Fix BOOST_PREFIX in Makefile

.gitignore

@@ -1,6 +1,9 @@
 boost*
 S4/lib
 S4/include
-setup.py
 OpenBLAS
 doc/build
+build/
+*.egg-info/
+__pycache__/
+*.pov

Makefile

@@ -79,6 +79,7 @@ S4_PROF = 0
 # Specify custom compilers if needed
 CXX = g++
 CC  = gcc
+PYTHON ?= python3
 
 #CFLAGS += -O3 -fPIC
 CFLAGS = -Wall -O3 -m64 -march=native -mtune=native -msse3 -msse2 -msse -fPIC
@@ -96,7 +97,7 @@ S4r_LIBNAME = $(OBJDIR)/libS4r.a
 #### and PREFIX if you want to install boost to a different location
 
 # Specify the paths to the boost include and lib directories
-BOOST_-L$(BOOST_PREFIX)/lib/PREFIX=${CURDIR}/S4
+BOOST_PREFIX=${CURDIR}/S4
 BOOST_INC = -I$(BOOST_PREFIX)/include
 BOOST_LIBS =  -lboost_serialization
 BOOST_URL=https://sourceforge.net/projects/boost/files/boost/1.74.0/boost_1_74_0.tar.gz
@@ -348,8 +349,11 @@ FunctionSampler2D.so: modules/function_sampler_2d.c modules/function_sampler_2d.
 #### Python extension
 
 S4_pyext: objdir $(S4_LIBNAME)
-	sh gensetup.py.sh $(OBJDIR) $(S4_LIBNAME) "$(LIBS)" $(BOOST_PREFIX)
-	pip3 install --upgrade --use-pep517 --no-build-isolation ./
+	S4_OBJDIR="$(OBJDIR)" \
+	S4_LIBFILE="$(S4_LIBNAME)" \
+	S4_LINK_FLAGS='$(LIBS)' \
+	BOOST_PREFIX="$(BOOST_PREFIX)" \
+	$(PYTHON) -m pip install --upgrade --no-build-isolation .
 
 clean:
-	rm -rf $(OBJDIR)
+	rm -rf $(OBJDIR)

README.md

@@ -5,7 +5,7 @@ If you are looking for a more user-friendly interface to S4 (wavelength-dependen
 ## Python prerequisites
 
 ```
-pip install numpy wheel setuptools
+pip install numpy wheel setuptools setuptools-scm
 ```
 
 ## Key steps:
@@ -23,6 +23,42 @@ using Homebrew (see below). If you want to use Boost libraries in a different lo
 **Note for users of new (late 2020 onwards) Apple machines with M1/Apple silicon/ARM chips: you will need to use Makefile.m1
 to compile successfully, see notes below on how to do this.**
 
+## Python Package Information
+
+- **Distribution name**: `s4-fmm`
+- **Python import**: `import S4`
+- **Supported Python versions**: Python >=3.10,<3.14
+- **Supported NumPy versions**: NumPy >=1.26,<3 at runtime, NumPy >=2,<3 when building wheels
+
+These are initial maintained support ranges pending automated compatibility testing.
+
+## Conda Development Environment
+
+For development, you can use the provided conda environment:
+
+```bash
+conda env create -f environment.yml
+conda activate s4-dev
+make S4_pyext
+```
+
+Note that native libraries (BLAS, LAPACK, FFTW3, SuiteSparse, Boost) still need to be installed separately according to the platform-specific instructions below.
+
+## Versioning
+
+S4 now uses Git tags for versioning via setuptools-scm. To create a release:
+
+```bash
+git tag -a v1.1.0 -m "S4 Python package version 1.1.0"
+git push origin v1.1.0
+```
+
+The installed version can be checked with:
+
+```bash
+python -c "from importlib.metadata import version; print(version('s4-fmm'))"
+```
+
 ## Installing relevant libraries etc.:
 
 **On Ubuntu (with a working version of Python3):**
@@ -47,17 +83,6 @@ brew install fftw suite-sparse openblas lapack boost
 
 You can get the make and git commands from homebrew, or through Apple Developer Tools. If the packages are installed/symlinked by Homebrew to the default location (/usr/local/include) you should not have to modify the Makefile, and you should be able to use the same Makefile as Ubuntu/Linux (i.e. no need to use Makefile.osx).
 
-*If you have multiple Python versions, you may need to modify the S4_pyext part of the Makefile:*
-
-````
-pip3 install --upgrade ./
-````
-
-to e.g.:
-```
-[path of target python or virtual environment] setup.py install
-```
-
 You can install S4 into a virtual environment automatically by just activating that environment in your terminal before running `make S4_pyext`.
 
 See [here](https://rayflare.readthedocs.io/en/latest/Installation/installation.html) for more extensive instructions.

