build:
 
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
@@ -29,19 +35,13 @@ jobs:
     - name: Set gfortran link on macos-latest
       if: matrix.os == 'macos-latest'
       run: |
-        set -x
-        sudo ln -s /usr/local/bin/gfortran-11 /usr/local/bin/gfortran
+        ln -s $FC $(dirname $(which $FC))/gfortran
         gfortran --version
 
     - name: Install via pip
       run: |
-        python -m pip install --upgrade pip wheel
-        python -m pip install numpy pytest pytest-cov
-        python -m pip install -e .
-
-    - name: Install extra dependencies (camb)
-      run: |
-        python -m pip install camb
+        python -m pip install --upgrade pip setuptools wheel meson ninja meson-python numpy
+        python -m pip install --no-build-isolation --editable '.[test]'
 
     - name: Download test data
       run: |
@@ -51,18 +51,20 @@ jobs:
 
     - name: Unit tests
       run: |
-        pytest -vv pspy --cov=pspy --cov-report=xml:coverage.xml --ignore=pspy/tests/test_pspy_namaster.py
+        pytest -vv pspy --cov=pspy --cov-report=xml --cov-report annotate --ignore=pspy/tests/test_pspy_namaster.py
 
     - name: Report Coverage (codecov)
       if: matrix.os == 'ubuntu-latest'
       uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
-    - name: Test notebooks (Only on Linux for saving time)
-      if: matrix.os == 'ubuntu-latest'
-      run: |
-        python -m pip install jupyter ipykernel
-        python -m ipykernel install --user --name=pspy
-        jupyter nbconvert --to notebook --execute docs/source/notebooks/tutorial_io.ipynb
+    # - name: Test notebooks (Only on Linux for saving time)
+    #   if: matrix.os == 'ubuntu-latest'
+    #   run: |
+    #     python -m pip install '.[notebook]'
+    #     python -m ipykernel install --user --name=pspy
+    #     jupyter nbconvert --to notebook --execute docs/source/notebooks/tutorial_io.ipynb
 
     - name: Comparing pspy to NaMaster
       if: matrix.os == 'ubuntu-latest'

.github/workflows/wheels.yml

@@ -14,49 +14,25 @@ concurrency:
 
 jobs:
   build_wheels:
-    name: Build wheels on ${{ matrix.os }} for ${{ matrix.cp }}
+    name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # macos-13 is an intel runner, macos-14 is apple silicon
         os: [ubuntu-latest, macos-13, macos-14]
-        cp: [cp38, cp39, cp310, cp311]
-        include:
-          - cp: cp38
-            numpyver: "1.22"
-          - cp: cp39
-            numpyver: "1.22"
-          - cp: cp310
-            numpyver: "1.22"
-          - cp: cp311
-            numpyver: "1.22"
 
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set gfortran link for macos-13
-        if: matrix.os == 'macos-13'
-        run: |
-          set -x
-          sudo ln -s /usr/local/bin/gfortran-11 /usr/local/bin/gfortran
-          
-      - name: Set gfortran link for macos-14
-        if: matrix.os == 'macos-14'
-        run: |
-          set -x
-          sudo ln -s /opt/homebrew/bin/gfortran-11 /usr/local/bin/gfortran
-
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.17.0
+        uses: pypa/cibuildwheel@v2.21.1
         env:
-          CIBW_BEFORE_BUILD: "python -m pip install numpy==${{ matrix.numpyver }}"
-          CIBW_BUILD_VERBOSITY: 3
-          CIBW_BUILD: "${{ matrix.cp }}-*"
-          CIBW_SKIP: "*-musllinux_* *i686*"
+          FC: gfortran-14
+          CC: gcc-14
+          MACOSX_DEPLOYMENT_TARGET: ${{ matrix.os == 'macos-13' && '13.0' || '14.0' }}
 
       - uses: actions/upload-artifact@v4
         with:
-          name: cibw-wheels-${{ matrix.os }}-${{ matrix.cp }}
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
           retention-days: 1
 
@@ -69,19 +45,14 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: '3.8'
-
-      - name: Brew packages
-        if: matrix.os == 'macos-13'
-        run: |
-          set -x
-          sudo ln -s /usr/local/bin/gfortran-11 /usr/local/bin/gfortran
-          gfortran --version
+          python-version: '3.10'
 
       - name: Build sdist
         run: |
+          python -m pip install --upgrade pip setuptools wheel
           python -m pip install numpy
-          python setup.py sdist
+          python -m pip install build
+          python -m build --sdist
 
       - uses: actions/upload-artifact@v4
         with:

MANIFEST.in

@@ -37,19 +37,29 @@ You can test your installation by running
 
     test-pspy
 
-If everything goes fine, no errors will occur. Otherwise, you can report your problem on the `Issues tracker <https://github.com/simonsobs/pspy/issues>`_.
+If everything goes fine, no errors will occur. Otherwise, you can report your problem on the `Issues
+tracker <https://github.com/simonsobs/pspy/issues>`_.
 
