Use meson-build and pyproject.toml

.github/workflows/ci-ubuntu.yml

@@ -19,10 +19,9 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']        
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
     - uses: actions/checkout@main
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@main
@@ -34,10 +33,10 @@ jobs:
         python -m pip install --upgrade pip
     - name: Install the package
       run: |
-        export SETUPTOOLS_ENABLE_FEATURES="legacy-editable"
-        pip install -e .
-        # Show f2py compiler info for debug
-        f2py -c --help-fcompiler        
+        # https://mesonbuild.com/meson-python/how-to-guides/editable-installs.html
+        python -m pip install -v .
     - name: Run tests
       run: |
+        # Force to use the installed package and not the one from the local repo.
+        rm pypolsys/__init__.py
         python -m pypolsys.test

.github/workflows/ci-windows.yml

@@ -19,7 +19,7 @@ jobs:
       - uses: conda-incubator/setup-miniconda@main
         with:
           activate-environment: polsys_env
-          python-version: 3.11
+          python-version: 3.12
           auto-activate-base: false
           miniconda-version: "latest"
           auto-update-conda: true
@@ -29,19 +29,15 @@ jobs:
           # Use conda to manage the building toolchain, but is now outdated
           # https://numpy.org/doc/stable/f2py/windows/index.html
           conda install m2w64-toolchain libpython
-          # numpy is required for pypolsys building. Better to install it with conda.
-          # Sometime it fails when installed by pip thought `build-system` requirement from `pyproject.toml` 
-          # Limit setuptools version because of numpy.distutils
-          conda install numpy "setuptools<60.0" wheel
       - name: Build
         shell: bash -l {0}
         run: |
             # Ignore `pyproject.toml` to avoid conda/pip mix in numpy version            
-            python -m pip install -e . --no-use-pep517
-            # Show f2py compiler info for debug
-            f2py -c --help-fcompiler            
+            python -m pip install -v .  
       - name: Test
         shell: bash -l {0}
         run: |
+            # force to use the installed package and not the one from the local repo.
+            rm pypolsys/__init__.py
             python -m pypolsys.test
 

README.md

@@ -37,48 +37,37 @@ To facilitate the build of this module, a copy of `POLSYS_PLP` *original* source
 ## Installation
 
 You'll need :
-  * python (tested for v >= 3.5);
+  * python (tested for v >= 3.8);
   * pip (optional);
   * fortran compiler (tested with `gfortran` and with `m2w64-toolchain` on windows)
   * lapack and blas installation (only on linux). The useful lapack/blas routines are also shipped with `POLSYS_PLP` sources and built by default on Window or on demand on linux (see below). Optimized library are preferred and often already present on linux systems. If not, library like `openblas` and the required development files can be installed with `sudo apt install libopenblas-dev` on debian based distribution (including ubuntu).
 
-If needed, please see the steps given in the continuous integration script [workflows](.github/workflows/ci-ubuntu.yml).
+If needed, please see the steps given in the continuous integration scripts [ci-ubuntu](.github/workflows/ci-ubuntu.yml) or [ci-windows](.github/workflows/ci-windows.yml). 
 
-### Using pip (preferred)
+### Using pip
 You can install `pypolsys` from pip:
 ```
 pip install pypolsys [--user]
 ```
-You can also install `pypolsys` after a download from github:
+You can also install `pypolsys` after a download from github or after cloning the repos:
 ```
 pip install path/to/pypolsys-version.tar.gz [--user]
 ```
-or in _editable_ mode if you want to modify the sources
+Installation can be done _editable_ mode if you want to modify the sources:
 ```
-pip install -e path/to/pypolsys
+python -m pip install --no-build-isolation --editable .
 ```
-after cloning the repos.
+In this case, compatible version of meson, meson-python and ninja have to be installed before (see `pyproject.toml` file).
 
-`pip` will install `numpy` (mandatory) and `sympy` and `scipy` (optional, required only for tests).
-
-Note that on ubuntu, you will need to use `pip3` instead of `pip` and `python3` instead of `python`.
-
-On linux, if you want to force the building with `POLSYS_PLP` lapack sources, you can tell it to pip with
+### Running tests
+To execute the full test suite, run :
 ```
-pip install --no-use-pep517 --install-option="--buildLapack" path/to/pypolsys
+python -m pypolsys.test
 ```
-The flag `--no-use-pep517` avoids side effect of `install-option` that disable wheels.
-Using `POLSYS_PLP` lapack sources is the standard behavior on windows.
 
 ### Troubleshooting
 With old `gfortran` version present on ubuntu 16.04 (see [here](https://gcc.gnu.org/bugzilla/show_bug.cgi?id=84276)) the building may failed. To avoid this, `intent(in, out)` statement has to be removed from the original `pypolsys/801/polsys_plp.f90`. It seems to work out of the box with `gfortan-8`.
 