S4/main_python.c

@@ -1488,7 +1488,7 @@ static PyObject *S4Sim_GetFieldsOnGridNumpy(S4Sim *self, PyObject *args, PyObjec
   /* strides[0] = strides[1]; */
   /* strides[1] = temp; */
   /* PyArray_UpdateFlags(Earr, NPY_ARRAY_UPDATE_ALL); */
-  PyArray_ENABLEFLAGS(Earr, NPY_ARRAY_OWNDATA);
+  PyArray_ENABLEFLAGS((PyArrayObject*)Earr, NPY_ARRAY_OWNDATA);
   /* PyArray_ENABLEFLAGS(Earr,  NPY_ARRAY_F_CONTIGUOUS); */
   PyObject *Harr;
   Harr = PyArray_SimpleNewFromData(3, dims, NPY_COMPLEX128, Hfields);
@@ -1499,7 +1499,7 @@ static PyObject *S4Sim_GetFieldsOnGridNumpy(S4Sim *self, PyObject *args, PyObjec
   /* strides[1] = temp; */
 
   /* PyArray_UpdateFlags(Harr, NPY_ARRAY_UPDATE_ALL); */
-  PyArray_ENABLEFLAGS(Harr, NPY_ARRAY_OWNDATA);
+  PyArray_ENABLEFLAGS((PyArrayObject*)Harr, NPY_ARRAY_OWNDATA);
   /* Harr->flags |= NPY_OWNDATA */
 
   /* PyArray_ENABLEFLAGS(Harr,  NPY_ARRAY_F_CONTIGUOUS); */

environment.yml

@@ -0,0 +1,20 @@
+# Conda development environment for S4 Python packaging
+# 
+# This file establishes Python-level development constraints only.
+# Native S4 build dependencies (BLAS, LAPACK, FFTW3, SuiteSparse, Boost)
+# are still installed separately according to existing platform instructions.
+# Full conda packaging of native dependencies will be addressed in a later task.
+
+name: s4-dev
+
+channels:
+  - conda-forge
+
+dependencies:
+  - python=3.12
+  - numpy>=2,<3
+  - pip
+  - setuptools>=80
+  - setuptools-scm>=9.2
+  - python-build>=1.2
+  - matplotlib>=3.8

pyproject.toml

@@ -0,0 +1,35 @@
+[build-system]
+requires = [
+    "setuptools>=80",
+    "setuptools-scm>=9.2",
+    "numpy>=2,<3",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "s4-fmm"
+dynamic = ["version"]
+description = "Stanford Stratified Structure Solver (S4): Fourier Modal Method"
+readme = "README.md"
+requires-python = ">=3.10"
+license = { text = "GPL" }
+dependencies = [
+    "numpy>=1.26,<3",
+]
+
+[project.optional-dependencies]
+examples = [
+    "matplotlib>=3.8",
+]
+dev = [
+    "build>=1.2",
+    "matplotlib>=3.8",
+]
+
+[tool.setuptools]
+# S4 is a C extension, not a Python package directory structure
+# We only build the S4 extension module, no package discovery needed
+py-modules = []
+
+[tool.setuptools_scm]
+fallback_version = "1.1.0"

setup.py

@@ -0,0 +1,77 @@
+#!/usr/bin/env python3
+"""
+Setuptools-based build configuration for S4 Python extension.
+
+This is a transitional wrapper around the existing Make-based native build.
+The native S4 library (libS4.a) must be built first using the Makefile.
+"""
+
+from pathlib import Path
+import os
+import shlex
+from setuptools import Extension, setup
+import numpy as np
+
+
+def parse_linker_flags(flags_str: str):
+    """
+    Parse linker flags from Makefile LIBS variable.
+
+    Converts flags like '-lfoo -L/path' into appropriate setuptools parameters.
+    Preserves order for linker-sensitive flags.
+    """
+    libraries = []
+    library_dirs = []
+    extra_link_args = []
+
+    for token in shlex.split(flags_str):
+        if token.startswith('-l'):
+            libraries.append(token[2:])
+        elif token.startswith('-L'):
+            library_dirs.append(token[2:])
+        else:
+            extra_link_args.append(token)
+
+    return libraries, library_dirs, extra_link_args
+
+
+def main():
+    # Get build configuration from environment variables (set by Makefile)
+    objdir = os.environ.get('S4_OBJDIR', './build')
+    libfile = os.environ.get('S4_LIBFILE', './build/libS4.a')
+    link_flags = os.environ.get('S4_LINK_FLAGS', '')
+    boost_prefix = os.environ.get('BOOST_PREFIX', f'{Path(__file__).parent.resolve()}/S4')
+
+    # Parse linker flags
+    libs, lib_dirs, extra_link_args = parse_linker_flags(link_flags)
+
+    # Base libraries required for S4 extension
+    libs.extend(['S4', 'stdc++'])
+    lib_dirs.extend([objdir, f'{boost_prefix}/lib'])
+
+    # Include directories
+    include_dirs = [
+        f'{boost_prefix}/include',
+        np.get_include(),
+    ]
+
+    # Extension configuration
+    S4module = Extension(
+        'S4',
+        sources=['S4/main_python.c'],
+        libraries=libs,
+        library_dirs=lib_dirs,
+        include_dirs=include_dirs,
+        extra_objects=[libfile],
+        runtime_library_dirs=[f'{boost_prefix}/lib'],
+        extra_compile_args=['-std=gnu99'],
+    )
+
+    # Setup configuration (metadata comes from pyproject.toml)
+    setup(
+        ext_modules=[S4module],
+    )
+
+
+if __name__ == '__main__':
+    main()