 If you plan to develop ``pspy``, it is better to checkout the latest version by doing
 
 .. code:: shell
 
     git clone https://github.com/simonsobs/pspy.git /where/to/clone
 
+Once downloaded, you can install using ``pip install .`` inside the project directory. We use the
+``meson`` build system, which should be understood by ``pip`` (it will build in an isolated
+environment).
+
+To run an editable install, you will need to do so in a way that does not have build isolation (as
+the backend build system, ``meson`` and ``ninja``, actually perform micro-builds on usage in this
+case):
+
 Then you can install the ``pspy`` library and its dependencies *via*
 
 .. code:: shell
 
-    pip install -e /where/to/clone
+    pip install --upgrade pip setuptools meson ninja meson-python numpy
+    pip install --no-build-isolation --editable /where/to/clone
 
 The ``-e`` option allow the developer to make changes within the ``pspy`` directory without having
 to reinstall at every changes.

README.rst

@@ -0,0 +1,67 @@
+# Main build file for pspy, helping with building the fortran
+project(
+  'pspy',
+  ['c', 'fortran']
+)
+
+py = import('python').find_installation(pure: false)
+
+# Dependencies
+py_dep = py.dependency()
+omp_dep = dependency('openmp')
+
+# Libraries
+cc = meson.get_compiler('c')
+c_m_dep = cc.find_library('m', required: true)
+
+fc = meson.get_compiler('fortran')
+fortran_m_dep = fc.find_library('m', required: true)
+
+# Directories
+library_install_dir = py.get_install_dir() / 'pspy'
+
+# Includes
+
+# Need to massage these into relative paths to keep meson happy.
+# It does not allow for absolute paths.
+incdir_numpy = run_command(
+    py,
+    ['-c', 'import numpy; import os; print(os.path.relpath(numpy.get_include()))'],
+    check: true
+).stdout().strip()
+
+incdir_f2py = run_command(
+    py,
+    ['-c', 'import numpy.f2py; import os; print(os.path.relpath(numpy.f2py.get_include()))'],
+    check: true
+).stdout().strip()
+
+# Build fortran extensions
+fortran_include = include_directories(incdir_numpy, incdir_f2py)
+
+fortran_sources = {
+    'pspy/mcm_fortran/mcm_fortran.f90': '_mcm_fortran',
+    'pspy/cov_fortran/cov_fortran.f90': '_cov_fortran',
+}
+
+foreach source_name, module_name : fortran_sources
+    f2py_output = custom_target(
+        input: source_name,
+        output: [module_name + '-f2pywrappers2.f90', module_name + 'module.c'],
+        command: [py, '-m', 'numpy.f2py', '@INPUT@', '-m', module_name, '--lower'],
+    )
+
+    py.extension_module(
+        module_name,
+        [source_name, f2py_output],
+        'pspy/wigner3j/wigner3j_sub.f',
+        incdir_f2py / 'fortranobject.c',
+        include_directories: fortran_include,
+        dependencies: [py_dep, omp_dep, c_m_dep, fortran_m_dep],
+        install: true,
+        subdir: 'pspy'
+    )
+endforeach
+
+subdir('pspy')
+subdir('scripts')

codecov.yml

@@ -1,8 +1,22 @@
-from __future__ import absolute_import, print_function
+from importlib.metadata import PackageNotFoundError, version
 
-from pspy import (mcm_fortran, pspy_utils, so_config, so_cov, so_dict, so_map,
-                  so_map_preprocessing, so_mcm, so_misc, so_mpi, so_spectra,
-                  so_window, sph_tools, flat_tools)
+from pspy import (
+    flat_tools,
+    pspy_utils,
+    so_config,
+    so_cov,
+    so_dict,
+    so_map,
+    so_map_preprocessing,
+    so_mcm,
+    so_misc,
+    so_mpi,
+    so_spectra,
+    so_window,
+    sph_tools,
+)
 
-from . import _version
-__version__ = _version.get_versions()['version']
+try:
+    __version__ = version("pspy")
+except PackageNotFoundError:
+    __version__ = "unknown"