-### Running tests
-
-To execute the full test suite, run :
-```
-python -m pypolsys.test
-```
 
 ## Usage
 Note that this projet is a work in progress and the API may change.
@@ -204,9 +193,10 @@ Before submitting a PR, run the tests suite ;-)
 If you need to modify `wrapper.f90` fortran source file. You will need to re-build the Fortran extension. This should be done into 2 steps
   1. The pyf file that avoid trouble with user_defined fortran type should be updated with `f2py` utilities :
 
-    ```
-    f2py -m polsys -h polsys.pyf wrapper.f90 --overwrite-signature
-    ```
+     ```
+     f2py -m polsys -h polsys.pyf wrapper.f90 --overwrite-signature
+     ```
+
   2. Re run the install
 
 

meson.build

@@ -0,0 +1,108 @@
+project(
+    'pypolsys',
+    'c',
+    version: run_command('pypolsys/version.py', check: true).stdout().strip(),
+    license: 'GNU General Public License v3 (GPLv3)',
+    meson_version: '>=0.64.0',
+    default_options: ['warning_level=2', 'buildtype=release'],
+)
+
+add_languages('fortran', native: true)
+# load meson python module
+py_mod = import('python')
+py = py_mod.find_installation(pure: false)
+py_dep = py.dependency()
+
+# Get include from numpy and f2py
+# based on https://numpy.org/doc/stable/f2py/buildtools/meson.html
+incdir_numpy = run_command(
+    py,
+    [
+        '-c',
+        'import os; os.chdir(".."); import numpy; print(numpy.get_include())',
+    ],
+    check: true,
+).stdout().strip()
+
+incdir_f2py = run_command(
+    py,
+    [
+        '-c',
+        'import os; os.chdir(".."); import numpy.f2py; print(numpy.f2py.get_include())',
+    ],
+    check: true,
+).stdout().strip()
+
+inc_np = include_directories(incdir_numpy, incdir_f2py)
+
+# Need to call f2py to process pyf files
+# Based on https://numpy.org/doc/stable/f2py/buildtools/meson.html and
+# https://github.com/scipy/scipy/blob/5e986a24f0ab03fbb382ed67ef15895024334481/scipy/io/meson.build#L4
+# From https://numpy.org/doc/stable/f2py/buildtools/index.html
+# For Fortran 90 programs, f2py generates for an input file blah.f90
+#  blahmodule.c
+#  blah-f2pywrappers.f, makes subroutines for functions, it rewrites assumed shape arrays as automatic arrays (empty for pypolsys).
+#  blah-f2pywrappers2.f90, handles code which is subdivided into modules
+
+# Copy .f2py_f2cmap in buildir (f2py needs it in the working dir)
+fs = import('fs')
+fs.copyfile('.f2py_f2cmap')
+_polsys_module = custom_target(
+    'polsys',
+    output: [
+        'polsysmodule.c',
+        'polsys-f2pywrappers2.f90',
+        'polsys-f2pywrappers.f',
+    ],
+    input: ['pypolsys/src/polsys.pyf'],
+    command: [py, '-m', 'numpy.f2py', '@INPUT@', '--lower'],
+)
+# Pypolsys extension own src files
+src_files = [
+    _polsys_module,
+    'pypolsys/801/polsys_plp.f90',
+    'pypolsys/src/wrapper.f90',
+]
+# Lapack
+lapack_dep = dependency('lapack', required: false)
+if not lapack_dep.found()
+    # Need to compile lapack too
+    src_files += 'pypolsys/801/lapack_plp.f'
+endif
+
+# Assumes that f2py was run before in _polsys_module
+py.extension_module(
+    'polsys',
+    src_files,
+    incdir_f2py / 'fortranobject.c',
+    include_directories: inc_np,
+    # No problem if lapack_dep is not found, meson just ignore it
+    dependencies: [py_dep, lapack_dep],
+    install: true,
+    link_language: 'fortran',
+    native: true,
+    subdir: 'pypolsys',  # Folder relative to site-packages to install to
+)
+
+# Add pure python files
+# Another approach is to split in two meso.build files
+python_sources = [
+    'pypolsys/__init__.py',
+    'pypolsys/test.py',
+    'pypolsys/utils.py',
+    'pypolsys/version.py',
+]
+
+# Install pure Python
+# see https://mesonbuild.com/Python-module.html
+py.install_sources(
+    python_sources,
+    pure: false,  # Will be installed next to binaries
+    subdir: 'pypolsys',  # Folder relative to site-packages to install to
+)
+
+# Add package_data used for tests as source files
+install_dir = py.get_install_dir(subdir: 'pypolsys/examples/data')
+install_data('pypolsys/examples/data/toy_model.npz', install_dir: install_dir)  # / 'examples' / 'data'
+
+

pypolsys/version.py

@@ -1 +1,5 @@
-__version__ = '0.1.4'
+#!/usr/bin/env python3
+__version__ = '0.1.5'
+
+if __name__ == '__main__':
+    print(__version__)

pyproject.toml

@@ -1,2 +1,33 @@
 [build-system]
-requires=['setuptools<60.0', 'wheel', 'numpy']
+build-backend = 'mesonpy'
+requires = ['meson-python>=0.15.0', 'cython', 'numpy']
+
+[project]
+name = 'pypolsys'
+dynamic = ["version"]
+description = "A python wrapper to `POLSYS_PLP` fortran90 package from Layne T. Watson, Steven M. Wise, Andrew J. Sommese, August, 1998."
+readme = 'README.md'
+license = {file = 'LICENSE'}
+requires-python = '>=3.8'
+authors = [
+  {name = "B. Nennig", email = '[email protected]'},
+]
+dependencies = [
+  "numpy",
+  "scipy",
+  "sympy",
+]
+classifiers = [
+  # How mature is this project?
+  "Development Status :: 5 - Production/Stable",
+  # Indicate who your project is intended for
+  "Topic :: Scientific/Engineering",  
+  # Specify the Python versions you support here.
+  "Programming Language :: Python :: 3",
+  "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+  "Operating System :: OS Independent",
+]
+
+[project.urls]
+homepage = "https://github.com/nennigb/pypolsys"
+